@article {8993, title = {Compositional characterisation of colostrum and proline rich polypeptides of indigenous cattle (Bos indicus family) and Holstein Friesian (Bos taurus) and their crossbred Karan Fries cattle [Mass Spectrometry Facility]}, journal = {International Dairy Journal}, year = {2025}, pages = {106264}, abstract = {

Proline-rich polypeptides (PRPs) are polypeptides characterized by a high proportion of hydrophobic amino acids (\~{} 45\%) and over 20\% proline, with molecular weights ranging from 0.5 to 17 kDa. Colostrum is the only source of PRPs; therefore, excess colostrum could be utilized for PRPs production. These PRPs mostly originate from caseins, such as β-casein and α-casein. The role of PRPs in preventing pathological processes in the central nervous system is well established and many formulations included PRPs or colostrum in their medications. Present study envisages composition of colostrum and quantify PRPs content across select indigenous breeds with exotic breed (Holstein Friesian, HF) and one cross breed of HF and Tharparkar (Karan Fries, KF), with time period after parturition. Furthermore, PRPs were characterized using SDS-PAGE, HPLC, amino acid composition, and LC-ESI-MS/MS to understand molecular weight distribution and sequential changes. The HF and Sahiwal breed consistently exhibited the higher PRPs yields at 12, 24 and 36 h postpartum. HF (114.10{\textpm}19.41 mg/L of colostrum) and Sahiwal (102.20{\textpm}2.35 mg/L of colostrum) showed the highest PRPs concentrations at 12 h, followed by a decline, highlighting colostrum collected within 24 h of parturition as the optimal PRPs source. Indigenous breeds such as Sahiwal (24.50\%), Gir (21.91\%), and Tharparkar (22.30\%) has shown higher concentrations of proline compared to the crossbred KF (17.49\%) and the exotic HF (18.25\%).

}, keywords = {Amino acid profile, Colostrinin, Colostrum, Composition, Immunonoglobulins, Proline-rich polypeptides}, issn = {0958-6946}, doi = {https://doi.org/10.1016/j.idairyj.2025.106264}, url = {https://www.sciencedirect.com/science/article/pii/S0958694625000834}, author = {Mamta Kumari and Usha Devi and T.M. Amrutha and Sandeep N and M.H. Sathish Kumar and Suman Kapila and Abdul S. Hussain and C.T. Manoj Kumar} } @article {8961, title = {Integrated omics analysis of rice gene expression profiles and microRNAs identifies crucial target genes for nitrogen use efficiency [Next Gen Genomics Facility]}, journal = {Plant Physiology Reports}, year = {2025}, month = {Feb}, abstract = {

Nitrogen use efficiency is a complex trait in rice involving nitrogen uptake, utilization, and assimilation. The coding mRNAs and non-coding regulatory RNAs have combinatorial involvement in molecular mechanisms underlying nutrient use efficiency. In this study, we generated the microRNA expression profiles of panicle tissues in N-efficient (Basmati370, Thurur bhog) and non-efficient genotypes (Kola Joha3, IC463254) at the booting stage using microRNA sequencing and microarray expression profiles of root and shoot tissues at the seedling stage in N-efficient (Varadhan) and non-efficient (Prasanna) genotypes under hydroponic condition with N (+) and without N supplementation N (-) using Affymetrix rice microarray chip. To understand holistically the differential expression of mRNAs and microRNAs regulating NUE, we integrated the newly generated microRNA sequencing and microarray datasets with earlier generated mRNA gene expression profile data using bioinformatics tools. We present a consolidated set of genes operating tissue and stage-wise in rice for NUE. The microRNAs viz. miR2118o, miR1442, miR5149 were up-regulated and miR164, miR2867, miR171i were down-regulated in N efficient genotypes under low N conditions. Interestingly, we have identified the consistent differential expression of known and novel microRNAs in N efficient genotypes viz. miR1859 (down-regulated), miR1441, miR3979-5p, miR5149 (up-regulated) under low nitrogen conditions. The GARP-MYB/SANT domain, early nodulin genes were exclusively present in the shoot of Varadhan; genes related to polycomb complex, enhancer of zeste, were downregulated under N0 condition. Under low N conditions, brassinosteroid insensitive receptor kinase-1, IAA31, DUF581, DUF617, DUF803, NIN, nodulin, oligopeptide transporter, OsPOP1, calmodulin kinases were upregulated across roots and shoots. The genes upregulated in efficient genotypes expressed in shoots as well as in panicle tissues and regulated by downregulation of their miRNAs are targets for further studies. Remarkably, the downregulation of specific metabolic pathways was observed as an adaptive strategy to cope with nitrogen limitation, highlighting the complexity of NUE regulation in rice. These findings elucidate the intricate molecular networks governing NUE in rice and underscore the potential of specific microRNAs and genes as targets for precision breeding strategies aimed at enhancing nitrogen utilization efficiency in rice cultivation. The integrative transcriptomic approach presented here provides a foundation for further functional genomic studies, facilitating the development of novel breeding strategies to optimize NUE in rice.

}, issn = {2662-2548}, doi = {10.1007/s40502-024-00846-9}, url = {https://doi.org/10.1007/s40502-024-00846-9}, author = {Barbadikar, Kalyani M. and Talapanti, Krishna Kant and Bej, Sonali and Karre, Suman and Kothandaraman, Harish and Malathi, S. and Puskur, Raghuveer Rao and Mangrauthia, Satendra Kumar and Desiraju, Subrahmanyam and Voleti, S. R. and Sureshrao Sakhare, Akshay and Anantha, M. S. and Sundaram, R. M. and Chirravuri, Neeraja N.} } @article {8677, title = {Distinct developmental patterns in Anopheles stephensi organ systems [Electron Microscopy (Micro-CT) Facility]}, journal = {Dev Biol}, year = {2024}, month = {2024 Jan 23}, abstract = {

Anatomical profiles of insects inform vector biology, comparative development and evolutionary studies with applications in forensics, agriculture and disease control. This study presents a comprehensive, high-resolution developmental profile of Anopheles stephensi, encompassing larval, pupal, and adult stages, obtained through microCT scanning. The results indicate in situ anatomical changes in most organ systems, including the central nervous system, eyes, musculature, alimentary canal, salivary glands, and ovaries, among other organ systems, except for the developing heart. We find significant differences in the mosquito gut, body-wall, and flight muscle development during metamorphosis from other dipterans like Drosophila. Specifically, indirect flight muscle specification and growth can be traced back at least to the 4th instar A. stephensi larvae, as opposed to post-puparial development in other Dipterans like Drosophila and Calliphora. Further, while Drosophila larval body-wall muscles and gut undergo histolysis, changes to these organs during mosquito metamorphosis are less pronounced. These observations, and raw data therein may serve as a reference for studies on the development and the genetics of mosquitoes. Overall, the detailed developmental profile of A. stephensi presented here illuminates the unique anatomy and developmental processes of Culicidae, with important implications for vector biology, disease control, and comparative evolutionary studies.

}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2024.01.008}, author = {Agrawal, Khushboo and Prabhakar, Sunil and Bakthavachalu, Baskar and Chaturvedi, Dhananjay} } @article {8863, title = {LC/MS Based Characterization Workflow of GLP-1 Therapeutic Peptide Liraglutide and Its Impurities [Agilent Technologies - C-CAMP Collaboration]}, year = {2024}, abstract = {

This application note demonstrates the power of the Agilent 1290 Infinity II liquid chromatograph (LC) coupled with the Agilent 6545XT AdvanceBio liquid chromatography/quadrupole time-of-flight mass spectrometer (LC/Q-TOF MS) for identification and characterization of therapeutic peptides. This application is exemplified for the GLP-1 agonist liraglutide and its impurities. The therapeutic peptide workflow within Agilent MassHunter BioConfirm software allows for accurate mass-based identification, sequence conformation, and identification of impurities, with extra or missing amino acid impurities that can arise during solid phase synthesis. These impurities may pose a potential safety risk and eventually may impact the efficacy of the product.

}, url = {https://www.agilent.com/cs/library/applications/an-liraglutide-impurities-characterization-5994-7727en-agilent.pdf}, author = {Shadab Ahmad and Nirpendra Singh and Ashish Pargaonkar and Dheeraj Vig and Mike Knierman} } @article {8465, title = {Characterization and techno-functional properties of Tenebrio molitor larvae protein concentrate [Mass Spectrometry - Proteomics Facility]}, journal = {Food Bioscience}, volume = {54}, year = {2023}, month = {07/2023}, abstract = {

Global population growth and an alarming rate of global warming conditions have driven the need for protein from alternative non-conventional sources, namely, insect proteins, through a sustainable approach. The protein concentrate of\ Tenebrio molitor\ larvae was examined for its suitability and applicability as a\ food\ ingredient. Protein was extracted through the acid-alkali method with \~{}79\% of extraction efficiency. The protein-bound polyphenols were extracted and quantified, and the anti-oxidant potential of protein-bound polyphenols and protein concentrate was assessed. The colour parameters of protein concentrate showed brighter colour (L*, 57.3) than the whole insect powder (L*, 39.0). The surface\ hydrophobicity\ of protein concentrate increased to 650, and an increase in the total and free sulfhydryl content (15.39 and 9.158\ μmol/g, respectively) was also observed compared to the whole insect powder. Significantly higher protein solubility was observed at pH 2 (72.3\%) and pH 11 (66.4\%), as compared to near the pI (6.9\% at pH 5 and 30.15\% at pH 4). Several prominent proteins, including 86 and 56\ kDa early-staged encapsulation-inducing proteins, cuticle proteins, and\ structural proteins\ were identified in protein concentrate. The techno-functional properties revealed that mealworm protein concentrate was superior to whole insect powder and comparable to\ whey protein isolate. These findings confirmed the excellent functional properties of mealworm protein concentrate, which can be further explored as a\ novel food ingredient.

}, doi = {https://doi.org/10.1016/j.fbio.2023.102882}, url = {https://www.sciencedirect.com/science/article/abs/pii/S2212429223005333}, author = {Siddaraju Anusha and Pradeep Singh Negi} } @article {8466, title = {Cryo-EM structure of GABA transporter 1 reveals substrate recognition and transport mechanism [National Cryo-Electron Microscopy Facility]}, journal = {Nat Struct Mol Biol}, year = {2023}, month = {2023 Jul 03}, abstract = {

The inhibitory neurotransmitter γ-aminobutyric acid (GABA) is cleared from the synaptic cleft by the sodium- and chloride-coupled GABA transporter GAT1. Inhibition of GAT1 prolongs the GABAergic signaling at the synapse and is a strategy to treat certain forms of epilepsy. In this study, we present the cryo-electron microscopy structure of Rattus norvegicus GABA transporter 1 (rGAT1) at a resolution of 3.1 {\r A}. The structure elucidation was facilitated by epitope transfer of a fragment-antigen binding (Fab) interaction site from the Drosophila dopamine transporter (dDAT) to rGAT1. The structure reveals rGAT1 in a cytosol-facing conformation, with a linear density in the primary binding site that accommodates a molecule of GABA, a displaced ion density proximal to Na site 1 and a bound chloride ion. A unique insertion in TM10 aids the formation of a compact, closed extracellular gate. Besides yielding mechanistic insights into ion and substrate recognition, our study will enable the rational design of specific antiepileptics.

}, issn = {1545-9985}, doi = {10.1038/s41594-023-01011-w}, url = {https://www.nature.com/articles/s41594-023-01011-w}, author = {Nayak, Smruti Ranjan and Joseph, Deepthi and H{\"o}fner, Georg and Dakua, Archishman and Athreya, Arunabh and Wanner, Klaus T and Kanner, Baruch I and Penmatsa, Aravind} } @article {8508, title = {Defining a research agenda for environmental wastewater surveillance of pathogens.}, journal = {Nat Med}, year = {2023}, month = {2023 Aug 03}, issn = {1546-170X}, doi = {10.1038/s41591-023-02457-7}, author = {Shaw, Alexander G and Troman, Catherine and Akello, Joyce Odeke and O{\textquoteright}Reilly, Kathleen M and Gauld, Jillian and Grow, Stephanie and Grassly, Nicholas and Steele, Duncan and Blazes, David and Kumar, Supriya} } @article {8544, title = {Distinct evolution of type I glutamine synthetase in Plasmodium and its species-specific requirement [Mass Spectrometry Facility - Metabolomics]}, journal = {Nat Commun}, volume = {14}, year = {2023}, month = {2023 Jul 14}, pages = {4216}, abstract = {

Malaria parasite lacks canonical pathways for amino acid biosynthesis and depends primarily on hemoglobin degradation and extracellular resources for amino acids. Interestingly, a putative gene for glutamine synthetase (GS) is retained despite glutamine being an abundant amino acid in human and mosquito hosts. Here we show Plasmodium GS has evolved as a unique type I enzyme with distinct structural and regulatory properties to adapt to the asexual niche. Methionine sulfoximine (MSO) and phosphinothricin (PPT) inhibit parasite GS activity. GS is localized to the parasite cytosol and abundantly expressed in all the life cycle stages. Parasite GS displays species-specific requirement in Plasmodium falciparum (Pf) having asparagine-rich proteome. Targeting PfGS affects asparagine levels and inhibits protein synthesis through eIF2α phosphorylation leading to parasite death. Exposure of artemisinin-resistant Pf parasites to MSO and PPT inhibits the emergence of viable parasites upon artemisinin treatment.

