@article {8675, title = {Generation and characterization of retinal pigment epithelium from patient iPSC line to model oculocutaneous albinism (OCA)1A disease [EyeStem Research Pvt. Ltd. - a C-CAMP Startup and Discovery to Innovation Accelerator, C-CAMP]}, journal = {J. Biosciences }, volume = {49}, year = {2024}, month = {01/2024}, abstract = {

Oculocutaneous albinism (OCA) is characterized by reduced melanin biosynthesis affecting the retina, thus impairing visual function. The disease pathology of OCA is poorly understood at the cellular level due to unavailability of suitable biological model systems. This study aimed to develop a disease-specific\ in vitro\ model for OCA type 1A, the most severe form caused by\ TYR\ (tyrosinase) gene mutations, using retinal pigment epithelium (RPE) differentiated from patient-derived human-induced pluripotent stem cells (hiPSCs). A comparative study between healthy and OCA1A RPE cells revealed that while healthy RPE cells exhibited timely onest of pigmentation during differentiation, OCA1A RPE cells failed to pigment even after an extended culture period. This observation was validated by ultrastructural studies using electron microscopy, hinting at melanosome-specific defects. Immunocytochemistry demonstrated abnormal expression patterns of melanogenesis-specific protein markers in OCA1A RPE cells, indicating reduced or absence of melanin synthesis. Next, a quantitative assay was\ performed to\ confirm the\ absence of melanin production in\ OCA1A RPE cells. Tyrosinase assay showed no activity in OCA1A compared with healthy RPE, suggesting non-functionality of\ TYR, further corroborated by western blot analysis showing complete absence of the protein. Gene expression by RNA sequencing of healthy and OCA1A RPE cells uncovered differential gene expression associated with lens development, visual perception, transmembrane transporter activity, and key signaling pathways. This disease-in-a-dish model of OCA1A provides an excellent platform to understand disease mechanism, identify potential therapeutic targets, and facilitate gene therapy or gene correction.

}, doi = {/doi.org/10.1007/s12038-023-00406-7}, url = {https://link.springer.com/article/10.1007/s12038-023-00406-7}, author = {Janavi Subramani and Niharika Patlolla and Rajani Battu and Taslimarif Saiyed and Rajarshi Pal} } @article {8441, title = {Gene flow drives genomic diversity in Asian Pikas distributed along the core and range-edge habitats in the Himalayas [Next Gen Genomics Facility (INT)]}, journal = {Ecol Evol.}, volume = {13}, year = {2023}, month = {05/2023}, chapter = {e10129}, abstract = {

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

}, keywords = {gene flow, genetic diversity, Himalayas, pika}, doi = {10.1002/ece3.10129}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10208896/}, author = {Nishma Dahal and Melia G. Romine and Sunita Khatiwara and Uma Ramakrishnan and Sangeet Lamichhaney} } @article {8886, title = {Grain Characteristics, Moisture, and Specific Peptides Produced by Contribute to False Smut Disease in Rice ( L.) [Mass Spectrometry - Proteomics Facility]}, journal = {Biomolecules}, volume = {13}, year = {2023}, month = {2023 Apr 12}, abstract = {

The fungus the causative agent of false smut in rice ( L.), is responsible for one of the severe grain diseases that lead to significant losses worldwide. In this research, microscopic and proteomic analyses were performed by comparing infected and non-infected grains of the susceptible and resistant rice varieties to provide insights into the molecular and ultrastructural factors involved in false smut formation. Prominent differentially expressed peptide bands and spots were detected due to false smut formation as revealed by sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional gel electrophoresis (2-DE) SDS-PAGE profiles and were identified using liquid chromatography-mass spectrometry (LC-MS/MS). The proteins identified from the resistant grains were involved in diverse biological processes such as cell redox homeostasis, energy, stress tolerance, enzymatic activities, and metabolic pathways. It was found that produces diverse degrading enzymes such as β-1, 3-endoglucanase, subtilisin-like protease, putative nuclease S1, transaldolase, putative palmitoyl-protein thioesterase, adenosine kinase, and DNase 1 that could discretely alter the host morphophysiology resulting in false smut. The fungus also produced superoxide dismutase, small secreted proteins, and peroxidases during the smut formation. This study revealed that the dimension of rice grain spikes, their elemental composition, moisture content, and the specific peptides produced by the grains and the fungi play a vital role in the formation of false smut.

