@article {8708, title = {Multiplexed fluorescence and scatter detection with single cell resolution using on-chip fiber optics for droplet microfluidic applications [Discovery to Innovation Accelerator, C-CAMP]}, journal = {Microsyst Nanoeng}, volume = {10}, year = {2024}, month = {2024}, pages = {35}, abstract = {

Droplet microfluidics has emerged as a critical component of several high-throughput single-cell analysis techniques in biomedical research and diagnostics. Despite significant progress in the development of individual assays, multiparametric optical sensing of droplets and their encapsulated contents has been challenging. The current approaches, most commonly involving microscopy-based high-speed imaging of droplets, are technically complex and require expensive instrumentation, limiting their widespread adoption. To address these limitations, we developed the OptiDrop platform; this platform is a novel optofluidic setup that leverages the principles of flow cytometry. Our platform enables on-chip detection of the scatter and multiple fluorescence signals from the microfluidic droplets and their contents using optical fibers. The highly customizable on-chip optical fiber-based signal detection system enables simplified, miniaturized, low-cost, multiparametric sensing of optical signals with high sensitivity and single-cell resolution within each droplet. To demonstrate the ability of the OptiDrop platform, we conducted a differential expression analysis of the major histocompatibility complex (MHC) protein in response to IFN stimulation. Our results showed the platform{\textquoteright}s ability to sensitively detect cell surface biomarkers using fluorescently labeled antibodies. Thus, the OptiDrop platform combines the versatility of flow cytometry with the power of droplet microfluidics to provide wide-ranging, scalable optical sensing solutions for research and diagnostics.

}, issn = {2055-7434}, doi = {10.1038/s41378-024-00665-w}, author = {Gupta, Preksha and Mohan, Ambili and Mishra, Apurv and Nair, Atindra and Chowdhury, Neeladri and Balekai, Dhanush and Rai, Kavyashree and Prabhakar, Anil and Saiyed, Taslimarif} } @article {8098, title = {Analysis of smart biomaterial containing umbilical cord blood serum protein conjugated with P-(NIPAAM) using spectroscopy [Bio-incubation Services]}, journal = {Materials Today: Proceedings}, year = {2023}, abstract = {

Human Umbilical Cord Blood Serum (HUCBS) is a complex and evolving collection of proteins that promote fetal development. In the realm of regenerative medicine, the important proteins found in HUCBS are of great interest. The smart biomaterial generated from HUCBS is described in this paper. To characterize this novel biomaterial, human umbilical cord blood was obtained in sterile vacutainers from mothers and left to clot for 24\ h at 37 {\textdegree}C. The supernatant serum was collected, centrifuged and lyophilized. The lyophilized HUCBS was homogenized with smart polymer. This sample was subjected to physico-chemical characterization using Attenuated Total Reflectance-Fourier-Transform Infrared (ATR-FTIR) Spectroscopy and Nuclear Magnetic Resonance (NMR). The quantification of protein-polymer conjugate using ATR-FTIR revealed peaks ranging between 3264 and 531\ cm-1 and that of NMR showed wide resonances in the region 0{\textendash}5\ ppm. ATR-FTIR and NMR investigations were used to determine the structural stability of protein molecules in protein-polymer complex which helps in understanding the possible clinical effectiveness of the smart biomaterial in drug delivery.

}, keywords = {ATR-FTIR, H NMR, HUCBS, P-NIPAAM, Protein-polymer conjugate}, issn = {2214-7853}, doi = {https://doi.org/10.1016/j.matpr.2023.01.285}, url = {https://www.sciencedirect.com/science/article/pii/S2214785323003759}, author = {Manasa Biligowda Latha and Ashmitha Kishan Shetty and Rajamanickam Deveswaran and Ashish Jagannath Rai and Serene Joy and Hadonahalli Munegowda Shashanka and Siddique Sha Muhammad Hussain and Suraksha Shetty} } @article {8462, title = {A curated list of targeted optimized promiscuous ketoreductases (TOP-K). [Bugworks Research Pvt. Ltd., a C-CAMP Startup]}, journal = {Biochem J}, volume = {480}, year = {2023}, month = {2023 Jul 12}, pages = {975-997}, abstract = {

Enzymes are either specific or promiscuous catalysts in nature. The latter is portrayed by protein families like CYP450Es, Aldo-ketoreductases and short/medium-chain dehydrogenases which participate in detoxification or secondary metabolite production. However, enzymes are evolutionarily {\textquoteright}blind{\textquoteright} to an ever-increasing synthetic substrate library. Industries and laboratories have circumvented this by high-throughput screening or site-specific engineering to synthesize the product of interest. However, this paradigm entails cost and time-intensive one-enzyme, one-substrate catalysis model. One of the superfamilies regularly used for chiral alcohol synthesis are short-chain dehydrogenases/reductases (SDRs). Our objective is to determine a superset of promiscuous SDRs that can catalyze multiple ketones. They are typically classified into shorter {\textquoteright}Classical{\textquoteright} and longer {\textquoteright}Extended{\textquoteright} type ketoreductases. However, current analysis of modelled SDRs reveals a length-independent conserved N-terminus Rossmann-fold and a variable substrate-binding C-terminus substrate-binding region for both categories. The latter is recognized to influence the enzyme{\textquoteright}s flexibility and substrate promiscuity and we hypothesize these properties are directly linked with each other. We tested this by catalyzing ketone intermediates with the essential and specific enzyme: FabG_E, as well as non-essential SDRs such as UcpA and IdnO. The experimental results confirmed this biochemical-biophysical association, making it an interesting filter for ascertaining promiscuous enzymes. Hence, we created a dataset of physicochemical properties derived from the protein sequences and employed machine learning algorithms to examine potential candidates. This resulted in 24 targeted optimized ketoreductases (TOP-K) from 81 014 members. The experimental validation of select TOP-Ks demonstrated the correlation between the C-terminal lid-loop structure, enzyme flexibility and turnover rate on pro-pharmaceutical substrates.

}, keywords = {ketoreductases, machine learning, medium-chain dehydrogenases, short-chain dehydrogenases}, issn = {1470-8728}, doi = {10.1042/BCJ20230051}, url = {https://pubmed.ncbi.nlm.nih.gov/37335080/}, author = {Shanbhag, Anirudh P and Rajagopal, Sreenath and Ghatak, Arindam and Katagihallimath, Nainesh and Subramanian, Ramaswamy and Datta, Santanu} } @article {8441, title = {Gene flow drives genomic diversity in Asian Pikas distributed along the core and range-edge habitats in the Himalayas [Next Gen Genomics Facility (INT)]}, journal = {Ecol Evol.}, volume = {13}, year = {2023}, month = {05/2023}, chapter = {e10129}, abstract = {

Studying the genetic variation among different species distributed across their core and range-edge habitats can provide valuable insights into how genetic variation changes across the species{\textquoteright} distribution range. This information can be important for understanding local adaptation, as well as for conservation and management efforts. In this study, we have carried out genomic characterization of six species of Asian Pikas distributed along their core and range-edge habitats in the Himalayas. We utilized a population genomics approach using ~28,000 genome-wide SNP markers obtained from restriction-site associated DNA sequencing. We identified low nucleotide diversity and high inbreeding coefficients in all six species across their core and range-edge habitats. We also identified evidence of gene flow among genetically diverse species. Our results provide evidence of reduced genetic diversity in Asian pikas distributed across the Himalayas and the neighboring regions and indicate that recurrent gene flow is possibly a key mechanism for maintaining genetic diversity and adaptive potential in these pikas. However, full-scale genomics studies that utilize whole-genome sequencing approaches will be needed to quantify the direction and timing of gene flow and functional changes associated with introgressed regions in the genome. Our results represent an important step toward understanding the patterns and consequences of gene flow in species, sampled at the least studied, yet climatically vulnerable part of their habitat that can be further used to inform conservation strategies that promote connectivity and gene flow between populations.

}, keywords = {gene flow, genetic diversity, Himalayas, pika}, doi = {10.1002/ece3.10129}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10208896/}, author = {Nishma Dahal and Melia G. Romine and Sunita Khatiwara and Uma Ramakrishnan and Sangeet Lamichhaney} } @article {8097, title = {Identification of key amino acid residues in OqxB mediated efflux of fluoroquinolones using site-directed mutagenesis [Bugworks Research Pvt. Ltd., a C-CAMP Startup]}, journal = {Res Microbiol}, year = {2023}, month = {2023 Feb 02}, pages = {104039}, abstract = {

OqxB belongs to the RND (Resistance-Nodulation-Division) efflux pump family, recognized widely as a major contributor towards enhancing antimicrobial resistance. It is known to be predominantly present in all Klebsiella spp. and is attributed for its role in increasing resistance against an array of antibiotics like nitrofurantoin, quinolones, β-lactams and colistin. However, the presence of oqxB encoding this efflux pump is not limited only to Klebsiella spp., but is also found to occur via horizontal gene transfer in other bacterial genera like Escherichia coli, Enterobacter cloacae and Salmonella spp. Recently, we reported the crystal structure of OqxB and its structure-function relationship required for the efflux of fluoroquinolones. Extending these findings further, we characterized the structural architecture of this efflux pump along with identifying some critical amino acids at the substrate binding domain of OqxB. Based on our in silico modelling studies, both, hydrophobic residues (F180, L280, L621, F626) and polar residues (R48, E50, E184, R157, R774) were found to be located at this site. The present work reports the importance of these key amino acid residues and the crucial ion-pair interactions at the substrate-binding pocket, thereby establishing their role in OqxB mediated efflux and the resultant resistance development against fluoroquinolones.

}, issn = {1769-7123}, doi = {10.1016/j.resmic.2023.104039}, author = {Bhowmik, Purnendu and Bharatham, Nagakumar and Murakami, Satoshi and Ramachandran, Vasanthi and Datta, Santanu} } @article {8556, title = {Purification and characterization of an asialofetuin specific lectin from the rhizome of Xanthosoma violaceum Schott [Mass Spectrometry - Proteomics Facility]}, journal = {Protein Expr Purif}, year = {2023}, month = {2023 Aug 29}, pages = {106357}, abstract = {

Lectins are proteins or glycoproteins that bind specifically and reversibly to the carbohydrate or glycoconjugates. A new lectin is purified from the rhizome of Xanthosoma violaceum Schott. by successive steps of ammonium sulfate fractionation and affinity chromatography with asialofetuin as ligand. The purified lectin was found to be a homotetramer of approximately 49 kDa with a subunit molecular weight of 12 kDa linked by non-covalent bonds. Characterization of the lectin shows that the hemagglutination activity is inhibited by asialofetuin and d-galacturonic acid. Hemagglutination activity is shown only in rabbit RBC but not in the human RBC of all blood groups. It is a metal ion-independent glycoprotein of 1.87\% carbohydrate content, stable upto 40 {\textdegree}C and pH from 5.5 to 9. The lectin shows its optimum hemagglutination activity at 0 {\textdegree}C-40 {\textdegree}C and pH 6 to 8.5. From LC-MS/MS analysis it is confirmed that the purified lectin was not purified and characterized earlier.

}, issn = {1096-0279}, doi = {10.1016/j.pep.2023.106357}, author = {Devi, Oinam Sangita and Singh, Senjam Sunil and Rana, K and Singh, Sorokhaibam Jibankumar and Singh, Wayenbam Sobhachandra} } @article {5253, title = {Analysis of water soluble fractions of crude oil by gas chromatography: Mass spectroscopy [Mass Spectrometry - Metabolomics Facility]}, journal = {The Pharma Innovation Journal}, volume = {SP-11(4)}, year = {2022}, month = {06/2022}, chapter = {1119}, abstract = {

Crude oil is the major source of energy in the modern society to meet the global energy demand by which exploitation of crude oil and its transportation increasing rapidly leading to frequent catastrophic oil spills. When oil spill occurs or when oil is discharged into aquatic environment the components of the crude oil present in it are mostly volatile, evaporates into the environment and the fraction of the oil soluble in water (i.e., WSF) is available to the organisms directly which is the main determinant of crude oil toxicity to aquatic organisms. Although this fraction is present only in relatively low concentrations, it is this fraction which is in most intimate contact with fish and other pelagic organisms with carcinogenic and mutagenic potential. So, the aim of the study was to determine different hydrocarbons dissolved in water soluble fraction (WSF) of crude oil qualitatively and quantitatively. The determination of different hydrocarbons present in water soluble fraction of crude oil can be used as reference point for many studies in future for determining the toxicity of water soluble fraction of crude oil to fishes.

}, keywords = {crude oil, gas chromatography, Water soluble fraction}, url = {https://www.thepharmajournal.com/archives/2022/vol11issue4S/PartP/S-11-4-135-968.pdf}, author = {Rishika, V. and Lakshmipathi, M.T. and Sampath Kumar, B.} } @article {2916, title = {Characterization of ACE inhibitory and antioxidant peptides in yak and cow milk hard chhurpi cheese of the Sikkim Himalayan region [Mass Spectrometry Proteomics Facility]}, journal = {Food Chemistry: X}, volume = {13}, year = {2022}, month = {03/2022}, pages = {100231}, type = {Journal Article}, abstract = {

In this study, simulated in vitro GI digestion of the Himalayan hard chhurpi cheese resulted in the increase of hydrolyzed protein content, antioxidant and ACE-inhibitory activities. LC-MS/MS-based peptidomics revealed a total of 1473 peptides in the samples originating from different milk proteins, including α-S1-casein, α-S2-casein, β-casein, κ-casein, α-lactalbumin, and β-lactoglobulin, out of which 60 peptides have been reported for different functional properties. A total of 101 peptides were predicted to be antihypertensive using the bioactivity prediction web servers, AHTpin and mAHTPred. In silico molecular docking studies predicted 20 antihypertensive peptides, exhibiting non-bond interactions between hard chhurpi peptides and ACE catalytic residues. A peptide, SLVYPFPGPI, identified in GI digested cow hard chhurpi and undigested, and GI digested samples of yak hard chhurpi, showed a stronger binding affinity towards ACE. Identifying antioxidant and ACE inhibitory peptides in hard cheese products adds value to them as functional foods of the Himalayan region.

}, keywords = {Antihypertensive, Bioactive peptides, Hard chhurpi, Molecular docking, Proteomics, Sikkim Himalaya}, doi = {https://doi.org/10.1016/j.fochx.2022.100231}, url = {https://www.sciencedirect.com/science/article/pii/S2590157522000293}, author = {Abedin, Md Minhajul and Chourasia, Rounak and Phukon, Loreni Chiring and Singh, Sudhir P and Rai, Amit Kumar} } @article {3704, title = {Genome-wide SNP markers from fecal samples reveal anthropogenic impacts on connectivity: case of a small carnivore in the central Indian landscape [Next Gen Genomics Facility]}, journal = {Animal Conservation}, year = {2022}, month = {03/2022}, abstract = {

Maintaining gene flow among fragmented habitat patches is critical for the long-term persistence of wild species. Landscape genetics tools are often used to understand the impact of landscape features on gene flow among fragmented populations. The ability to detect the relationship between gene flow and landscape depends on the power of the genetic tools used, which increases with the number of genotyped loci. Next-generation sequencing (NGS) based methods allow genotyping of a high number of loci but are challenging to implement for non-invasive samples, which are commonly used in conservation genetics research. Here we assess the impact of landscape heterogeneity on jungle cat (Felis chaus) movement using genome-wide single nucleotide polymorphism (SNP) markers obtained from fecal samples, using a methylation-based DNA (MBD) enrichment method. We successfully genotyped 20 jungle cat individuals at 2246 SNP loci and compared our results to a previous study that used microsatellite markers and 93 individuals. Our results demonstrate the efficiency and robustness of the MBD enrichment approach with fecal samples in generating genome-wide data for endangered and cryptic species of conservation concern. Our landscape analyses revealed that roads and human-dominated land-use negatively impact jungle cat movement in central India. We explicitly quantified the uncertainty in our analyses and concluded that several thousand SNPs from fewer individuals provide more power than tens of microsatellites from more individuals, in quantifying the effects of landscape on gene flow. Our results provide insight into the impacts of anthropogenic habitat modification on an often-ignored small carnivore species. Insights on connectivity for such species can help policymakers and wildlife managers move beyond connectivity contingent on charismatic species to devise holistic landscape-level management plans for multiple carnivores.

}, doi = {https://doi.org/10.1111/acv.12770}, author = {Tyagi, A. and Khan, A. and Thatte, P. and Ramakrishnan, U.} } @article {3630, title = {Immune profile and responses of a novel dengue DNA vaccine encoding an EDIII-NS1 consensus design based on Indo-African sequences [C-CAMP Bioincubation Facility]}, journal = {Molecular Therapy - Cell Press}, year = {2022}, month = {2022 Jan 07}, type = {Journal Article}, abstract = {

The ongoing COVID-19 pandemic highlights the need to tackle viral variants, expand the number of antigens, and assess diverse delivery systems for vaccines against emerging viruses. In the present study, a DNA vaccine candidate was generated by combining in tandem envelope protein domain III (EDIII) of dengue virus serotypes 1-4 and a dengue virus (DENV)-2 non-structural protein 1 (NS1) protein-coding region. Each domain was designed as a serotype-specific consensus coding sequence derived from different genotypes based on the whole genome sequencing of clinical isolates in\ India and complemented with data from Africa. This sequence was further optimized for protein expression. In silico structural analysis of the EDIII consensus sequence revealed that epitopes are structurally conserved and immunogenic. The vaccination of mice with this construct induced pan-serotype neutralizing antibodies and antigen-specific T\ cell responses. Assaying intracellular interferon (IFN)-γ staining, immunoglobulin IgG2(a/c)/IgG1 ratios, and immune gene profiling suggests a strong Th1-dominant immune\ response. Finally, the passive transfer of immune sera protected AG129 mice challenged with a virulent, non-mouse-adapted DENV-2 strain. Our findings collectively suggest an alternative strategy for dengue vaccine design by offering a novel vaccine candidate with a possible broad-spectrum protection and a successful clinical translation either as a stand alone or in a mix and match strategy.

}, keywords = {antibody-dependent enhancement, consensus sequence, dengue, dengue surveillance, DNA vaccine, EDIII domain, NS1 protein}, issn = {1525-0024}, doi = {10.1016/j.ymthe.2022.01.013}, url = {https://www.cell.com/molecular-therapy-family/molecular-therapy/fulltext/S1525-0016(22)00013-2$\#$secsectitle0165}, author = {Sankaradoss, Arun and Jagtap, Suraj and Nazir, Junaid and Moula, Shefta E and Modak, Ayan and Fialho, Joshuah and Iyer, Meenakshi and Shastri, Jayanthi S and Dias, Mary and Gadepalli, Ravisekhar and Aggarwal, Alisha and Vedpathak, Manoj and Agrawal, Sachee and Pandit, Awadhesh and Nisheetha, Amul and Kumar, Anuj and Bordoloi, Mahasweta and Shafi, Mohamed and Shelar, Bhagyashree and Balachandra, Swathi S and Damodar, Tina and Masika, Moses Muia and Mwaura, Patrick and Anzala, Omu and Muthumani, Kar and Sowdhamini, Ramanathan and Medigeshi, Guruprasad R and Roy, Rahul and Pattabiraman, Chitra and Krishna, Sudhir and Sreekumar, Easwaran} } @article {3480, title = {Production and characterization of bioactive peptides from rice beans using Bacillus subtilis [Mass Spectrometry - Proteomics Facility]}, journal = {Bioresource Technology}, year = {2022}, month = {01/2022}, pages = {126932}, type = {Journal Article}, abstract = {

A bioprocess was developed for production of bioactive peptides on microbial fermentation of rice beans using proteolytic Bacillus subtilis strains. The peptides produced were identified by LC-MS/MS analysis, revealing the presence of many unique peptide sequences to individual hydrolysates. On functional properties prediction, antihypertensive peptides (3.90\%) were found to be higher in comparison to other bioactive peptides. Among different strains, B. subtilis KN2B fermented hydrolysate exhibited highest angiotensin converting enzyme (ACE)-inhibitory activity (45.73\%). Furthermore, 19 selected peptides, including the common and unique peptides were examined for their affinity towards the binding cavity of ACE using molecular docking. The results showed a common peptide PFPIPFPIPIPLP, and another IPFPPIPFLPPI unique to B. subtilis KN2B fermented hydrolysate exhibited promising binding at the ACE binding site with substantial free binding energy. The process developed can be used for the production of bioactive peptides from rice bean for application in nutraceutical industries.

}, keywords = {ACE-inhibitory peptide, Bacillus subtilis, Fermented legume, Molecular docking, Rice bean}, doi = {https://doi.org/10.1016/j.biortech.2022.126932}, url = {https://www.sciencedirect.com/science/article/abs/pii/S0960852422002619}, author = {Padhi, Srichandan and Chourasia, Rounak and Kumari, Megha and Singh, Sudhir P and Rai, Amit Kumar} } @article {7323, title = {Ultrashort Peptide-Based Hydrogel for the Healing of Critical Bone Defects in Rabbits [C-CAMP BIG Grantee/Startup]}, journal = {ACS Appl Mater Interfaces}, year = {2022}, month = {2022 Nov 19}, abstract = {

The use of hydrogels as scaffolds for three-dimensional (3D) cell growth is an active area of research in tissue engineering. Herein, we report the self-assembly of an ultrashort peptide, a tetrapeptide, Asp-Leu-IIe-IIe, the shortest peptide sequence from a highly fibrillogenic protein TDP-43, into the hydrogel. The hydrogel was mechanically strong and highly stable, with storage modulus values in MPa ranges. The hydrogel supported the proliferation and successful differentiation of bone marrow-derived mesenchymal stem cells (BMSCs) in its matrix as assessed by cell viability, calcium deposition, alkaline phosphatase (ALP) activity, and the expression of osteogenic marker gene studies. To check whether the hydrogel supports 3D growth and regeneration in conditions, a rabbit critical bone defect model was used. Micro-computed tomography (CT) and X-ray analysis demonstrated the formation of mineralized neobone in the defect areas, with significantly higher bone mineralization and relative bone densities in animals treated with the peptide hydrogel compared to nontreated and matrigel treatment groups. The ultrashort peptide-based hydrogel developed in this work holds great potential for its further development as tissue regeneration and/or engineering scaffolds.

