@article {9105, title = {Macrophage metabolic reprogramming during dietary stress influences adult body size in Drosophila [Central Imaging and Flow Cytometry Facility (INT)]}, journal = {EMBO Rep}, year = {2025}, month = {2025 Sep 09}, abstract = {

Immune cells are increasingly recognized as nutrient sensors; however, their developmental role in regulating growth under homeostasis or dietary stress remains elusive. Here, we show that Drosophila larval macrophages, in response to excessive dietary sugar (HSD), reprogram their metabolic state by activating glycolysis, thereby enhancing TCA-cycle flux, and increasing lipogenesis-while concurrently maintaining a lipolytic state. Although this immune-metabolic configuration correlates with growth retardation under HSD, our genetic analyses reveal that enhanced lipogenesis supports growth, whereas glycolysis and lipolysis are growth-inhibitory. Notably, promoting immune-driven lipogenesis offsets early growth inhibition in imaginal discs caused by glycolytic and lipolytic immune-metabolic states. Our findings reveal a model of immune-metabolic imbalance, where growth-suppressive states (glycolysis, lipolysis) dominate over a growth-supportive lipogenic state, thereby impairing early organ size control and ultimately affecting adult size. Overall, this study provides important insights into dietary stress-induced immune-metabolic reprogramming and its link to organ size regulation and early developmental plasticity.

}, issn = {1469-3178}, doi = {10.1038/s44319-025-00574-7}, author = {Mahanta, Anusree and Najar, Sajad Ahmad and Hariharan, Nivedita and Bhowmick, Ajit and Rizvi, Syed Iqra and Goyal, Manisha and Parupalli, Preethi and Subramanian, Ramaswamy and Giangrande, Angela and Palakodeti, Dasaradhi and Mukherjee, Tina} } @article {9118, title = {Metabolic coupling of ROS generation and antioxidant synthesis by the GABA shunt pathway in myeloid-like blood progenitor cells of Drosophila. [CIFF \& Metabolomics Facility]}, journal = {PLoS Genet}, volume = {21}, year = {2025}, month = {2025 Sep}, pages = {e1011602}, abstract = {

Redox balance is crucial for normal development of stem and progenitor cells that reside in oxidative environments. In this study, we explore the mechanisms of redox homeostasis in such niches and show that myeloid-like blood progenitor cells of the Drosophila larval lymph gland, that generate reactive oxygen species (ROS), moderate it developmentally by de novo synthesizing glutathione (GSH) to ensure redox balance. During lymph gland development, as the blood-progenitor cells oxidize pyruvate via the TCA cycle leading to the generation of ROS, GABA-shunt restricts pyruvate dehydrogenase (PDH) activity and consequently TCA cycle flux. This moderation enables a metabolic rerouting of TCA-derived oxaloacetate (OAA) to pyruvate via gluconeogenesis, which is necessary to sustain serine levels, the rate-limiting precursor for de novo GSH synthesis. Disruption of GABA metabolism causes metabolic imbalance, marked by excessive PDH activity and heightened TCA cycle flux. This results in reduced OAA availability, impaired gluconeogenic capacity, and insufficient serine/GSH production, ultimately leading to ROS dysregulation. Overall, this study identifies a unique metabolic framework in blood progenitor cells, where the GABA shunt, by restraining PDH and TCA cycle activity, maintains ROS at developmental levels. By coupling TCA-derived metabolites to GSH production, this state enables the TCA cycle to support both ROS generation and ROS scavenging, ensuring the developmental roles of ROS while preserving progenitor homeostasis.

}, keywords = {Animals, Antioxidants, Citric Acid Cycle, Drosophila, Drosophila melanogaster, Drosophila Proteins, gamma-Aminobutyric Acid, Gluconeogenesis, Glutathione, Hematopoietic Stem Cells, Larva, Myeloid Cells, Oxidation-Reduction, Oxidative Stress, Pyruvic Acid, Reactive Oxygen Species}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1011602}, author = {Goyal, Manisha and Tiwari, Sakshi and Arora, Jagriti and Cooper, Bruce and Subramanian, Ramaswamy and Mukherjee, Tina} } @article {9122, title = {Microwave-assisted synthesis of silica quantum dots: a novel approach for targeting PI3K/AKT signaling in breast cancer therapy [Central Imaging and Flow Cytometry Facility, CIFF, Bangalore Life Science Cluster - NCBS - C-CAMP - InStem - TIGS]}, journal = {RSC Adv}, volume = {15}, year = {2025}, month = {2025 Oct 20}, pages = {39677-39688}, abstract = {