}, keywords = {Amino Acids, Animals, Artemisinins, Asparagine, Glutamate-Ammonia Ligase, Glutamine, Humans, Parasites, Plasmodium falciparum}, issn = {2041-1723}, doi = {10.1038/s41467-023-39670-4}, author = {Ghosh, Sourav and Kundu, Rajib and Chandana, Manjunatha and Das, Rahul and Anand, Aditya and Beura, Subhashree and Bobde, Ruchir Chandrakant and Jain, Vishal and Prabhu, Sowmya Ramakant and Behera, Prativa Kumari and Mohanty, Akshaya Kumar and Chakrapani, Mahabala and Satyamoorthy, Kapaettu and Suryawanshi, Amol Ratnakar and Dixit, Anshuman and Padmanaban, Govindarajan and Nagaraj, Viswanathan Arun} } @article {8319, title = {Significance of Plasmodium berghei Amino Acid Transporter 1 in Food Vacuole Functionality and Its Association with Cerebral Pathogenesis [Mass Spectrometry Facility - Metabolomics]}, journal = {Microbiol Spectr}, year = {2023}, month = {2023 Mar 28}, pages = {e0494322}, abstract = {

The food vacuole plays a central role in the blood stage of parasite development by digesting host hemoglobin acquired from red blood cells and detoxifying the host heme released during hemoglobin digestion into hemozoin. Blood-stage parasites undergo periodic schizont bursts, releasing food vacuoles containing hemozoin. Clinical studies in malaria-infected patients and animal studies have shown the association of hemozoin with disease pathogenesis and abnormal host immune responses in malaria. Here, we perform a detailed characterization of putative Plasmodium berghei amino acid transporter 1 localized in the food vacuole to understand its significance in the malaria parasite. We show that the targeted deletion of amino acid transporter 1 in Plasmodium berghei leads to a swollen food vacuole phenotype with the accumulation of host hemoglobin-derived peptides. Plasmodium berghei amino acid transporter 1-knockout parasites produce less hemozoin, and the hemozoin crystals display a thin morphology compared with wild-type parasites. The knockout parasites show reduced sensitivity to chloroquine and amodiaquine by showing recrudescence. More importantly, mice infected with the knockout parasites are protected from cerebral malaria and display reduced neuronal inflammation and cerebral complications. Genetic complementation of the knockout parasites restores the food vacuole morphology with hemozoin levels similar to that of wild-type parasites, causing cerebral malaria in the infected mice. The knockout parasites also show a significant delay in male gametocyte exflagellation. Our findings highlight the significance of amino acid transporter 1 in food vacuole functionality and its association with malaria pathogenesis and gametocyte development. Food vacuoles of the malaria parasite are involved in the degradation of red blood cell hemoglobin. The amino acids derived from hemoglobin degradation support parasite growth, and the heme released is detoxified into hemozoin. Antimalarials such as quinolines target hemozoin formation in the food vacuole. Food vacuole transporters transport hemoglobin-derived amino acids and peptides from the food vacuole to the parasite cytosol. Such transporters are also associated with drug resistance. Here, we show that the deletion of amino acid transporter 1 in Plasmodium berghei leads to swollen food vacuoles with the accumulation of hemoglobin-derived peptides. The transporter-deleted parasites generate less hemozoin with thin crystal morphology and show reduced sensitivity to quinolines. Mice infected with transporter-deleted parasites are protected from cerebral malaria. There is also a delay in male gametocyte exflagellation, affecting transmission. Our findings uncover the functional significance of amino acid transporter 1 in the life cycle of the malaria parasite.

}, issn = {2165-0497}, doi = {10.1128/spectrum.04943-22}, author = {Anand, Aditya and Chandana, Manjunatha and Ghosh, Sourav and Das, Rahul and Singh, Nalini and Vaishalli, Pradeep Mini and Gantasala, Nagavara Prasad and Padmanaban, Govindarajan and Nagaraj, Viswanathan Arun} } @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 {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 {3918, title = {Profilin is involved in G1 to S phase progression and mitotic spindle orientation during Leishmania donovani cell division cycle [Mass Spectrometry - Proteomics Facility]}, journal = {PLoS One}, volume = {17}, year = {2022}, month = {2022}, pages = {e0265692}, abstract = {

Profilin is a multi-ligand binding protein, which is a key regulator of actin dynamics and involved in regulating several cellular functions. It is present in all eukaryotes, including trypanosomatids such as Leishmania. However, not much is known about its functions in these organisms. Our earlier studies have shown that Leishmania parasites express a single homologue of profilin (LdPfn) that binds actin, phosphoinositides and poly- L- proline motives, and depletion of its intracellular pool to 50\%of normal levels affects the cell growth and intracellular trafficking. Here, we show, employing affinity pull-down and mass spectroscopy, that LdPfn interacted with a large number of proteins, including those involved in mRNA processing and protein translation initiation, such as eIF4A1. Further, we reveal, using mRNA Seq analysis, that depletion of LdPfn in Leishmania cells (LdPfn+/-) resulted in significantly reduced expression of genes which encode proteins involved in cell cycle regulation, mRNA translation initiation, nucleosides and amino acids transport. In addition, we show that in LdPfn+/- cells, cellular levels of eIF4A1 protein were significantly decreased, and during their cell division cycle, G1-to-S phase progression was delayed and orientation of mitotic spindle altered. These changes were, however, reversed to normal by episomal expression of GFP-LdPfn in LdPfn+/- cells. Taken together, our results indicate that profilin is involved in regulation of G1-to-S phase progression and mitotic spindle orientation in Leishmania cell cycle, perhaps through its interaction with elF4A1 protein.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0265692}, author = {Ambaru, Bindu and Gangadharan, Ganesh Muthu and Subramanya, Hosahalli S and Gupta, Chhitar M} } @article {6120, title = {Quantitative insight into the metabolism of isoprene-producing Synechocystis sp. PCC 6803 using steady state C-MFA. [Mass Spectrometry Facility]}, journal = {Photosynth Res}, year = {2022}, month = {2022 Sep 07}, abstract = {

Cyanobacteria are photosynthetic bacteria, widely studied for the conversion of atmospheric carbon dioxide to useful platform chemicals. Isoprene is one such industrially important chemical, primarily used for production of synthetic rubber and biofuels. Synechocystis sp. PCC 6803, a genetically amenable cyanobacterium, produces isoprene on heterologous expression of isoprene synthase gene, albeit in very low quantities. Rationalized metabolic engineering to re-route the carbon flux for enhanced isoprene production requires in-dept knowledge of the metabolic flux distribution in the cell. Hence, in the present study, we undertook steady state 13C-metabolic flux analysis of glucose-tolerant wild-type (GTN) and isoprene-producing recombinant (ISP) Synechocystis sp. to understand and compare the carbon flux distribution in the two strains. The R-values for amino acids, flux analysis predictions and gene expression profiles emphasized predominance of Calvin cycle and glycogen metabolism in GTN. Alternatively, flux analysis predicted higher activity of the anaplerotic pathway through phosphoenolpyruvate carboxylase and malic enzyme in ISP. The striking difference in the Calvin cycle, glycogen metabolism and anaplerotic pathway activity in GTN and ISP suggested a possible role of energy molecules (ATP and NADPH) in regulating the carbon flux distribution in GTN and ISP. This claim was further supported by the transcript level of selected genes of the electron transport chain. This study provides the first quantitative insight into the carbon flux distribution of isoprene-producing cyanobacterium, information critical for developing Synechocystis sp. as a single cell factory for isoprenoid/terpenoid production.

}, keywords = {Cyanobacterium, Flux analysis, MEP pathway, Metabolic model, qRT-PCR}, issn = {1573-5079}, doi = {10.1007/s11120-022-00957-0}, url = {https://link.springer.com/article/10.1007/s11120-022-00957-0}, author = {Nirati, Yasha and Purushotham, Nidhish and Alagesan, Swathi} } @article {4451, title = {SARS-CoV-2 infection of human-induced pluripotent stem cells-derived lung lineage cells evokes inflammatory and chemosensory responses by targeting mitochondrial pathways [Eyestem Research Pvt. Ltd., a C-CAMP Startup]}, journal = {J Cell Physiol}, year = {2022}, month = {2022 Apr 23}, abstract = {

The COVID-19 disease caused by severe acute respiratory syndrome coronavirus 2\ (SARS-CoV-2) primarily affects the lung, particularly the proximal airway and distal alveolar cells. NKX2.1+ primordial lung progenitors of the foregut (anterior) endoderm are the developmental precursors to all adult lung epithelial lineages and are postulated to play an important role in viral tropism. Here, we show that SARS-CoV-2 readily infected and replicated in human-induced pluripotent stem cell-derived proximal airway cells, distal alveolar cells, and lung progenitors. In addition to the upregulation of antiviral defense and immune responses, transcriptomics data uncovered a robust epithelial cell-specific response, including perturbation of metabolic processes and disruption in the alveolar maturation program. We also identified spatiotemporal dysregulation of mitochondrial heme oxygenase 1 (HMOX1), which is associated with defense against antioxidant-induced lung injury. Cytokines, such as TNF-α, INF-γ, IL-6, and IL-13, were upregulated in infected cells sparking mitochondrial ROS production and change in electron transport chain complexes. Increased mitochondrial ROS then activated additional proinflammatory cytokines leading to an aberrant cell cycle resulting in apoptosis. Notably, we are the first to report a chemosensory response resulting from SARS-CoV-2 infection similar to that seen in COVID-19 patients. Some of our key findings were validated using COVID-19-affected postmortem lung tissue sections. These results suggest that our in vitro system could serve as a suitable model to investigate the pathogenetic mechanisms of SARS-CoV-2 infection and to discover and test therapeutic drugs against COVID-19 or its consequences.

}, issn = {1097-4652}, doi = {10.1002/jcp.30755}, author = {Surendran, Harshini and Kumar, Saurabh and Narasimhaiah, Swathi and Ananthamurthy, Anuradha and Varghese, P S and D{\textquoteright}Souza, George A and Medigeshi, Guruprasad and Pal, Rajarshi} } @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 {1866, title = {Alterations of Primary Metabolites in Root Exudates of Intercropped Cajanus cajan{\textendash}Zea mays Modulate the Adaptation and Proteome of Ensifer (Sinorhizobium) fredii NGR234 [Mass Spectrometry - Proteomics Facility]}, journal = {Microbial Ecology}, year = {2021}, month = {08/2021}, pages = {1{\textendash}18}, type = {Journal Article}, abstract = {

Legume-cereal intercropping systems, in the context of diversity, ecological function, and better yield have been widely studied. Such systems enhance nutrient phytoavailability by balancing root-rhizosphere interactions. Root exudates (RE) play an important role in the rhizospheric interactions of plant-plant and/or plant-microbiome interaction. However, the influence of the primary metabolites of RE on plant-rhizobia interactions in a legume-cereal intercrop system is not known. To understand the plant communication with rhizobia, Cajanus cajan-Zea mays intercropped plants and the broad host range legume nodulating Ensifer fredii NGR234 as the model plants and rhizobium used respectively. A metabolomics-based approach revealed a clear separation between intercropped and monocropped RE of the two plants. Intercropped C. cajan showed an increase in the myo-inositol, and proline, while intercropped Z. mays showed enhanced galactose, D-glucopyranoside, and arginine in the RE. Physiological assays of NGR234 with the RE of intercropped C. cajan exhibited a significant enhancement in biofilm formation, while intercropped Z. mays RE accelerated the bacterial growth in the late log phase. Further, using label-free proteomics, we identified a total of 2570 proteins of NGR234 covering 50\% annotated protein sequences upon exposure to Z. mays RE. Furthermore, intercropped Z. mays RE upregulated bacterioferritin comigratory protein (BCP), putative nitroreductase, IlvD, LeuC, D (branched-chain amino acid proteins), and chaperonin proteins GroEL2. Identification offered new insights into the metabolome of the legume-cereal intercrop and proteome of NGR234-Z. mays interactions that underline the new molecular candidates likely to be involved in the fitness of rhizobium in the intercropping system.