}, issn = {1944-8252}, doi = {10.1021/acsami.2c18733}, author = {Yadav, Nitin and Kumar, Utkarsh and Roopmani, Purandhi and Krishnan, Uma Maheswari and Sethuraman, Swaminathan and Chauhan, Meenakshi K and Chauhan, Virander S} } @article {2598, title = {Validated In Silico Model for Biofilm Formation in Escherichia coli [Bugworks Research Pvt. Ltd., a C-CAMP Startup]}, journal = {ACS Synthetic Biology}, year = {2022}, month = {01/2022}, abstract = {

Using\ Escherichia coli\ as the representative biofilm former, we report here the development of an in silico model built by simulating events that transform a free-living bacterial entity into self-encased multicellular biofilms. Published literature on \~{}300 genes associated with pathways involved in biofilm formation was curated, static maps were created, and suitably interconnected with their respective metabolites using ordinary differential equations. Precise interplay of genetic networks that regulate the transitory switching of bacterial growth pattern in response to environmental changes and the resultant multicomponent synthesis of the extracellular matrix were appropriately represented. Subsequently, the in silico model was analyzed by simulating time-dependent changes in the concentration of components by using the R and python environment. The model was validated by simulating and verifying the impact of key gene knockouts (KOs) and systematic knockdowns on biofilm formation, thus ensuring the outcomes were comparable with the reported literature. Similarly, specific gene KOs in laboratory and pathogenic\ E. coli\ were constructed and assessed. MiaA, YdeO, and YgiV were found to be crucial in biofilm development. Furthermore, qRT-PCR confirmed the elevation of expression in biofilm-forming clinical isolates. Findings reported in this study offer opportunities for identifying biofilm inhibitors with applications in multiple industries. The application of this model can be extended to the health care sector specifically to develop novel adjunct therapies that prevent biofilms in medical implants and reduce emergence of biofilm-associated resistant polymicrobial-chronic infections. The in silico framework reported here is open source and accessible for further enhancements.

}, doi = {10.1021/acssynbio.1c00445}, url = {https://doi.org/10.1021/acssynbio.1c00445}, author = {Bhowmik, Purnendu and Rajagopal, Sreenath and Hmar, Rothangamawi Victoria and Singh, Purnima and Saxena, Pragya and Amar, Prakruthi and Thomas, Teby and Ravishankar, Rajani and Nagaraj, Savitha and Katagihallimath, Nainesh and Sarangapani, Ramanujan Kadambi and Ramachandran, Vasanthi and Datta, Santanu} } @article {1858, title = {Azaindole Based Potentiator of Antibiotics against Gram-Negative Bacteria [C-CAMP Startup Bugworks]}, journal = {ACS Infectious Diseases}, year = {2021}, month = {10/2021}, type = {Journal Article}, abstract = {
We discovered azaindole-based compounds with weak innate activity that exhibit substantial potentiation of antibacterial activities of different antibiotics, viz., rifampicin, erythromycin, solithromycin, and novobiocin in Gram-negative bacteria. In the presence of the azaindole derivatives, these antibiotics exhibited submicromolar minimum inhibitory concentrations (MICs) against Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. The fold improvements in MIC of these antibiotics that were otherwise weak or inactive on their own against these bacteria were also observed against drug-resistant clinical isolates. Our studies indicate that this selective potentiation is probably through destabilization of the outer membrane{\textquoteright}s integrity, known to be regulated by the lipopolysaccharides (LPS). Thus, the azaindole based compounds described here open opportunities for those antibiotics that are otherwise ineffective due to LPS mediated entry barriers in Gram-negative bacteria.
}, keywords = {Azaindole, Bacterial Permeability, Lipopolysachhardies (LPS), Polymyxin, Synergy}, doi = {10.1021/acsinfecdis.1c00171}, url = {https://pubs.acs.org/doi/abs/10.1021/acsinfecdis.1c00171$\#$}, author = {Sharma, Sreevalli and Rao, Ranga and Reeve, Stephanie M and Phelps, Gregory A and Bharatham, Nagakumar and Katagihallimath, Nainesh and Ramachandran, Vasanthi and Raveendran, Savitha and Sarma, Maitrayee and Nath, Anubha} } @article {1761, title = {Elucidation of the liver proteome in response to an antioxidant intake in rabbits [Mass Spectrometry - Proteomics Facility]}, journal = {Egyptian Liver Journal }, volume = {11}, year = {2021}, month = {06/2021}, abstract = {

Background

Antioxidant intakes are one of the most cherished dietary approaches for the management of oxidative stress-induced liver damages. These antioxidants exist as the bioactive compounds present in plants and other natural sources functioning in varieties of ways from acting as direct scavengers of the free radicals to acting as the modifiers of genes and proteins expressions.\ Chlorella vulgaris\ is one of such antioxidants; it is a unicellular microalga and a rich source of polyphenols which has been reported for its capacity of reducing oxidative stress by upregulation of antioxidant genes. However, there are scarce reports on its effect on antioxidant protein expressions and functions in the liver. This situation necessitates untargeted proteomic profiling of the liver due to the antioxidant intakes as carried out in this present study. Sixteen laboratory weaner rabbits of 8 weeks old with initial average bodyweight of 1060 {\textpm} 29.42 g were randomly divided into two groups (n\ = 8 per group); the first group served as control while the second served as the treatment group were used for this study.

Results

After a period of 120 days daily consumption of 500 mg of\ Chlorella vulgaris\ biomass per kg bodyweight of the rabbit models, the animals were sacrificed and their livers were harvested followed by protein extraction for the untargeted proteomic profiling using LC-MS/Orbitrap Fusion Tribrid{\texttrademark} peptides quantifier and sequencer. Also, there was an assessment of the oxidative stress biomarkers in the liver and serum of the rabbits. Five-hundred and forty-four (544) proteins were identified out of which 204 were unique to the control, 198 were unique to the treatment group, while 142 were common to both groups of the rabbits. Antioxidant proteins commonly found in both groups were upregulated in the treatment group and were significantly associated with oxidative stress-protective activities. There was a reduction in oxidative stress biomarkers of the supplemented group as indicated by the assessment of the liver malondialdehyde concentrations (p\ \< 0.05), total antioxidant capacities (p\ \< 0.05), and antioxidant enzyme activities (p\ \< 0.05). Similarly, these biomarkers were significantly reduced in the serum of the supplemented rabbits (p\ \< 0.05).

Conclusion

The study concluded that\ Chlorella vulgaris\ is an antioxidant agent that could be suitable for reducing liver oxidative stress damage and it is a potential drug candidate for protecting the liver against oxidative stress damages as revealed in the rabbit models.

}, doi = {https://doi.org/10.1186/s43066-021-00118-3}, url = {https://link.springer.com/article/10.1186/s43066-021-00118-3$\#$Ack1}, author = {Akeem Babatunde Sikiru and Arunachalam Arangasamy and Stephen Sunday Acheneje Egena and Sejian Veerasamy and Ippala Janardhan Reddy and Bhatta Raghavendra} } @article {1691, title = {Geometry encoded functional programming of tumor homing peptides for targeted drug delivery [Image Analysis Support]}, journal = {J Control Release}, year = {2021}, month = {2021 Mar 12}, abstract = {

Poly-peptide molecules have shown promising applications in drug delivery and tumor targeting. A series of tumor homing peptides were designed by exhaustively sampling low energy geometrical basins of amino acids at specific sites of a peptide molecule to induce a conformational lock. This peptide library was pruned to a limited set of eight molecules, employing electrostatic interactions, docking, and molecular dynamics simulations. These designed and optimized peptides were synthesized and tested on various cell lines, including breast cancer (MDA-MB-231), cervical cancer (HeLa), osteosarcoma (U2-OS), and non-cancerous mammary epithelial cells (MCF-10A) using confocal microscopy and flow cytometry. Peptides show differential uptake in cancerous MDA-MB-231, HeLa, U2-OS, and non-cancerous MCF-10A cells. Confocal imaging verified their ability to penetrate even in 3D tumorospheres of MDA-MB-231 cells. Further, experiments of mitochondrial membrane potential depolarization and Caspase-3 activation confirmed that their cytotoxic effects are by apoptosis. Homing ability of the designed peptides in in vivo system and fluorescence imaging with clinical samples of human origin have further confirmed that the in vitro studies are qualitatively identical and quantitatively comparable in their ability to selectively recognize tumor cells. Overall, we present a roadmap for the functional programming of peptide-based homing and penetrating molecules that can perform selective tumor targeting.

}, issn = {1873-4995}, doi = {10.1016/j.jconrel.2021.03.010}, author = {Goyal, Ruchika and Jerath, Gaurav and Akhil, R and Chandrasekharan, Aneesh and Puppala, Eswara Rao and Ponneganti, Srikanth and Sarma, Anupam and Naidu, V G M and Santhoshkumar, T R and Ramakrishnan, Vibin} } @article {1776, title = {Investigation of chemical and biological properties of an acidic polysaccharide fraction from Pleurotus eous (Berk.) Sacc}, journal = {Food Bioscience}, year = {2021}, month = {06/2021}, abstract = {

Pleurotus eous, pink oyster mushroom and functional food, is widely cultivated in Southern India. In this study, we successfully attempted, to isolate a new acidic polysaccharide fraction (PEPA-1a) possessing a molecular weight of 8.926 {\texttimes} 104 Da from the fruiting bodies of Pleurotus eous through ion-exchange and gel-filtration chromatographic techniques. A monosaccharide composition comprising glucose, galactose, rhamnose, mannose, and N-acetyl galactosamine were found to have the corresponding mole percentages of 20.25, 56.75, 3.06, 11.07, and 8.86, respectively. The antioxidant activity was assessed through seven in vitro tests, PEPA-1a showed significant antioxidant activity in a dose-dependent way, with EC50 values stretching from 1.08 to 4.91 mg/mL. Analyses of PEPA-1a towards in vitro anti-tumour showed high activity against HT29 (IC50 = 233.50 μg/mL) and PC3 cells (IC50 = 230.80 μg/mL). The anticoagulant activity was estimated through APTT, PT and TT tests which show effective anticoagulant activity. Also, the congo red analysis revealed the triple-helical structures of carbohydrates. The results indicate that consumption of P eous polysaccharide may be beneficial for health and will serve as an exceptionally accessible natural source for food and pharmaceutical industries.

}, keywords = {Anti-tumour activity, Anticoagulant activity, Antioxidant activity, Characterization, Pleurotus eous, Polysaccharides}, doi = {doi.org/10.1016/j.fbio.2021.101209}, url = {https://www.sciencedirect.com/science/article/abs/pii/S2212429221003345$\#$!}, author = {Sasikala Gunasekaran and Sudha Govindan and Prasanna Ramani} } @article {1678, title = {Methanol Skin Mucus Extract of Mrigal (Cirrhinus mrigala) Fish Peptide Targeting Viral Particles of Infectious Pancreatic Necrosis Virus (IPNV) and Infectious Salmon Anemia Virus (ISAV): an in silico Approach [Mass Spectrometry Facility]}, journal = {International Journal of Peptide Research and Therapeutics}, volume = {71}, year = {2021}, month = {02/2021}, type = {Research Article}, abstract = {

The teleost fish skin mucus acts as an important physical and biological barrier that prevents fish from the surrounding environment. Many studies reported the presence of various immunological molecules in fish skin mucus that involve in protection against invading microbes. In the present study, the skin mucus proteins of freshwater fish\ Cirrhinus mrigala\ (mrigal) were extracted using organic solvent (methanol) and further analyzed by liquid chromatography-tandem mass spectrometry (LC{\textendash}MS/MS) to identify proteins by database retrieval. LC{\textendash}MS/MS analysis revealed the presence of diverse proteins in the methanol skin mucus extract. The identified proteins were classified into biological process, cellular process and molecular functions by Gene Ontology (GO) enrichment analysis. A peptide was selected, modelled and compared with other antimicrobial peptides sequences through phylogenetic analysis and showed that the modelled peptide shared high similarity with Arminin-1 of Cnidaria animals. We also investigated the potentiality of the modelled peptide against Infectious Pancreatic Necrosis Virus sub viral particle and Infectious Salmon Anemia Virus hemagglutinin-esterase protein through protein-peptide docking using ClusPro. The docking results confirmed that the modelled peptide has good interactions with viral particles. Therefore, these results suggest that the modelled peptide molecule from\ C. mrigala\ methanol skin mucus extract can be further studied that aid in the development of novel peptide candidate for the control of aquaculture viral diseases.

}, doi = {https://doi.org/10.1007/s10989-021-10179-y}, author = {Arun Sridhar and Dinesh Babu Manikandan and Sathish Kumar Marimuthu and Manikandan Murugesan and Thirumurugan Ramasamy} } @article {1917, title = {Novel non intrusive continuous use ZeBox technology to trap and kill airborne microbes [Biomoneta Research Pvt. Ltd., a C-CAMP Startup / Electron Microscopy Facility]}, journal = {Scientific Reports}, volume = {11}, year = {2021}, month = {11/2021}, pages = {Article number: 22779 }, abstract = {

Preventing nosocomial infection is a major unmet need of our times. Existing air decontamination technologies suffer from demerits such as toxicity of exposure, species specificity, noxious gas emission, environment-dependent performance and high power consumption. Here, we present a novel technology called {\textquotedblleft}ZeBox{\textquotedblright} that transcends the conventional limitations and achieves high microbicidal efficiency. In ZeBox, a non-ionizing electric field extracts naturally charged microbes from flowing air and deposits them on engineered microbicidal surfaces. The surface{\textquoteright}s three dimensional topography traps the microbes long enough for them to be inactivated. The electric field and chemical surfaces synergistically achieve rapid inactivation of a broad spectrum of microbes. ZeBox achieved near complete kill of airborne microbes in challenge tests (5{\textendash}9 log reduction) and\ \>90\%\ efficiency in a fully functional stem cell research facility in the presence of humans. Thus, ZeBox fulfills the dire need for a real-time, continuous, safe, trap-and-kill air decontamination technology.

}, doi = {doi.org/10.1038/s41598-021-02184-4}, author = {Kruttika S. Phadke and Deepak G. Madival and Janani Venkataraman and Debosmita Kundu and K. S. Ramanujan and Nisha Holla and Jaywant Arakeri and Gaurav Tomar and Santanu Datta and Arindam Ghatak} } @article {1864, title = {Organic mineral supplementation on differential protein profile of Osmanabadi bucks (Capra hircus) [Mass Spectrometry - Proteomics Facility]}, journal = {Reproductive Biology}, volume = {21}, year = {2021}, month = {07/2021}, pages = {100533}, type = {Journal Article}, abstract = {

The present study aimed to determine the differential protein profile of seminal plasma proteins of bucks supplemented with trace minerals. Forty bucks of uniform size and body weight were assigned as ten groups (n = 4). The control group (T1) was fed with the control diet (concentration mixture and roughages) whereas the remaining groups were supplemented the control diet with Zn20 mg (T2), Zn40 mg (T3), Zn60 mg (T4), Cu12.5 mg (T5), Cu25 mg (T6), Cu37.5 mg (T7), Zn20 mg + Cu12.5 mg (T8), Zn40 mg + Cu25 mg (T9), and Zn60 mg + Cu37.5 mg (T10) for eight months. Seminal plasma proteins from each group were subjected to two-dimensional electrophoresis and fifteen differential proteins were selected based on differential expression, subjected to identification using Nano-LC{\textendash}MS/MS (LTQ-Qrbitrap-MS). The identified proteins were Triacylglycerol lipase, EGF like repeats and discoidin domains 3, Lipocalin, Iodothyronine deiodinase, Transcription factor AP2-delta, 60S ribosomal protein L13, IST1 factor associated with ESCRT-III, Lysozyme, Uncharacterized protein (BRI3-binding protein), Uncharacterized protein, Histone deacetylase 11, General transcription factor IIF subunit 2, Nudix hydrolase 6, Protein kinase cAMP-activated catalytic subunit beta and Elongin C. The organic Cu supplemented group is the better than the organic Zn and organic Zn + Cu supplemented groups.

}, keywords = {Bucks, Differential protein, Fecundity, Organic mineral, Seminal plasma}, doi = {https://doi.org/10.1016/j.repbio.2021.100533}, url = {https://www.sciencedirect.com/science/article/abs/pii/S1642431X21000541$\#$}, author = {Sekar, Backialakshmi and Arangasamy, Arunachalam and Naidu, Sharanya Jeevendra and Reddy, Ippala Janardhan and Bhatta, Raghavendra} } @article {1861, title = {Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae [Bugworks, a C-CAMP startup]}, journal = {Nature communications}, volume = {12}, year = {2021}, month = {09/2021}, pages = {1{\textendash}12}, type = {Journal Article}, abstract = {

OqxB is an RND (Resistance-Nodulation-Division) efflux pump that has emerged as a factor contributing to the antibiotic resistance in Klebsiella pneumoniae. OqxB underwent horizontal gene transfer and is now seen in other Gram-negative bacterial pathogens including Escherichia coli, Enterobacter cloacae and Salmonella spp., further disseminating multi-drug resistance. In this study, we describe crystal structure of OqxB with n-dodecyl-β-D-maltoside (DDM) molecules bound in its substrate-binding pocket, at 1.85 {\r A} resolution. We utilize this structure in computational studies to predict the key amino acids contributing to the efflux of fluoroquinolones by OqxB, distinct from analogous residues in related transporters AcrB and MexB. Finally, our complementation assays with mutated OqxB and minimum inhibitory concentration (MIC) experiments with clinical isolates of E. coli provide further evidence that the predicted structural features are indeed involved in ciprofloxacin efflux.

}, doi = {https://doi.org/10.1038/s41467-021-25679-0}, url = {https://www.nature.com/articles/s41467-021-25679-0}, author = {Bharatham, Nagakumar and Bhowmik, Purnendu and Aoki, Maho and Okada, Ui and Sharma, Sreevalli and Yamashita, Eiki and Shanbhag, Anirudh P and Rajagopal, Sreenath and Thomas, Teby and Sarma, Maitrayee and others} } @article {1848, title = {SUMOylation of Arginyl tRNA Synthetase Modulates the Drosophila Innate Immune Response [Transgenic Fly Facility]}, journal = {Frontiers in Cell and Developmental Biology }, year = {2021}, month = {09/2021}, abstract = {

SUMO conjugation of a substrate protein can modify its activity, localization, interaction or function. A large number of SUMO targets in cells have been identified by Proteomics, but biological roles for SUMO conjugation for most targets remains elusive. The multi-aminoacyl tRNA synthetase complex (MARS) is a sensor and regulator of immune signaling. The proteins of this 1.2 MDa complex are targets of SUMO conjugation, in response to infection. Arginyl tRNA Synthetase (RRS), a member of the sub-complex II of MARS, is one such SUMO conjugation target. The sites for SUMO conjugation are Lys 147 and 383. Replacement of these residues by Arg (RRSK147R,K383R), creates a SUMO conjugation resistant variant (RRSSCR). Transgenic Drosophila lines for RRSWT and RRSSCR were generated by expressing these variants in a RRS loss of function (lof) animal, using the UAS-Gal4 system. The RRS-lof line was itself generated using CRISPR/Cas9 genome editing. Expression of both RRSWT and RRSSCR rescue the RRS-lof lethality. Adult animals expressing RRSWT and RRSSCR are compared and contrasted for their response to bacterial infection by gram positive M. luteus and gram negative Ecc15. We find that RRSSCR, when compared to RRSWT\ shows modulation of the transcriptional response, as measured by quantitative 3' mRNA sequencing. Our study uncovers a possible non-canonical role for SUMOylation of RRS, a member of the MARS complex, in host-defense.

}, keywords = {ArgRS, Cas9, CRISPR, MARS complex, NFkB, signaling}, doi = {https://doi.org/10.3389/fcell.2021.695630}, url = {https://www.frontiersin.org/articles/10.3389/fcell.2021.695630/full$\#$h9}, author = {Prajna Nayak and Aarti Kejriwal and Girish S. Ratnaparkhi} } @article {1677, title = {The truth about scats and dogs: Next-generation sequencing and spatial capture{\textendash}recapture models offer opportunities for conservation monitoring of an endangered social canid [Next Gen Genomics Facility (INT)].}, journal = {Biological Conservation}, volume = {256}, year = {2021}, pages = {109028}, abstract = {

Obtaining accurate population counts of endangered species is central to conservation biology, with implications for gaining ecological insights, informing management strategies, and judicial use of conservation funds. Despite decades of progress in methodological developments in the realm of population ecology, reliable density estimates are unavailable for many species of conservation concern. The dhole (Asiatic wild dog Cuon alpinus) is one such endangered large carnivore found in the tropical forests of south and southeast Asia. Here, we (i) develop next-generation sequencing resources to identify individual dholes from genetic samples, (ii) apply these methods to identify individuals in the wild, from scat (fecal) samples collected through systematic field surveys and (iii) generate reliable estimates of dhole densities in Wayanad Wildlife Sanctuary (Western Ghats, India) using Spatial Capture{\textendash}Recapture {\textquoteleft}SCR{\textquoteright} models. We estimate dhole densities to be 12{\textendash}14.2 individuals/100 sq. km based on a set of SCR models, with \ 50 individuals within Wayanad{\textquoteright}s administrative boundary. Our study presents a methodological improvement in generating population estimates of an important apex predator while also offering ecologically informative insights on a species in dire need of science-based management efforts. Replicating this study across connected reserves and over time can serve as a unified framework for understanding population dynamics, population structures, landscape connectivity and metapopulation-level conservation requirements. We propose that the approach presented here may be adopted as an economically and logistically feasible protocol for conservation monitoring of dholes and other ecologically important species plagued by similar issues of data-deficiency, and insufficient funding and resources.