In this study, a facile and efficient approach was adopted for the first time to synthesize silica quantum dots (SiQDs) using tetraethyl orthosilicate (TEOS) as a precursor and ascorbic acid as a reducing agent. The synthesis was achieved microwave-assisted hydrolysis of TEOS in the presence of ascorbic acid, resulting in the formation of stable, highly fluorescent SiQDs. Extensive high-throughput characterization techniques were employed to investigate the optical, morphological, and structural properties of the as-prepared SiQDs, confirming their uniform size distribution, strong photoluminescence, and moderate stability. The therapeutic potential of SiQDs was explored against breast cancer cell lines (MCF-7 and MDA-MB-231), where they exhibited significant cytotoxicity and selective anticancer activity. Mechanistic investigations revealed that SiQDs effectively induce apoptosis in cancer cells by downregulating the PI3K/AKT signaling pathway, a critical regulator of cell survival and proliferation. These findings underscore the potential of SiQDs as promising anticancer agents in precision cancer therapy, offering a novel strategy for targeted cancer treatment. The study also paves the way for the design and development of silica-based nanomaterials with tailored properties for biomedical applications.

}, issn = {2046-2069}, doi = {10.1039/d5ra04715c}, author = {Selvaraj, Anitha and Ponnuchamy, Kumar} } @article {8824, title = {Macrophage-conditioned medium enhances tunneling nanotube formation in breast cancer cells via PKC, Src, NF-κB, and p38 MAPK signaling [Next Gen Genomics Facility]}, journal = {Cell Signal}, year = {2024}, month = {2024 Jun 25}, pages = {111274}, abstract = {

Tumor-associated macrophages (TAMs) secrete cytokines, chemokines, and growth factors in the tumor microenvironment (TME) to support cancer progression. Higher TAM infiltration in the breast TME is associated with a poor prognosis. Previous studies have demonstrated the role of macrophages in stimulating long-range intercellular bridges referred to as tunneling nanotubes (TNTs) in cancer cells. Intercellular communication between cancer cells via TNTs promotes cancer growth, invasion, metastasis, and therapy resistance. Given the important role of TNTs and macrophages in cancer, the role of macrophage-induced TNTs in chemotherapy drug doxorubicin resistance is not known. Furthermore, the mechanism of macrophage-mediated TNT formation is elusive. In this study, it is shown that the macrophage-conditioned medium (MΦCM) partially mimicked inflammatory TME, induced an EMT phenotype, and increased migration in MCF-7 breast cancer cells. Additionally, secreted proteins in MΦCM induced TNT formation in MCF-7 cells, which led to increased resistance to doxorubicin. Transcriptomic analysis of MΦCM-treated MCF-7 cells showed enrichment of the NF-κB and focal adhesion pathways, as well as upregulation of genes involved in EMT, extracellular remodeling, and actin cytoskeleton reorganization. Interestingly, inhibitors of PKC, Src, NF-κB, and p38 decreased macrophage-induced TNT formation in MCF-7 cells. These results reveal the novel role of PKC and Src in inducing TNT formation in cancer cells and suggest that inhibition of PKC and Src activity may likely contribute to reduced macrophage-breast cancer cell interaction and the potential therapeutic strategy of cancer.

}, issn = {1873-3913}, doi = {10.1016/j.cellsig.2024.111274}, author = {Melwani, Pooja Kamal and Balla, Murali Mohan Sagar and Bhamani, Aman and Nandha, Shivani R and Checker, Rahul and Pandey, Badri Narain} } @article {8708, title = {Multiplexed fluorescence and scatter detection with single cell resolution using on-chip fiber optics for droplet microfluidic applications [Discovery to Innovation Accelerator, C-CAMP]}, journal = {Microsyst Nanoeng}, volume = {10}, year = {2024}, month = {2024}, pages = {35}, abstract = {

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

}, issn = {2055-7434}, doi = {10.1038/s41378-024-00665-w}, author = {Gupta, Preksha and Mohan, Ambili and Mishra, Apurv and Nair, Atindra and Chowdhury, Neeladri and Balekai, Dhanush and Rai, Kavyashree and Prabhakar, Anil and Saiyed, Taslimarif} } @article {8472, title = {Marinobacterium lacunae sp. nov. isolated from estuarine sediment [Next Gen Genomics Facility]}, journal = {Arch Microbiol}, volume = {205}, year = {2023}, month = {2023 Jul 22}, pages = {294}, abstract = {