}, keywords = {Cajanus cajan Zea mays, Ensifer fredii NGR234, Metabolomics, Proteomics, Root exudates (RE)}, doi = {https://doi.org/10.1007/s00248-021-01818-4}, url = {https://link.springer.com/article/10.1007/s00248-021-01818-4}, author = {Vora, Siddhi M and Ankati, Sravani and Patole, Chhaya and Podile, Appa Rao and Archana, G} } @article {1679, title = {Chemical intervention for enhancing growth and reducing grain arsenic accumulation in rice [Mass Spectrometry - Metabolomics Facility]}, journal = {Environ Pollut}, volume = {276}, year = {2021}, month = {2021 Feb 13}, pages = {116719}, abstract = {

Arsenic (As) is a ubiquitous environmental carcinogen that enters the human food chain mainly through rice grains. In the present study, we evaluated the potential of thiourea (TU; non-physiological reactive oxygen species scavenger) in mitigating the negative effects of arsenic (As) stress in indica rice variety IR64, with the overall aim to reduce grain As accumulation. At seedling stage, As\ +\ TU treatment induced the formation of more numerous and longer crown roots compared with As alone. The As accumulation in main root, crown root, lower leaf and upper leaf was significantly reduced to 0.1-, 0.14-, 0.16-, 0.14-fold, respectively in As\ +\ TU treated seedlings compared with those of As alone. This reduced As accumulation was also coincided with light-dependent suppression in the expression levels of aquaporins and photosynthesis-related genes in As\ +\ TU treated roots. In addition, the foliar-supplemented TU under As-stress maintained reducing redox conditions which decreased the rate of As accumulation in flag leaves and, eventually grain As by 0.53-fold compared with those of As treatment. The agronomic feasibility of TU was validated under naturally As contaminated sites of Nadia (West Bengal, India). The tiller numbers and crop productivity (kg seed/ha) of TU-sprayed plants were increased by 1.5- and 1.18-fold, respectively; while, grain As accumulation was reduced by 0.36-fold compared with those of water-sprayed control. Thus, this study established TU application as a sustainable solution for cultivating rice in As-contaminated field conditions.

}, issn = {1873-6424}, doi = {10.1016/j.envpol.2021.116719}, author = {Srivastava, Ashish Kumar and Pandey, Manish and Ghate, Tejashree and Kumar, Vikash and Upadhyay, Munish Kumar and Majumdar, Arnab and Sanjukta, Abhay Kumar and Agrawal, Ashish Kumar and Bose, Sutapa and Srivastava, Sudhakar and Suprasanna, Penna} } @article {1865, title = {Chrysin modulates protein kinase IKK$\varepsilon$/TBK1, insulin sensitivity and hepatic fatty infiltration in diet-induced obese mice [Mass Spectrometry - Lipidomics]}, journal = {Drug Development Research}, year = {2021}, month = {08/2021}, type = {Journal Article}, abstract = {

Nuclear factor kappa B cells (NF-κB) activation causes induction of the noncanonical IκB kinases (I-kappa-B kinase epsilon (IKKε) and TANK-binding kinase 1 (TBK1) in liver and fat after high fat diet which followed activating of cascade of counter-inflammation that conserves energy storage. Chrysin (5,7-dihydroxyflavone), a natural flavonoid, present in many plants, honey and propolis, used conventionally to treat numerous ailments. The present study was aimed to identify the protective role of chrysin on the glucose lowering and insulin sensitivity in diet induced obese (DIO) mice by regulating IKKε/TBK1. Chrysin administered therapeutically (60, 100, 200 mg/kg body weight) and preventive mode (200 mg/kg body weight) for 4 and 10 weeks respectively to DIO mice. At last fasting blood glucose, oral glucose tolerance test, serum lipid profile, as well as the expression level of IKKε/TBK1 and triglyceride in the liver tissue were assessed. DIO mice showed impaired glucose tolerance, reduced weight gain, elevated hepatic IKKε/TBK1 expression, fatty acid infiltration triglyceride and increased in plasma insulin and glucose. Chrysin in both therapeutic and preventive mode normalized the altered levels of the same. Overall chrysin improves glycemic control and insulin sensitivity through regulating expression of IKKε/TBK1 in liver of DIO mice.

}, keywords = {chrysin, DIO, high fat diet, IKKε/TBK1, insulin.}, doi = {https://doi.org/10.1002/ddr.21859}, url = {https://onlinelibrary.wiley.com/doi/10.1002/ddr.21859}, author = {Amir Siddiqui, Mohammad and Akhtar, Juber and Uddin, Shahab and Chandrashekharan, Sidda Madappa and Ahmad, Mohammad and Khan, Mohammad Irfan and Khalid, Mohammad} } @article {1760, title = {Effect of nanoparticle exposure in a living system: probed by quantification of Fetuin-B in plasma proteome and kidney tissue imaging using MALDI imaging mass spectrometry in a rat model [Mass Spectrometry - Proteomics Facility]}, journal = {Journal of Nanoparticle Research }, volume = {23}, year = {2021}, type = {Article number: 125}, abstract = {

Nanoparticles have gained importance in various biomedical field viz cosmetics, diagnostics, therapeutics, and food additives. Due to small size, NPs penetrate tissues and cells, thereby interacting with biomolecules such as proteins and nucleic acids. This raises the major concern to investigate the effect of NPs in a living system. Previously, we reported downregulation of Fetuin-B in rat plasma, with the increasing dose level of NP-Fe4(P2O7)3, in rats treated with NP-Fe4(P2O7)3 as a food-fortificant. In the present study, we validated the dose response of Fetuin-B in rats exposed to NP-Fe4(P2O7)3, NP-ZnO, and NP-SiO2. Fetuin-B showed similar dose responses in all the groups irrespective of their physicochemical properties. Previously, we hypothesized that the immune response was triggered upon exposure to NP-Fe4(P2O7)3 in vivo, which led to the differential regulation of Fetuin-B. To evaluate the hypothesis, immunological response was assessed in rats by estimating the pro-inflammatory cytokines in plasma. We observed Interleukin-1α and Interleukin-1β increased with the increasing dose levels of the three NPs. The impact of NPs on the proteomic profile in the kidney tissues of rats exposed to three NPs, showed differential spatial distribution of α-Enolase across the medulla and the cortex region with respect to the control group, suggesting an overexpression of α-Enolase. Overexpression of α-Enolase might be an indicative of cellular apoptosis in response to cytotoxicity caused due to NP perforation across the cellular membrane. In the present study, we propose that Fetuin-B might be considered a plasma biomarker to detect nanotoxicity at an early stage in a living system.

}, doi = {://doi.org/10.1007/s11051-021-05251-z}, url = {https://link.springer.com/article/10.1007/s13204-021-01914-4}, author = {Bindu Y. Srinivasu and Arun Arumugaperumal and Amrita Mitra and Monita Muralidharan and Rajdeep Das and Amit Kumar Mandal} } @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 {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 {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 {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 {1288, title = {Microbial Diversity and Metabolite Profiles of Palm Wine Produced From Three Different Palm Tree Species in C{\^o}te d{\textquoteright}Ivoire [Mass Spectrometry - Metabolomics Facility]}, journal = {Sci Rep}, volume = {10}, year = {2020}, month = {2020 Feb 03}, pages = {1715}, abstract = {

Palm wine, the most commonly consumed traditional alcoholic beverage in Western Africa, harbours a complex microbiota and metabolites, which plays a crucial role in the overall quality and value of the product. In the present study, a combined metagenomic and metabolomic approach was applied to describe the microbial community structure and metabolites profile of fermented saps from three palm species (Elaeis guineensis, Raphia hookeri, Borassus aethiopum) in C{\^o}te d{\textquoteright}Ivoire. Lactobacillaceae (47\%), Leuconostocaceae (16\%) and Acetobacteriaceae (28\%) were the most abundant bacteria and Saccharomyces cerevisiae (87\%) the predominant yeasts in these beverages. The microbial community structure of Raphia wine was distinctly different from the others. Multivariate analysis based on the metabolites profile clearly separated the three palm wine types. The main differentiating metabolites were putatively identified as gevotroline hydrochloride, sesartemin and methylisocitrate in Elaeis wine; derivative of homoserine, mitoxantrone in Raphia wine; pyrimidine nucleotide sugars (UDP-D-galacturonate) and myo-Inositol derivatives in Borassus wine. The enriched presence of gevotroline (an antipsychotic agent) and mitoxantrone (an anticancer drug) in palm wine supports its therapeutic potential. This work provides a valuable insight into the microbiology and biochemistry of palm wines and a rationale for selecting functional microorganisms for potential biotechnology applications.

}, issn = {2045-2322}, doi = {10.1038/s41598-020-58587-2}, author = {Djeni, Theodore N and Kouame, Karen H and Ake, Francine D M and Amoikon, Laurent S T and Dje, Marcellin K and Jeyaram, Kumaraswamy} } @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 {1161, title = {Chronic Pressure Overload Results in Deficiency of Mitochondrial Membrane Transporter ABCB7 Which Contributes to Iron Overload, Mitochondrial Dysfunction, Metabolic Shift and Worsens Cardiac Function [Mass Spectrometry - Metabolomics Facility].}, journal = {Sci Rep}, volume = {9}, year = {2019}, month = {2019 Sep 11}, pages = {13170}, abstract = {

We examined the hitherto unexplored role of mitochondrial transporters and iron metabolism in advancing metabolic and mitochondrial dysfunction in the heart during long term pressure overload. We also investigated the link between mitochondrial dysfunction and fluctuation in mitochondrial transporters associated with pressure overload cardiac hypertrophy. Left ventricular hypertrophy (LVH) was induced in 3-month-old male Wistar rats by constriction of the aorta using titanium clips. After sacrifice at the end of 6 and 15 months after constriction, tissues from the left ventricle (LV) from all animals were collected for histology, biochemical studies, proteomic and metabolic profiling, and gene and protein expression studies. LV tissues from rats with LVH had a significant decrease in the expression of ABCB7 and mitochondrial oxidative phosphorylation (mt-OXPHOS) enzymes, an increased level of lipid metabolites, decrease in the level of intermediate metabolites of pentose phosphate pathway and elevated levels of cytoplasmic and mitochondrial iron, reactive oxygen species (ROS) and autophagy-related proteins. Knockdown of ABCB7 in H9C2 cells and stimulation with angiotensin II resulted in increased ROS levels, ferritin, and transferrin receptor expression and iron overload in both mitochondria and cytoplasm. A decrease in mRNA and protein levels of mt-OXPHOS specific enzymes, mt-dynamics and autophagy clearance and activation of IGF-1 signaling were also seen in these cells. ABCB7 overexpression rescued all these changes. ABCB7 was found to interact with mitochondrial complexes IV and V. We conclude that in chronic pressure overload, ABCB7 deficiency results in iron overload and mitochondrial dysfunction, contributing to heart failure.

}, issn = {2045-2322}, doi = {10.1038/s41598-019-49666-0}, author = {Kumar, Vikas and A, Aneesh Kumar and Sanawar, Rahul and Jaleel, Abdul and Santhosh Kumar, T R and Kartha, C C} } @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 {893, title = {Deep sequencing identified potential miRNAs involved in defence response, stress and plant growth characteristics of wild genotypes of cardamom [Next Gen Genomics Facility]}, journal = {Plant Biol (Stuttg)}, volume = {21}, year = {2019}, month = {2019 Jan}, pages = {3-14}, abstract = {

Cardamom has long been used as a food flavouring agent and in ayurvedic medicines for mouth ulcers, digestive problems and even depression. Extensive occurrence of pests and diseases adversely affect its cultivation and result in substantial reductions in total production and productivity. Numerous studies revealed the significant role of miRNAs in plant biotic stress responses. In the current study, miRNA profiling of cultivar and wild cardamom genotypes was performed using an Ion Proton sequencer. We identified 161 potential miRNAs representing 42 families, including monocot/tissue-specific and 14 novel miRNAs in both genotypes. Significant differences in miRNA family abundance between the libraries were observed in read frequencies. A total of 19 miRNAs (from known miRNAs) displayed a twofold difference in expression between wild and cultivar genotypes. We found 1168 unique potential targets for 40 known miRNA families in wild and 1025 potential targets for 42 known miRNA families in cultivar genotypes. The differential expression analysis revealed that most miRNAs identified were highly expressed in cultivars and, furthermore, lower expression of miR169 and higher expression of miR529 in wild cardamom proved evidence that wild genotypes have stronger drought stress tolerance and floral development than cultivars. Potential targets predicted for the newly identified miRNAs from the miRNA libraries of wild and cultivar cardamom genotypes involved in metabolic and developmental processes and in response to various stimuli. qRT-PCR confirmed miRNAs were differentially expressed between wild and cultivar genotypes. Furthermore, four target genes were validated experimentally to confirm miRNA-mRNA target pairing using RNA ligase-mediated 5{\textquoteright} Rapid Amplification of cDNA Ends (5{\textquoteright}RLM-RACE) PCR.