}, keywords = {Carnivores, Conservation monitoring, Genetic markers, Non-invasive surveys, Population estimation, Single nucleotide polymorphisms, Tropics}, issn = {0006-3207}, doi = {https://doi.org/10.1016/j.biocon.2021.109028}, url = {https://www.sciencedirect.com/science/article/pii/S000632072100080X}, author = {Arjun Srivathsa and Ryan G. Rodrigues and Kok Ben Toh and Arun Zachariah and Ryan W. Taylor and Madan K. Oli and Uma Ramakrishnan} } @article {1442, title = {Caspar SUMOylation regulates lifespan [Transgenic Fly Facility]}, journal = {MicroPubl Biol}, volume = {2020}, year = {2020}, month = {2020 Aug 02}, issn = {2578-9430}, doi = {10.17912/micropub.biology.000288}, author = {Kaduskar, Bhagyashree and Trivedi, Deepti and Ratnaparkhi, Girish S} } @article {1323, title = {Dataset for the combined transcriptome assembly of M. oleifera and functional annotation [Next Gen Genomics Facility (INT)]}, journal = {Data in Brief}, year = {2020}, pages = {105416}, abstract = {

In this paper, we present the data acquired during transcriptome analysis of the plant Moringa oleifera [1] from five different tissues (root, stem, leaf, flower and seed) by RNA sequencing. A total of 271 million reads were assembled with an N50 of 2094bp. The combined transcriptome was assessed for transcript abundance across five tissues. The protein coding genes identified from the transcripts were annotated and used for orthology analysis. Further, enzymes involved in the biosynthesis of select medicinally important secondary metabolites, vitamins and ion transporters were identified and their expression levels across tissues were examined. The data generated by RNA sequencing has been deposited to NCBI public repository under the accession number PRJNA394193 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA394193).

}, keywords = {Annotation, Enrichment analysis, Gene Expression, Metabolic pathway, Orthology, Transcriptome}, issn = {2352-3409}, doi = {https://doi.org/10.1016/j.dib.2020.105416}, url = {http://www.sciencedirect.com/science/article/pii/S2352340920303103}, author = {K. Mohamed Shafi and Adwait G. Joshi and Iyer Meenakshi and Shaik Naseer Pasha and K. Harini and Jarjapu Mahita and Radha Sivarajan Sajeevan and Snehal D. Karpe and Pritha Ghosh and Sathyanarayanan Nitish and A. Gandhimathi and Oommen K. Mathew and Subramanian Hari Prasanna and Manoharan Malini and Eshita Mutt and Mahantesha Naika and Nithin Ravooru and Rajas M. Rao and Prashant N. Shingate and Anshul Sukhwal and Margaret S. Sunitha and Atul K. Upadhyay and Rithvik S. Vinekar and Ramanathan Sowdhamini} } @article {1447, title = {Dietary supplementation of extracts of red sea weed (Kappaphycus alvarezii) improves growth, intestinal morphology, expression of intestinal genes and immune responses in broiler chickens [Sea6Energy Pvt. Ltd, a C-CAMP Startup]}, journal = {Journal of the Science of Food and Agriculture}, year = {2020}, month = {08, 2020}, type = {Research Article}, abstract = {

BACKGROUND

Effects of supplementation of dried alkaline (referred to as MVP1) and aqueous (referred to as PBD1) extracts of\ K. alvarezii\ , were evaluated in broiler (Vencobb 400) chickens (1{\textendash}35 d post-hatch). In experiment I, each of the seven diets (basal diet with three levels (0.5, 1.5 or 5.0 g kg-1\ diet) of MVP1 or PBD1 and a negative control) was fed to twelve pen replicates containing five birds in each. In experiment II, each of three diets (a negative control, and PBD1 at two levels (1.0 or 1.5 g kg-1\ diet)) was fed to sixteen pen replicates of five chicks in each.

RESULTS

Concentrations of total phenolics, phycobillins and free radical scavenging activity were higher (P\<0.01) whereas carrageenan was lower in PBD1 than in MVP1. In the experiment I, PBD1 at 1.5 g kg-1\ diet improved (P\<0.05) body weight (7.11\% higher). In the experiment II, both the treatments improved (P\<0.01) BW (9.18\% and 8.47\%, respectively) as compared to control. The group fed with PBD1@ 1.0 g kg-1\ had higher (P\<0.05) HI titre, expression of intestinal claudin 2, TLR2A, NOD1, avian beta defensin 4, interleukin 2 and 6 genes than control. Treatments did not influence feed efficiency or levels of most of the antioxidant enzymes. Villus width and crypt depth were significantly higher in the group fed with 1.5 g kg-1\ of PBD1.

CONCLUSION

Supplementing dried aqueous extract of\ Kappaphycus alvarezii\ at 1 g kg-1\ diet may be an effective strategy to increase growth and immunity in broiler chicken.

}, doi = {https://doi.org/10.1002/jsfa.10708}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jsfa.10708}, author = {Paul, Shyam Sundar and Venkata, Hemanth Giri Rao Vantharam and Raju, MVLN and Rama Rao, SV and Nori, Sri Sailaja and Suryanarayan, Shrikumar and Kumar, Vikas and Perveen, Zeba and Srinivas Prasad, Cadaba} } @article {1530, title = {Elucidating the processes and pathways enriched in buffalo sperm proteome in regulating semen quality [Mass Spectrometry Facility - Proteomics]}, journal = {Cell Tissue Res}, year = {2020}, month = {2020 Nov 05}, abstract = {

Sperm carries a reservoir of proteins regulating the molecular functions to attain functional competence. Semen samples collected from buffalo bulls were assessed for sperm functional attributes (n\ =\ 11) and proteome profiling (n\ =\ 6). Sperm proteins were extracted and profiled by employing LC-MS/MS. Overall, the buffalo sperm contained 1365 proteins, of which 458 were common between the groups. The unique proteins were 477 and 430 in good and poor quality semen, respectively. In the whole proteome of buffalo sperm, sexual reproduction with phosphatidylethanolamine-binding protein1 (PEBP1), fetuin-B (FETUB) and acrosin (ACR) was the most enriched (p\ =\ 8.44E-19) biological process, also with thermogenesis (p\ =\ 0.003), oocyte meiosis (p\ =\ 0.007) and vascular smooth muscle contraction (p\ =\ 0.009) apart from metabolic pathways. In good quality semen, mesenchyme migration (p\ =\ 1.24E-07) and morphogenesis (p\ =\ 0.001) were abundant biological processes. In good quality semen, the fluid shear stress (p\ =\ 0.01) and, in poor quality semen, valine, leucine and isoleucine degradation (p\ =\ 3.8E-05) pathways were enriched. In good quality semen, 7 proteins were significantly (p\ \<\ 0.05) upregulated and 33 proteins were significantly (p\ \<\ 0.05) downregulated. On validating the abundantly expressed sperm proteins, serine protease inhibitor Kazal-type 2-like (SPINK2; 2.17-fold) and neddylin (NEDD8; 1.13-fold) were upregulated and YBX2 was downregulated (0.41-fold) in good quality semen as compared with poor quality semen (1-fold). The present findings revealed the importance of sperm proteins in oocyte maturation, fertilization process and early embryonic development. The variations in the proteomic composition can be used as potential markers for the selection of breeding bulls.

}, issn = {1432-0878}, doi = {10.1007/s00441-020-03303-9}, author = {Binsila, Bala Krishnan and Archana, Santhanahalli Siddalingappa and Ramya, Laxman and Swathi, Divakar and Selvaraju, Sellappan and Gowda, N K Shivakumar and Pal, Din Taran and Rafay, Abu and Bhatta, Raghavendra} } @article {1475, title = {Inhibition of plant pathogenic fungi by endophytic Trichoderma spp. through mycoparasitism and volatile organic compounds}, journal = {Microbiological Research}, year = {2020}, pages = {126595}, abstract = {

Antagonism of plant pathogenic fungi by endophytic fungi is a well-known phenomenon. In plate assays, the antagonism could be due to mycoparasitism, competition for space or antibiosis, involving a chemical diffusate, or a volatile organic compound (VOC). In this study, we demonstrate that besides mycoparasitism, VOCs play a major role in antagonism of pathogenic fungi by four endophytic fungi belonging to the genus Trichoderma. Using a double-plate assay, we show that all the four endophytic Trichoderma species significantly inhibited mycelial growth of three of the four pathogens, (Sclerotinia sclerotiorum-TSS, Sclerotium rolfsii-CSR and Fusarium oxysporum-CFO), while that of Macrophomina phaseolina-CMP was not affected. GC-MS analysis of the pure cultures of one of the endophytic fungi studied, namely, Trichoderma longibrachiatum strain 2 (Acc. No. MK751758) and the pathogens, F. oxysporum-CFO and M. phaseolina-CMP revealed the presence of several VOCs including hydrocarbons, alcohols, ketones, aldehydes, esters, acids, ethers and different classes of terpenes. In mixed double plates, where the endophyte was grown along with either of the two plant pathogens, F. oxysporum-CFO or M. phaseolina-CMP, there was an induction of a number of new VOCs that were not detected in the pure cultures of either the endophyte or pathogens. Several of these new VOCs are reported to possess antifungal and cytotoxic activity. We discuss these results and highlight the importance of such interactions in endophyte-pathogen interactions.

}, keywords = {Biological control, Endophytic fungi, Fungal antagonism, Soil-borne pathogenic fungi}, issn = {0944-5013}, doi = {https://doi.org/10.1016/j.micres.2020.126595}, url = {http://www.sciencedirect.com/science/article/pii/S0944501320304638}, author = {P. Rajani and Rajasekaran C. and M.M. Vasanthakumari and Shannon B. Olsson and Ravikanth G. and Uma Shaanker R.} } @article {1465, title = {A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways [Next Gen Genomics Facility (INT)]}, journal = {MethodsX}, year = {2020}, pages = {101053}, abstract = {

This protocol describes a stepwise process to identify proteins of interest from a query proteome derived from NGS data. We implemented this protocol on Moringa oleifera transcriptome to identify proteins involved in secondary metabolite and vitamin biosynthesis and ion transport. This knowledge-driven protocol identifies proteins using an integrated approach involving sensitive sequence search and evolutionary relationships. We make use of functionally important residues (FIR) specific for the query protein family identified through its homologous sequences and literature. We screen protein hits based on the clustering with true homologues through phylogenetic tree reconstruction complemented with the FIR mapping. The protocol was validated for the protein hits through qRT-PCR and transcriptome quantification. Our protocol demonstrated a higher specificity as compared to other methods, particularly in distinguishing cross-family hits. This protocol was effective in transcriptome data analysis of M. oleifera as described in Pasha et. al.{\textbullet}Knowledge-driven protocol to identify secondary metabolite synthesizing protein in a highly specific manner.{\textbullet}Use of functionally important residues for screening of true hits.{\textbullet}Beneficial for metabolite pathway reconstruction in any (species, metagenomics) NGS data.

}, keywords = {functionally important residue, homology, multiple sequence alignment, Pathway, phylogenetic analysis}, issn = {2215-0161}, doi = {https://doi.org/10.1016/j.mex.2020.101053}, url = {http://www.sciencedirect.com/science/article/pii/S2215016120302739}, author = {Adwait G. Joshi and K. Harini and Iyer Meenakshi and K. Mohamed Shafi and Shaik Naseer Pasha and Jarjapu Mahita and Radha Sivarajan Sajeevan and Snehal D. Karpe and Pritha Ghosh and Sathyanarayanan Nitish and A. Gandhimathi and Oommen K. Mathew and Subramanian Hari Prasanna and Manoharan Malini and Eshita Mutt and Mahantesha Naika and Nithin Ravooru and Rajas M. Rao and Prashant N. Shingate and Anshul Sukhwal and Margaret S. Sunitha and Atul K. Upadhyay and Rithvik S. Vinekar and Ramanathan Sowdhamini} } @article {1637, title = {Metabolic control of cellular immune-competency by odors in Drosophila [Mass Spectrometry - Metabolomics Facility (INT)]}, journal = {Elife}, volume = {9}, year = {2020}, month = {2020 Dec 29}, abstract = {

Studies in different animal model systems have revealed the impact of odors on immune cells; however, any understanding on why and how odors control cellular immunity remained unclear. We find that employ an olfactory-immune cross-talk to tune a specific cell type, the lamellocytes, from hematopoietic-progenitor cells. We show that neuronally released GABA derived upon olfactory stimulation is utilized by blood-progenitor cells as a metabolite and through its catabolism, these cells stabilize Sima/HIFα protein. Sima capacitates blood-progenitor cells with the ability to initiate lamellocyte differentiation. This systemic axis becomes relevant for larvae dwelling in wasp-infested environments where chances of infection are high. By co-opting the olfactory route, the preconditioned animals elevate their systemic GABA levels leading to the upregulation of blood-progenitor cell Sima expression. This elevates their immune-potential and primes them to respond rapidly when infected with parasitic wasps. The present work highlights the importance of the olfaction in immunity and shows how odor detection during animal development is utilized to establish a long-range axis in the control of blood-progenitor competency and immune-priming.

}, issn = {2050-084X}, doi = {10.7554/eLife.60376}, author = {Madhwal, Sukanya and Shin, Mingyu and Kapoor, Ankita and Goyal, Manisha and Joshi, Manish K and Ur Rehman, Pirzada Mujeeb and Gor, Kavan and Shim, Jiwon and Mukherjee, Tina} } @article {1342, title = {Metagenomics analysis reveals features unique to Indian distal gut microbiota [Next Gen Genomics Facility]}, journal = {PLoS One}, volume = {15}, year = {2020}, month = {2020}, pages = {e0231197}, abstract = {

Various factors including diet, age, geography, culture and socio-economic status have a role in determining the composition of the human gut microbiota. The human gut microbial composition is known to be altered in disease conditions. Considering the important role of the gut microbiome in maintaining homeostasis and overall health, it is important to understand the microbial diversity and the functional metagenome of the healthy gut. Here, we characterized the microbiota of 31 fecal samples from healthy individuals of Indian ethnic tribes from Ladakh, Jaisalmer and Khargone by shotgun metagenomic sequencing. Sequence analysis revealed that Bifidobacterium and Prevotella were the key microbes contributing to the differences among Jaisalmer, Khargone and Ladakh samples at the genus level. Our correlation network study identified carbohydrate-active enzymes and carbohydrate binding proteins that are associated with specific genera in the different Indian geographical regions studied. Network analysis of carbohydrate-active enzymes and genus abundance revealed that the presence of different carbohydrate-active enzymes is driven by differential abundance of genera. The correlation networks were different in the different geographical regions, and these interactions suggest the role of less abundant genera in shaping the gut environment. We compared our data with samples from different countries and found significant differences in taxonomic composition and abundance of carbohydrate-active enzymes in the gut microbiota as compared to the other countries.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0231197}, author = {Kaur, Kamaldeep and Khatri, Indu and Akhtar, Akil and Subramanian, Srikrishna and Ramya, T N C} } @article {1274, title = {Ozone enhanced production of potentially useful exopolymers from the cyanobacterium Nostoc muscorum [Mass Spectrometry - Glycomics]}, journal = {Polymer Testing}, volume = {84}, year = {2020}, pages = {106385}, abstract = {

Extracellular polysaccharides (EPS) from Nostoc muscorum, a heterocystous, filamentous cyanobacterium isolated from a jhumland (shifting cultivation) soil of Assam, North-East India, was physico-chemically characterized to find out its potential applications and to improve its production with some stress source like ozone. Using Response Surface Methodology (RSM), EPS production was improved. Accordingly, with magnesium sulfate (MgSO4{\textperiodcentered}7H2O) at 62\ mg\ L-1, Sodium Chloride (NaCl) at 58\ mg\ L-1 and 56\ mg\ L-1 di-potassium hydrogen phosphate (K2HPO4), a yield of 126.73\ μg\ mL-1 of EPS in 12 days was obtained which was four-fold higher than un-optimised control. An important finding of this study is that EPS production could be further enhanced by over 50\% with a mild stress by a strong oxidizing agent ozone (O3). Physico-chemical properties of this Ozone induced EPS was evaluated and found identical to uninduced EPS. EPS was composed of the hexoses- Glucose (14.80\%), Galactose (18.01\%) and Mannose (12.64\%), the pentoses- Arabinose (17.86\%) and Xylose (11.66\%), the deoxyhexose- Fucose (12.53\%) and Rhamnose (12.50\%). Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy (ATR-FTIR) analysis revealed the presence of the functional groups uronic acid and traces of sulfate group. The Zeta potential analysis revealed that the emulsions were stabilized electrosterically rather than by pure electrostatic repulsion and steric stabilization. EPS at 1\% in hydrocarbons and vegetable oils was observed to be an excellent emulsifier (99\%), with reasonable stability. Rheological study revealed that the EPS (1\%) was a non- Newtonian weak gel, useful for emulsification activity. Unlike petroleum-based emulsifiers now in use, bio-based EPS are renewable, economical and eco-friendly. The physico-chemical characteristics suggest their utility in a wide variety of other applications including bioremediation, manufacture of paints, shear reduction in oil drilling etc.

}, keywords = {Cyanobacteria, Extracellular polysaccharides (EPS), Optimization, Ozone (O), Stress induction}, issn = {0142-9418}, doi = {https://doi.org/10.1016/j.polymertesting.2020.106385}, url = {http://www.sciencedirect.com/science/article/pii/S0142941819320951}, author = {Dharitri Borah and Gayathri Rethinam and Subramanian Gopalakrishnan and Jayashree Rout and Naiyf S. Alharbi and Sulaiman Ali Alharbi and Thajuddin Nooruddin} } @article {1627, title = {RNA-binding proteins La and HuR cooperatively modulate translation repression of PDCD4 mRNA [Mass Spectrometry Facility - Proteomics]}, journal = {J Biol Chem .}, volume = {doi: 10.1074/jbc.RA120.014894. Online ahead of print.}, year = {2020}, month = {12/2020}, abstract = {

Post-transcriptional regulation of gene expression plays a critical role in controlling the inflammatory response. An uncontrolled inflammatory response results in chronic inflammation, often leading to tumorigenesis. Programmed cell death 4 (PDCD4) is a pro-inflammatory tumor-suppressor gene which helps to prevent the transition from chronic inflammation to cancer. PDCD4 mRNA translation is regulated by an interplay between the oncogenic microRNA miR-21 and the RNA-binding protein (RBP) HuR in response to LPS stimulation, but the role of other regulatory factors remain unknown. Here we report that the RBP Lupus antigen (La) interacts with the 3{\textquoteright}UTR of PDCD4 mRNA and prevents miR-21-mediated translation repression. While LPS causes nuclear-cytoplasmic translocation of HuR, it enhances cellular La expression. Remarkably, La and HuR were found to bind cooperatively to the PDCD4 mRNA and mitigate miR-21-mediated translation repression. The cooperative action of La and HuR reduced cell proliferation and enhanced apoptosis, reversing the pro-oncogenic function of miR-21. Together, these observations demonstrate a cooperative interplay between two RBPs, triggered differentially by the same stimulus, which exerts a synergistic effect on PDCD4 expression and thereby helps maintain a balance between inflammation and tumorigenesis.

}, author = {Kumar, Ravi and Poria, Dipak Kumar and Ray, Partho Sarothi} } @article {1343, title = {Tracing the origin of olive ridley turtles entangled in ghost nets in the Maldives: A phylogeographic assessment of populations at risk [Next Gen Genomics Facility]}, journal = {Biological Conservation}, volume = {245}, year = {2020}, pages = {108499}, abstract = {

Abandoned, lost or discarded fishing nets, (ghost nets) represent a major threat to marine vertebrates. However, thorough assessments of their impact on threatened species are largely missing. In the Maldives, olive ridley sea turtles (Lepidochelys olivacea) are frequently caught in ghost nets however the archipelago does not support a significant nesting population. Our aim in this study was to determine the origin of olive ridleys entangled in ghost nets found in the Maldives and evaluate potential impacts on respective source populations. Based on a citizen science and conservation program, we recorded 132 olive ridley turtles entangled in ghost nets in just one year. Genetic analyses (mtDNA) of entangled individuals and of potential source populations revealed that most captured olive ridleys originated from Sri Lanka and eastern India. Oman could be excluded as source population, even during the prevalence of the south west monsoon. Based on our results and already available published literature, we were able to estimate that the recorded ghost net entanglements accounted for a relatively small amount (0.48\%) of the eastern Indian population. However, the entangled turtles accounted for a much larger percentage (41\%) of the Sri Lankan populations. However, it should be noted that our estimates of population-level mortality are linked to substantial uncertainty due to the lack of reliable information on population dynamics. Consequently, any precautionary protection measures applied should be complemented with improved quantification of turtle recruitment and life-stage specific mortalities.

}, keywords = {Citizen science, Entanglement, Ghost nets, mtDNA, Phylogenetics, Plastics}, issn = {0006-3207}, doi = {https://doi.org/10.1016/j.biocon.2020.108499}, url = {http://www.sciencedirect.com/science/article/pii/S0006320719313874}, author = {Martin Stelfox and Alfred Burian and Kartik Shanker and Alan F. Rees and Claire Jean and Ma{\"\i}a S. Willson and Nashwa Ahmed Manik and Michael Sweet} } @article {1524, title = {Tracking the time-dependent and tissue-specific processes of arsenic accumulation and stress responses in rice (Oryza sativa L.) [Mass Spectrometry - Metabolomics Facility]}, journal = {Journal of Hazardous Materials}, year = {2020}, pages = {124307}, abstract = {

The present study analysed time (0.5h to 24h) and tissue [roots, old leaves (OL) and young leaves (YL)] dependent nature of arsenic (As) accumulation and ensuing responses in two contrasting varieties of rice (Oryza sativa L.); Pooja (tolerant) and CO-50 (moderately sensitive). Arsenic accumulation was 5.4-, 4.7- and 7.3-fold higher at 24h in roots, OL and YL, respectively of var. CO-50 than that in var. Pooja. Arsenic accumulation in YL depicted a delayed accumulation; at 2h onwards in var. Pooja (0.23{\textmu}gg-1 dw) while at 1h onwards in var. CO50 (0.26{\textmu}gg-1 dw). The responses of oxidative stress parameters, antioxidant enzymes, metabolites and ions were also found to be tissue- and time-dependent and depicted differential pattern in the two varieties. Among hormone, salicylic acid and abscisic acid showed variable response in var. Pooja and var. CO-50. Metabolite analysis depicted an involvement of various metabolites in As stress responses of two varieties. In conclusion, an early sensing of the As stress, proper coordination of hormones, biochemical responses, ionic and metabolic profiles allowed var. Pooja to resist As stress and reduce As accumulation more effectively as compared to that of var. CO-50.