A novel motile bacterium was isolated from a sediment sample collected in Kochi backwaters, Kerala, India. This bacterium is Gram negative, rod shaped, 1.0-1.5\ {\textmu}m wide, and 2.0-3.0\ {\textmu}m long. It was designated as strain AK27. Colonies were grown on marine agar displayed circular, off-white, shiny, moist, translucent, flat, margin entire, 1-2\ mm in diameter. The major fatty acids identified in this strain were C ω7c, C, and summed in feature 3. The composition of polar lipids in the strain AK27 included phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unidentified amino lipid, two unidentified aminophospholipids, two unidentified phospholipids, and six unidentified lipids. The genomic DNA of strain AK27 exhibited a G+C content of 56.4\ mol\%. Based on the analysis of 16S rRNA gene sequence, strain AK27 showed sequence similarity to M. ramblicola D7 and M. zhoushanense WM3 as 98.99\% and 98.58\%, respectively. Compared to other type strains of the Marinobacterium genus, strain AK27 exhibited sequence similarities ranging from 91.7\% to 96.4\%. When compared to Marinobacterium zhoushanense WM3 and Marinobacterium ramblicola D7, strain AK27 exhibited average nucleotide identity values of 80.25\% and 79.97\%, and dDDH values of 22.9\% and 22.6\%, respectively. The genome size of the strain AK27 was 4.55\ Mb, with 4,229 coding sequences. Based on the observed phenotypic and chemotaxonomic features, and the results of phylogenetic and phylogenomic analysis, this study proposes the classification of strain AK27 as a novel species within the genus Marinobacterium. The proposed name for this novel species is Marinobacterium lacunae sp. nov.

}, keywords = {Agar, Alteromonadaceae, Cardiolipins, Phylogeny, RNA, Ribosomal, 16S}, issn = {1432-072X}, doi = {10.1007/s00203-023-03627-4}, author = {Tanuku, Srinivas Naga Radha and Pinnaka, Anil Kumar and Behera, Swarnaprava and Singh, Aditya and Pydi, Sudharani and Vasudeva, Gunjan and Vaidya, Bhumika and Sharma, Gunjan and Ganta, Sampath Kumar and Garbhapu, Naveen Sagar} } @article {1678, title = {Methanol Skin Mucus Extract of Mrigal (Cirrhinus mrigala) Fish Peptide Targeting Viral Particles of Infectious Pancreatic Necrosis Virus (IPNV) and Infectious Salmon Anemia Virus (ISAV): an in silico Approach [Mass Spectrometry Facility]}, journal = {International Journal of Peptide Research and Therapeutics}, volume = {71}, year = {2021}, month = {02/2021}, type = {Research Article}, abstract = {

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

}, doi = {https://doi.org/10.1007/s10989-021-10179-y}, author = {Arun Sridhar and Dinesh Babu Manikandan and Sathish Kumar Marimuthu and Manikandan Murugesan and Thirumurugan Ramasamy} } @article {1862, title = {Mito-targeted antioxidant prevents cardiovascular remodelling in spontaneously hypertensive rat by modulation of energy metabolism [Mass Spectrometry - Proteomics Facility]}, journal = {Clinical and Experimental Pharmacology and Physiology}, year = {2021}, month = {08/2021}, type = {Journal Article}, abstract = {

Hypertension induced left ventricular hypertrophy (LVH) augments the risk of cardiovascular anomalies. Mitochondrial alterations result in oxidative stress, accompanied by decrease in fatty acid oxidation, leading to the activation of the hypertrophic program. Targeted antioxidants are expected to reduce mitochondrial reactive oxygen species more effectively than general antioxidants. This study was designed to assess whether the mito-targeted antioxidant, Mito-Tempol (Mito-TEMP) is more effective than the general oxidant, Tempol (TEMP) in reduction of hypertension and hypertrophy and prevention of shift in cardiac energy metabolism. Spontaneously hypertensive rats were administered either TEMP (20 mg/kg/day) or Mito-TEMP (2 mg/kg/day) intraperitoneally for 30 days. Post treatment, animals were subjected to 2D-echocardiography. Myocardial lysates were subjected to RPLC {\textendash} LTQ-Orbitrap-MS analysis. Mid-ventricular sections were probed for markers of energy metabolism and fibrosis. The beneficial effect on cardiovascular structure and function was significantly higher for Mito-TEMP. Increase in mitochondrial antioxidants and stimulation of fatty acid metabolism; with significant improvement in cardiovascular function was apparent in spontaneously hypertensive rats (SHR) treated with Mito-TEMP. The study indicates that Mito-TEMP is superior to its non- targeted isoform in preventing hypertension induced LVH, and the beneficial effects on heart are possibly mediated by reversal of metabolic remodelling.