}, issn = {1438-8677}, doi = {10.1111/plb.12888}, author = {Nadiya, F and Anjali, N and Thomas, J and Gangaprasad, A and Sabu, K K} } @article {1138, title = {Discovery of a deeply divergent new lineage of vine snake (Colubridae: Ahaetuliinae: Proahaetulla gen. nov.) from the southern Western Ghats of Peninsular India with a revised key for Ahaetuliinae [Next Gen Genomics Facility].}, journal = {PLoS One}, volume = {14}, year = {2019}, month = {2019}, pages = {e0218851}, abstract = {

The Western Ghats are well known as a biodiversity hotspot, but the full extent of its snake diversity is yet to be uncovered. Here, we describe a new genus and species of vine snake Proahaetulla antiqua gen. et sp. nov., from the Agasthyamalai hills in the southern Western Ghats. It was found to be a member of the Ahaetuliinae clade, which currently comprises the arboreal snake genera Ahaetulla, Dryophiops, Dendrelaphis and Chrysopelea, distributed in South and Southeast Asia. Proahaetulla shows a sister relationship with all currently known taxa belonging to the genus Ahaetulla, and shares ancestry with Dryophiops. In addition to its phylogenetic position and significant genetic divergence, this new taxon is also different in morphology from members of Ahaetuliinae in a combination of characters, having 12-13 partially serrated keels on the dorsal scale rows, 20 maxillary teeth and 3 postocular scales. Divergence dating reveals that the new genus is ancient, dating back to the Mid-Oligocene, and is one of the oldest persisting monotypic lineages of snakes in the Western Ghats. This discovery adds to the growing list of ancient lineages endemic to the Agasthyamalai hills and underscores the biogeographic significance of this isolated massif in the southern Western Ghats.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0218851}, author = {Mallik, Ashok Kumar and Achyuthan, N Srikanthan and Ganesh, Sumaithangi R and Pal, Saunak P and Vijayakumar, S P and Shanker, Kartik} } @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 {1196, title = {Hypoxic Non-replicating Persistent Develops Thickened Outer Layer That Helps in Restricting Rifampicin Entry [Electron Microscopy Facility]}, journal = {Front Microbiol}, volume = {10}, year = {2019}, month = {2019}, pages = {2339}, abstract = {

Bacteria undergo adaptive morphological changes to survive under stress conditions. The present work documents the morphological changes in () cells cultured under hypoxic condition using Wayne{\textquoteright}s hypoxia model involving non-replicating persistence stages 1 and 2 (NRP stage 1 and NRP stage 2) and reveals their physiological significance. Transmission electron microscopy of the NRP stage 2 cells showed uneven but thick outer layer (TOL), unlike the evenly thin outer layer of the actively growing mid-log phase (MLP) cells. On the contrary, the saprophytic NRP stage 2 cells lacked TOL. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) of the NRP stage 2 cells confirmed the rough uneven surface unlike the smooth surface of the MLP cells. Zeta potential measurements showed high negative charge on the surface of NRP stage 2 cells and polysaccharide specific calcofluor white (CFW) staining of the cells revealed high content of polysaccharide in the TOL. This observation was supported by the real-time PCR data showing high levels of expression of the genes involved in the synthesis of sugars, such as trehalose, mannose and others, which are implicated in polysaccharide synthesis. Experiments to understand the physiological significance of the TOL revealed restricted entry of the biologically low-active 5-carboxyfluorescein-rifampicin (5-FAM-RIF), at concentrations equivalent to microbicidal concentrations of the unconjugated biologically active rifampicin, into the NRP stage 2 cells, unlike in the MLP cells. Further, as expected, mechanical removal of the TOL by mild bead beating or release of the NRP stage 2 cells from hypoxia into normoxia in fresh growth medium also significantly increased 5-FAM-RIF permeability into the NRP stage 2 cells to an extent comparable to that into the MLP cells. Taken together, these observations revealed that cells under hypoxia develop TOL that helps in restricting rifampicin entry, thereby conferring rifampicin tolerance.

}, issn = {1664-302X}, doi = {10.3389/fmicb.2019.02339}, author = {Jakkala, Kishor and Ajitkumar, Parthasarathi} } @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 {1014, title = {Loss of Hepatic Oscillatory Fed microRNAs Abrogates Refed Transition and Causes Liver Dysfunctions [Next Gen Genomics Facility].}, journal = {Cell Rep}, volume = {26}, year = {2019}, month = {2019 Feb 19}, pages = {2212-2226.e7}, abstract = {

Inability to mediate fed-fast transitions in the liver is known to cause metabolic dysfunctions and diseases. Intuitively, a failure to inhibit futile translation of state-specific transcripts during fed-fast cycles would abrogate dynamic physiological transitions. Here, we have discovered hepatic fed microRNAs that target fasting-induced genes and are essential for a refed transition. Our findings highlight the role of these fed microRNAs in orchestrating system-level control over liver physiology and whole-body energetics. By targeting SIRT1, PGC1α, and their downstream genes, fed microRNAs regulate metabolic and mitochondrial pathways. MicroRNA expression, processing, and RISC loading oscillate during these cycles and possibly constitute an anticipatory mechanism. Fed-microRNA oscillations are deregulated during aging. Scavenging of hepatic fed microRNAs causes uncontrolled gluconeogenesis and failure in\ the catabolic-to-anabolic switching upon feeding, which are hallmarks of metabolic diseases. Besides identifying mechanisms that enable efficient physiological toggling, our study highlights fed microRNAs as candidate therapeutic targets.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2019.01.087}, author = {Maniyadath, Babukrishna and Chattopadhyay, Tandrika and Verma, Srikant and Kumari, Sujata and Kulkarni, Prineeta and Banerjee, Kushal and Lazarus, Asmitha and Kokane, Saurabh S and Shetty, Trupti and Anamika, Krishanpal and Kolthur-Seetharam, Ullas} } @article {1011, title = {Molecular mechanism of interactions between Chrysin and I-kappa-B kinase epsilon (IKKe)/Tank Binding Kinase-1(TBK1): Cell based assay and insilico molecular docking studies [High Throughput Screening Facility].}, journal = {J Biomol Struct Dyn}, year = {2019}, month = {2019 Feb 15}, pages = {1-9}, abstract = {

Chrysin, a bioactive flavonoid, was investigated for its potential to inhibit the activity of I-kappa-B kinase epsilon (IKKe) / Tank Binding Kinase-1(TBK1) an enzyme responsible for production of pro inflammatory cytokine and suppression of energy expenditure genes, finally causing insulin resistance and obesity. Expressions of majority of polyinosinic-polycytidylic acid (poly IC) mediated genes are mediated through Toll/interleukin-1 receptor domainߝcontaining adapter-inducing interferon (TRIF) dependent signalling pathway. To check the therapeutic potential of chrysin its effect was examined on Toll/interleukin-1 receptor domainߝcontaining adapter-inducing interferon (TRIF) dependent pathway. Chrysin showed significant inhibition of I-kappa-B kinase epsilon (IKKe) / Tank Binding Kinase-1(TBK1) enzyme activity by kinase assay. Chrysin suppressed the I-kappa-B kinase epsilon expression induced by polyinosinic-polycytidylic acid resulting into decrease expression of target genes interferon gamma-induced protein 10 (IP10), monocyte chemoattractant protein-1 (MCP-1) and interleukin-6 (IL-6) in macrophage-like cell line. Chrysin also showed increase in oxygen consumption in osteosarcoma cell line hence alleviating energy expenditure and thermogenesis. Moreover, insilico analysis shows that chrysin interact weakly with I-kappa-B kinase epsilon (IKKe) but displayed good interaction with Tank Binding Kinase-1 (TBK1). Overall these results suggested that I-kappa-B kinase epsilon (IKKe) / Tank Binding Kinase-1(TBK1) may be a novel target for chrysin that possesses anti-inflammatory and insulin sensitivity effects at I-kappa-B kinase epsilon (IKKe) / Tank Binding Kinase-1(TBK1) binding sites.

}, issn = {1538-0254}, doi = {10.1080/07391102.2019.1581086}, author = {Siddiqui, Amir M and Akhtar, Juber and M S, Shahab Uddin and Khan, Mohammad Irfan and Khalid, Mohammad} } @article {1139, title = {Post-translational modifications in capsid proteins of recombinant adeno-associated virus (AAV) 1-rh10 serotypes [Mass Spectrometry Facility - Proteomics \& Glycomics].}, journal = {FEBS J}, year = {2019}, month = {2019 Jul 22}, abstract = {

Post-translational modifications in viral capsids are known to fine-tune and regulate several aspects of the infective life cycle of several viruses in the host. Recombinant viruses that are generated in a specific producer cell line are likely to inherit unique post-translational modifications during intra-cellular maturation of its capsid proteins. Data on such post-translational modifications in the capsid of recombinant adeno-associated virus serotypes (AAV1-rh10) is limited. We have employed liquid chromatography and mass spectrometry analysis to characterize post-translational modifications in AAV1-rh10 capsid protein. Our analysis revealed a total of 52 post-translational modifications in AAV2-AAVrh10 capsids, including ubiquitination (17\%), glycosylation (36\%), phosphorylation (21\%), SUMOylation (13\%) and acetylation (11\%). While AAV1 had no detectable post-translational modification, at least four AAV serotypes had \>7 post-translational modifications in their capsid protein. About 82\% of these post-translational modifications are novel. A limited validation of AAV2 capsids by MALDI-TOF and western blot analysis demonstrated minimal glycosylation and ubiquitination of AAV2 capsids. To further validate this, we disrupted a glycosylation site identified in AAV2 capsid (AAV2-N253Q), which severely compromised its packaging efficiency (~100-fold vs AAV2 wildtype vectors). In order to confirm other post-translational modifications detected such as SUMOylation, mutagenesis of a SUMOylation site(K258Q) in AAV2 was performed. This mutant vector demonstrated reduced levels of SUMO-1/2/3 proteins and negligible transduction, two weeks after ocular gene transfer. Our study underscores the heterogeneity of post-translational modifications in AAV vectors. The data presented here, should facilitate further studies to understand the biological relevance of post-translational modifications in AAV life cycle and the development of novel bioengineered AAV vectors for gene therapy applications. This article is protected by copyright. All rights reserved.

}, issn = {1742-4658}, doi = {10.1111/febs.15013}, author = {Mary, Bertin and Maurya, Shubham and Arumugam, Sathyathithan and Kumar, Vikas and Jayandharan, Giridhara R} } @article {1016, title = {Serum biomarkers identification by iTRAQ and verification by MRM: S100A8/S100A9 levels predict tumor-stroma involvement and prognosis in Glioblastoma [Mass Spectrometry - Metabolomics Facility].}, journal = {Sci Rep}, volume = {9}, year = {2019}, month = {2019 Feb 26}, pages = {2749}, abstract = {

Despite advances in biology and treatment modalities, the prognosis of glioblastoma (GBM) remains poor. Serum reflects disease macroenvironment and thus provides a less invasive means to diagnose and monitor a diseased condition. By employing 4-plex iTRAQ methodology, we identified 40 proteins with differential abundance in GBM sera. The high abundance of serum S100A8/S100A9 was verified by multiple reaction monitoring (MRM). ELISA and MRM-based quantitation showed a significant positive correlation. Further, an integrated investigation using stromal, tumor purity and cell type scores demonstrated an enrichment of myeloid cell lineage in the GBM tumor microenvironment. Transcript levels of S100A8/S100A9 were found to be independent poor prognostic indicators in GBM. Medium levels of pre-operative and three-month post-operative follow-up serum S100A8 levels predicted poor prognosis in GBM patients who lived beyond median survival. In vitro experiments showed that recombinant S100A8/S100A9 proteins promoted integrin signalling dependent glioma cell migration and invasion up to a threshold level of concentrations. Thus, we have discovered GBM serum marker by iTRAQ and verified by MRM. We also demonstrate interplay between tumor micro and macroenvironment and identified S100A8 as a potential marker with diagnostic and prognostic value in GBM.

}, issn = {2045-2322}, doi = {10.1038/s41598-019-39067-8}, author = {Arora, Anjali and Patil, Vikas and Kundu, Paramita and Kondaiah, Paturu and Hegde, A S and Arivazhagan, A and Santosh, Vani and Pal, Debnath and Somasundaram, Kumaravel} } @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 {1175, title = {Stromal cells downregulate miR-23a-5p to activate protective autophagy in acute myeloid leukemia [Next Gen Genomics Facility (INT)].}, journal = {Cell Death Dis}, volume = {10}, year = {2019}, month = {2019 Sep 30}, pages = {736}, abstract = {

Complex molecular cross talk between stromal cells and the leukemic cells in bone marrow is known to contribute significantly towards drug-resistance. Here, we have identified the molecular events that lead to stromal cells mediated therapy-resistance in acute myeloid leukemia (AML). Our work demonstrates that stromal cells downregulate miR-23a-5p levels in leukemic cells to protect them from the chemotherapy induced apoptosis. Downregulation of miR-23a-5p in leukemic cells leads to upregulation of protective autophagy by targeting TLR2 expression. Further, autophagy inhibitors when used as adjuvants along with conventional drugs can improve drug sensitivity in vitro as well in vivo in a mouse model of leukemia. Our work also demonstrates that this mechanism of bone marrow stromal cell mediated regulation of miR-23a-5p levels and subsequent molecular events are relevant predominantly in myeloid leukemia. Our results illustrate the critical and dynamic role of the bone marrow microenvironment in modulating miRNA expression in leukemic cells which could contribute significantly to drug resistance and subsequent relapse, possibly through persistence of minimal residual disease in this environment.