}, keywords = {Arsenic, Hormones, Metabolites, ROS, Signalling, Stress}, issn = {0304-3894}, doi = {https://doi.org/10.1016/j.jhazmat.2020.124307}, url = {http://www.sciencedirect.com/science/article/pii/S0304389420322974}, author = {Poonam Yadav and Sudhakar Srivastva and Tanmayi Patil and Rishiraj Raghuvanshi and Ashish K. Srivastava and Penna Suprasanna} } @article {1145, title = {Aspartic protease from Aspergillus niger: Molecular characterization and interaction with pepstatin A [Mass Spectrometry Facility - Proteomics].}, journal = {Int J Biol Macromol}, year = {2019}, month = {2019 Jul 30}, abstract = {

In the pursuit of industrial aspartic proteases, aspergillopepsin A-like endopeptidase from the fungi Aspergillus niger, was identified and cultured by solid state fermentation. Conventional chromatographic techniques were employed to purify the extracellular aspartic protease to apparent homogeneity. The enzyme was found to have single polypeptide chain with a molecular mass of 50 {\textpm} 0.5 kDa. The optimum pH and temperature for the purified aspartic protease was found to be 3.5 and 60 {\textdegree}C respectively. The enzyme was stable for 60 min at 50 {\textdegree}C. The purified enzyme had specific activity of 40,000 {\textpm} 1800 U/mg. The enzyme had 85\% homology with the reported aspergillopepsin A-like aspartic endopeptidase from Aspergillus niger CBS 513.88, based on tryptic digestion and peptide analysis. Pepstatin A reversibly inhibited the enzyme with a K value of 0.045 μM. Based on homology modeling and predicted secondary structure, it was inferred that the aspartic protease is rich in β-structures, which was also confirmed by CD measurements. Interaction of pepstatin A with the enzyme did not affect the conformation of the enzyme as evidenced by CD and fluorescence measurements. Degree of hydrolysis of commercial substrates indicated the order of cleaving ability of the enzyme to be hemoglobin \> defatted soya flour \> gluten \> gelatin \> skim milk powder. The enzyme also improved the functional characteristics of defatted soya flour. This aspartic protease was found to be an excellent candidate for genetic manipulation for biotechnological application in food and feed industries, due to its high catalytic turn over number and thermostability.

}, issn = {1879-0003}, doi = {10.1016/j.ijbiomac.2019.07.133}, author = {Purushothaman, Kavya and Bhat, Sagar Krishna and Singh, Sridevi Annapurna and Marathe, Gopal Kedihithlu and Appu Rao, Appu Rao G} } @article {1017, title = {Comparative analysis of the gut microbiota in centenarians and young adults shows a common signature across genotypically non-related populations [Mass Spectrometry - Metabolomics Facility].}, journal = {Mech Ageing Dev}, volume = {179}, year = {2019}, month = {2019 Feb 06}, pages = {23-35}, abstract = {

Gut microbiota is among the factors that may be involved in healthy aging. Broader and geographically spread studies on gut microbiota of centenarians can help in identifying a common signature of longevity. We identified an endogamous Indian population with high centenarian prevalence. Here, we compared the gut microbiota composition and fecal metabolites of a centenarians group (\~{}100 years) with young people (25-45 years) of the region with the high centenarian prevalence and the nearby region of low centenarian prevalence to decipher microbial-related longevity signatures. Also, we compared our results with publicly available datasets of similar groups including 125 centenarians from three countries (Italy, Japan, China). Our comparative analysis resulted in higher biodiversity within Ruminococcaceae in centenarians, with respect to younger adults, irrespective of their nationality. We observed bacterial signatures that are common among extremely old people of different nationality. Comparative metabolites profiling identified the fecal metabolic signature of extreme aging in the Indian study population. Our analysis of the co-occurrence network and bimodal distribution of several taxa suggested the establishment of a pervasive change in the gut ecology during extreme aging. Our study might pave the way to develop gut microbiota based biomarkers for healthy aging.

}, issn = {1872-6216}, doi = {10.1016/j.mad.2019.02.001}, author = {Tuikhar, Ngangyola and Keisam, Santosh and Labala, Rajendra Kumar and Ramakrishnan, Padma and Arunkumar, Moirangthem Cha and Ahmed, Giasuddin and Biagi, Elena and Jeyaram, Kumaraswamy} } @article {1061, title = {Differentiating Human Induced Pluripotent Stem Cells (iPSCs) Into Lung Epithelial Cells. [Eyestem, a C-CAMP Startup]}, journal = {Curr Protoc Stem Cell Biol}, year = {2019}, month = {2019 Apr 18}, pages = {e86}, abstract = {

Human induced pluripotent\ stem cells\ (hiPSCs) not only offer great opportunities for the study of human development but also have tremendous potential for future clinical\ cell-based therapies.\ The protocol outlined here is used to differentiate hiPSCs into lung epithelial cell types through a process that faithfully recapitulates the stepwise events observed in vivo. From pluripotency, cells are differentiated to a definitive endoderm fate, followed by progression into anteriorized foregut endoderm that has the ability to give rise to both proximal and distal epithelial cells. Furthermore, this methodology allows for the study of lung dysfunction and disease modeling using patient-derived cells, as well as high-throughput pharmacological screening and eventually personalized therapies. Recently we were able to reproduce this protocol using the working cell bank of an hiPSC line made under current Good Manufacturing Practice (cGMP) conditions, a necessary step for the future clinical application of these\ cells. {\textcopyright} 2019 by John Wiley \& Sons, Inc.

}, issn = {1938-8969}, doi = {10.1002/cpsc.86}, author = {Surendran, Harshini and Rajamoorthy, Mohanapriya and Pal, Rajarshi} } @article {986, title = {Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway [Discovery to Innovation Accelerator]}, journal = {Nat Commun}, volume = {10}, year = {2019}, month = {2019 Jan 09}, pages = {89}, abstract = {

The importance of gut microbiota in human health and pathophysiology is undisputable. Despite the abundance of metagenomics data, the functional dynamics of gut microbiota in human health and disease remain elusive. Urolithin A (UroA), a major microbial metabolite derived from polyphenolics of berries and pomegranate fruits displays anti-inflammatory, anti-oxidative, and anti-ageing activities. Here, we show that UroA and its potent synthetic analogue (UAS03) significantly enhance gut barrier function and inhibit unwarranted inflammation. We demonstrate that UroA and UAS03 exert their barrier functions through activation of aryl hydrocarbon receptor (AhR)- nuclear factor erythroid 2-related factor 2 (Nrf2)-dependent pathways to upregulate epithelial tight junction proteins. Importantly, treatment with these compounds attenuated colitis in pre-clinical models by remedying barrier dysfunction in addition to anti-inflammatory activities. Cumulatively, the results highlight how microbial metabolites provide two-pronged beneficial activities at gut epithelium by enhancing barrier functions and reducing inflammation to protect from colonic diseases.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-07859-7}, author = {Singh, Rajbir and Chandrashekharappa, Sandeep and Bodduluri, Sobha R and Baby, Becca V and Hegde, Bindu and Kotla, Niranjan G and Hiwale, Ankita A and Saiyed, Taslimarif and Patel, Paresh and Vijay-Kumar, Matam and Langille, Morgan G I and Douglas, Gavin M and Cheng, Xi and Rouchka, Eric C and Waigel, Sabine J and Dryden, Gerald W and Alatassi, Houda and Zhang, Huang-Ge and Haribabu, Bodduluri and Vemula, Praveen K and Jala, Venkatakrishna R} } @article {1115, title = {Hematite Nanoparticles: synthesis, characterization and aquatic ecotoxicity effects [Central Imaging and Flow Cytometry Facility]}, journal = {Research Journal of Biotechnology}, volume = {14}, year = {2019}, chapter = {21}, abstract = {

Iron oxide nanoparticles have been investigated recently for their useful applications in numerous biomedical areas, in environmental remediation and in different industrial applications. In any case, additional risks have been identified with the release of nanoparticles into the environment. In the present study the toxicity of hematite nanoparticles to marine algae, Chlorella vulgaris was studied with focus on oxidative stress and cytotoxicity analysis. The synthesized hematite nanoparticles are in the range of 26-50 nm. Result showed that Chlorella vulgaris growth reduced with increasing concentrations. The nanoparticles induced oxidative stress was the main toxic mechanism. The nanoparticles and Chlorella vulgaris cell physical interaction also contributed to the nanotoxicity. Field Emission Scanning Electron Microscope shows the morphological changes and cell damage. In 24h, treatment mortality was 20 {\textendash} 70 \% and LC50 value for 24h was 393.60 mg/L. Toxicity study on copepod showed mortality increased from 20- 100\% for 48hr and LC50 value for 44h was 221.34 mg/L.

}, author = {Suman Thodhal Yoganandham and Radhika Rajasree Santha Ravindranath* and Gayathri Sathyamoorthy and Remya Rajan Renuka and Aranganathan Lakshminarayanan} } @article {1458, title = {The Hox gene uses Doublesex as a cofactor to promote neuroblast apoptosis in the central nervous system [Transgenic Fly Facility]}, journal = {Development}, volume = {146}, year = {2019}, month = {2019 08 22}, abstract = {

Highly conserved DM domain-containing transcription factors (Doublesex/MAB-3/DMRT1) are responsible for generating sexually dimorphic features. In the central nervous system, a set of Doublesex (Dsx)-expressing neuroblasts undergo apoptosis in females whereas their male counterparts proliferate and give rise to serotonergic neurons crucial for adult mating behaviour. Our study demonstrates that the female-specific isoform of Dsx collaborates with Hox gene () to bring about this apoptosis. Biochemical results suggest that proteins AbdB and Dsx interact through their highly conserved homeodomain and DM domain, respectively. This interaction is translated into a cooperative binding of the two proteins on the apoptotic enhancer in the case of females but not in the case of males, resulting in female-specific activation of apoptotic genes. The capacity of AbdB to use the sex-specific isoform of Dsx as a cofactor underlines the possibility that these two classes of protein are capable of cooperating in selection and regulation of target genes in a tissue- and sex-specific manner. We propose that this interaction could be a common theme in generating sexual dimorphism in different tissues across different species.

}, keywords = {Animals, Apoptosis, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Female, Gene Expression Regulation, Developmental, Genes, Homeobox, Homeodomain Proteins, Male, Neural Stem Cells, Protein Isoforms, Sex Characteristics}, issn = {1477-9129}, doi = {10.1242/dev.175158}, author = {Ghosh, Neha and Bakshi, Asif and Khandelwal, Risha and Rajan, Sriivatsan Govinda and Joshi, Rohit} } @article {1151, title = {Isolation and Characterization of Conotoxin Protein from Conus inscriptus and Its Potential Anticancer Activity Against Cervical Cancer (HeLa-HPV 16 Associated) Cell Lines [Mass Spectrometry - Proteomics/Glycomics]}, journal = {International Journal of Peptide Research and Therapeutics}, year = {2019}, month = {Aug}, abstract = {

Marine snails are abundant sources of biologically important conopeptides with their potential applications in drug development. The present study aimed to identify the potential conopeptides from the venom duct of Conus inscriptus. After extraction conopeptides were characterized by liquid chromatography{\textendash}mass spectrometric analysis showing totally 29 protein sequences with disulfide linkages of different molecular mass distributed in the range of 387{\textendash}1536\ m/z and the peptides showing mostly to T-superfamily of conotoxins with 78\ kDa heat shock proteins. The venom peptides showed six different molecular weight bands (37, 51, 60, 70, 80 and 90\ kDa) above 30\ kDa after in-gel enzymatic digestion. Furthermore, the conopeptides exhibit potential cytotoxic activity against HeLa-HPV 16 associated, Vero (normal) cell lines and brine shrimp. Fourier transform infra-red spectroscopy analysis confirms the structural and functional groups. The observed results suggests the venom peptides from C. inscriptus as a potential anticancer agent.

}, issn = {1573-3904}, doi = {10.1007/s10989-019-09907-2}, url = {https://doi.org/10.1007/s10989-019-09907-2}, author = {Kumari, Anjali and Ameri, Shijin and Ravikrishna, Palavancha and Dhayalan, Arul and Kamala-Kannan, S. and Selvankumar, T. and Govarthanan, M.} } @article {1160, title = {Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway [National Cryo-Electron Microscopy Facility (INT)]}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {09, 2019}, type = {Article}, chapter = {4127}, abstract = {Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.}, keywords = {Bacterial structural biology, Cryoelectron microscopy, Multienzyme complexes}, author = {Nitish Sathyanarayanan and Giuseppe Cannone and Lokesh Gakhar and Nainesh Katagihallimath and Ramanathan Sowdhamini and Subramanian Ramaswamy and Kutti R. Vinothkumar} } @article {1136, title = {Mon1 constitutes a novel node in the brain-gonad axis that is essential for female germline maturation. [Transgenic Fly Facility]}, journal = {Development}, volume = {146}, year = {2019}, month = {2019 Jul 10}, abstract = {

Monensin-sensitive 1 (Mon1) is an endocytic regulator that participates in the conversion of Rab5-positive early endosomes to Rab7-positive late endosomes. In , loss of leads to sterility as the mutant females have extremely small ovaries with complete absence of late stage egg chambers - a phenotype reminiscent of mutations in the insulin pathway genes. Here, we show that expression of many insulin-like peptides (ILPs) is reduced in mutants and feeding adults an insulin-rich diet can rescue the ovarian defects. Surprisingly, however, functions in the tyramine/octopaminergic neurons (OPNs) and not in the ovaries or the insulin-producing cells (IPCs). Consistently, knockdown of in only the OPNs is sufficient to mimic the ovarian phenotype, while expression of the gene in the OPNs alone can {\textquoteright}rescue{\textquoteright} the mutant defect. Last, we have identified and as critical targets of This study thus identifies as a novel molecular player in the brain-gonad axis and underscores the significance of inter-organ systemic communication during development.

}, issn = {1477-9129}, doi = {10.1242/dev.166504}, author = {Dhiman, Neena and Shweta, Kumari and Tendulkar, Shweta and Deshpande, Girish and Ratnaparkhi, Girish S and Ratnaparkhi, Anuradha} } @article {1178, title = {Serotonin is essential for eye regeneration in planaria Schmidtea~mediterranea [Mass Spectrometry (Metabolomics) and Central Imaging \& Flow Cytometry Facilities (INT)]}, journal = {FEBS Lett}, year = {2019}, month = {2019 Sep 17}, abstract = {

Planaria is an ideal system to study factors involved in regeneration and tissue homeostasis. Little is known about the role of metabolites and small molecules in stem cell maintenance and lineage specification in planarians. Using liquid chromatography and mass spectrometry (LC-MS)-based quantitative metabolomics, we determined the relative levels of metabolites in stem cells, progenitors, and differentiated cells of the planarian Schmidtea\ mediterranea. Tryptophan and its metabolic product serotonin are significantly enriched in stem cells and progenitor population. Serotonin biosynthesis in these cells is brought about by a noncanonical enzyme, phenylalanine hydroxylase. Knockdown of Smed-pah leads to complete disappearance of eyes in regenerating planaria, while exogenous supply of serotonin and its precursor rescues the eyeless phenotype. Our results demonstrate a key role for serotonin in eye regeneration.

}, issn = {1873-3468}, doi = {10.1002/1873-3468.13607}, author = {Sarkar, Arunabha and Mukundan, Namita and Sowndarya, Sai and Dubey, Vinay Kumar and Babu, Rosana and Lakshmanan, Vairavan and Rangiah, Kannan and Panicker, Mitradas M and Palakodeti, Dasaradhi and Subramanian, Sabarinath Peruvemba and Subramanian, Ramaswamy} } @article {1202, title = {Small molecule modulator of aggrephagy regulates neuroinflammation to curb pathogenesis of neurodegeneration [Discovery to Innovation Accelerator (INT)].}, journal = {EBioMedicine}, year = {2019}, month = {2019 Nov 11}, abstract = {

BACKGROUND: Plethora of efforts fails to yield a single drug to reverse the pathogenesis of Parkinson{\textquoteright}s disease (PD) and related α-synucleopathies.

METHODS: Using chemical biology, we identified a small molecule inhibitor of c-abl kinase, PD180970 that could potentially clear the toxic protein aggregates. Genetic, molecular, cell biological and immunological assays were performed to understand the mechanism of action. In vivo preclinical disease model of PD was used to assess its neuroprotection efficacy.

FINDINGS: In this report, we show the ability of a small molecule inhibitor of tyrosine kinases, PD180970, to induce autophagy (cell lines and mice midbrain) in an mTOR-independent manner and ameliorate the α-synuclein mediated toxicity. PD180970 also exerts anti-neuroinflammatory potential by inhibiting the release of proinflammatory cytokines such as IL-6 (interleukin-6) and MCP-1 (monocyte chemoattractant protein-1) through reduction of TLR-4 (toll like receptor-4) mediated NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) activation. In vivo studies show that PD180970 is neuroprotective by degrading the toxic protein oligomers through induction of autophagy and subsiding the microglial activation.

INTERPRETATION: These protective mechanisms ensure the negation of Parkinson{\textquoteright}s disease related motor impairments. FUND: This work was supported by Wellcome Trust/DBT India Alliance Intermediate Fellowship (500159-Z-09-Z), DST-SERB grant (EMR/2015/001946), DBT (BT/INF/22/SP27679/2018) and JNCASR intramural funds to RM, and SERB, DST (SR/SO/HS/0121/2012) to PAA, and DST-SERB (SB/YS/LS-215/2013) to JPC and BIRAC funding to ETA C-CAMP.

}, issn = {2352-3964}, doi = {10.1016/j.ebiom.2019.10.036}, author = {Sn, Suresh and Pandurangi, Janhavi and Murumalla, Ravi and Dj, Vidyadhara and Garimella, Lakshmi and Acharya, Achyuth and Rai, Shashank and Paul, Abhik and Yarreiphang, Haorei and Pillai, Malini S and Giridharan, Mridhula and Clement, James P and Alladi, Phalguni Anand and Saiyed, Taslimarif and Manjithaya, Ravi} } @article {1007, title = {SOD1 activity threshold and TOR signalling modulate VAP(P58S) aggregation via reactive oxygen species-induced proteasomal degradation in a model of amyotrophic lateral sclerosis. [High Throughput Screening Facility]}, journal = {Dis Model Mech}, volume = {12}, year = {2019}, month = {2019 Feb 07}, abstract = {

Familial amyotrophic lateral sclerosis (ALS) is an incurable, late-onset motor neuron disease, linked strongly to various causative genetic loci. codes for a missense mutation, P56S, in VAMP-associated protein B (VAPB) that causes the protein to misfold and form cellular aggregates. Uncovering genes and mechanisms that affect aggregation dynamics would greatly help increase our understanding of the disease and lead to potential therapeutics. We developed a quantitative high-throughput S2R+ cell-based kinetic assay coupled with fluorescent microscopy to score for genes involved in the modulation of aggregates of the fly orthologue, VAP(P58S), fused with GFP. A targeted RNA interference screen against 900 genes identified 150 hits that modify aggregation, including the ALS loci and (also known as ), as well as genes belonging to the mTOR pathway. Further, a system to measure the extent of VAP(P58S) aggregation in the larval brain was developed in order to validate the hits from the cell-based screen. In the larval brain, we find that reduction of SOD1 levels or decreased mTOR signalling reduces aggregation, presumably by increasing the levels of cellular reactive oxygen species (ROS). The mechanism of aggregate clearance is, primarily, proteasomal degradation, which appears to be triggered by an increase in ROS. We have thus uncovered an interesting interplay between SOD1, ROS and mTOR signalling that regulates the dynamics of VAP aggregation. Mechanistic processes underlying such cellular regulatory networks will lead to better understanding of the initiation and progression of ALS.This article has an associated First Person interview with the first author of the paper.

}, issn = {1754-8411}, doi = {10.1242/dmm.033803}, author = {Chaplot, Kriti and Pimpale, Lokesh and Ramalingam, Balaji and Deivasigamani, Senthilkumar and Kamat, Siddhesh S and Ratnaparkhi, Girish S} } @article {1228, title = {Transcriptome analysis reveals plasticity in gene regulation due to environmental cues in Primula sikkimensis, a high altitude plant species [Next Gen Genomics Facility (INT)].}, journal = {BMC Genomics}, volume = {20}, year = {2019}, month = {2019 Dec 17}, pages = {989}, abstract = {

BACKGROUND: Studying plasticity in gene expression in natural systems is crucial, for predicting and managing the effects of climate change on plant species. To understand the contribution of gene expression level variations to abiotic stress compensation in a Himalaya plant (Primula sikkimensis), we carried out a transplant experiment within (Ambient), and beyond (Below Ambient and Above Ambient) the altitudinal range limit of species. We sequenced nine transcriptomes (three each from each altitudinal range condition) using Illumina sequencing technology. We compared the fitness variation of transplants among three transplant conditions.

RESULTS: A large number of significantly differentially expressed genes (DEGs) between below ambient versus ambient (109) and above ambient versus ambient (85) were identified. Transcripts involved in plant growth and development were mostly up-regulated in below ambient conditions. Transcripts involved in signalling, defence, and membrane transport were mostly up-regulated in above ambient condition. Pathway analysis revealed that most of the genes involved in metabolic processes, secondary metabolism, and flavonoid biosynthesis were differentially expressed in below ambient conditions, whereas most of the genes involved in photosynthesis and plant hormone signalling were differentially expressed in above ambient conditions. In addition, we observed higher reproductive fitness in transplant individuals at below ambient condition compared to above ambient conditions; contrary to what we expect from the cold adaptive P. sikkimensis plants.

CONCLUSIONS: We reveal P. sikkimensis{\textquoteright}s capacity for rapid adaptation to climate change through transcriptome variation, which may facilitate the phenotypic plasticity observed in morphological and life history traits. The genes and pathways identified provide a genetic resource for understanding the temperature stress (both the hot and cold stress) tolerance mechanism of P. sikkimensis in their natural environment.