}, keywords = {Chromatography, Liquid, Edible Grain, Oryza, Peptides, Proteomics, Tandem Mass Spectrometry}, issn = {2218-273X}, doi = {10.3390/biom13040669}, author = {Jose, Robinson C and Kanchal, Thangjam and Louis, Bengyella and Talukdar, Narayan C and Chowdhury, Devasish} } @article {8416, title = {Grain Characteristics, Moisture, and Specific Peptides Produced by Ustilaginoidea virens Contribute to False Smut Disease in Rice (Oryza\ sativa L.) [Mass Spectrometry - Proteomics Facility]}, journal = {Biomolecules}, volume = {13}, year = {2023}, abstract = {

The fungus Ustilaginoidea virens, the causative agent of false smut in rice (Oryza sativa L.), is responsible for one of the severe grain diseases that lead to significant losses worldwide. In this research, microscopic and proteomic analyses were performed by comparing U. virens infected and non-infected grains of the susceptible and resistant rice varieties to provide insights into the molecular and ultrastructural factors involved in false smut formation. Prominent differentially expressed peptide bands and spots were detected due to false smut formation as revealed by sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional gel electrophoresis (2-DE) SDS-PAGE profiles and were identified using liquid chromatography-mass spectrometry (LC-MS/MS). The proteins identified from the resistant grains were involved in diverse biological processes such as cell redox homeostasis, energy, stress tolerance, enzymatic activities, and metabolic pathways. It was found that U. virens produces diverse degrading enzymes such as β-1, 3-endoglucanase, subtilisin-like protease, putative nuclease S1, transaldolase, putative palmitoyl-protein thioesterase, adenosine kinase, and DNase 1 that could discretely alter the host morphophysiology resulting in false smut. The fungus also produced superoxide dismutase, small secreted proteins, and peroxidases during the smut formation. This study revealed that the dimension of rice grain spikes, their elemental composition, moisture content, and the specific peptides produced by the grains and the fungi U. virens play a vital role in the formation of false smut.

}, issn = {2218-273X}, doi = {10.3390/biom13040669}, url = {https://www.mdpi.com/2218-273X/13/4/669}, author = {Jose, Robinson C. and Kanchal, Thangjam and Louis, Bengyella and Talukdar, Narayan C. and Chowdhury, Devasish} } @article {3704, title = {Genome-wide SNP markers from fecal samples reveal anthropogenic impacts on connectivity: case of a small carnivore in the central Indian landscape [Next Gen Genomics Facility]}, journal = {Animal Conservation}, year = {2022}, month = {03/2022}, abstract = {

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

}, doi = {https://doi.org/10.1111/acv.12770}, author = {Tyagi, A. and Khan, A. and Thatte, P. and Ramakrishnan, U.} } @article {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 {1860, title = {Glycomic and glycotranscriptomic profiling of mucin-type O-glycans in planarian Schmidtea mediterranea [Mass Spectrometry - Glycomics]}, journal = {Glycobiology}, year = {2021}, month = {09/2021}, type = {Journal Article}, abstract = {