}, issn = {2041-4889}, doi = {10.1038/s41419-019-1964-8}, author = {Ganesan, Saravanan and Palani, Hamenth Kumar and Lakshmanan, Vairavan and Balasundaram, Nithya and Alex, Ansu Abu and David, Sachin and Venkatraman, Arvind and Korula, Anu and George, Biju and Balasubramanian, Poonkuzhali and Palakodeti, Dasaradhi and Vyas, Neha and Mathews, Vikram} } @article {1020, title = {Transcriptomics analysis of propiconazole-treated Cochliobolus sativus reveals new putative azole targets in the plant pathogen [Next Gen Genomics Facility].}, journal = {Funct Integr Genomics}, year = {2019}, month = {2019 Mar 06}, abstract = {

Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is a filamentous fungus from the class Dothideomycetes. It is a pathogen of cereals including wheat and barley, and causes foliar spot blotch, root rot, black point on grains, head blight, leaf blight, and seedling blight diseases. Annual yields of these economically important cereals are severely reduced due to this pathogen attack. Evolution of fungicide resistant pathogen strains, availability of a limited number of potent antifungal compounds, and their efficacy are the acute issues in field management of phytopathogenic fungi. Propiconazole is a widely used azole fungicide to control the disease in fields. The known targets of azoles are the demethylase enzymes involved in ergosterol biosynthesis. Nonetheless, azoles have multiple modes of action, some of which have not been explored yet. Identifying the off-target effects of fungicides by dissecting gene expression profiles in response to them can provide insights into their modes of action and possible mechanisms of fungicide resistance. Moreover it can also reveal additional targets for development of new fungicides. Hence, we analyzed the global gene expression profile of C. sativus on exposure to sub-lethal doses of propiconazole in a time series. The gene expression patterns were confirmed using quantitative reverse transcriptase PCR (qRT-PCR). This study revealed overexpression of target genes from the sterol biosynthesis pathway supporting the reported mode of resistance against azoles. In addition, some new potential targets have also been identified, which could be explored to develop new fungicides and plant protection strategies.

}, issn = {1438-7948}, doi = {10.1007/s10142-019-00660-9}, author = {Somani, Deepika and Adhav, Ragini and Prashant, Ramya and Kadoo, Narendra Y} } @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 {775, title = {Genome-wide differential expression profiling in wild and cultivar genotypes of cardamom reveals regulation of key pathways in plant growth and development [Next Gen Genomics Facility]}, journal = {Agri Gene}, volume = {8}, year = {2018}, pages = {18 - 27}, keywords = {Cardamom, Differential expression, Down regulation, Essential oil biosynthesis, Transcriptome, Up regulation}, issn = {2352-2151}, doi = {https://doi.org/10.1016/j.aggene.2018.03.002}, url = {http://www.sciencedirect.com/science/article/pii/S2352215118300060}, author = {F Nadiya and N Anjali and Jinu Thomas and AGangaprasad and K K Sabu} } @article {1013, title = {Highly Sensitive LC-MS/MS-ESI method Development for the Determination of 5,7-dihydroxyflavone in Mouse Plasma and Pharmacokinetic Study in Lean and Diet Induced Obese Mice [High Throughput Screening Facility].}, journal = {Der Pharmacia Lettre}, volume = {10}, year = {2018}, type = {Research Article}, chapter = {1-12}, abstract = {

Diet-induced obese (DIO) mice have been commonly used extensively as an animal model of obesity and diabetes in the efficacy assessment for new drug candidates. Physiological and biochemical alterations are reported in DIO mice due to modulations of drug-metabolizing enzymes and high calorie intake. Limited studies have been reported regarding the effect of obesity/diabetes on pharmacokinetics (PK) in animals. A simple, specific and sensitive rapid LC-ESI-MS/MS method has been developed and validated for the quantification of chrysin (5,7-dihydroxyflavone) using tolbutamide as an internal standard (IS) as per regulatory guidelines. Sample preparation was accomplished through a simple protein precipitation. Chromatographic separation of 5,7-dihydroxyflavone and IS was performed on Atlantis C-18 column using an isocratic mobile phase comprising 0.2\% formic acid in water and acetonitrile (20:80, v/v) at a flow rate of 0.9 mL/min. Elution of 5,7-dihydroxyflavone and IS occurred at ~2.49 and 2.34 min, respectively. The total chromatographic run time was 3.2 min. A linear response function was established in the concentration range of 4.50-4500 ng/mL. This novel method has been applied to a pharmacokinetic study in lean and DIO mice.

}, author = {Amir Siddiqui and . Badruddeen and Juber Akhtar and Shahab Uddin MS and Chandrashekaran S and Mohammad Irfan Khan and Mohammad Khalid} } @article {890, title = {Identification and characterization of drought responsive microRNAs and their target genes in cardamom (Elettaria cardamomum Maton) [Next Gen Genomics Facility]}, journal = {Plant Growth Regulation}, year = {2018}, month = {Dec}, abstract = {

Plant miRNAs are found to be present throughout the genome and they regulate gene expression either by cleaving mRNA or inhibiting the translational process at the post transcriptional level. Drought is one of the major limiting factors that negatively affect productivity of plants. Cardamom cultivation is having good production potential but the plants are vulnerable to biotic and abiotic stress factors. To date, nothing is known about the regulatory roles of miRNAs in response to drought stress in cardamom. Ion Torrent sequencing of two small RNA libraries prepared from control (C) and treated (T) plants raised under well irrigated and drought stressed treatments respectively created 3,938,342 and 4,083,181 primary reads. A total of 150 conserved and 20 novel microRNAs were identified from both the control and treated libraries. Discovery of 17 differentially expressed miRNAs under drought stress suggests that these miRNAs might have involved in various biological processes to improve plant tolerance to water stress. Several target genes for drought stress regulating miRNAs were identified including miR156l and miR169c which cleave the target mRNA involved in response to water deprivation. miR530b and miR156a target mRNAs which respond to water deprivation and inhibit the translational process. The expression patterns of some of the miRNAs and their targets were validated by qRT-PCR. This study is the first report of drought responsive miRNAs and their targets in cardamom. The outcome of this research could provide insights into the miRNA based regulatory mechanisms in response to drought stress in monocot plants.

}, issn = {1573-5087}, doi = {10.1007/s10725-018-0462-9}, url = {https://doi.org/10.1007/s10725-018-0462-9}, author = {Anjali, N. and Nadiya, F. and Thomas, Jinu and Sabu, K. K.} } @article {1012, title = {A Naturally Occurring Flavone (Chrysin): Chemistry, Occurrence, Pharmacokinetic, Toxicity, Molecular Targets and Medicinal Properties [High Throughput Screening Facility].}, journal = {Journal of Biologically Active Products from Nature}, volume = {8}, year = {2018}, pages = {208-227}, doi = {10.1080/22311866.2018.1498750}, url = {https://doi.org/10.1080/22311866.2018.1498750}, author = {Amir Siddiqui and . Badruddeen and Juber Akhtar and Shahab Uddin M.S. and Mohammad Irfan Khan and Mohammad Khalid and Mohammad Ahmad} } @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 {685, title = {S-Glutathionylation of p47phox sustains superoxide generation in activated neutrophils. [Mass Spectrometry Facility - Proteomics]}, journal = {Biochim Biophys Acta}, volume = {1865}, year = {2018}, month = {2018 Feb}, pages = {444-454}, abstract = {

Post-translational modifications (PTMs) induced conformational changes of proteins can cause their activation or inactivation. Neutrophils clear pathogen through phagocytosis and oxidative burst generation, while participate in inflammation through sustained and uncontrolled generation of ROS. In activated PMNs, cytosolic NOX-2 subunit p47phox following phosphorylation interacts with p67phox, p40phox and along with Rac2 translocate to the membrane. Phosphorylation of p47phox subunit occurs in both short spurts as well as sustained ROS generation, suggesting towards the unidentified molecular mechanism(s) driving these two diverse outcomes by various stimuli. The present study demonstrates that in PMA or NO treated neutrophils a subunit of NOX2, p47phox gets glutathionylated to sustain ROS generation along with a decrease in catalase, Grx-1 activity and change in GSH/GSSG ratio. Surprisingly, fMLP treated cells neither showed sustained ROS production nor glutathionylation of p47phox. S-Glutathionylation was always secondary to phosphorylation of p47phox and inhibition of glutathionylation did not alter phosphorylation but specifically impaired sustained ROS production. Interestingly, forced S-glutathionylation of p47phox converted the fMLP induced ROS generation into sustained release of ROS. We then identified the glutathionylation susceptible cysteine residues of p47phox by LC-MS/MS with IAM switch mapping. Site-directed mutagenesis of cysteine residues further mitigated p47phox S-glutathionylation. Thus, we demonstrate that p47phox S-glutathionylation plays an essential key role in the sustained ROS generation by human neutrophils.

}, issn = {0006-3002}, doi = {10.1016/j.bbamcr.2017.11.014}, author = {Nagarkoti, Sheela and Dubey, Megha and Awasthi, Deepika and Kumar, Vikas and Chandra, Tulika and Kumar, Sachin and Dikshit, Madhu} } @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 {892, title = {Data on identification of conserved and novel miRNAs in Elettaria cardamomum [Next Gen Genomics Facility]}, journal = {Data Brief}, volume = {14}, year = {2017}, month = {2017 Oct}, pages = {789-792}, abstract = {

(L.) Maton, or small cardamom referred as {\textquoteright}queen of spices{\textquoteright}, is a perennial herbaceous rhizomatous monocot of the family Zingiberaceae. Cardamom seeds and fruits are the economically significant parts and effectively used as a traditional medicine, food additive and flavoring agent. In the present study, using Ion Proton next generation sequencing technology we performed the small RNA sequencing, conserved and novel miRNA predictions of a wild and five cultivar genotypes of cardamom. Small RNA sequencing generated a total of 5,451,328 and 2,756,250 raw reads for wild and cultivar cardamom respectively. The raw data was submitted to SRA database of NCBI under the accession numbers and SRX2273863 (wild) and SRX2273862 (cultivars). The raw reads were quality filtered and predicted conserved and novel miRNAs for wild and cultivar cardamom. The predicted miRNAs, miRNA-targets and functional annotations might provide valuable insights into differences between wild progenitor and cultivated cardamom.

}, issn = {2352-3409}, doi = {10.1016/j.dib.2017.08.037}, author = {Nadiya, F and Anjali, N and Thomas, Jinu and Gangaprasad, A and Sabu, K K} } @article {8888, title = {Genome-wide changes in microRNA expression during short and prolonged heat stress and recovery in contrasting rice cultivars [Next Gen Genomics Facility]}, journal = {J Exp Bot}, volume = {68}, year = {2017}, month = {2017 Apr 01}, pages = {2399-2412}, abstract = {

MicroRNAs (miRNAs) are known to regulate expression of genes under stress. We report here the deep sequencing of small RNAs expressed during control, short and prolonged heat stress and recovery. Genome-wide identification of miRNAs in tolerant (Nagina 22) and susceptible (Vandana) rice cultivars was performed in 16 samples representing root and shoot of 13-day-old seedlings. The expression profile of miRNAs was analysed in 36 pairwise combinations to identify the genotype-, treatment- and tissue-dependent expression of miRNAs. Small-RNA sequencing of 16 libraries yielded ~271 million high-quality raw sequences; 162 miRNA families were identified. The highly expressed miRNAs in rice tissues were miR166, miR168, miR1425, miR529, mR162, miR1876, and miR1862. Expression of osa-miR1436, osa-miR5076, osa-miR5161, and osa-miR6253 was observed only in stressed tissue of both genotypes indicating their general role in heat stress response. Expression of osa-miR1439, osa-miR1848, osa-miR2096, osa-miR2106, osa-miR2875, osa-miR3981, osa-miR5079, osa-miR5151, osa-miR5484, osa-miR5792, and osa-miR5812 was observed only in Nagina 22 during high temperature, suggesting a specific role of these miRNAs in heat stress tolerance. This study provides details of the repertoire of miRNAs expressed in root and shoot of heat susceptible and tolerant rice genotypes under heat stress and recovery.

}, keywords = {Gene Expression Regulation, Plant, Genome, Plant, High-Throughput Nucleotide Sequencing, Hot Temperature, MicroRNAs, Oryza, RNA, Plant, Seedlings, Sequence Analysis, RNA, Time Factors}, issn = {1460-2431}, doi = {10.1093/jxb/erx111}, author = {Mangrauthia, Satendra K and Bhogireddy, Sailaja and Agarwal, Surekha and Prasanth, Vishnu V and Voleti, S R and Neelamraju, Sarla and Subrahmanyam, Desiraju} } @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 {1019, title = {Insulin Plant (Costus pictus) Extract Restores Thyroid Hormone Levels in Experimental Hypothyroidism [Mass Spectrometry - Metabolomics Facility].}, journal = {Pharmacognosy Res}, volume = {9}, year = {2017}, month = {2017 Jan-Mar}, pages = {51-59}, abstract = {

BACKGROUND: The aim of the present study was to investigate the preventive effect of leaf extract in experimental hypothyroidism.