}, issn = {1471-2164}, doi = {10.1186/s12864-019-6354-1}, author = {Gurung, Priya Darshini and Upadhyay, Atul Kumar and Bhardwaj, Pardeep Kumar and Sowdhamini, Ramanathan and Ramakrishnan, Uma} } @article {1084, title = {The transcriptome enables the identification of candidate genes behind medicinal value of Drumstick tree (Moringa oleifera) [Next Gen Genomics Facility (INT)].}, journal = {Genomics}, year = {2019}, month = {2019 Apr 29}, abstract = {

Moringa oleifera is a plant well-known for its nutrition value, drought resistance and medicinal properties. cDNA libraries from five different tissues (leaf, root, stem, seed and flower) of M. oleifera cultivar Bhagya were generated and sequenced. We developed a bioinformatics pipeline to assemble transcriptome, along with the previously published M. oleifera genome, to predict 17,148 gene models. Few candidate genes related to biosynthesis of secondary metabolites, vitamins and ion transporters were identified. Expressions were further confirmed by real-time quantitative PCR experiments for few promising leads. Quantitative estimation of metabolites, as well as elemental analysis, was also carried out to support our observations. Enzymes in the biosynthesis of vitamins and metabolites like quercetin and kaempferol are highly expressed in leaves, flowers and seeds. The expression of iron transporters and calcium storage proteins were observed in root and leaves. In general, leaves retain the highest amount of small molecules of interest.

}, issn = {1089-8646}, doi = {10.1016/j.ygeno.2019.04.014}, author = {Pasha, Shaik Naseer and Shafi, K Mohamed and Joshi, Adwait G and Meenakshi, Iyer and Harini, K and Mahita, Jarjapu and Sajeevan, Radha Sivarajan and Karpe, Snehal D and Ghosh, Pritha and Nitish, Sathyanarayanan and Gandhimathi, A and Mathew, Oommen K and Prasanna, Subramanian Hari and Malini, Manoharan and Mutt, Eshita and Naika, Mahantesha and Ravooru, Nithin and Rao, Rajas M and Shingate, Prashant N and Sukhwal, Anshul and Sunitha, Margaret S and Upadhyay, Atul K and Vinekar, Rithvik S and Sowdhamini, Ramanathan} } @article {690, title = {Automation aided optimization of cloning, expression and purification of enzymes of the bacterial sialic acid catabolic and sialylation pathways enzymes for structural studies. [Protein Technology (INT)]}, year = {2018}, author = {Sneha Bairy and Lakshmi Narayanan Gopalan and Thanuja Gangi Setty and Sathya Srinivasachari and Lavanyaa Manjunath and Jay Prakash Kumar and Sai R Guntupalli and Sucharita Bose and Vinod Nayak and Swagatha Ghosh and Nitish Sathyanarayanan and Rhawnie Caing-Carlsson and Weixiao Yuan Wahlgren and Rosmarie Friemann and S. Ramaswamy and Muniasamy Neerathilingam} } @article {770, title = {Biolubricant potential of exopolysaccharides from the cyanobacterium Cyanothece epiphytica. [Mass Spectrometry - Glycomics]}, journal = {Appl Microbiol Biotechnol}, volume = {102}, year = {2018}, month = {2018 Apr}, pages = {3635-3647}, abstract = {

Exopolysaccaharides (EPS) are carbohydrate polymers secreted by microbial cells, as a protective layer termed sheath or capsule. Their composition is variable. Optimisation of nutrient factors and the effect of some simple stresses on the ability of Cyanothece epiphytica to produce EPS were tested. Of the tested stresses, exposure to ozone for 50\ s at 0.06\ mg/L resulted in a relatively high EPS yield, without any damage to cell structure. EPS was characterised physicochemically. Chemically, it was found to be composed of pentoses arabinose and xylose; hexoses glucose, galactose and mannose; and the deoxyhexose fucose sugars which were sulphated and with different functional groups. EPS from C. epiphytica was found to be a good hydrophobic dispersant, an excellent emulsifier as well as a flocculant. Its potential as a biolubricant with characteristics better than the conventional lubricant {\textquoteright}grease{\textquoteright} was revealed through analysis. This study gave the clue for developing a commercial technology to produce a less expensive and more environment-friendly natural lubricant from the cyanobacterium C. epiphytica for tribological applications.

}, issn = {1432-0614}, doi = {10.1007/s00253-018-8892-x}, author = {Borah, Dharitri and Nainamalai, Sangeetha and Gopalakrishnan, Subramanian and Rout, Jayashree and Alharbi, Naiyf S and Alharbi, Sulaiman Ali and Nooruddin, Thajuddin} } @article {686, title = {Exploiting a water network to achieve enthalpy-driven, bromodomain-selective BET inhibitors}, journal = {Bioorganic \& Medicinal Chemistry}, volume = {26}, year = {2018}, pages = {25 - 36}, issn = {0968-0896}, doi = {https://doi.org/10.1016/j.bmc.2017.10.042}, url = {http://www.sciencedirect.com/science/article/pii/S0968089617315948}, author = {William R. Shadrick and Peter J. Slavish and Sergio C. Chai and Brett Waddell and Michele Connelly and Jonathan A. Low and Cynthia Tallant and Brandon M. Young and Nagakumar Bharatham and Stefan Knapp and Vincent A. Boyd and Marie Morfouace and Martine F. Roussel and Taosheng Chen and Richard E. Lee and R. Kiplin Guy and Anang A. Shelat and Philip M. Potter} } @article {888, title = {Gene expression is implicated in the ability of pikas to occupy Himalayan elevational gradient. [Next Gen Genomics Facility (INT)]}, journal = {PLoS One}, volume = {13}, year = {2018}, month = {2018}, pages = {e0207936}, abstract = {

Species are shifting their ranges due to climate change, many moving to cooler and higher locations. However, with elevation increase comes oxygen decline, potentially limiting a species{\textquoteright} ability to track its environment depending on what mechanisms it has available to compensate for hypoxic stress. Pikas (Family Ochotonidae), cold-specialist small mammal species, are already undergoing elevational range shifts. We collected RNA samples from one population of Ochotona roylei in the western Himalaya at three sites- 3,600, 4,000, and 5,000 meters-and found no evidence of significant population genetic structure nor positive selection among sites. However, out of over 10,000 expressed transcripts, 26 were significantly upregulated at the 5,000 m site and were significantly enriched for pathways consistent with physiological compensation for limited oxygen. These results suggest that differences in gene expression may play a key role in enabling hypoxia tolerance on this local scale, indicating elevational flexibility that may facilitate successful range shifts in response to climate change.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0207936}, author = {Solari, Katherine A and Ramakrishnan, Uma and Hadly, Elizabeth A} } @article {1062, title = {Generation of Transplantable Retinal Pigmented Epithelial (RPE) Cells for Treatment of Age-Related Macular Degeneration (AMD). [Eyestem, a C-CAMP Startup]}, journal = {Methods Mol Biol}, year = {2018}, month = {2018 Jun 13}, abstract = {

Age-related macular degeneration (AMD) is the foremost cause of blindness in people over the age of 60 worldwide. Clinically, this disease starts with distortion in central vision eventually leading to legal blindness. Vision loss has a significant impact on quality of life and incurs a substantial cost to the economy. Furthermore, AMD is a complex and progressive neurodegenerative disorder that triggers visual impairment due to the loss of retinal pigmented epithelium (RPE) and the light-sensitive photoreceptors that they support, protect and provide nutrition. Currently, there is no curative treatment for the most common form of this disease, i.e., dry AMD. A novel approach to treat AMD involves the transplantation of RPE cells derived from human induced pluripotent stem cells (iPSCs) in the outer retina. These iPSC-derived RPE cells not only show characteristics similar to native RPE but also could replace as well as regenerate damaged pathologic RPE and produce supportive growth factors and cytokines. Several clinical trials are being conducted taking advantage of a variety of cell- and tissue engineering-based approaches. Here, we present a simple, cost effective, and scalable cell-culture model for generation of purified RPE thus providing the foundation for developing an allogeneic cell therapy for AMD.

}, issn = {1940-6029}, doi = {10.1007/7651_2018_140}, author = {Surendran, Harshini and Rathod, Reena J and Pal, Rajarshi} } @article {1006, title = {Mass Spectrometric Quantification of Arousal Associated Neurochemical Changes in Single Honey Bee Brains and Brain Regions. [Mass Spectrometry Facility - Metabolomics (INT)]}, journal = {ACS Chem Neurosci}, year = {2018}, month = {2018 Oct 26}, abstract = {

Honey bee foragers show a strong diurnal rhythm of foraging activity, and such behavioral changes are likely under the control of specific neuromodulators. To identify and quantify neuromodulators involved in regulating rest and arousal in honey bees, we established a mass spectrometric method for quantifying 14 different neurochemicals and precursor molecules. We measured forager type and brain region specific differences in amine levels from individual honey bee brains and brain regions. The observed differences in amine levels between resting and aroused foragers resemble findings in other species indicating a conserved molecular mechanism by glutamate and GABA in regulating arousal. Subesophageal ganglion specific changes in the histaminergic system and global increases in aspartate during arousal suggest a possible role of histamine and aspartate in feeding and arousal, respectively. More aminergic systems were significantly affected due to arousal in nectar foragers than in pollen foragers, implying that forager phenotypes differ not only in their food preference but also in their neuromodulatory signaling systems (brain states). Finally, we found that neurotransmitter precursors were better at distinguishing brain states in the central brain, while their end products correlated with arousal associated changes in sensory regions like the optic and antennal lobes.

}, issn = {1948-7193}, doi = {10.1021/acschemneuro.8b00254}, author = {Ramesh, Divya and Brockmann, Axel} } @article {1015, title = {Mechanochemical feedback control of dynamin independent endocytosis modulates membrane tension in adherent cells. [Microfluidics and Microfabrication Facility (INT)]}, journal = {Nat Commun}, volume = {9}, year = {2018}, month = {2018 10 11}, pages = {4217}, abstract = {

Plasma membrane tension regulates many key cellular processes. It is modulated by, and can modulate, membrane trafficking. However, the cellular pathway(s) involved in this interplay is poorly understood. Here we find that, among a number of endocytic processes operating simultaneously at the cell surface, a dynamin independent pathway, the CLIC/GEEC (CG) pathway, is rapidly and specifically upregulated upon a sudden reduction of tension. Moreover, inhibition (activation) of the CG pathway results in lower (higher) membrane tension. However, alteration in membrane tension does not directly modulate CG endocytosis. This requires vinculin, a mechano-transducer recruited to focal adhesion in adherent cells. Vinculin acts by controlling the levels of a key regulator of the CG pathway, GBF1, at the plasma membrane. Thus, the CG pathway directly regulates membrane tension and is in turn controlled via a mechano-chemical feedback inhibition, potentially leading to homeostatic regulation of membrane tension in adherent cells.

}, keywords = {Animals, Biomechanical Phenomena, Cell Adhesion, Cell Membrane, Dynamins, Endocytosis, Feedback, Physiological, Mechanotransduction, Cellular, Mice, Signal Transduction, Temperature, Vinculin}, issn = {2041-1723}, doi = {10.1038/s41467-018-06738-5}, author = {Thottacherry, Joseph Jose and Kosmalska, Anita Joanna and Kumar, Amit and Vishen, Amit Singh and Elosegui-Artola, Alberto and Pradhan, Susav and Sharma, Sumit and Singh, Parvinder P and Guadamillas, Marta C and Chaudhary, Natasha and Vishwakarma, Ram and Trepat, Xavier and Del Pozo, Miguel A and Parton, Robert G and Rao, Madan and Pullarkat, Pramod and Roca-Cusachs, Pere and Mayor, Satyajit} } @article {764, title = {Nitrothiophene carboxamides, a novel narrow spectrum antibacterial series: Mechanism of action and Efficacy [Bugworks Res. Pvt. Ltd., a C-CAMP Startup]}, journal = {Sci Rep}, volume = {8}, year = {2018}, month = {2018 May 08}, pages = {7263}, abstract = {

The mechanism of efflux is a tour-de-force in the bacterial armoury that has thwarted the development of novel antibiotics. We report the discovery of a novel chemical series with potent antibacterial properties that was engineered to overcome efflux liability. Compounds liable to efflux specifically via the Resistance Nodulation and cell Division (RND) pump, AcrAB-TolC were chosen for a hit to lead progression. Using structure-based design, the compounds were optimised to lose their binding to the efflux pump, thereby making them potent on wild-type bacteria. We discovered these compounds to be pro-drugs that require activation in E. coli by specific bacterial nitroreductases NfsA and NfsB. Hit to lead chemistry led to the generation of compounds that were potent on wild-type and multi-drug resistant clinical isolates of E. coli, Shigella spp., and Salmonella spp. These compounds are bactericidal and efficacious in a mouse thigh infection model.

}, issn = {2045-2322}, doi = {10.1038/s41598-018-25407-7}, author = {Hameed P, Shahul and Bharatham, Nagakumar and Katagihallimath, Nainesh and Sharma, Sreevalli and Nandishaiah, Radha and Shanbhag, Anirudh P and Thomas, Teby and Narjari, Riya and Sarma, Maitrayee and Bhowmik, Purnendu and Amar, Prakruthi and Ravishankar, Rajani and Jayaraman, Ramesh and Muthan, Kubendran and Subbiah, Ramesh and Ramachandran, Vasanthi and Balasubramanian, V and Datta, Santanu} } @article {1018, title = {Pharmacokinetics of colistin in patients with multidrug-resistant Gram-negative infections: A pilot study [Mass Spectrometry - Metabolomics Facility].}, journal = {Indian J Med Res}, volume = {147}, year = {2018}, month = {2018 04}, pages = {407-412}, abstract = {

Background \& objectives: There is little information concerning intravenously (i.v.) administered colistin in patients with multidrug-resistant (MDR) Gram-negative infections. Thus, this pilot prospective study was undertaken to characterize efficacy and pharmacokinetics of colistin in patients with MDR Gram-negative infections.

Methods: Nine patients with age \>12 yr and MDR Gram-negative infections were included, of whom six were given colistin at the doses of 2 MU, while three patients were given 1 MU i.v. dose every 8 h. Blood samples were collected at different time intervals. Determination of colistin concentration was done by a ultra-high-performance liquid chromatography/mass spectrometry/selected reaction monitoring assay.

Results: The area under the plasma concentration-versus-time curve over eight hours (AUC) for colistin after the 1 dose ranged from 3.3 to 16.4 mg{\texttimes}h/l (median, 4.59). After the 5 dose, AUCfor colistin ranged from 4.4 to 15.8 mg{\texttimes}h/l (median, 6.0). With minimal inhibitory concentration (MIC) value of 0.125 mg/l, AUC/MIC ranged from 26.7 to 131.4 (median, 36.7) and 35.5 to 126.0 (median, 48.0) after the 1 and the 5 doses of 2 MU every 8 h, respectively.

Interpretation \& conclusions: As there is a paucity of information on AUC/MIC for colistin, it may not be possible to conclude whether AUC/MIC values in our patients were adequate. There is a microbiological clearance of organism, which goes in favour of the dosing schedule being adequate. Further studies need to be done to understand the pharmacokinetics of colistin in patients with infections.

}, keywords = {Anti-Bacterial Agents, Colistin, Drug Resistance, Multiple, Bacterial, Gram-Negative Bacterial Infections, Humans, Pilot Projects, Prospective Studies}, issn = {0971-5916}, doi = {10.4103/ijmr.IJMR_1464_16}, author = {Gautam, Vikas and Shafiq, Nusrat and Mouton, Johan W and Malhotra, Sameer and Kaur, Satinder and Ray, Pallab} } @article {815, title = {Quantification of Neurotransmitters from Intact and Regenerating Planarians Using UHPLC-MS/SRM Method. [Mass Spectrometry - Metabolomics Facility (INT)]}, journal = {Methods Mol Biol}, volume = {1774}, year = {2018}, month = {2018}, pages = {555-570}, abstract = {

Freshwater planarian species S. mediterranea is an emerging stem cell model because of its capability of regenerating large portions of missing body parts. It is one of the best model systems available to address the basic biological mechanisms in the regeneration processes. Absolute quantification of metabolites from planarians is imperative to understand their role in the regeneration processes. Here we describe a stable isotope dilution ultrahigh performance liquid chromatography/mass spectrometry/selected reaction monitoring (UHPLC-MS/SRM) assay for a sensitive and quantitative assessment of neurotransmitters (NTs) in planaria. We used this method for the simultaneous quantification of 16 NTs from both intact and regenerating planarians.

}, issn = {1940-6029}, doi = {10.1007/978-1-4939-7802-1_25}, author = {Rangiah, Kannan and Palakodeti, Dasaradhi} } @article {768, title = {Species-specific and differential expression of BSP-5 and other BSP variants in normozoospermic and asthenozoospermic buffalo (Bubalus bubalis) and cattle (Bos taurus) seminal plasma. [Mass Spectrometry Facility - Proteomics]}, journal = {Theriogenology}, volume = {106}, year = {2018}, month = {2018 Jan 15}, pages = {279-286}, abstract = {

Binder of sperm-5 (BSP-5) is one of the fertility-associated proteins of cattle seminal plasma. Binding of sperm to the oviductal epithelium is mediated by BSP group of proteins. However, it is not clear, whether this protein is also involved in sperm motility. In the present study, attempts were made to characterize BSP-5 protein in both normozoospermic (NS) and asthenozoospermic (AS) Murrah buffalo (n~=~18; Bubalus bubalis), Holstein Friesian (n~=~8, Bos taurus) and Jersey cattle (n~=~8; Bos taurus) bull seminal plasma and also study its expression pattern in these species. 1-D Western blot demonstrated three major BSP-5 immunoreactive protein bands (24.2~kDa, 20.5~kDa, and 12.3~kDa) in buffalo seminal plasma. Of these, the intensities of 24.2 and 20.5~kDa protein bands reduced significantly (P~<=~0.05) in seminal plasma of AS group compared to that of NS group. On the contrary, the expression of 12.3~kDa protein band did not vary significantly between the groups. In Holstein Friesian seminal plasma, at least six BSP-5 immunoreactive protein bands (25.1, 23.6, 19.5, 13.8, 13.1 and 12.3~kDa) could be detected. Of these, the intensities of 23.6, 13.8/13.1 and 12.3~kDa protein bands decreased (P~=~0.058, 0.111, 0.053) in AS group bulls compared to NS bulls. Holstein Friesian bull seminal plasma demonstrated a BSP-5 immunoreactive duplex protein band of 13.8/13.1~kDa, which was not evident in buffalo seminal plasma. In 2-D Western blot, a train of five BSP-5 immunoreactive duplex protein spots (Mr 21.0-27.6~kDa, pI of \~{}3.9-5.1) was detected. Mass spectrometry of one of the representative duplex spot confirmed that these were BSP-5 and BSP-3 proteins, respectively. Indirect immunofluorescence studies showed that BSP-5 is primarily localized to the mid-piece/mitochondrial region of buffalo spermatozoa. To conclude, the findings of the present study could establish the significance and association of BSP-5 proteins in sperm motility and how their level differ in semen from two different clinical groups of buffalo bull (NS vs. AS). Further, the study also demonstrated that the expression pattern of BSP-5 and other BSP variants in seminal plasma of bulls is species-specific.

}, issn = {1879-3231}, doi = {10.1016/j.theriogenology.2017.10.014}, author = {Divyashree, B C and Roy, Sudhir C} } @article {889, title = {A strategy to identify a ketoreductase that preferentially synthesizes pharmaceutically relevant (S)-alcohols using whole-cell biotransformation [Bugworks Res. Pvt. Ltd., a C-CAMP Startup]}, journal = {Microb Cell Fact}, volume = {17}, year = {2018}, month = {2018 Dec 03}, pages = {192}, abstract = {

INTRODUCTION: Chemical industries are constantly in search of an expeditious and environmentally benign method for producing chiral synthons. Ketoreductases have been used as catalysts for enantioselective conversion of desired prochiral ketones to their corresponding alcohol. We chose reported promiscuous ketoreductases belonging to different protein families and expressed them in E.\ coli to evaluate their ability as whole-cell catalysts for obtaining chiral alcohol intermediates of pharmaceutical importance. Apart from establishing a method to produce high value (S)-specific alcohols that have not been evaluated before, we propose an in silico analysis procedure\ to predict product chirality.

RESULTS: Six enzymes originating from Sulfolobus\ sulfotaricus, Zygosaccharomyces\ rouxii, Hansenula\ polymorpha, Corynebacterium sp. ST-10, Synechococcus sp. PCC\ 7942 and Bacillus sp. ECU0013 with reported efficient activity for dissimilar substrates are compared here to arrive at an optimal enzyme for the method. Whole-cell catalysis of ketone intermediates for drugs like Aprepitant, Sitagliptin and Dolastatin using E.\ coli over-expressing these enzymes yielded (S)-specific chiral alcohols. We explain this chiral specificity for the best-performing enzyme, i.e., Z.\ rouxii ketoreductase using in silico modelling and MD simulations. This rationale was applied to five additional ketones that are used in the synthesis of Crizotinib, MA-20565\ (an antifungal agent), Sulopenem, Rivastigmine, Talampanel and Barnidipine and predicted the yield of (S) enantiomers. Experimental evaluation matched the in silico analysis wherein ~ 95\% (S)-specific alcohol with a chemical yield of 23-79\% was obtained through biotransformation. Further, the cofactor re-cycling was optimized by switching the carbon source from glucose to sorbitol that improved the chemical yield to 85-99\%.

CONCLUSIONS: Here, we present a strategy to synthesize pharmaceutically relevant chiral alcohols by ketoreductases using a cofactor balanced whole-cell catalysis scheme that is useful for the industry. Based on the results obtained in these trials, Zygosaccharomyces\ rouxii ketoreductase was identified as a proficient enzyme to obtain (S)-specific alcohols from their respective ketones. The whole-cell catalyst when combined with nutrient modulation of using sorbitol as a carbon source helped obtain high enantiomeric and chemical yield.