O-Glycans on cell surfaces play important roles in cell-cell, cell-matrix, and receptor-ligand interaction. Therefore, glycan-based interactions are important for tissue regeneration and homeostasis. Free-living flatworm Schmidtea mediterranea, because of its robust regenerative potential, is of great interest in the field of stem cell biology and tissue regeneration. Nevertheless, information on the composition and structure of O-glycans in planaria is unknown. Using mass spectrometry and in silico approaches, we characterized the glycome and the related transcriptome of mucin-type O-glycans of planarian S. mediterranea. Mucin-type O-glycans were composed of multiple isomeric, methylated, and unusually extended mono- and di-substituted O-GalNAc structures. Extensions made of hexoses and 3-O methyl hexoses were the glycoforms observed. From glycotranscriptomic analysis, sixty genes belonging to five distinct enzyme classes were identified to be involved in mucin-type O-glycan biosynthesis. These genes shared homology with those in other invertebrate systems. While a majority of the genes involved in mucin-type O-glycan biosynthesis was highly expressed during organogenesis and in differentiated cells, a few select genes in each enzyme class were specifically enriched during early embryogenesis. Our results indicate a unique temporal and spatial role for mucin-type O-glycans during embryogenesis and organogenesis and in adulthood. In summary, this is the first report on O-glycans in planaria. This study expands the structural and biosynthetic possibilities in cellular glycosylation in the invertebrate glycome and provides a framework towards understanding the biological role of mucin-type O-glycans in tissue regeneration using planarians.

}, keywords = {Flatworm, GC-MS, Invertebrates, MALDI-TOF mass spectrometry, ScRNAseq}, doi = {https://doi.org/10.1093/glycob/cwab097}, url = {https://academic.oup.com/glycob/advance-article-abstract/doi/10.1093/glycob/cwab097/6361079}, author = {Subramanian, Sabarinath Peruvemba and Lakshmanan, Vairavan and Palakodeti, Dasaradhi and Subramanian, Ramaswamy} } @article {888, title = {Gene expression is implicated in the ability of pikas to occupy Himalayan elevational gradient. [Next Gen Genomics Facility (INT)]}, journal = {PLoS One}, volume = {13}, year = {2018}, month = {2018}, pages = {e0207936}, abstract = {

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

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

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

}, issn = {1940-6029}, doi = {10.1007/7651_2018_140}, author = {Surendran, Harshini and Rathod, Reena J and Pal, Rajarshi} } @article {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 {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 {538, title = {Genome analysis of rice-blast fungus Magnaporthe oryzae field isolates from southern India.}, journal = {Genom Data}, volume = {5}, year = {2015}, month = {2015 Sep}, pages = {284-91}, abstract = {

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

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

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

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

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

}, keywords = {Gene Expression Regulation, Plant, Genome, Plant, India, Ocimum, Plant Leaves, Plants, Medicinal}, issn = {1471-2229}, doi = {10.1186/s12870-015-0562-x}, author = {Upadhyay, Atul K and Chacko, Anita R and Gandhimathi, A and Ghosh, Pritha and Harini, K and Joseph, Agnel P and Joshi, Adwait G and Karpe, Snehal D and Kaushik, Swati and Kuravadi, Nagesh and Lingu, Chandana S and Mahita, J and Malarini, Ramya and Malhotra, Sony and Malini, Manoharan and Mathew, Oommen K and Mutt, Eshita and Naika, Mahantesha and Nitish, Sathyanarayanan and Pasha, Shaik Naseer and Raghavender, Upadhyayula S and Rajamani, Anantharamanan and Shilpa, S and Shingate, Prashant N and Singh, Heikham Russiachand and Sukhwal, Anshul and Sunitha, Margaret S and Sumathi, Manojkumar and Ramaswamy, S and Gowda, Malali and Sowdhamini, Ramanathan} } @article {475, title = {Genetic transformation of structural and functional circuitry rewires the Drosophila brain. [Drosophila Facility]}, journal = {Elife}, volume = {3}, year = {2014}, month = {2014 Dec 29}, abstract = {

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

}, keywords = {Animals, Brain, Cell Lineage, Drosophila, Morphogenesis, Neurons}, issn = {2050-084X}, doi = {10.7554/eLife.04407}, author = {Sen, Sonia and Cao, Deshou and Choudhary, Ramveer and Biagini, Silvia and Wang, Jing W and Reichert, Heinrich and VijayRaghavan, K} } @article {534, title = {Glycans in regeneration.}, journal = {ACS Chem Biol}, volume = {9}, year = {2014}, month = {2014 Jan 17}, pages = {96-104}, abstract = {

Glycans participate in many key cellular processes during development and in physiology and disease. In this review, the functional role of various glycans in the regeneration of neurons and body parts in adult metazoans is discussed. Understanding glycosylation may facilitate research in the field of stem cell biology and regenerative medicine.