}, keywords = {cardiac hypertrophy, cardiac metabolism, LC-MS, mitochondria targeted antioxidant, proteomic analysis, spontaneously hypertensive rat}, doi = {https://doi.org/10.1111/1440-1681.13585}, url = {https://onlinelibrary.wiley.com/doi/10.1111/1440-1681.13585}, author = {Potnuri, Ajay Godwin and Purushothaman, Sreeja and Saheera, Sherin and Nair, Renuka R} } @article {1637, title = {Metabolic control of cellular immune-competency by odors in Drosophila [Mass Spectrometry - Metabolomics Facility (INT)]}, journal = {Elife}, volume = {9}, year = {2020}, month = {2020 Dec 29}, abstract = {

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

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

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

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0231197}, author = {Kaur, Kamaldeep and Khatri, Indu and Akhtar, Akil and Subramanian, Srikrishna and Ramya, T N C} } @article {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 {1480, title = {A microfluidic flow analyzer with integrated lensed optical fibers [Discovery to Innovation Accelerator]}, journal = {Biomicrofluidics}, volume = {14}, year = {2020}, pages = {054104}, doi = {10.1063/5.0013250}, url = {https://doi.org/10.1063/5.0013250}, author = {Mohan,A. and Gupta,P. and Nair,A. P. and Prabhakar,A. and Saiyed,T.} } @article {1160, title = {Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway [National Cryo-Electron Microscopy Facility (INT)]}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {09, 2019}, type = {Article}, chapter = {4127}, abstract = {Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.}, keywords = {Bacterial structural biology, Cryoelectron microscopy, Multienzyme complexes}, author = {Nitish Sathyanarayanan and Giuseppe Cannone and Lokesh Gakhar and Nainesh Katagihallimath and Ramanathan Sowdhamini and Subramanian Ramaswamy and Kutti R. Vinothkumar} } @article {1193, title = {Molecular Engineering of Adeno-Associated Virus Capsid Improves Its Therapeutic Gene Transfer in Murine Models of Hemophilia and Retinal Degeneration [Mass Spectrometry - Proteomics Facility]}, journal = {Mol Pharm}, year = {2019}, month = {2019 Oct 22}, abstract = {

Recombinant adeno-associated virus (AAV)-based gene therapy has been promising, but several host-related transduction or immune challenges remain. For this mode of therapy to be widely applicable, it is crucial to develop high transduction and permeating vectors that infect the target at significantly low doses. Because glycosylation of capsid proteins is known to be rate limiting in the life cycle of many viruses, we reasoned that perturbation of glycosylation sites in AAV2 capsid will enhance gene delivery. In our first set experiments, pharmacological modulation of the glycosylation status in host cells, modestly decreased (1-fold) AAV2 packaging efficacy while it improved their gene expression (\~{}74\%) in vitro. We then generated 24 mutant AAV2 vectors modified to potentially create or disrupt a glycosylation site in its capsid. Three of them demonstrated a 1.3-2.5-fold increase in transgene expression in multiple cell lines (HeLa, Huh7, and ARPE-19). Hepatic gene transfer of these vectors in hemophilia B mice, resulted in a 2-fold increase in human coagulation factor (F)IX levels, while its T/B-cell immunogenic response was unaltered. Subsequently, intravitreal gene transfer of glycosylation site-modified vectors in C57BL6/J mice demonstrated an increase in green fluorescence protein expression (\~{}2- to 4-fold) and enhanced permeation across retina. Subretinal administration of these modified vectors containing RPE65 gene further rescued the photoreceptor response in a murine model of Leber congenital amarousis. Our studies highlight the translational potential of glycosylation site-modified AAV2 vectors for hepatic and ocular gene therapy applications.