}, issn = {1475-2859}, doi = {10.1186/s12934-018-1036-2}, author = {Haq, Saiful F and Shanbhag, Anirudh P and Karthikeyan, Subbulakshmi and Hassan, Imran and Thanukrishnan, Kannan and Ashok, Abhishek and Sukumaran, Sunilkumar and Ramaswamy, S and Bharatham, Nagakumar and Datta, Santanu and Samant, Shalaka and Katagihallimath, Nainesh} } @article {868, title = {A versatile LC-MS/MS approach for comprehensive, quantitative analysis of central metabolic pathways. [Mass Spectrometry - Lipidomics \& Metabolomics (INT)]}, journal = {Wellcome Open Res}, volume = {3}, year = {2018}, month = {2018}, pages = {122}, abstract = {

Liquid chromatography-mass spectrometry (LC-MS/MS) based approaches are widely used for the identification and quantitation of specific metabolites, and are a preferred approach towards analyzing cellular metabolism. Most methods developed come with specific requirements such as unique columns, ion-pairing reagents and pH conditions, and typically allow measurements in a specific pathway alone. Here, we present a single column-based set of methods for simultaneous coverage of multiple pathways, primarily focusing on central carbon, amino acid, and nucleotide metabolism. We further demonstrate the use of this method for quantitative, stable isotope-based metabolic flux experiments, expanding its use beyond steady-state level measurements of metabolites. The expected kinetics of label accumulation pertinent to the pathway under study are presented with some examples. The methods discussed here are broadly applicable, minimize the need for multiple chromatographic resolution methods, and highlight how simple labeling experiments can be valuable in facilitating a comprehensive understanding of the metabolic state of cells.

}, issn = {2398-502X}, doi = {10.12688/wellcomeopenres.14832.1}, author = {Walvekar, Adhish and Rashida, Zeenat and Maddali, Hemanth and Laxman, Sunil} } @article {683, title = {Combinatorial action of Grainyhead, Extradenticle and Notch in regulating Hox mediated apoptosis in Drosophila larval CNS.}, journal = {PLoS Genet}, volume = {13}, year = {2017}, month = {2017 Oct}, pages = {e1007043}, abstract = {

Hox mediated neuroblast apoptosis is a prevalent way to pattern larval central nervous system (CNS) by different Hox genes, but the mechanism of this apoptosis is not understood. Our studies with Abdominal-A (Abd-A) mediated larval neuroblast (pNB) apoptosis suggests that AbdA, its cofactor Extradenticle (Exd), a helix-loop-helix transcription factor Grainyhead (Grh), and Notch signaling transcriptionally contribute to expression of RHG family of apoptotic genes. We find that Grh, AbdA, and Exd function together at multiple motifs on the apoptotic enhancer. In vivo mutagenesis of these motifs suggest that they are important for the maintenance of the activity of the enhancer rather than its initiation. We also find that Exd function is independent of its known partner homothorax in this apoptosis. We extend some of our findings to Deformed expressing region of sub-esophageal ganglia where pNBs undergo a similar Hox dependent apoptosis. We propose a mechanism where common players like Exd-Grh-Notch work with different Hox genes through region specific enhancers to pattern respective segments of larval central nervous system.

}, keywords = {Amino Acid Sequence, Animals, Apoptosis, Central Nervous System, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Enhancer Elements, Genetic, Female, Gene Expression Regulation, Developmental, Genes, Homeobox, Homeodomain Proteins, Larva, Male, Nuclear Proteins, Receptors, Notch, Transcription Factors}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1007043}, author = {Khandelwal, Risha and Sipani, Rashmi and Govinda Rajan, Sriivatsan and Kumar, Raviranjan and Joshi, Rohit} } @article {471, title = {Gut microbial degradation of organophosphate insecticides-induces glucose intolerance via gluconeogenesis. [Next Generation Genomics facility]}, journal = {Genome Biol}, volume = {18}, year = {2017}, month = {2017 Jan 24}, pages = {8}, abstract = {

BACKGROUND: Organophosphates are the most frequently and largely applied insecticide in the world due to their biodegradable nature. Gut microbes were shown to degrade organophosphates and cause intestinal dysfunction. The diabetogenic nature of organophosphates was recently reported but the underlying molecular mechanism is unclear. We aimed to understand the role of gut microbiota in organophosphate-induced hyperglycemia and to unravel the molecular mechanism behind this process.

RESULTS: Here we demonstrate a high prevalence of diabetes among people directly exposed to organophosphates in rural India (n = 3080). Correlation and linear regression analysis reveal a strong association between plasma organophosphate residues and HbA1c but no association with acetylcholine esterase was noticed. Chronic treatment of mice with organophosphate for 180\ days confirms the induction of glucose intolerance with no significant change in acetylcholine esterase. Further fecal transplantation and culture transplantation experiments confirm the involvement of gut microbiota in organophosphate-induced glucose intolerance. Intestinal metatranscriptomic and host metabolomic analyses reveal that gut microbial organophosphate degradation produces short chain fatty acids like acetic acid, which induces gluconeogenesis and thereby accounts for glucose intolerance. Plasma organophosphate residues are positively correlated with fecal esterase activity and acetate level of human diabetes.

CONCLUSION: Collectively, our results implicate gluconeogenesis as the key mechanism behind organophosphate-induced hyperglycemia, mediated by the organophosphate-degrading potential of gut microbiota. This study reveals the gut microbiome-mediated diabetogenic nature of organophosphates and hence that the usage of these insecticides should be reconsidered.

}, issn = {1474-760X}, doi = {10.1186/s13059-016-1134-6}, author = {Velmurugan, Ganesan and Ramprasath, Tharmarajan and Swaminathan, Krishnan and Mithieux, Gilles and Rajendhran, Jeyaprakash and Dhivakar, Mani and Parthasarathy, Ayothi and Babu, D D Venkatesh and Thumburaj, Leishman John and Freddy, Allen J and Dinakaran, Vasudevan and Puhari, Shanavas Syed Mohamed and Rekha, Balakrishnan and Christy, Yacob Jenifer and Anusha, Sivakumar and Divya, Ganesan and Suganya, Kannan and Meganathan, Boominathan and Kalyanaraman, Narayanan and Vasudevan, Varadaraj and Kamaraj, Raju and Karthik, Maruthan and Jeyakumar, Balakrishnan and Abhishek, Albert and Paul, Eldho and Pushpanathan, Muthuirulan and Rajmohan, Rajamani Koushick and Velayutham, Kumaravel and Lyon, Alexander R and Ramasamy, Subbiah} } @article {706, title = {Dynein Clusters into Lipid Microdomains on Phagosomes to Drive Rapid Transport toward Lysosomes.}, journal = {Cell}, volume = {164}, year = {2016}, month = {2016 Feb 11}, pages = {722-34}, abstract = {

Diverse cellular processes are driven by motor proteins that are recruited to and generate force on lipid membranes. Surprisingly little is known about how membranes control the force from motors and how this may impact specific cellular functions. Here, we show that dynein motors physically cluster into microdomains on the membrane of a phagosome as it matures inside cells. Such geometrical reorganization allows many dyneins within a cluster to generate cooperative force on a single microtubule. This results in rapid directed transport of the phagosome toward microtubule minus ends, likely promoting phagolysosome fusion and pathogen degradation. We show that lipophosphoglycan, the major molecule implicated in immune evasion of Leishmania donovani, inhibits phagosome motion by disrupting the clustering and therefore the cooperative force generation of dynein. These findings appear relevant to several pathogens that prevent phagosome-lysosome fusion by targeting lipid microdomains on phagosomes.

}, keywords = {Animals, Biological Transport, Cell Line, Dictyostelium, Dyneins, Glycosphingolipids, Leishmania donovani, Lysosomes, Membrane Microdomains, Mice, Phagosomes}, issn = {1097-4172}, doi = {10.1016/j.cell.2015.12.054}, author = {Rai, Ashim and Pathak, Divya and Thakur, Shreyasi and Singh, Shampa and Dubey, Alok Kumar and Mallik, Roop} } @article {540, title = {A method for comparative metabolomics in urine using high resolution mass spectrometry.}, journal = {J Chromatogr A}, volume = {1443}, year = {2016}, month = {2016 Apr 22}, pages = {83-92}, abstract = {

Developing a workflow for metabolite profiling from biological fluids using mass spectrometry is imperative to extract accurate information. In this study, urine samples from smokers (n=10) and nonsmokers (n=10) were analyzed using an ultrahigh performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) system. For the analysis, two different chromatographic methods [Reversed phase chromatography (RPC) and Hydrophilic interaction liquid chromatography (HILIC)], in two ionization modes (positive and negative) were used. Spiked reserpine (positive ion mode) or taurocholate (negative ion mode) were used for data extraction and normalization. Quality controls (QCs), prepared by pooling urine samples from both smokers and non-smokers (each n=10), were used to assess the reproducibility of the method. The final data output from SIEVE 2.2 after applying a cut-off for QC coefficient of variation (CV) \<20\% and p-value \<0.05 showed 165, 83, 177 and 100 unique components in RP positive/negative, HILIC positive/negative modes, respectively. Statistical analysis showed clustering of the two groups and the QCs, while the variable importance in projection (VIP) scores for the top fifteen metabolites in each of the four modes indicated the metabolites most responsible for the differences. Application of the developed workflow for comparative metabolomic analysis of urine in different diseased models will be of great use in the field of clinical metabolomics.

}, keywords = {Chromatography, Liquid, Chromatography, Reverse-Phase, Hydrophobic and Hydrophilic Interactions, Mass Spectrometry, Metabolomics, Reproducibility of Results, Urinalysis}, issn = {1873-3778}, doi = {10.1016/j.chroma.2016.02.080}, author = {Ramakrishnan, Padma and Nair, Sreenath and Rangiah, Kannan} } @article {509, title = {Structure of a heterogeneous, glycosylated, lipid-bound, in vivo-grown protein crystal at atomic resolution from the viviparous cockroach Diploptera punctata. [Mass spectrometry - Glycomics]}, journal = {IUCrJ}, volume = {3}, year = {2016}, month = {2016 Jul 01}, pages = {282-93}, abstract = {

Macromolecular crystals for X-ray diffraction studies are typically grown in vitro from pure and homogeneous samples; however, there are examples of protein crystals that have been identified in vivo. Recent developments in micro-crystallography techniques and the advent of X-ray free-electron lasers have allowed the determination of several protein structures from crystals grown in cellulo. Here, an atomic resolution (1.2 {\r A}) crystal structure is reported of heterogeneous milk proteins grown inside a living organism in their functional niche. These in vivo-grown crystals were isolated from the midgut of an embryo within the only known viviparous cockroach, Diploptera punctata. The milk proteins crystallized in space group P1, and a structure was determined by anomalous dispersion from the native S atoms. The data revealed glycosylated proteins that adopt a lipocalin fold, bind lipids and organize to form a tightly packed crystalline lattice. A single crystal is estimated to contain more than three times the energy of an equivalent mass of dairy milk. This unique storage form of nourishment for developing embryos allows access to a constant supply of complete nutrients. Notably, the crystalline cockroach-milk proteins are highly heterogeneous with respect to amino-acid sequence, glycosylation and bound fatty-acid composition. These data present a unique example of protein heterogeneity within a single in vivo-grown crystal of a natural protein in its native environment at atomic resolution.

}, doi = {10.1107/S2052252516008903}, author = {Banerjee, Sanchari and Coussens, Nathan P and Gallat, Fran{\c c}ois-Xavier and Sathyanarayanan, Nitish and Srikanth, Jandhyam and Yagi, Koichiro J and Gray, James S S and Tobe, Stephen S and Stay, Barbara and Chavas, Leonard M G and Ramaswamy, Subramanian} } @article {499, title = {Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree. [Mass spectrometry - Metabolomics]}, journal = {PeerJ}, volume = {3}, year = {2015}, month = {2015}, pages = {e1066}, abstract = {

Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC-600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are the major active principles isolated from neem seed. Absolutely nothing is known about the biochemical pathways of these metabolites in neem tree. To identify genes and pathways in neem, we sequenced neem genomes and transcriptomes using next generation sequencing technologies. Assembly of Illumina and 454 sequencing reads resulted in 267 Mb, which accounts for 70\% of estimated size of neem genome. We predicted 44,495 genes in the neem genome, of which 32,278 genes were expressed in neem tissues. Neem genome consists about 32.5\% (87 Mb) of repetitive DNA elements. Neem tree is phylogenetically related to citrus, Citrus sinensis. Comparative analysis anchored 62\% (161 Mb) of assembled neem genomic contigs onto citrus chromomes. Ultrahigh performance liquid chromatography-mass spectrometry-selected reaction monitoring (UHPLC-MS/SRM) method was used to quantify azadirachtin, nimbin, and salanin from neem tissues. Weighted Correlation Network Analysis (WCGNA) of expressed genes and metabolites resulted in identification of possible candidate genes involved in azadirachtin biosynthesis pathway. This study provides genomic, transcriptomic and quantity of top three neem metabolites resource, which will accelerate basic research in neem to understand biochemical pathways.

}, doi = {10.7717/peerj.1066}, author = {Kuravadi, Nagesh A and Yenagi, Vijay and Rangiah, Kannan and Mahesh, H B and Rajamani, Anantharamanan and Shirke, Meghana D and Russiachand, Heikham and Loganathan, Ramya Malarini and Shankara Lingu, Chandana and Siddappa, Shilpa and Ramamurthy, Aishwarya and Sathyanarayana, B N and Gowda, Malali} } @article {473, title = {A dPIP5K dependent pool of phosphatidylinositol 4,5 bisphosphate (PIP2) is required for G-protein coupled signal transduction in Drosophila photoreceptors.[Drosophila facility]}, journal = {PLoS Genet}, volume = {11}, year = {2015}, month = {2015 Jan}, pages = {e1004948}, abstract = {

Multiple PIP2 dependent molecular processes including receptor activated phospholipase C activity occur at the neuronal plasma membranes, yet levels of this lipid at the plasma membrane are remarkably stable. Although the existence of unique pools of PIP2 supporting these events has been proposed, the mechanism by which they are generated is unclear. In Drosophila photoreceptors, the hydrolysis of PIP2 by G-protein coupled phospholipase C activity is essential for sensory transduction of photons. We identify dPIP5K as an enzyme essential for PIP2 re-synthesis in photoreceptors. Loss of dPIP5K causes profound defects in the electrical response to light and light-induced PIP2 dynamics at the photoreceptor membrane. Overexpression of dPIP5K was able to accelerate the rate of PIP2 synthesis following light induced PIP2 depletion. Other PIP2 dependent processes such as endocytosis and cytoskeletal function were unaffected in photoreceptors lacking dPIP5K function. These results provide evidence for the existence of a unique dPIP5K dependent pool of PIP2 required for normal Drosophila phototransduction. Our results define the existence of multiple pools of PIP2 in photoreceptors generated by distinct lipid kinases and supporting specific molecular processes at neuronal membranes.

}, keywords = {Animals, Cell Membrane, Cytoskeleton, Drosophila, Drosophila melanogaster, Light Signal Transduction, Membrane Proteins, Ocular Physiological Phenomena, Phosphatidylinositol 4,5-Diphosphate, Phosphoinositide Phospholipase C, Phosphotransferases (Alcohol Group Acceptor), Photoreceptor Cells, Retina, Signal Transduction}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1004948}, author = {Chakrabarti, Purbani and Kolay, Sourav and Yadav, Shweta and Kumari, Kamalesh and Nair, Amit and Trivedi, Deepti and Raghu, Padinjat} } @article {538, title = {Genome analysis of rice-blast fungus Magnaporthe oryzae field isolates from southern India.}, journal = {Genom Data}, volume = {5}, year = {2015}, month = {2015 Sep}, pages = {284-91}, abstract = {

The Indian subcontinent is the center of origin and diversity for rice (Oryza sativa L.). The O. sativa ssp. indica is a major food crop grown in India, which occupies the first and second position in area and production, respectively. Blast disease caused by Magnaporthe oryzae is a major constraint to rice production. Here, we report the analysis of genome architecture and sequence variation of two field isolates, B157 and MG01, of the blast fungus from southern India. The 40\ Mb genome of B157 and 43\ Mb genome of MG01 contained 11,344 and 11,733 predicted genes, respectively. Genomic comparisons unveiled a large set of SNPs and several isolate specific genes in the Indian blast isolates. Avr genes were analyzed in several sequenced Magnaporthe strains; this analysis revealed the presence of Avr-Pizt and Avr-Ace1 genes in all the sequenced isolates. Availability of whole genomes of field isolates from India will contribute to global efforts to understand genetic diversity of M. oryzae population and to track the emergence of virulent pathotypes.

}, doi = {10.1016/j.gdata.2015.06.018}, author = {Gowda, Malali and Shirke, Meghana D and Mahesh, H B and Chandarana, Pinal and Rajamani, Anantharamanan and Chattoo, Bharat B} } @article {498, title = {Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties.[Mass spectrometry - Metabolomics]}, journal = {BMC Plant Biol}, volume = {15}, year = {2015}, month = {2015 Aug 28}, pages = {212}, abstract = {

BACKGROUND: Krishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and medicinal importance in India. The common name of this plant is {\textquoteright}Tulsi{\textquoteright} (or {\textquoteright}Tulasi{\textquoteright} or {\textquoteright}Thulasi{\textquoteright}) and is considered sacred by Hindus. We present the draft genome of Ocimum tenuiflurum L (subtype Krishna Tulsi) in this report. The paired-end and mate-pair sequence libraries were generated for the whole genome sequenced with the Illumina Hiseq 1000, resulting in an assembled genome of 374\ Mb, with a genome coverage of 61\ \% (612\ Mb estimated genome size). We have also studied transcriptomes (RNA-Seq) of two subtypes of O. tenuiflorum, Krishna and Rama Tulsi and report the relative expression of genes in both the varieties.

RESULTS: The pathways leading to the production of medicinally-important specialized metabolites have been studied in detail, in relation to similar pathways in Arabidopsis thaliana and other plants. Expression levels of anthocyanin biosynthesis-related genes in leaf samples of Krishna Tulsi were observed to be relatively high, explaining the purple colouration of Krishna Tulsi leaves. The expression of six important genes identified from genome data were validated by performing q-RT-PCR in different tissues of five different species, which shows the high extent of urosolic acid-producing genes in young leaves of the Rama subtype. In addition, the presence of eugenol and ursolic acid, implied as potential drugs in the cure of many diseases including cancer was confirmed using mass spectrometry.

CONCLUSIONS: The availability of the whole genome of O.tenuiflorum and our sequence analysis suggests that small amino acid changes at the functional sites of genes involved in metabolite synthesis pathways confer special medicinal properties to this herb.

}, keywords = {Gene Expression Regulation, Plant, Genome, Plant, India, Ocimum, Plant Leaves, Plants, Medicinal}, issn = {1471-2229}, doi = {10.1186/s12870-015-0562-x}, author = {Upadhyay, Atul K and Chacko, Anita R and Gandhimathi, A and Ghosh, Pritha and Harini, K and Joseph, Agnel P and Joshi, Adwait G and Karpe, Snehal D and Kaushik, Swati and Kuravadi, Nagesh and Lingu, Chandana S and Mahita, J and Malarini, Ramya and Malhotra, Sony and Malini, Manoharan and Mathew, Oommen K and Mutt, Eshita and Naika, Mahantesha and Nitish, Sathyanarayanan and Pasha, Shaik Naseer and Raghavender, Upadhyayula S and Rajamani, Anantharamanan and Shilpa, S and Shingate, Prashant N and Singh, Heikham Russiachand and Sukhwal, Anshul and Sunitha, Margaret S and Sumathi, Manojkumar and Ramaswamy, S and Gowda, Malali and Sowdhamini, Ramanathan} } @article {497, title = {Protective effect of Euphorbia hirta and its components against snake venom induced lethality. [Mass spectrometry - Metabolomics]}, journal = {J Ethnopharmacol}, volume = {165}, year = {2015}, month = {2015 May 13}, pages = {180-90}, abstract = {

ETHNOPHARMACOLOGICAL RELEVANCE: Despite the use of snake anti-venom therapy, herbal medicine is still in practice to treat snakebites. Euphorbia hirta is traditionally used as antidote for snakebites and also for numerous other ailments. However, the scientific evidence for its anti-snake venom property is still lacking.

MATERIALS AND METHODS: Methanolic extract of E. hirta was evaluated for anti-venom activity under in vitro and ex vivo conditions. Histopathological changes in the vital organs of the mice were also monitored. UHPLC-SRM/MS was used to estimate the phenolic constituents whereas GC-MS analysis was performed to analyze the volatile metabolites present. The major compound was further evaluated for its contribution to the overall inhibitory potential of the extract.

RESULTS: Methanolic extract of E. hirta completely inhibited the venom enzymes under in vitro and reduced the edema ratio. The extract increased the survival time (\>24h) of mice which was further evidenced by histopathological analysis of vital organs. Phytochemical analysis revealed higher content of phenolic (144 mg/g extract) compounds in the extract. UHPLC-SRM/MS demonstrated that ellagic acid, gallic acid and quinic acid are the major phenolics whereas GC-MS analysis revealed pyrogallol as the major constituent (60.07\%) among the volatile components of the extract. It was also shown that pyrogallol has the ability to differentially inhibit venom protease but not phospholipase A2.

CONCLUSION: The present study confirmed that E. hirta methanolic extract was able to completely inhibit Naja naja venom induced toxicity under in vitro as well as ex vivo conditions, thus providing scientific evidence to its traditional use.