MATERIALS AND METHODS: Forty male Wistar rats were randomly divided into four groups with ten rats in each group: Control (C), hypothyroid (H), control+extract (C+E), and hypothyroid+extract (H+E). Rats in C group did not receive any intervention throughout the experimental period. The rats in the C+E and H+E groups received pretreatment with leaf extract for 4 weeks. Subsequently, for the next 6 weeks, rats in the H group received 0.05\% propylthiouracil in drinking water while C+E group received leaf extract and H+E group received propyl thiouracil and leaf extract.

RESULTS: Hypothyroid group rats exhibited dramatic increase in thyroid-stimulating hormone (TSH) levels with concomitant depletion in the levels of thyroid hormones. Treatment with the extract resulted in remarkable improvement in thyroid profile. Extract produced 10.59-fold increase in plasma free T3, 8.65-fold increase in free T4, and 3.59-fold decrease in TSH levels in H+E group in comparison with H group. Treatment with the extract ameliorated hypercholesterolemia, decreased levels of plasma C-reactive protein and tumor necrosis factor alpha, suppressed tissue oxidative stress and prevented hepatic and renal damage caused due to thyroid hormone depletion in the H+E group. Pentacyclic triterpenes alpha and beta amyrins were identified and quantified in the extract.

CONCLUSIONS: This is the first study to reveal that extract has therapeutic potential to restore thyroid hormone levels and prevent the biochemical complications due to thyroid hormone insufficiency in the animal model of experimental hypothyroidism.

SUMMARY: The preventive effect of leaf extract in experimental hypothyroidism was evaluated in the present study.Hypothyroidism was induced in the experimental animals by giving 0.05\% propylthiouracil in drinking water.Hypothyroid rats exhibited dramatic increase in thyroid-stimulating hormone (TSH) levels with concomitant depletion in the levels of thyroid hormones.Treatment with leaf extract in hypothyroid rats significantly improved the thyroid profile. It also ameliorated hypercholesterolemia, decreased the levels of plasma inflammatory markers, suppressed tissue oxidative stress and prevented hepatic and renal damage caused due to thyroid hormone depletion.The possible active principles alpha and beta amyrins were identified and quantified in the extract through LC-MS. APCI: Atmospheric pressure chemical ionization; AST: Aspartate aminotransferase; ALT: Alanine aminotransferase; C group: Control group; C+E group: Control+extract group; : ; CRP: C-reactive protein; DPPH: 2,2-diphenyl-1-picrylhydrazyl; FRAP: Ferric reducing antioxidant power; HDL: High-density lipoprotein; H group: Hypothyroid group; H+E group: Hypothyroid+extract group; LDL: Low-density lipoprotein; LC-MS: Liquid chromatography-mass spectrometry; MDA: Malondialdehyde; PTU: 6-Propyl-2-thiouracil; SRM: Single reaction monitoring; TSH: Thyroid-stimulating hormone; TPTZ: 2,4,6-tri-(2-pyridyl)-5-triazine; TBA: 2-Thiobarbituric acid; TG: Triglyceride; TNFα: Tumor necrosis factor alpha; TAS: Total antioxidant status.

}, issn = {0976-4836}, doi = {10.4103/0974-8490.199766}, author = {Ashwini, S and Bobby, Zachariah and Sridhar, M G and Cleetus, C C} } @article {532, title = {Targeted, Site-specific quantitation of N- and O-glycopeptides using (18)O-labeling and product ion based mass spectrometry.}, journal = {Glycoconj J}, volume = {34}, year = {2017}, month = {2017 Feb}, pages = {95-105}, abstract = {

The site-specific quantitation of N- and O-glycosylation is vital to understanding the function(s) of different glycans expressed at a given site of a protein under physiological and disease conditions. Most commonly used precursor ion intensity based quantification method is less accurate and other labeled methods are expensive and require enrichment of glycopeptides. Here, we used glycopeptide product (y and Y0) ions and (18)O-labeling of C-terminal carboxyl group as a strategy to obtain quantitative information about fold-change and relative abundance of most of the glycoforms attached to the glycopeptides. As a proof of concept, the accuracy and robustness of this targeted, relative quantification LC-MS method was demonstrated using Rituximab. Furthermore, the N-glycopeptide quantification results were compared with a biosimilar of Rituximab and validated with quantitative data obtained from 2-AB-UHPLC-FL method. We further demonstrated the intensity fold-change and relative abundance of 46 unique N- and O-glycopeptides and aglycopeptides from innovator and biosimilar samples of Etanercept using both the normal-MS and product ion based quantitation. The results showed a very similar site-specific expression of N- and O-glycopeptides between the samples but with subtle differences. Interestingly, we have also been able to quantify macro-heterogeneity of all N- and O-glycopetides of Etanercept. In addition to applications in biotherapeutics, the developed method can also be used for site-specific quantitation of N- and O-glycopeptides and aglycopeptides of glycoproteins with known glycosylation pattern.

}, issn = {1573-4986}, doi = {10.1007/s10719-016-9733-8}, author = {Srikanth, Jandhyam and Agalyadevi, Rathinasamy and Babu, Ponnusamy} } @article {8889, title = {Transcriptional transitions in Alphonso mango (Mangifera indica L.) during fruit development and ripening explain its distinct aroma and shelf life characteristics [Next Gen Genomics Facility]}, journal = {Sci Rep}, volume = {7}, year = {2017}, month = {2017 Aug 18}, pages = {8711}, abstract = {

Alphonso is known as the "King of mangos" due to its unique flavor, attractive color, low fiber pulp and long shelf life. We analyzed the transcriptome of Alphonso mango through Illumina sequencing from seven stages of fruit development and ripening as well as flower. Total transcriptome data from these stages ranged between 65 and 143 Mb. Importantly, 20,755 unique transcripts were annotated and 4,611 were assigned enzyme commission numbers, which encoded 142 biological pathways. These included ethylene and flavor related secondary metabolite biosynthesis pathways, as well as those involved in metabolism of starch, sucrose, amino acids and fatty acids. Differential regulation (p-value <= 0.05) of thousands of transcripts was evident in various stages of fruit development and ripening. Novel transcripts for biosynthesis of mono-terpenes, sesqui-terpenes, di-terpenes, lactones and furanones involved in flavor formation were identified. Large number of transcripts encoding cell wall modifying enzymes was found to be steady in their expression, while few were differentially regulated through these stages. Novel 79 transcripts of inhibitors of cell wall modifying enzymes were simultaneously detected throughout Alphonso fruit development and ripening, suggesting controlled activity of these enzymes involved in fruit softening.

}, keywords = {Cell Wall, Enzyme Inhibitors, Flowers, Fruit, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Gene Ontology, Genes, Plant, Glycoside Hydrolases, Mangifera, Odorants, Phylogeny, Reproducibility of Results, RNA, Messenger, Transcription, Genetic, Transcriptome}, issn = {2045-2322}, doi = {10.1038/s41598-017-08499-5}, author = {Deshpande, Ashish B and Anamika, Krishanpal and Jha, Vineet and Chidley, Hemangi G and Oak, Pranjali S and Kadoo, Narendra Y and Pujari, Keshav H and Giri, Ashok P and Gupta, Vidya S} } @article {688, title = {Transcriptome profiling of Elettaria cardamomum (L.) Maton (small cardamom).}, journal = {Genom Data}, volume = {11}, year = {2017}, month = {2017 Mar}, pages = {102-103}, abstract = {

Elettaria cardamomum (L.) Maton, known as {\textquoteright}queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base) and 24,889,197 (75 base) raw reads accounting for approximately 8.21GB and 7.65GB of sequence data for wild and cultivar genotypes of cardamom respectively. The raw data were submitted to SRA database of NCBI under the accession numbers SRX1141272 (wild) and SRX1141276 (cultivars). The raw reads were quality filtered and assembled using MIRA assembler resulted with 112,208 and 264,161contigs having N50 value 616 and 664 for wild and cultivar cardamom respectively. The assembled unigenes were functionally annotated using several databases including PlantCyc for pathway annotation. This work represents the first report on cardamom transcriptome sequencing. In order to generate a comprehensive reference transcriptome, we further assembled the raw reads of wild and cultivar genotypes which might enrich the plant transcriptome database and trigger advanced research in cardamom genomics.

}, issn = {2213-5960}, doi = {10.1016/j.gdata.2016.12.013}, author = {Nadiya, F and Anjali, N and Thomas, Jinu and Gangaprasad, A and Sabu, K K} } @article {8885, title = {Comparative Metagenomics Reveal Phylum Level Temporal and Spatial Changes in Mycobiome of Belowground Parts of Crocus sativus [Next Gen Genomics Facility]}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016}, pages = {e0163300}, abstract = {

Plant-fungal associations have been explored by routine cultivation based approaches and cultivation based approaches cannot catalogue more than 5\% of fungal diversity associated with any niche. In the present study, an attempt has been made to catalogue fungal diversity associated with belowground parts i.e. rhizosphere and cormosphere, of Crocus sativus (an economically important herb) during two growth stages, using cultivation independent ITS gene targeted approach, taking bulk soil as reference. The 454 pyrosequencing sequence data analysis suggests that the fungal diversity was niche and growth stage specific. Fungi diversity, in the present case, was not only different between the two organs (roots and corm) but the dominance pattern varies between the cormosphere during two growth stages. Zygomycota was dominant fungal phylum in the rhizosphere whereas Basidiomycota was dominant in cormosphere during flowering stage. However in cormosphere though Basidiomycota was dominant phylum during flowering stage but Zygomycota was dominant during dormant stage. Interestingly, in cormosphere, the phyla which was dominant at dormant stage was rare at flowering stage and vice-versa (Basidiomycota: Flowering = 93.2\% Dormant = 0.05\% and Zygomycota: Flowering = 0.8\% Dormant = 99.7\%). At genus level, Rhizopus was dominant in dormant stage but was rare in flowering stage (Rhizopus: Dormant = 99.7\% Flowering = 0.55\%). This dynamics is not followed by the bulk soil fungi which was dominated by Ascomycota during both stages under study. The genus Fusarium, whose species F. oxysporum causes corm rot in C. sativus, was present during both stages with slightly higher abundance in roots. Interestingly, the abundance of Rhizopus varied a great deal in two stages in cormosphere but the abundance of Fusarium was comparable in two growth stages (Bulk soil Flowering = 0.05\%, Rhizosphere Flowering = 1.4\%, Cormosphere Flowering = 0.06\%, Bulk soil Dormant = 2.47\% and cormosphere dormant = 0.05\%). This is the first report on the fungal diversity associated with the root of Crocus sativus and first report on the fungi associated with corm of any plant with the temporal and spatial variation in the fungal community structure.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0163300}, author = {Ambardar, Sheetal and Singh, Heikham Russiachand and Gowda, Malali and Vakhlu, Jyoti} } @article {780, title = {Exploring Packaged Microvesicle Proteome Composition of Chinese Hamster Ovary Secretome [Mass Spectrometry - Proteomics]}, journal = {Journal of Bioprocessing \& Biotechniques}, volume = {6}, year = {2016}, pages = {1-11}, keywords = {

CHO, Microvesicles, Proteome, Recombinant protein production

, Secretome}, issn = {2155-9821}, doi = {10.4172/2155-9821.1000274}, url = {https://www.omicsonline.org/open-access/exploring-packaged-microvesicle-proteome-composition-of-chinesehamster-ovary-secretome-2155-9821-1000274.php?aid=71599}, author = {Niraj Kumar and Dixat Gopal Gupta and Srikant Kumar and et. al.} } @article {8884, title = {Genome Sequence, Comparative Analysis, and Evolutionary Insights into Chitinases of Entomopathogenic Fungus Hirsutella thompsonii [Next Gen Genomics Facility]}, journal = {Genome Biology and Evolution}, volume = {7}, year = {2015}, month = {02}, pages = {916-930}, abstract = {

{Hirsutella thompsonii (Ht) is a fungal pathogen of acarines and the primary cause of epizootics among mites. The draft genomes of two isolates of Ht (MTCC 3556: Ht3, 34.6 Mb and MTCC 6686: Ht6, 34.7 Mb) are presented and compared with the genomes of Beauveria bassiana (Bb) ARSEF 2860 and Ophiocordyceps sinensis (Os) CO18. Comparative analysis of carbohydrate active enzymes, pathogen{\textendash}host interaction genes, metabolism-associated genes, and genes involved in biosynthesis of secondary metabolites in the four genomes was carried out. Reduction in gene family sizes in Ht3 and Os as compared with Ht6 and Bb is observed. Analysis of the mating type genes in Ht reveals the presence of MAT idiomorphs which is suggestive of cryptic sexual traits in Ht. We further identify and classify putative chitinases that may function as virulence factors in fungal entomopathogens due to their role in degradation of arthropod cuticle.}

}, issn = {1759-6653}, doi = {10.1093/gbe/evv037}, url = {https://doi.org/10.1093/gbe/evv037}, author = {Agrawal, Yamini and Khatri, Indu and Subramanian, Srikrishna and Shenoy, Belle Damodara} } @article {496, title = {Insulin plant (Costus pictus) extract improves insulin sensitivity and ameliorates atherogenic dyslipidaemia in fructose induced insulin resistant rats: Molecular mechanism [Mass spectrometry - Metabolomics]}, journal = {Journal of Functional Foods}, volume = {17}, year = {2015}, pages = {749 - 760}, abstract = {

Abstract The preventative effect of insulin plant (Costus pictus) leaf extract on hyperglycaemia, insulin sensitivity and dyslipidaemia in fructose-fed insulin resistant rats was investigated in the present study, further the possible underlying mechanism was also explored. It was observed that under insulin resistant condition this plant extract decreases hyperinsulinaemia by improving insulin sensitivity at the peripheral level through its antioxidant and anti-inflammatory effects. At molecular level decreased activation of molecules involved in stress sensitive signalling cascade and down regulation of pro-inflammatory cytokines were noticed. Furthermore the effects of this plant extract on adipokine profile and plasma homocysteine were evaluated. The possible active components responsible for the beneficial effect exerted by this plant extract have also been identified and quantified. To the best of our knowledge this is the first study on insulin plant extract on the aforementioned animal model.