}, issn = {1543-8392}, doi = {10.1021/acs.molpharmaceut.9b00959}, author = {Mary, Bertin and Maurya, Shubham and Kumar, Mohit and Bammidi, Sridhar and Kumar, Vikas and Jayandharan, Giridhara R} } @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 {1136, title = {Mon1 constitutes a novel node in the brain-gonad axis that is essential for female germline maturation. [Transgenic Fly Facility]}, journal = {Development}, volume = {146}, year = {2019}, month = {2019 Jul 10}, abstract = {

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

}, issn = {1477-9129}, doi = {10.1242/dev.166504}, author = {Dhiman, Neena and Shweta, Kumari and Tendulkar, Shweta and Deshpande, Girish and Ratnaparkhi, Girish S and Ratnaparkhi, Anuradha} } @article {1025, title = {Myosin heavy chain mutations that cause Freeman-Sheldon syndrome lead to muscle structural and functional defects in Drosophila. [Transgenic Fly Facility]}, journal = {Dev Biol}, volume = {449}, year = {2019}, month = {2019 May 15}, chapter = {90}, abstract = {

Missense mutations in the MYH3 gene encoding myosin heavy chain-embryonic (MyHC-embryonic) have been reported to cause two skeletal muscle contracture syndromes, Freeman Sheldon Syndrome (FSS) and Sheldon Hall Syndrome (SHS). Two residues in MyHC-embryonic that are most frequently mutated, leading to FSS, R672 and T178, are evolutionarily conserved across myosin heavy chains in vertebrates and Drosophila. We generated transgenic Drosophila expressing myosin heavy chain (Mhc) transgenes with the FSS mutations and characterized the effect of their expression on Drosophila muscle structure and function. Our results indicate that expressing these mutant Mhc transgenes lead to structural abnormalities in the muscle, which increase in severity with age and muscle use. We find that flies expressing the FSS mutant Mhc transgenes in the muscle exhibit shortening of the inter-Z disc distance of sarcomeres, reduction in the Z-disc width, aberrant deposition of Z-disc proteins, and muscle fiber splitting. The ATPase activity of the three FSS mutant MHC proteins are reduced compared to wild type MHC, with the most severe reduction observed in the T178I mutation. Structurally, the FSS mutations occur close to the ATP binding pocket, disrupting the ATPase activity of the protein. Functionally, expression of the FSS mutant Mhc transgenes in muscle lead to significantly reduced climbing capability in adult flies. Thus, our findings indicate that the FSS contracture syndrome mutations lead to muscle structural defects and functional deficits in Drosophila, possibly mediated by the reduced ATPase activity of the mutant MHC proteins.

}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2019.02.017}, author = {Das, Shreyasi and Kumar, Pankaj and Verma, Aakanksha and Maiti, Tushar K and Mathew, Sam J} } @article {1006, title = {Mass Spectrometric Quantification of Arousal Associated Neurochemical Changes in Single Honey Bee Brains and Brain Regions. [Mass Spectrometry Facility - Metabolomics (INT)]}, journal = {ACS Chem Neurosci}, year = {2018}, month = {2018 Oct 26}, abstract = {

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

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

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

}, keywords = {Animals, Biomechanical Phenomena, Cell Adhesion, Cell Membrane, Dynamins, Endocytosis, Feedback, Physiological, Mechanotransduction, Cellular, Mice, Signal Transduction, Temperature, Vinculin}, issn = {2041-1723}, doi = {10.1038/s41467-018-06738-5}, author = {Thottacherry, Joseph Jose and Kosmalska, Anita Joanna and Kumar, Amit and Vishen, Amit Singh and Elosegui-Artola, Alberto and Pradhan, Susav and Sharma, Sumit and Singh, Parvinder P and Guadamillas, Marta C and Chaudhary, Natasha and Vishwakarma, Ram and Trepat, Xavier and Del Pozo, Miguel A and Parton, Robert G and Rao, Madan and Pullarkat, Pramod and Roca-Cusachs, Pere and Mayor, Satyajit} } @article {869, title = {Methionine coordinates a hierarchically organized anabolic program enabling proliferation. [Mass Spectrometry - Lipidomics \& Metabolomics and Next Gen Sequencing Facilities (INT)]}, journal = {Mol Biol Cell}, year = {2018}, month = {2018 Oct 24}, pages = {mbcE18080515}, abstract = {