}, keywords = {Animals, Extremities, Glycosylation, Humans, Hydra, Nerve Regeneration, Neurons, Polysaccharides, Regeneration, Regenerative Medicine}, issn = {1554-8937}, doi = {10.1021/cb400784j}, author = {Babu, Ponnusamy} } @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 {484, title = {Genomic analysis reveals epistatic silencing of "expensive" genes in Escherichia coli K-12. [Next Generation Genomics facility]}, journal = {Mol Biosyst}, volume = {9}, year = {2013}, month = {2013 Aug}, pages = {2021-33}, abstract = {

A barrier for horizontal gene transfer is high gene expression, which is metabolically expensive. Silencing of horizontally-acquired genes in the bacterium Escherichia coli is caused by the global transcriptional repressor H-NS. The activity of H-NS is enhanced or diminished by other proteins including its homologue StpA, and Hha and YdgT. The interconnections of H-NS with these regulators and their role in silencing gene expression in E. coli are not well understood on a genomic scale. In this study, we use transcriptome sequencing to show that there is a bi-layered gene silencing system - involving the homologous H-NS and StpA - operating on horizontally-acquired genes among others. We show that H-NS-repressed genes belong to two types, termed "epistatic" and "unilateral". In the absence of H-NS, the expression of "epistatically controlled genes" is repressed by StpA, whereas that of "unilaterally controlled genes" is not. Epistatic genes show a higher tendency to be non-essential and recently acquired, when compared to unilateral genes. Epistatic genes reach much higher expression levels than unilateral genes in the absence of the silencing system. Finally, epistatic genes contain more high affinity H-NS binding motifs than unilateral genes. Therefore, both the DNA binding sites of H-NS as well as the function of StpA as a backup system might be selected for silencing highly transcribable genes.

}, keywords = {Binding Sites, DNA-Binding Proteins, Epistasis, Genetic, Escherichia coli K12, Escherichia coli Proteins, Fimbriae Proteins, Gene Expression Regulation, Bacterial, Gene Silencing, Gene Transfer, Horizontal, Genome, Bacterial, Molecular Chaperones, Protein Binding, Repressor Proteins, Sequence Analysis, DNA, Transcription, Genetic, Transcriptome}, issn = {1742-2051}, doi = {10.1039/c3mb70035f}, author = {Srinivasan, Rajalakshmi and Chandraprakash, Deepti and Krishnamurthi, Revathy and Singh, Parul and Scolari, Vittore F and Krishna, Sandeep and Seshasayee, Aswin Sai Narain} } @article {490, title = {Genome sequence of the halotolerant bacterium Imtechella halotolerans K1T. [Next Generation Genomics facility]}, journal = {J Bacteriol}, volume = {194}, year = {2012}, month = {2012 Jul}, pages = {3731}, abstract = {

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

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

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

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

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

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

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

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

}, keywords = {Animals, Blood Glucose, Diabetes Mellitus, Experimental, DNA Methylation, Epididymis, Germ Cells, Humans, Hyperglycemia, Male, Mice, Ploidies, Sperm Count, Spermatogenesis, Spermatozoa, Streptozocin, Testosterone}, issn = {1573-7330}, doi = {10.1007/s10815-012-9873-0}, author = {Bose, Rohini and Adiga, Satish K and D{\textquoteright}Souza, Fiona and Salian, Sujith R and Uppangala, Shubhashree and Kalthur, Guruprasad and Jain, Navya and Radhakrishnan, Raghu A and Bhat, Nalini and Krishnamurthy, Hanumantappa and Kumar, Pratap} }