}, keywords = {Insulin plant}, issn = {1756-4646}, doi = {http://dx.doi.org/10.1016/j.jff.2015.06.024}, url = {//www.sciencedirect.com/science/article/pii/S1756464615003187}, author = {S. Ashwini and Zachariah Bobby and Manoj Joseph and Sajini Elizabeth Jacob and Ramamoorthy Padmapriya} } @article {520, title = {Isolation of Exosomes from Blood Plasma: Qualitative and Quantitative Comparison of Ultracentrifugation and Size Exclusion Chromatography Methods. (Mass spectrometry - Proteomics)}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0145686}, abstract = {

BACKGROUND: Exosomes are emerging targets for biomedical research. However, suitable methods for the isolation of blood plasma-derived exosomes without impurities have not yet been described.

AIM: Therefore, we investigated the efficiency and purity of exosomes isolated with potentially suitable methods; differential ultracentrifugation (UC) and size exclusion chromatography (SEC).

METHODS AND RESULTS: Exosomes were isolated from rat and human blood plasma by various UC and SEC conditions. Efficiency was investigated at serial UC of the supernatant, while in case of SEC by comparing the content of exosomal markers of various fractions. Purity was assessed based on the presence of albumin. We found that the diameter of the majority of isolated particles fell into the size range of exosomes, however, albumin was also present in the preparations, when 1h UC at 4{\textdegree}C was applied. Furthermore, with this method only a minor fraction of total exosomes could be isolated from blood as deduced from the constant amount of exosomal markers CD63 and TSG101 detected after serial UC of rat blood plasma samples. By using UC for longer time or with shorter sedimentation distance at 4{\textdegree}C, or UC performed at 37{\textdegree}C, exosomal yield increased, but albumin impurity was still observed in the isolates, as assessed by transmission electron microscopy, dynamic light scattering and immunoblotting against CD63, TSG101 and albumin. Efficiency and purity were not different in case of using further diluted samples. By using SEC with different columns, we have found that although a minor fraction of exosomes can be isolated without significant albumin content on Sepharose CL-4B or Sephacryl S-400 columns, but not on Sepharose 2B columns, the majority of exosomes co-eluted with albumin.

CONCLUSION: Here we show that it is feasible to isolate exosomes from blood plasma by SEC without significant albumin contamination albeit with low vesicle yield.

}, keywords = {Animals, Chromatography, Gel, Exosomes, Male, Plasma, Rats, Wistar, Ultracentrifugation}, issn = {1932-6203}, doi = {10.1371/journal.pone.0145686}, author = {Baranyai, Tam{\'a}s and Herczeg, Kata and On{\'o}di, Zs{\'o}fia and Voszka, Istv{\'a}n and M{\'o}dos, K{\'a}roly and Marton, Nikolett and Nagy, Gy{\"o}rgy and M{\"a}ger, Imre and Wood, Matthew J and El Andaloussi, Samir and P{\'a}link{\'a}s, Zolt{\'a}n and Kumar, Vikas and Nagy, P{\'e}ter and Kittel, {\'A}gnes and Buz{\'a}s, Edit Ir{\'e}n and Ferdinandy, P{\'e}ter and Giricz, Zolt{\'a}n} } @article {513, title = {L-Plastin S-glutathionylation promotes reduced binding to β-actin and affects neutrophil functions. (Mass Spectrometry)}, journal = {Free Radic Biol Med}, volume = {86}, year = {2015}, month = {2015 Sep}, pages = {1-15}, abstract = {

Posttranslational modifications (PTMs) of cytoskeleton proteins due to oxidative stress associated with several pathological conditions often lead to alterations in cell function. The current study evaluates the effect of nitric oxide (DETA-NO)-induced oxidative stress-related S-glutathionylation of cytoskeleton proteins in human PMNs. By using in vitro and genetic approaches, we showed that S-glutathionylation of L-plastin (LPL) and β-actin promotes reduced chemotaxis, polarization, bactericidal activity, and phagocytosis. We identified Cys-206, Cys-283, and Cys-460as S-thiolated residues in the β-actin-binding domain of LPL, where cys-460 had the maximum score. Site-directed mutagenesis of LPL Cys-460 further confirmed the role in the redox regulation of LPL. S-Thiolation diminished binding as well as the bundling activity of LPL. The presence of S-thiolated LPL was detected in neutrophils from both diabetic patients and db/db mice with impaired PMN functions. Thus, enhanced nitroxidative stress may results in LPL S-glutathionylation leading to impaired chemotaxis, polarization, and bactericidal activity of human PMNs, providing a mechanistic basis for their impaired functions in diabetes mellitus.

}, keywords = {Actins, Adult, Amino Acid Sequence, Animals, Case-Control Studies, Cell Polarity, Chemotaxis, Diabetes Mellitus, Female, Glutathione, HEK293 Cells, Humans, Male, Mice, Inbred C57BL, Mice, Obese, Microfilament Proteins, Middle Aged, Molecular Sequence Data, Neutrophils, Nitric Oxide, Oxidative Stress, Protein Binding, Protein Processing, Post-Translational, Young Adult}, issn = {1873-4596}, doi = {10.1016/j.freeradbiomed.2015.04.008}, author = {Dubey, Megha and Singh, Abhishek K and Awasthi, Deepika and Nagarkoti, Sheela and Kumar, Sachin and Ali, Wahid and Chandra, Tulika and Kumar, Vikas and Barthwal, Manoj K and Jagavelu, Kumaravelu and S{\'a}nchez-G{\'o}mez, Francisco J and Lamas, Santiago and Dikshit, Madhu} } @article {710, title = {Production and characterization of lipopeptide from Bacillus cereus SNAU01 under solid state fermentation and its potential application as anti-biofilm agent. Biocatalysis and Agricultural Biotechnology 5 (2016):123{\textendash}132}, year = {2015}, author = {S. Nalini et al.} } @article {684, title = {Role of Homothorax in region specific regulation of Deformed in embryonic neuroblasts.}, journal = {Mech Dev}, volume = {138 Pt 2}, year = {2015}, month = {2015 Nov}, pages = {190-7}, abstract = {

The expression and regulation of Hox genes in developing central nervous system (CNS) lack important details like specific cell types where Hox genes are expressed and the transcriptional regulatory players involved in these cells. In this study we have investigated the expression and regulation of Drosophila Hox gene Deformed (Dfd) in specific cell types of embryonic CNS. Using Dfd neural autoregulatory enhancer we find that Dfd autoregulates itself in cells of mandibular neuromere. We have also investigated the role of a Hox cofactor Homothorax (Hth) for its role in regulating Dfd expression in CNS. We find that Hth exhibits a region specific role in controlling the expression of Dfd, but has no direct role in mandibular Dfd neural autoregulatory circuit. Our results also suggest that homeodomain of Hth is not required for regulating Dfd expression in embryonic CNS.

}, keywords = {Animals, Central Nervous System, Drosophila, Drosophila Proteins, Enhancer Elements, Genetic, Gene Expression Regulation, Developmental, Genes, Homeobox, Homeodomain Proteins, Neural Stem Cells, Organogenesis}, issn = {1872-6356}, doi = {10.1016/j.mod.2015.09.003}, author = {Kumar, Raviranjan and Chotaliya, Maheshvari and Vuppala, Sruthakeerthi and Auradkar, Ankush and Palasamudrum, Kalyani and Joshi, Rohit} } @article {8356, title = {Lunatimonas lonarensis gen. nov., sp. nov., a haloalkaline bacterium of the family Cyclobacteriaceae with nitrate reducing activity [Next Gen Genomics Facility]}, journal = {Syst Appl Microbiol}, volume = {37}, year = {2014}, month = {2014 Feb}, pages = {10-6}, abstract = {

Novel pinkish-orange pigmented, Gram-negative staining, half-moon shaped, non-motile, strictly aerobic strains designated AK24(T) and AK26 were isolated from water and sediment samples of Lonar Lake, Buldhana district, Maharahstra, India. Both strains were positive for oxidase, catalase and β-galactosidase activities. The predominant fatty acids were iso-C15:0 (41.5\%), anteiso-C15:0 (9.7\%), iso-C17:0 3OH (9.6\%), iso-C17:1 ω9c (10.2\%) and C16:1 ω7c/C16:1 ω6c/iso-C15:0 2OH (summed feature 3) (14.4\%). The strains contained MK-7 as the major respiratory quinone, and phosphatidylethanolamine and five unidentified lipids as the polar lipids. Blast analysis of the 16S rRNA gene sequence of strain AK24(T) showed that it was closely related to Aquiflexum balticum, with a pair-wise sequence similarity of 91.6\%, as well as to Fontibacter ferrireducens, Belliella baltica and Indibacter alkaliphilus (91.3, 91.2 and 91.2\% pair-wise sequence similarity, respectively), but it only had between 88.6 and 91.0\% pair-wise sequence similarity to the rest of the family members. The MALDI-TOF assay reported no significant similarities for AK24(T) and AK26, since they potentially represented a new species. A MALDI MSP dendrogram showed close similarity between the two strains, but they maintained a distance from their phylogenetic neighbors. The genome of AK24(T) showed the presence of heavy metal tolerance genes, including the genes providing resistance to arsenic, cadmium, cobalt and zinc. A cluster of heat shock resistance genes was also found in the genome. Two lantibiotic producing genes, LanR and LasB, were also found in the genome of AK24(T). Strains AK24(T) and AK26 were very closely related to each other with 99.5\% pair-wise sequence similarity. Phylogenetic analysis indicated that the strains were members of the family Cyclobacteriaceae and they clustered with the genus Mariniradius, as well as with the genera Aquiflexum, Cecembia, Fontibacter, Indibacter, and Shivajiella. DNA-DNA hybridization between strains AK24(T) and AK26 showed a relatedness of 82\% and their rep-PCR banding patterns were very similar. Based on data from the current polyphasic study, it is proposed that the isolates be placed in a new genus and species with the name Lunatimonas lonarensis gen. nov., sp. nov. The type strain of Lunatimonas lonarensis is AK24(T) (=JCM 18822(T)=MTCC 11627(T)).