}, keywords = {Animals, Chromatography, High Pressure Liquid, Cobra Venoms, Euphorbia, Male, Mass Spectrometry, Mice, Phytotherapy, Plant Extracts, Snake Bites, Snake Venoms}, issn = {1872-7573}, doi = {10.1016/j.jep.2015.02.044}, author = {Gopi, Kadiyala and Renu, Kadali and Sannanaik Vishwanath, Bannikuppe and Jayaraman, Gurunathan} } @article {501, title = {A quantitative metabolomics peek into planarian regeneration. [Mass spectrometry - Metabolomics]}, journal = {Analyst}, volume = {140}, year = {2015}, month = {2015 May 21}, pages = {3445-64}, abstract = {

The fresh water planarian species Schmidtea mediterranea is an emerging stem cell model because of its capability to regenerate a whole animal from a small piece of tissue. It is one of the best model systems to address the basic mechanisms essential for regeneration. Here, we are interested in studying the roles of various amines, thiols and nucleotides in planarian regeneration, stem cell function and growth. We developed mass spectrometry based quantitative methods and validated the differential enrichment of 35 amines, 7 thiol metabolites and 4 nucleotides from both intact and regenerating planarians. Among the amines, alanine in sexual and asparagine in asexual are the highest (\>1000 ng/mg) in the intact planarians. The levels of thiols such as cysteine and GSH are 651 and 1107 ng mg(-1) in planarians. Among the nucleotides, the level of cGMP is the lowest (0.03 ng mg(-1)) and the level of AMP is the highest (187 ng mg(-1)) in both of the planarian strains. We also noticed increasing levels of amines in both anterior and posterior regenerating planarians. The blastema from day 3 regenerating planarians also showed higher amounts of many amines. Interestingly, the thiol (cysteine and GSH) levels are well maintained during planarian regeneration. This suggests an inherent and effective mechanism to control induced oxidative stress because of the robust regeneration and stem cell proliferation. Like in intact planarians, the level of cGMP is also very low in regenerating planarians. Surprisingly, the levels of amines and thiols in head regenerating blastemas are \~{}3 times higher compared to those for tail regenerating blastemas. Thus our results strongly indicate the potential roles of amines, thiols and nucleotides in planarian regeneration.

}, keywords = {Animals, Calibration, Chromatography, High Pressure Liquid, Limit of Detection, Metabolomics, Planarians, Reference Standards, Regeneration, Reproduction, Asexual, Species Specificity, Tandem Mass Spectrometry}, issn = {1364-5528}, doi = {10.1039/c4an02037e}, author = {Natarajan, Nivedita and Ramakrishnan, Padma and Lakshmanan, Vairavan and Palakodeti, Dasaradhi and Rangiah, Kannan} } @article {533, title = {A rapid, nonradioactive assay for measuring heparan sulfate C-5 epimerase activity using hydrogen/deuterium exchange-mass spectrometry.}, journal = {Methods Mol Biol}, volume = {1229}, year = {2015}, month = {2015}, pages = {209-19}, abstract = {

Heparin and heparan sulfate (HS) glycosaminoglycans have important roles in anticoagulation, human development, and human diseases. HS C5-epimerase, which catalyzes the epimerization of GlcA to IdoA, is a crucial enzyme involved in the biosynthesis of heparin-related biomolecules. Here, we describe a detailed method for measuring the total activity of HS C5-epimerase that involves the following steps: H/D exchange upon epimerization of the substrate with HS C5-epimerase, low-pH nitrous acid treatment of the substrate, the separation of low-pH nitrous acid-cleaved disaccharides using HPLC, and mass spectrometry analysis. This nonradioactive method is rapid and sensitive and, importantly, allows us to study the reversible nature of HS C5-epimerase.

}, keywords = {Animals, Biocatalysis, Carbohydrate Epimerases, Chromatography, Ion Exchange, Chromatography, Liquid, Deuterium Exchange Measurement, Disaccharides, Enzyme Assays, Glucuronic Acid, Heparitin Sulfate, Humans, Iduronic Acid, Mass Spectrometry, Sf9 Cells}, issn = {1940-6029}, doi = {10.1007/978-1-4939-1714-3_19}, author = {Babu, Ponnusamy and Victor, Xylophone V and Raman, Karthik and Kuberan, Balagurunathan} } @article {472, title = {RDGBα, a PtdIns-PtdOH transfer protein, regulates G-protein-coupled PtdIns(4,5)P2 signalling during Drosophila phototransduction.[Drosophila Facility]}, journal = {J Cell Sci}, volume = {128}, year = {2015}, month = {2015 Sep 01}, pages = {3330-44}, abstract = {

Many membrane receptors activate phospholipase C (PLC) during signalling, triggering changes in the levels of several plasma membrane lipids including phosphatidylinositol (PtdIns), phosphatidic acid (PtdOH) and phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2]. It is widely believed that exchange of lipids between the plasma membrane and endoplasmic reticulum (ER) is required to restore lipid homeostasis during PLC signalling, yet the mechanism remains unresolved. RDGBα (hereafter RDGB) is a multi-domain protein with a PtdIns transfer protein (PITP) domain (RDGB-PITPd). We find that, in vitro, the RDGB-PITPd binds and transfers both PtdOH and PtdIns. In Drosophila photoreceptors, which experience high rates of PLC activity, RDGB function is essential for phototransduction. We show that binding of PtdIns to RDGB-PITPd is essential for normal phototransduction; however, this property is insufficient to explain the in vivo function because another Drosophila PITP (encoded by vib) that also binds PtdIns cannot rescue the phenotypes of RDGB deletion. In RDGB mutants, PtdIns(4,5)P2 resynthesis at the plasma membrane following PLC activation is delayed and PtdOH levels elevate. Thus RDGB couples the turnover of both PtdIns and PtdOH, key lipid intermediates during G-protein-coupled PtdIns(4,5)P2 turnover.

}, keywords = {Animals, Drosophila melanogaster, Drosophila Proteins, Eye Proteins, Light Signal Transduction, Membrane Proteins, Phosphatidic Acids, Phosphatidylinositol 4,5-Diphosphate, Type C Phospholipases}, issn = {1477-9137}, doi = {10.1242/jcs.173476}, author = {Yadav, Shweta and Garner, Kathryn and Georgiev, Plamen and Li, Michelle and Gomez-Espinosa, Evelyn and Panda, Aniruddha and Mathre, Swarna and Okkenhaug, Hanneke and Cockcroft, Shamshad and Raghu, Padinjat} } @article {475, title = {Genetic transformation of structural and functional circuitry rewires the Drosophila brain. [Drosophila Facility]}, journal = {Elife}, volume = {3}, year = {2014}, month = {2014 Dec 29}, abstract = {

Acquisition of distinct neuronal identities during development is critical for the assembly of diverse functional neural circuits in the brain. In both vertebrates and invertebrates, intrinsic determinants are thought to act in neural progenitors to specify their identity and the identity of their neuronal progeny. However, the extent to which individual factors can contribute to this is poorly understood. We investigate the role of orthodenticle in the specification of an identified neuroblast (neuronal progenitor) lineage in the Drosophila brain. Loss of orthodenticle from this neuroblast affects molecular properties, neuroanatomical features, and functional inputs of progeny neurons, such that an entire central complex lineage transforms into a functional olfactory projection neuron lineage. This ability to change functional macrocircuitry of the brain through changes in gene expression in a single neuroblast reveals a surprising capacity for novel circuit formation in the brain and provides a paradigm for large-scale evolutionary modification of circuitry.

}, keywords = {Animals, Brain, Cell Lineage, Drosophila, Morphogenesis, Neurons}, issn = {2050-084X}, doi = {10.7554/eLife.04407}, author = {Sen, Sonia and Cao, Deshou and Choudhary, Ramveer and Biagini, Silvia and Wang, Jing W and Reichert, Heinrich and VijayRaghavan, K} } @article {502, title = {Sensitive UHPLC-MS/SRM method for quantifying olanzapine metabolites and degradation products from sera}, journal = {Anal. Methods}, volume = {6}, year = {2014}, pages = {5250-5257}, abstract = {

In recent years{,} the use of antipsychotics like olanzapine has increased leading to potentially serious adverse metabolic effects. A sensitive method to quantify olanzapine and its metabolites is therefore highly needed. A stable isotope dilution ultrahigh performance liquid chromatography-mass spectrometry/selected reaction monitoring based quantitative assay has been developed for the simultaneous estimation of olanzapine and its metabolites. This method includes the parent drug olanzapine{,} its metabolites (desmethyl olanzapine and olanzapine-N-oxide) and degradation derived piperazinium chloride{,} lactam and cyclic amine impurities. All analytes were well resolved and showed a linear relationship across a large dynamic range (0.017-1.25 ng mL-1) for all olanzapine metabolites except the lactam{,} in which the linear relationship was demonstrated at concentrations five times higher (0.085-6.25 ng mL-1). All analytes had regression coefficients higher than 0.998{,} accuracies between 92-113\% and low coefficients of variation (0.94 to 9.3\%). The recovery for all of the analytes from the sera matrix was 80 to 115\%. This validated method is suitable for quantifying olanzapine and its metabolites from small volumes of sera samples with great sensitivity.

}, doi = {10.1039/C4AY00450G}, url = {http://dx.doi.org/10.1039/C4AY00450G}, author = {Rangiah, Kannan} } @article {535, title = {Unique, polyfucosylated glycan-receptor interactions are essential for regeneration of Hydra magnipapillata.}, journal = {ACS Chem Biol}, volume = {9}, year = {2014}, month = {2014 Jan 17}, pages = {147-55}, abstract = {

Cell-cell communications, cell-matrix interactions, and cell migrations play a major role in regeneration. However, little is known about the molecular players involved in these critical events, especially cell surface molecules. Here, we demonstrate the role of specific glycan-receptor interactions in the regenerative process using Hydra magnipapillata as a model system. Global characterization of the N- and O-glycans expressed by H. magnipapillata using ultrasensitive mass spectrometry revealed mainly polyfucosylated LacdiNAc antennary structures. Affinity purification showed that a putative C-type lectin (accession number Q6SIX6) is a likely endogenous receptor for the novel polyfucosylated glycans. Disruption of glycan-receptor interactions led to complete shutdown of the regeneration machinery in live Hydra. A time-dependent, lack-of-regeneration phenotype observed upon incubation with exogenous fuco-lectins suggests the involvement of a polyfucose receptor-mediated signaling mechanism during regeneration. Thus, for the first time, the results presented here provide direct evidence for the role of polyfucosylated glycan-receptor interactions in the regeneration of H. magnipapillata.

}, keywords = {Animals, Carbohydrate Sequence, Hydra, Lectins, C-Type, Molecular Sequence Data, Polysaccharides, Regeneration}, issn = {1554-8937}, doi = {10.1021/cb400486t}, author = {Sahadevan, Sonu and Antonopoulos, Aristotelis and Haslam, Stuart M and Dell, Anne and Ramaswamy, Subramanian and Babu, Ponnusamy} } @article {518, title = {Vertebrate Hedgehog is secreted on two types of extracellular vesicles with different signaling properties. (Mass spectrometry - Proteomics)}, journal = {Sci Rep}, volume = {4}, year = {2014}, month = {2014 Dec 08}, pages = {7357}, abstract = {

Hedgehog (Hh) is a secreted morphogen that elicits differentiation and patterning in developing tissues. Multiple proposed mechanisms to regulate Hh dispersion includes lipoprotein particles and exosomes. Here we report that vertebrate Sonic Hedgehog (Shh) is secreted on two types of extracellular-vesicles/exosomes, from human cell lines and primary chick notochord cells. Although largely overlapping in size as estimated from electron micrographs, the two exosomal fractions exhibited distinct protein and RNA composition. We have probed the functional properties of these vesicles using cell-based assays of Hh-elicited gene expression. Our results suggest that while both Shh-containing exo-vesicular fractions can activate an ectopic Gli-luciferase construct, only exosomes co-expressing Integrins can activate endogenous Shh target genes HNF3β and Olig2 during the differentiation of mouse ES cells to ventral neuronal progenitors. Taken together, our results demonstrate that primary vertebrate cells secrete Shh in distinct vesicular forms, and support a model where packaging of Shh along with other signaling proteins such as Integrins on exosomes modulates target gene activation. The existence of distinct classes of Shh-containing exosomes also suggests a previously unappreciated complexity for fine-tuning of Shh-mediated gradients and pattern formation.

}, keywords = {Animals, Chick Embryo, Exosomes, Extracellular Space, Hedgehog Proteins, HEK293 Cells, Humans, MicroRNAs, Models, Biological, Protein Transport, Signal Transduction, Vertebrates}, issn = {2045-2322}, doi = {10.1038/srep07357}, author = {Vyas, Neha and Walvekar, Ankita and Tate, Dhananjay and Lakshmanan, Vairavan and Bansal, Dhiru and Lo Cicero, Alessandra and Raposo, Graca and Palakodeti, Dasaradhi and Dhawan, Jyotsna} } @article {503, title = {Comprehensive analysis of neurotransmitters from regenerating planarian extract using an ultrahigh-performance liquid chromatography/mass spectrometry/selected reaction monitoring method.}, journal = {Rapid Commun Mass Spectrom}, volume = {27}, year = {2013}, month = {2013 Nov 15}, pages = {2439-52}, abstract = {

RATIONALE: Absolute quantification of neurotransmitters (NTs) from biological systems is imperative to track how changes in concentration of active neurochemicals may affect biological behavior. A sensitive method for the absolute quantification of multiple NTs in a single method is highly needed.

METHODS: A stable-isotope dilution ultrahigh-performance liquid chromatography/mass spectrometry/selected reaction monitoring (UHPLC/MS/SRM) assay has been developed for a sensitive and quantitative assessment of NTs in planaria. We used this method for the simultaneous quantification of 16 NTs. All analytes showed a linear relationship between concentrations (0.78-50 ng/mL), regression coefficients higher than 0.97, accuracy (91-109\%) and low coefficients of variation (CVs). The inter-day CVs for the lowest quality controls (1.56 ng/mL) were in the range between 2-11\%.

RESULTS: The levels of most of the NTs were similar in both sexual and asexual planarians except for glutamic acid, which was about two-fold higher in asexual compared to sexual planarians. We identified high levels of serotonin and failed to detect tryptamine suggesting that the pathway essential for the conversion of tryptophan into tryptamine is absent in planarians. Interestingly, we also found high levels of dopamine and L-DOPA in regenerating planarians suggesting their possible role in regeneration.

CONCLUSIONS: For the first time, we developed novel methodology based on UHPLC/MS/SRM and quantified 16 NTs with high sensitivity and specificity from sexual and asexual strains of planarian Schmidtea mediterranea. This method will also have great application in quantifying various NTs with great precision in different model systems.

}, keywords = {Animals, Chromatography, High Pressure Liquid, Glutamic Acid, Limit of Detection, Neurotransmitter Agents, Planarians, Reproduction, Reproduction, Asexual, Serotonin, Spectrometry, Mass, Electrospray Ionization, Tryptamines}, issn = {1097-0231}, doi = {10.1002/rcm.6706}, author = {Rangiah, Kannan and Palakodeti, Dasaradhi} } @article {521, title = {Draft Genome Sequence of Acinetobacter baumannii Strain MSP4-16. (Next Generation Genomics)}, journal = {Genome Announc}, volume = {1}, year = {2013}, month = {2013 Apr 04}, pages = {e0013713}, abstract = {

We report the 4.0-Mb draft genome sequence of Acinetobacter baumannii strain MSP4-16, isolated from a mangrove soil sample from Parangipettai (11{\textdegree}30{\textquoteright}N, 79{\textdegree}47{\textquoteright}E), Tamil Nadu, India. The draft genome sequence of strain MSP4-16 consists of 3,944,542\ bp, with a G+C content of 39\%, 5,387 protein coding genes, and 69 RNAs.

}, doi = {10.1128/genomeA.00137-13}, author = {Singh, Nitin Kumar and Kumar, Shailesh and Raghava, Gajendra Pal Singh and Mayilraj, Shanmugam} } @article {486, title = {Draft Genome Sequence of Amycolatopsis decaplanina Strain DSM 44594T. [Next Generation Genomics facility]}, journal = {Genome Announc}, volume = {1}, year = {2013}, month = {2013 Apr 04}, pages = {e0013813}, abstract = {

We report the 8.5-Mb genome sequence of Amycolatopsis decaplanina strain DSM 44594(T), isolated from a soil sample from India. The draft genome of strain DSM 44594(T) consists of 8,533,276\ bp with a 68.6\% G+C content, 7,899 protein-coding genes, and 57 RNAs.

}, doi = {10.1128/genomeA.00138-13}, author = {Kaur, Navjot and Kumar, Shailesh and Bala, Monu and Raghava, Gajendra Pal Singh and Mayilraj, Shanmugam} } @article {522, title = {Draft Genome Sequence of Rhodococcus qingshengii Strain BKS 20-40. (Next Generation Genomics)}, journal = {Genome Announc}, volume = {1}, year = {2013}, month = {2013 Mar 28}, pages = {e0012813}, abstract = {

We report the 5.8-Mb genome sequence of Rhodococcus qingshengii strain BKS 20-40, isolated from a palm tree rhizosphere soil sample from Bhitarkanika National Park, Odisha, India. The strain is capable of degrading cholesterol moiety. The draft genome of strain BKS 20-40 consists of 6,601,618\ bp, with 62.4\% G+C content.

}, doi = {10.1128/genomeA.00128-13}, author = {Bala, Monu and Kumar, Shailesh and Raghava, Gajendra Pal Singh and Mayilraj, Shanmugam} } @article {487, title = {Draft Genome Sequence of Rhodococcus ruber Strain BKS 20-38. [Next Generation Genomics facility]}, journal = {Genome Announc}, volume = {1}, year = {2013}, month = {2013 Apr 04}, pages = {e0013913}, abstract = {

We report the 6.1-Mb genome sequence of Rhodococcus ruber strain BKS 20-38, isolated from the palm tree rhizosphere soil of Bhitarkanika National Park, Odhisha, India. The draft genome sequence of strain BKS 20-38 consists of 6,126,900\ bp, with a G+C content of 69.72\%, 5,716 protein-coding genes, and 49 RNAs.

}, doi = {10.1128/genomeA.00139-13}, author = {Bala, Monu and Kumar, Shailesh and Raghava, Gajendra Pal Singh and Mayilraj, Shanmugam} } @article {485, title = {Draft Genome Sequence of Rhodococcus triatomae Strain BKS 15-14. [Next Generation Genomics facility]}, journal = {Genome Announc}, volume = {1}, year = {2013}, month = {2013 Mar 28}, pages = {e0012913}, abstract = {

We report the 5.8-Mb genome sequence of Rhodococcus triatomae BKS 15-14, isolated from an ant hill soil sample, collected from Bhitarkanika Mangrove Reserve Forest, Odisha, India. The draft genome of strain BKS 15-14 consists of 5,824,349 bp, with a G+C content of 69\%, 5,387 protein-coding genes, and 57 RNAs.

}, doi = {10.1128/genomeA.00129-13}, author = {Kumar, Shailesh and Bala, Monu and Raghava, Gajendra Pal Singh and Mayilraj, Shanmugam} } @article {523, title = {Draft Genome Sequence of Streptomyces gancidicus Strain BKS 13-15. (Next Generation Genomics)}, journal = {Genome Announc}, volume = {1}, year = {2013}, month = {2013 Apr 18}, pages = {e0015013}, abstract = {

We report the 7.3-Mbp genome sequence of Streptomyces gancidicus strain BKS 13-15, isolated from mangrove sediment samples collected from the Bhitar Kanika Mangrove Reserve Forest, Odissha, India. The draft genome of strain Streptomyces gancidicus strain BKS 13-15 consists of 7,300,479\ bp with 72.6\% G+C content, 6,631 protein-coding genes, and 71 RNAs.

}, doi = {10.1128/genomeA.00150-13}, author = {Kumar, Shailesh and Kaur, Navjot and Singh, Nitin Kumar and Raghava, Gajendra Pal Singh and Mayilraj, Shanmugam} } @article {1010, title = {Light driven ultrafast electron transfer in oxidative redding of Green Fluorescent Proteins. [Protein Technology Facility]}, journal = {Sci Rep}, volume = {3}, year = {2013}, month = {2013}, pages = {1580}, abstract = {

Fluorescent proteins undergoing green to red (G/R) photoconversion have proved to be potential tools for investigating dynamic processes in living cells and for photo-localization nanoscopy. However, the photochemical reaction during light induced G/R photoconversion of fluorescent proteins remains unclear. Here we report the direct observation of ultrafast time-resolved electron transfer (ET) during the photoexcitation of the fluorescent proteins EGFP and mEos2 in presence of electron acceptor, p-benzoquinone (BQ). Our results show that in the excited state, the neutral EGFP chromophore accepts electrons from an anionic electron donor, Glu222, and G/R photoconversion is facilitated by ET to nearby electron acceptors. By contrast, mEos2 fails to produce the red emitting state in the presence of BQ; ET depletes the excited state configuration en route to the red-emitting fluorophore. These results show that ultrafast ET plays a pivotal role in multiple photoconversion mechanisms and provide a method to modulate the G/R photoconversion process.

}, keywords = {Benzoquinones, Electron Transport, Green Fluorescent Proteins, Light, Oxidation-Reduction}, issn = {2045-2322}, doi = {10.1038/srep01580}, author = {Saha, Ranajay and Verma, Pramod Kumar and Rakshit, Surajit and Saha, Suvrajit and Mayor, Satyajit and Pal, Samir Kumar} } @article {711, title = {Microscopic elucidation of abundant endophytic bacteria colonizing the cell wall{\textendash}plasma membrane peri-space in the shoot-tip tissue of banana. Oxford Journal AoB PLANTS (2013) 5 : plt011}, year = {2013}, author = {Pious Thomas and Krishna M. Reddy.} } @article {713, title = {Active remodeling of cortical actin regulates spatiotemporal organization of cell surface molecules.}, journal = {Cell}, volume = {149}, year = {2012}, month = {2012 Jun 08}, pages = {1353-67}, abstract = {

Many lipid-tethered proteins and glycolipids exist as monomers and nanoclusters on the surface of living cells. The spatial distribution and dynamics of formation and breakup of nanoclusters does not reflect thermal and chemical equilibrium and is controlled by active remodeling of the underlying cortical actin. We propose a model for nanoclustering based on active hydrodynamics, wherein cell surface molecules bound to dynamic actin are actively driven to form transient clusters. This consistently explains all of our experimental observations. Using FCS and TIRF microscopy, we provide evidence for the existence of short, dynamic, polymerizing actin filaments at the cortex, a key assumption of the theoretical framework. Our theory predicts that lipid-anchored proteins that interact with dynamic actin must exhibit anomalous concentration fluctuations, and a cell membrane protein capable of binding directly to actin can form nanoclusters. These we confirm experimentally, providing an active mechanism for molecular organization and its spatiotemporal regulation on the plasma membrane.