Methionine availability during overall amino acid limitation metabolically reprograms cells to support proliferation, the underlying basis for which remains unclear. Here, we construct the organization of this methionine mediated anabolic program, using yeast. Combining comparative transcriptome analysis, biochemical and metabolic flux based approaches, we discover that methionine rewires overall metabolic outputs by increasing the activity of a key regulatory node. This comprises of: the pentose phosphate pathway (PPP) coupled with reductive biosynthesis, the glutamate dehydrogenase (GDH) dependent synthesis of glutamate/glutamine, and pyridoxal-5-phosphate (PLP) dependent transamination capacity. This PPP-GDH-PLP node provides the required cofactors and/or substrates for subsequent rate-limiting reactions in the synthesis of amino acids, and therefore nucleotides. These rate-limiting steps in amino acid biosynthesis are also induced in a methionine-dependent manner. This thereby results in a biochemical cascade establishing a hierarchically organized anabolic program. For this methionine mediated anabolic program to be sustained, cells co-opt a "starvation stress response" regulator, Gcn4p. Collectively, our data suggest a hierarchical metabolic framework explaining how methionine mediates an anabolic switch.

}, issn = {1939-4586}, doi = {10.1091/mbc.E18-08-0515}, author = {Walvekar, Adhish S and Srinivasan, Rajalakshmi and Gupta, Ritu and Laxman, Sunil} } @article {454, title = {Mechanism of apoptosis induction in human breast cancer MCF-7 cell by Ruviprase, a small peptide from Daboia russelii russelii venom.[Mass Spectrometry]}, journal = {Chem Biol Interact}, volume = {258}, year = {2016}, month = {2016 Oct 25}, pages = {297-304}, abstract = {

Ruviprase, a 4.4~kDa peptide isolated from Daboia russelii russelii venom demonstrated antiproliferative activity against EMT6/AR1, U-87MG, HeLa and MCF-7 cancer cells with an IC50 value of 23.0, 8.8, 5.8 and 4.0~μg ml(-1), respectively. However, it was nontoxic to non-cancerous human embryonic kidney cell and human peripheral blood lymphocytes. Flow-cytometric analysis confirmed the apoptosis induction in MCF-7 cells by Ruviprase where it induced DNA condensation but did not cause mitotic blockage or chromosomal aberration in treated-cells. Immunofluorescence microscopic analysis indicated Ruviprase induced apoptosis in MCF-7 cells through p53 and p21-mediated pathways. Ruviprase generated reactive oxygen species (ROS), altered the mitochondrial transmembrane potential, and significantly decreased the cellular glutathione (GSH) content of MCF-7 cells. Immunoblotting and quantitative real-time PCR (qRT-PCR) analyses suggested that Ruviprase down-regulated the expression of anti-apoptotic protein Bcl-2, increased cleavage of poly (ADP-ribose) polymerase (PARP) protein, and up-regulated the expression of pro-apoptotic protein Bax, as well as executer protein caspase-7 to induced apoptosis in MCF-7 cells via intrinsic pathway. This is the first report on the characterization of the anticancer potential of a small, non-toxic and anticoagulant peptide purified from Russell{\textquoteright}s viper venom.

}, issn = {1872-7786}, doi = {10.1016/j.cbi.2016.09.004}, author = {Thakur, Rupamoni and Kini, Sudarshan and Kurkalang, Sillarine and Banerjee, Atanu and Chatterjee, Purba and Chanda, Abhishek and Chatterjee, Anupam and Panda, Dulal and Mukherjee, Ashis K} } @article {540, title = {A method for comparative metabolomics in urine using high resolution mass spectrometry.}, journal = {J Chromatogr A}, volume = {1443}, year = {2016}, month = {2016 Apr 22}, pages = {83-92}, abstract = {

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

}, keywords = {Chromatography, Liquid, Chromatography, Reverse-Phase, Hydrophobic and Hydrophilic Interactions, Mass Spectrometry, Metabolomics, Reproducibility of Results, Urinalysis}, issn = {1873-3778}, doi = {10.1016/j.chroma.2016.02.080}, author = {Ramakrishnan, Padma and Nair, Sreenath and Rangiah, Kannan} } @article {711, title = {Microscopic elucidation of abundant endophytic bacteria colonizing the cell wall{\textendash}plasma membrane peri-space in the shoot-tip tissue of banana. Oxford Journal AoB PLANTS (2013) 5 : plt011}, year = {2013}, author = {Pious Thomas and Krishna M. Reddy.} }