}, keywords = {Bacterial Typing Techniques, Bacteroidetes, Cluster Analysis, DNA, Bacterial, DNA, Ribosomal, Fatty Acids, Fresh Water, Genome, Bacterial, Geologic Sediments, India, Molecular Sequence Data, Nitrates, Oxidation-Reduction, Phospholipids, Phylogeny, Quinones, RNA, Ribosomal, 16S, Sequence Analysis, DNA}, issn = {1618-0984}, doi = {10.1016/j.syapm.2013.10.003}, author = {Srinivas, T N R and Aditya, S and Bhumika, V and Kumar, P Anil} } @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 {512, title = {Biochemistry. Watch water flow.}, journal = {Science}, volume = {340}, year = {2013}, month = {2013 Jun 14}, pages = {1294-5}, keywords = {Aquaporins, Fungal Proteins, Pichia, Water}, issn = {1095-9203}, doi = {10.1126/science.1239270}, author = {Abramson, Jeff (C-CAMP) and Vartanian, Armand S} } @article {477, title = {A genetic RNAi screen for IP$_{3}$/Ca{\texttwosuperior}$^{+}$ coupled GPCRs in Drosophila identifies the PdfR as a regulator of insect flight. [Drosophila facility]}, journal = {PLoS Genet}, volume = {9}, year = {2013}, month = {2013}, pages = {e1003849}, abstract = {

Insect flight is regulated by various sensory inputs and neuromodulatory circuits which function in synchrony to control and fine-tune the final behavioral outcome. The cellular and molecular bases of flight neuromodulatory circuits are not well defined. In Drosophila melanogaster, it is known that neuronal IP3 receptor mediated Ca{\texttwosuperior}$^{+}$ signaling and store-operated Ca{\texttwosuperior}$^{+}$ entry (SOCE) are required for air-puff stimulated adult flight. However, G-protein coupled receptors (GPCRs) that activate intracellular Ca{\texttwosuperior}$^{+}$ signaling in the context of flight are unknown in Drosophila. We performed a genetic RNAi screen to identify GPCRs that regulate flight by activating the IPIP$_{3}$ receptor. Among the 108 GPCRs screened, we discovered 5 IPIP$_{3}$/Ca{\texttwosuperior}$^{+}$ linked GPCRs that are necessary for maintenance of air-puff stimulated flight. Analysis of their temporal requirement established that while some GPCRs are required only during flight circuit development, others are required both in pupal development as well as during adult flight. Interestingly, our study identified the Pigment Dispersing Factor Receptor (PdfR) as a regulator of flight circuit development and as a modulator of acute flight. From the analysis of PdfR expressing neurons relevant for flight and its well-defined roles in other behavioral paradigms, we propose that PdfR signaling functions systemically to integrate multiple sensory inputs and modulate downstream motor behavior.

}, keywords = {Adult, Animals, Calcium Signaling, Drosophila melanogaster, Drosophila Proteins, Flight, Animal, Humans, Inositol 1,4,5-Trisphosphate Receptors, Neurons, Receptors, G-Protein-Coupled, RNA Interference, Signal Transduction}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1003849}, author = {Agrawal, Tarjani and Sadaf, Sufia and Hasan, Gaiti} } @article {488, title = {Genome sequencing unveils a novel sea enterotoxin-carrying PVL phage in Staphylococcus aureus ST772 from India. [Next Generation Genomics facility]}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013}, pages = {e60013}, abstract = {

Staphylococcus aureus is a major human pathogen, first recognized as a leading cause of hospital-acquired infections. Community-associated S. aureus (CA-SA) pose a greater threat due to increase in severity of infection and disease among children and healthy adults. CA-SA strains in India are genetically diverse, among which is the sequence type (ST) 772, which has now spread to Australia, Europe and Japan. Towards understanding the genetic characteristics of ST772, we obtained draft genome sequences of five relevant clinical isolates and studied the properties of their PVL-carrying prophages, whose presence is a defining hallmark of CA-SA. We show that this is a novel prophage, which carries the structural genes of the hlb-carrying prophage and includes the sea enterotoxin. This architecture probably emerged early within the ST772 lineage, at least in India. The sea gene, unique to ST772 PVL, despite having promoter sequence characteristics typical of low expression, appears to be highly expressed during early phase of growth in laboratory conditions. We speculate that this might be a consequence of its novel sequence context. The crippled nature of the hlb-converting prophage in ST772 suggests that widespread mobility of the sea enterotoxin might be a selective force behind its {\textquoteright}transfer{\textquoteright} to the PVL prophage. Wild type ST772 strains induced strong proliferative responses as well as high cytotoxic activity against neutrophils, likely mediated by superantigen SEA and the PVL toxin respectively. Both proliferation and cytotoxicity were markedly reduced in a cured ST772 strain indicating the impact of the phage on virulence. The presence of SEA alongside the genes for the immune system-modulating PVL toxin may contribute to the success and virulence of ST772.

}, keywords = {Bacterial Toxins, Base Sequence, Enterotoxins, Exotoxins, Genome, Bacterial, Hemolysin Proteins, Humans, India, Leukocidins, Molecular Sequence Data, Prophages, RNA, Messenger, Sequence Analysis, DNA, Sphingomyelin Phosphodiesterase, Staphylococcus aureus}, issn = {1932-6203}, doi = {10.1371/journal.pone.0060013}, author = {Prabhakara, Sushma and Khedkar, Supriya and Shambat, Srikanth Mairpady and Srinivasan, Rajalakshmi and Basu, Atanu and Norrby-Teglund, Anna and Seshasayee, Aswin Sai Narain and Arakere, Gayathri} } @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 {495, title = {Draft genome sequence of Staphylococcus aureus 118 (ST772), a major disease clone from India. [Next Generation Genomics facility]}, journal = {J Bacteriol}, volume = {194}, year = {2012}, month = {2012 Jul}, pages = {3727-8}, abstract = {

We report the draft genome sequence of an ST772 Staphylococcus aureus disease isolate carrying staphylococcal cassette chromosome mec (SCCmec) type V from a pyomyositis patient. Our de novo short read assembly is \~{}2.8 Mb and encodes a unique Panton-Valentine leukocidin (PVL) phage with structural genes similar to those of ϕ7247PVL and novel lysogenic genes at the N termini.

}, keywords = {Cloning, Molecular, Genome, Bacterial, India, Molecular Sequence Data, Pyomyositis, Staphylococcal Infections, Staphylococcus aureus}, issn = {1098-5530}, doi = {10.1128/JB.00480-12}, author = {Prabhakara, Sushma and Khedkar, Supriya and Loganathan, Ramya Malarini and Chandana, S and Gowda, Malali and Arakere, Gayathri and Seshasayee, Aswin Sai Narain} } @article {494, title = {Draft genome sequence of Staphylococcus aureus ST672, an emerging disease clone from India. [Next Generation Genomics facility]}, journal = {J Bacteriol}, volume = {194}, year = {2012}, month = {2012 Dec}, pages = {6946-7}, abstract = {

We report the draft genome sequence of methicillin-resistant Staphylococcus aureus (MRSA) strain ST672, an emerging disease clone in India, from a septicemia patient. The genome size is about 2.82 Mb with 2,485 open reading frames (ORFs). The staphylococcal cassette chromosome mec (SCCmec) element (type V) and immune evasion cluster appear to be different from those of strain ST772 on preliminary examination.

}, keywords = {Bacteremia, Bacterial Proteins, Bacterial Typing Techniques, Base Sequence, DNA, Bacterial, Genome, Bacterial, Humans, Methicillin-Resistant Staphylococcus aureus, Molecular Sequence Data, Open Reading Frames, Penicillin-Binding Proteins, Sequence Analysis, DNA, Staphylococcal Infections}, issn = {1098-5530}, doi = {10.1128/JB.01868-12}, author = {Khedkar, Supriya and Prabhakara, Sushma and Loganathan, Ramya Malarini and S, Chandana and Gowda, Malali and Arakere, Gayathri and Seshasayee, Aswin Sai Narain} } @article {480, title = {Drosophila protein interaction map (DPiM): a paradigm for metazoan protein complex interactions. [Drosophila facility]}, journal = {Fly (Austin)}, volume = {6}, year = {2012}, month = {2012 Oct-Dec}, pages = {246-53}, abstract = {

Proteins perform essential cellular functions as part of protein complexes, often in conjunction with RNA, DNA, metabolites and other small molecules. The genome encodes thousands of proteins but not all of them are expressed in every cell type; and expressed proteins are not active at all times. Such diversity of protein expression and function accounts for the level of biological intricacy seen in nature. Defining protein-protein interactions in protein complexes, and establishing the when, what and where of potential interactions, is therefore crucial to understanding the cellular function of any protein-especially those that have not been well studied by traditional molecular genetic approaches. We generated a large-scale resource of affinity-tagged expression-ready clones and used co-affinity purification combined with tandem mass-spectrometry to identify protein partners of nearly 5,000 Drosophila melanogaster proteins. The resulting protein complex "map" provided a blueprint of metazoan protein complex organization. Here we describe how the map has provided valuable insights into protein function in addition to generating hundreds of testable hypotheses. We also discuss recent technological advancements that will be critical in addressing the next generation of questions arising from the map.

}, keywords = {Animals, Cell Line, Computational Biology, Drosophila melanogaster, Drosophila Proteins, Models, Biological, Protein Interaction Mapping, Protein Interaction Maps}, issn = {1933-6942}, doi = {10.4161/fly.22108}, author = {Guruharsha, K G and Obar, Robert A and Mintseris, Julian and Aishwarya, K and Krishnan, R T and VijayRaghavan, K and Artavanis-Tsakonas, Spyros} } @article {719, title = {Functional tumor infiltrating TH1 and TH2 effectors in large early-stage cervical cancer are suppressed by regulatory T cells.}, journal = {Int J Gynecol Cancer}, volume = {22}, year = {2012}, month = {2012 Sep}, pages = {1130-7}, abstract = {

OBJECTIVE: Analysis of tumor-infiltrating lymphocytes (TILs) is one of the cornerstones for the understanding of immune responses prevailing in the tumor microenvironment. We studied TILs from squamous cell carcinoma of the cervix ex vivo without proliferating them in vitro before analysis.

METHODS: Whereas TILs were magnetic activated cell separation enriched and flow sorted into CD4 CD25 (regulatory T cells [Tregs]), CD4 CD25 (effector T cells [Teffs]) were directly purified by flow cytometry, and both these subsets were characterized phenotypically and functionally. Tissue sections were probed for interleukin 4 (IL-4) and interferon γ.

RESULTS: Effector T cells constitutively expressed both interferon γ and IL-4 prototypical cytokines of TH1 and TH2, respectively, and were able to proliferate and secrete higher quantities of both cytokines in response to anti-CD3/anti-CD28 and autologous tumor lysates. Only 53\% of cervical cancer Tregs were FOXP3, elaborated transforming growth factor β1, and IL-10 and were able to inhibit both T helper subsets.

CONCLUSIONS: Intratumoral Teffs represented functionally active subsets of both TH1 and TH2 that were not anergic but were suppressed by multiple Treg subsets, which comprised FOXP3 + Tregs and Tregs secreting transforming growth factor β1 and IL-10. These results imply that the microenvironment of cervical carcinomas harbored both TH1 and TH2 subsets of CD4 Teffs that were functionally active but were perhaps unable to perform because of the overpowering effect of Tregs.

}, keywords = {Carcinoma, Squamous Cell, Cytokines, Female, Flow Cytometry, Humans, Immune Tolerance, Interferon-gamma, Lymphocyte Activation, Lymphocytes, Tumor-Infiltrating, Neoplasm Staging, T-Lymphocytes, Regulatory, Th1 Cells, Th2 Cells, Uterine Cervical Neoplasms}, issn = {1525-1438}, doi = {10.1097/IGC.0b013e318262aa53}, author = {Adurthi, Sreenivas and Mukherjee, Geetashree and Krishnamurthy, H and Sudhir, Krishna and Bafna, Uttamchand D and Umadevi, Kswamy and Jayshree, Rudrapatna Subramanyam} } @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 {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} } @article {483, title = {Inositol 1,4,5-trisphosphate receptor and dSTIM function in Drosophila insulin-producing neurons regulates systemic intracellular calcium homeostasis and flight. [Drosophila facility]}, journal = {J Neurosci}, volume = {30}, year = {2010}, month = {2010 Jan 27}, pages = {1301-13}, abstract = {

Calcium (Ca(2+)) signaling is known to regulate the development, maintenance and modulation of activity in neuronal circuits that underlie organismal behavior. In Drosophila, intracellular Ca(2+) signaling by the inositol 1,4,5-trisphosphate receptor and the store-operated channel (dOrai) regulates the formation and function of neuronal circuits that control flight. Here, we show that restoring InsP(3)R activity in insulin-producing neurons of flightless InsP(3)R mutants (itpr) during pupal development can rescue systemic flight ability. Expression of the store operated Ca(2+) entry (SOCE) regulator dSTIM in insulin-producing neurons also suppresses compromised flight ability of InsP(3)R mutants suggesting that SOCE can compensate for impaired InsP(3)R function. Despite restricted expression of wild-type InsP(3)R and dSTIM in insulin-producing neurons, a global restoration of SOCE and store Ca(2+) is observed in primary neuronal cultures from the itpr mutant. These results suggest that restoring InsP(3)R-mediated Ca(2+) release and SOCE in a limited subset of neuromodulatory cells can influence systemic behaviors such as flight by regulating intracellular Ca(2+) homeostasis in a large population of neurons through a non-cell-autonomous mechanism.

}, keywords = {Animals, Calcium, Calcium Signaling, Cell Membrane, Cells, Cultured, Central Nervous System, Drosophila, Drosophila Proteins, Flight, Animal, Homeostasis, Inositol 1,4,5-Trisphosphate Receptors, Insulin, Intracellular Fluid, Membrane Proteins, Mutation, Neural Pathways, Neurons, Pupa, Stromal Interaction Molecule 1}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3668-09.2010}, author = {Agrawal, Neha and Venkiteswaran, Gayatri and Sadaf, Sufia and Padmanabhan, Nisha and Banerjee, Santanu and Hasan, Gaiti} }