}, keywords = {Actins, Animals, Cell Line, Tumor, Cell Membrane, CHO Cells, Cricetinae, Cytoskeleton, Humans, Membrane Proteins, Models, Biological, Spectrometry, Fluorescence}, issn = {1097-4172}, doi = {10.1016/j.cell.2012.05.008}, author = {Gowrishankar, Kripa and Ghosh, Subhasri and Saha, Suvrajit and C, Rumamol and Mayor, Satyajit and Rao, Madan} } @article {720, title = {Antiproliferative property of n-hexane and chloroform extracts of Anisomeles malabarica (L). R. Br. in HPV16-positive human cervical cancer cells.}, journal = {J Pharmacol Pharmacother}, volume = {3}, year = {2012}, month = {2012 Jan}, pages = {26-34}, abstract = {

OBJECTIVES: To find the efficacy of serial extracts of Anisomeles malabarica in inhibiting proliferation of and inducing apoptosis in human cervical cancer cells, SiHa and ME 180, that are HPV 16-positive.

MATERIALS AND METHODS: The whole plant was extracted in n-hexane, chloroform, ethyl acetate, n-butanol, methanol, and water. The cells were treated with the extracts at increasing concentrations to find the IC(50), adopting MTT ([3-(4,5 dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide]) assay. Acridine orange (AO) and ethidium bromide (EB) and Hoechst 33258 staining were adopted to assess the mode of cell death, Annexin V-Cy3 staining to evaluate one of the early apoptotic features, JC-1 staining to assess the mitochondrial membrane depolarization, comet assay for DNA fragmentation, and cell cycle analysis for the distribution of cells after treatment.

RESULTS: n-Hexane and chloroform extracts were cytotoxic to the cervical cancer cells in dose- and duration-dependent manner. The cells that responded to the treatments revealed typical apoptotic features. Early features of apoptosis, phosphatidyl serine translocation and loss of mitochondrial trans-membrane potential, were observed in the treated cells, and comet assay revealed DNA damage. In the FACS analysis, the cells accumulated in the sub-G0/G1 phase of the cell cycle, except in n-hexane- and chloroform extract-treated SiHa cells at 24 h, which showed arrest in S- and G2/M phases.

CONCLUSIONS: n-Hexane and chloroform extracts of A. malabarica inhibit proliferation of and induce death in HPV16-positive cervical cancer cells, mostly by apoptosis and to some extent by necrosis.

}, issn = {0976-5018}, doi = {10.4103/0976-500X.92500}, author = {Preethy, Christo Paul and Padmapriya, Ramamoorthy and Periasamy, Vaiyapuri Subbarayan and Riyasdeen, Anvarbatcha and Srinag, Suresh and Krishnamurthy, Hanumanthappa and Alshatwi, Ali Abdullah and Akbarsha, Mohammad Abdulkader} } @article {717, title = {Developmental heterogeneity in DNA packaging patterns influences T-cell activation and transmigration.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012}, pages = {e43718}, abstract = {

Cellular differentiation programs are accompanied by large-scale changes in nuclear organization and gene expression. In this context, accompanying transitions in chromatin assembly that facilitates changes in gene expression and cell behavior in a developmental system are poorly understood. Here, we address this gap and map structural changes in chromatin organization during murine T-cell development, to describe an unusual heterogeneity in chromatin organization and associated functional correlates in T-cell lineage. Confocal imaging of DNA assembly in cells isolated from bone marrow, thymus and spleen reveal the emergence of heterogeneous patterns in DNA organization in mature T-cells following their exit from the thymus. The central DNA pattern dominated in immature precursor cells in the thymus whereas both central and peripheral DNA patterns were observed in na{\"\i}ve and memory cells in circulation. Na{\"\i}ve T-cells with central DNA patterns exhibited higher mechanical pliability in response to compressive loads in vitro and transmigration assays in vivo, and demonstrated accelerated expression of activation-induced marker CD69. T-cell activation was characterized by marked redistribution of DNA assembly to a central DNA pattern and increased nuclear size. Notably, heterogeneity in DNA patterns recovered in cells induced into quiescence in culture, suggesting an internal regulatory mechanism for chromatin reorganization. Taken together, our results uncover an important component of plasticity in nuclear organization, reflected in chromatin assembly, during T-cell development, differentiation and transmigration.

}, keywords = {Animals, Antigens, CD, Antigens, Differentiation, T-Lymphocyte, Bone Marrow Cells, Cell Lineage, Cell Movement, Cell Nucleus, Chromatin, DNA, Hematopoietic Stem Cells, Lectins, C-Type, Lymphocyte Activation, Mice, Microscopy, Confocal, Models, Biological, Models, Statistical, Sequence Analysis, DNA, Spleen, T-Lymphocytes}, issn = {1932-6203}, doi = {10.1371/journal.pone.0043718}, author = {Gupta, Soumya and Marcel, Nimi and Talwar, Shefali and Garg, Megha and R, Indulaxmi and Perumalsamy, Lakshmi R and Sarin, Apurva and Shivashankar, G V} } @article {714, title = {Distinct spatial and molecular features of notch pathway assembly in regulatory T cells.}, journal = {Sci Signal}, volume = {5}, year = {2012}, month = {2012 Jul 24}, pages = {ra53}, abstract = {

Variations in the spatial localization of signaling components and crosstalk among signaling cascades are mechanisms through which diversity in signaling networks is generated. The receptor Notch provides an example of regulation by spatial localization: In the canonical Notch signaling pathway, Notch is cleaved to produce the Notch intracellular domain (NICD, also known as NIC), which translocates to the nucleus to regulate gene expression. We describe a T cell receptor-dependent, non-nuclear distribution and function of the processed receptor Notch, which was associated with the improved survival of regulatory T cells (T(regs)) in vitro and in vivo and was compromised by T cell-specific deletion of Notch1. Unlike a nuclear-restricted mutant of NICD, mutant NICD that underwent nuclear export or was targeted to the plasma membrane protected Notch1(-/-) T(regs) from apoptosis induced by nutrient deprivation and oxidative stress. Notch signaling integrated with phosphatidylinositol 3-kinase signaling and mammalian target of rapamycin complex 2 (mTORC2) for this cell survival function. Biochemical and imaging approaches revealed a membrane-proximal complex containing NICD and the mTORC2 component Rictor, and this complex was stabilized by specific interactions with the Notch ligand Delta-like-1 and mediated the survival of T(regs). Together, our evidence for the spatial control of Notch and the crosstalk of Notch signaling with other pathways reveals coupling between the localization of Notch and diverse intracellular signaling pathways.

}, keywords = {Animals, Apoptosis, Blotting, Western, Carrier Proteins, Cell Line, Cell Membrane, Cell Survival, Flow Cytometry, Gene Knockout Techniques, Humans, Immunoprecipitation, Intercellular Signaling Peptides and Proteins, Mice, Mice, Inbred C57BL, Microscopy, Fluorescence, Phosphatidylinositol 3-Kinase, Rapamycin-Insensitive Companion of mTOR Protein, Receptor Cross-Talk, Receptor, Notch1, Signal Transduction, T-Lymphocytes, Regulatory, Trans-Activators, Transcription Factors}, issn = {1937-9145}, doi = {10.1126/scisignal.2002859}, author = {Perumalsamy, Lakshmi R and Marcel, Nimi and Kulkarni, Sneha and Radtke, Freddy and Sarin, Apurva} } @article {492, title = {Draft genome sequence of the nitrophenol-degrading actinomycete Rhodococcus imtechensis RKJ300. [Next Generation Genomics facility]}, journal = {J Bacteriol}, volume = {194}, year = {2012}, month = {2012 Jul}, pages = {3543}, abstract = {

We report the 8.231-Mb genome sequence of Rhodococcus imtechensis RKJ300, isolated from pesticide-contaminated soil in Punjab, India. The genome sequence of the strain RKJ300 will be helpful in exploring the molecular pathways involved in the degradation of nitrophenols.

}, keywords = {Biodegradation, Environmental, Genome, Bacterial, India, Molecular Sequence Data, Nitrophenols, Pesticides, Rhodococcus, Sequence Analysis, DNA, Soil Microbiology, Soil Pollutants}, issn = {1098-5530}, doi = {10.1128/JB.00532-12}, author = {Vikram, Surendra and Kumar, Shailesh and Subramanian, Srikrishna and Raghava, Gajendra Pal Singh} } @article {716, title = {Evidence for the existence of a secondary pathway for fibril growth during the aggregation of tau.}, journal = {J Mol Biol}, volume = {421}, year = {2012}, month = {2012 Aug 10}, pages = {296-314}, abstract = {

The mechanism of amyloid fibril formation by proteins has been classically described by the nucleation-dependent polymerization (NDP) model, which makes certain predictions regarding the kinetics of fibrillation. All proteins whose aggregation conforms to the NDP model display a t(2) time dependence for their initial reaction profile. However, there are proteins whose aggregation reactions have kinetic signatures of a flat lag phase followed by an exponential rise in fibril mass, which does not conform to the NDP model. Amyloid fibril formation by tau, a microtubule-associated protein whose aggregation to form neurofibrillary tangles is implicated in Alzheimer{\textquoteright}s disease and other tauopathies, in the presence of inducers such as heparin and fatty acid micelles, has always been traditionally described by a ligand-induced NDP model. In this study, the existence of a secondary pathway for fibril growth during the aggregation of the functional, repeat domain of tau in the presence of heparin has been established. Both kinetic and accessory evidence are provided for the existence of this pathway, which is shown to augment the primary homogeneous nucleation pathway. From the kinetic data, the main secondary pathway that is operative appears to be fibril fragmentation but other pathways such as branching or secondary nucleation may also be operative.

}, keywords = {Amyloid, Kinetics, Micelles, Microscopy, Atomic Force, Models, Chemical, tau Proteins}, issn = {1089-8638}, doi = {10.1016/j.jmb.2012.01.007}, author = {Ramachandran, Gayathri and Udgaonkar, Jayant B} } @article {490, title = {Genome sequence of the halotolerant bacterium Imtechella halotolerans K1T. [Next Generation Genomics facility]}, journal = {J Bacteriol}, volume = {194}, year = {2012}, month = {2012 Jul}, pages = {3731}, abstract = {

We report the 3.087-Mb genome sequence of Imtechella halotolerans K1(T), isolated from an estuarine water sample collected from Kochi, Kerala, India. Strain K1 was recently reported as a novel genus of the family Flavobacteriaceae.

}, keywords = {Gene Expression Regulation, Bacterial, Genome, Bacterial, Gram-Negative Aerobic Bacteria, Molecular Sequence Data}, issn = {1098-5530}, doi = {10.1128/JB.00506-12}, author = {Kumar, Shailesh and Vikram, Surendra and Subramanian, Srikrishna and Raghava, Gajendra Pal Singh and Pinnaka, Anil Kumar} } @article {489, title = {Genome sequence of the marine bacterium Marinilabilia salmonicolor JCM 21150T. [Next Generation Genomics facility]}, journal = {J Bacteriol}, volume = {194}, year = {2012}, month = {2012 Jul}, pages = {3746}, abstract = {

We report the 4.98-Mb genome sequence of Marinilabilia salmonicolor JCM 21150(T), which was isolated from marine mud in the year 1961. The draft genome of strain Marinilabilia salmonicolor JCM 21150(T) contains 4,982,627 bp with a G+C content of 41.92\% and 4,227 protein coding genes, 52 tRNAs, and 3 rRNAs.

}, keywords = {Bacteria, Gene Expression Regulation, Bacterial, Genome, Bacterial, Molecular Sequence Data}, issn = {1098-5530}, doi = {10.1128/JB.00649-12}, author = {Kumar, Shailesh and Subramanian, Srikrishna and Raghava, Gajendra Pal Singh and Pinnaka, Anil Kumar} } @article {723, title = {Germ cell abnormalities in streptozotocin induced diabetic mice do not correlate with blood glucose level.}, journal = {J Assist Reprod Genet}, volume = {29}, year = {2012}, month = {2012 Dec}, pages = {1405-13}, abstract = {

PURPOSE: To assess the effect of streptozotocin induced hyperglycemia on germ cell integrity, DNA ploidy and methylation status for a period of two spermatogenesis cycles in adult male Swiss albino mice.

METHODS: Streptozotocin injected mice were monitored for hyperglycemia at a regular interval for a period of 36 and 72\ days. The DNA integrity in epididymal spermatozoa was determined by the comet assay. Flow cytometric analysis was done in germ cells to assess the DNA ploidy. The global methylation analysis in germ cells was done by 5-methyl cytosine immunostaining.

RESULTS: Streptozotocin administration successfully resulted in hyperglycemic response which significantly affected serum testosterone level, sperm DNA integrity and DNA ploidy at the end of 36\ days. However, no changes were observed in either epididymal sperm concentration or germ cell methylation status. In contrast, at the end of 76\ days, although serum testosterone level, sperm DNA integrity and DNA ploidy status were unperturbed significantly in hyperglycemic group, the epididymal sperm concentration and methylation status of preleptotene/zygotene cells were significantly altered. Importantly, an attempt to find out the association between the blood glucose levels and the abnormalities in hyperglycemic group failed to demonstrate any correlation.

CONCLUSIONS: The germ cell abnormalities observed in hyperglycemic group could be interpreted as a primary effect of streptozotocin and not due to hyperglycemia. Our results call for further evaluation of streptozotocin before its application to study the hyperglycemic responses on male germ cells.

}, keywords = {Animals, Blood Glucose, Diabetes Mellitus, Experimental, DNA Methylation, Epididymis, Germ Cells, Humans, Hyperglycemia, Male, Mice, Ploidies, Sperm Count, Spermatogenesis, Spermatozoa, Streptozocin, Testosterone}, issn = {1573-7330}, doi = {10.1007/s10815-012-9873-0}, author = {Bose, Rohini and Adiga, Satish K and D{\textquoteright}Souza, Fiona and Salian, Sujith R and Uppangala, Shubhashree and Kalthur, Guruprasad and Jain, Navya and Radhakrishnan, Raghu A and Bhat, Nalini and Krishnamurthy, Hanumantappa and Kumar, Pratap} } @article {712, title = {An inhibitor of nonhomologous end-joining abrogates double-strand break repair and impedes cancer progression.}, journal = {Cell}, volume = {151}, year = {2012}, month = {2012 Dec 21}, pages = {1474-87}, abstract = {

DNA Ligase IV is responsible for sealing of double-strand breaks (DSBs) during nonhomologous end-joining (NHEJ). Inhibiting Ligase IV could result in amassing of DSBs, thereby serving as a strategy toward treatment of cancer. Here, we identify a molecule, SCR7 that inhibits joining of DSBs in cell-free repair system. SCR7 blocks Ligase IV-mediated joining by interfering with its DNA binding but not that of T4 DNA Ligase or Ligase I. SCR7 inhibits NHEJ in a Ligase IV-dependent manner within cells,\ and activates the intrinsic apoptotic pathway. More importantly, SCR7 impedes tumor progression in mouse models and when coadministered with DSB-inducing therapeutic modalities enhances their sensitivity significantly. This inhibitor to target NHEJ offers a strategy toward the treatment of cancer and improvement of existing regimens.

}, keywords = {Amino Acid Sequence, Animals, Cell Line, Tumor, Disease Models, Animal, DNA Breaks, Double-Stranded, DNA End-Joining Repair, DNA Ligase ATP, DNA Ligases, Drug Design, Drug Resistance, Neoplasm, Humans, Lymphocytes, Lymphoma, Male, Mice, Mice, Inbred BALB C, Mice, Nude, Models, Molecular, Molecular Sequence Data, Neoplasms, Protein Structure, Tertiary, Pyrimidines, Radiation Tolerance, Rats, Schiff Bases, Sequence Alignment}, issn = {1097-4172}, doi = {10.1016/j.cell.2012.11.054}, author = {Srivastava, Mrinal and Nambiar, Mridula and Sharma, Sheetal and Karki, Subhas S and Goldsmith, G and Hegde, Mahesh and Kumar, Sujeet and Pandey, Monica and Singh, Ram K and Ray, Pritha and Natarajan, Renuka and Kelkar, Madhura and De, Abhijit and Choudhary, Bibha and Raghavan, Sathees C} } @article {479, title = {Interaction with a kinesin-2 tail propels choline acetyltransferase flow towards synapse. [Drosophila facility]}, journal = {Traffic}, volume = {13}, year = {2012}, month = {2012 Jul}, pages = {979-91}, abstract = {

Bulk flow constitutes a substantial part of the slow transport of soluble proteins in axons. Though the underlying mechanism is unclear, evidences indicate that intermittent, kinesin-based movement of large protein-aggregates aids this process. Choline acetyltransferase (ChAT), a soluble enzyme catalyzing acetylcholine synthesis, propagates toward the synapse at an intermediate, slow rate. The presynaptic enrichment of ChAT requires heterotrimeric kinesin-2, comprising KLP64D, KLP68D and DmKAP, in Drosophila. Here, we show that the bulk flow of a recombinant Green Fluorescent Protein-tagged ChAT (GFP::ChAT), in Drosophila axons, lacks particulate features. It occurs for a brief period during the larval stages. In addition, both the endogenous ChAT and GFP::ChAT directly bind to the KLP64D tail, which is essential for the GFP::ChAT entry and anterograde flow in axon. These evidences suggest that a direct interaction with motor proteins could regulate the bulk flow of soluble proteins, and thus establish their asymmetric distribution.

}, keywords = {Animals, Animals, Genetically Modified, Axonal Transport, Carrier Proteins, Choline O-Acetyltransferase, Cholinergic Neurons, Drosophila, Drosophila Proteins, Fluorescence Recovery After Photobleaching, Kinesin, Larva, Microtubule-Associated Proteins, Protein Interaction Domains and Motifs, Synapses}, issn = {1600-0854}, doi = {10.1111/j.1600-0854.2012.01361.x}, author = {Sadananda, Aparna and Hamid, Runa and Doodhi, Harinath and Ghosal, Debnath and Girotra, Mukul and Jana, Swadhin Chandra and Ray, Krishanu} } @article {722, title = {Poor sperm quality and advancing age are associated with increased sperm DNA damage in infertile men.}, journal = {Andrologia}, volume = {44 Suppl 1}, year = {2012}, month = {2012 May}, pages = {642-9}, abstract = {

With increasing evidence for faulty paternal contribution to reproduction, there has been a steady increase in studies highlighting an association between sperm DNA damage, failed/delayed fertilisation and aberrant embryo development. Owing to prevailing ambiguity, the aims of the study were to analyse the genetic integrity of the male gamete and then to understand its association with age, standard semen parameters, lifestyle and occupational factors. The study included 504 subjects, attending university infertility clinic for fertility evaluation and treatment. Semen characteristics were analysed by standard criteria; terminal deoxynucelotidyl transferase-mediated nick end-labelling assay was employed for DNA damage assessment. The average incidence of sperm DNA damage in patients with normozoospermic semen parameters was \<10\%. Patients with oligozoospermia, severe oligozoospermia, oligoasthenoteratospermia, asthenoteratozoospermia and necrozoospermia had significantly higher level of sperm DNA damage (P \< 0.001). Patients above 40 years of age had significantly high levels of DNA damage (P \< 0.001) compared with their counterparts. Patients with varicocele and a history of alcohol consumption had higher incidence of spermatozoa with DNA damage (P \< 0.01). Poor sperm characteristics in the ejaculate are associated with increased sperm DNA damage. Age-related increase in sperm DNA damage and association of the same with varicocele and alcohol consumption are also demonstrated.

}, keywords = {Aging, DNA Damage, Humans, Infertility, Male, Life Style, Male, Occupations, Spermatozoa}, issn = {1439-0272}, doi = {10.1111/j.1439-0272.2011.01243.x}, author = {Varshini, J and Srinag, B S and Kalthur, G and Krishnamurthy, H and Kumar, P and Rao, S B-S and Adiga, S K} } @article {482, title = {A protein complex network of Drosophila melanogaster. [Drosophila facility]}, journal = {Cell}, volume = {147}, year = {2011}, month = {2011 Oct 28}, pages = {690-703}, abstract = {

Determining the composition of protein complexes is an essential step toward understanding the cell as an integrated system. Using coaffinity purification coupled to mass spectrometry analysis, we examined protein associations involving nearly 5,000 individual, FLAG-HA epitope-tagged Drosophila proteins. Stringent analysis of these data, based on a statistical framework designed to define individual protein-protein interactions, led to the generation of a Drosophila protein interaction map (DPiM) encompassing 556 protein complexes. The high quality of the DPiM and its usefulness as a paradigm for metazoan proteomes are apparent from the recovery of many known complexes, significant enrichment for shared functional attributes, and validation in human cells. The DPiM defines potential novel members for several important protein complexes and assigns functional links to 586 protein-coding genes lacking previous experimental annotation. The DPiM represents, to our knowledge, the largest metazoan protein complex map and provides a valuable resource for analysis of protein complex evolution.

}, keywords = {Animals, Drosophila melanogaster, Drosophila Proteins, Proteasome Endopeptidase Complex, Protein Interaction Mapping, Proteomics, SNARE Proteins}, issn = {1097-4172}, doi = {10.1016/j.cell.2011.08.047}, author = {Guruharsha, K G and Rual, Jean-Fran{\c c}ois and Zhai, Bo and Mintseris, Julian and Vaidya, Pujita and Vaidya, Namita and Beekman, Chapman and Wong, Christina and Rhee, David Y and Cenaj, Odise and McKillip, Emily and Shah, Saumini and Stapleton, Mark and Wan, Kenneth H and Yu, Charles and Parsa, Bayan and Carlson, Joseph W and Chen, Xiao and Kapadia, Bhaveen and VijayRaghavan, K and Gygi, Steven P and Celniker, Susan E and Obar, Robert A and Artavanis-Tsakonas, Spyros} }