Biology subjects

Pal, A.

Publications and source records attributed to Pal, A..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

A Bioluminescent Activity Dependent (BLADe) Platform for Converting Neuronal Activity to Photoreceptor Activation

Genetically encoded sensors and actuators have advanced the ability to observe and manipulate cellular activity, yet few non-invasive strategies enable cells to directly couple their intracellular states to user-defined outputs. We promote a bioluminescent activity-dependent (BLADe) platform that facilitates programmable feedback through genetically encoded light generation. Using calcium (Ca{superscript 2}) flux as a model, we engineered a Ca{superscript 2}-dependent luciferase that functions as an activity-gated light source capable of photoactivating light-sensing actuators. As an initial demonstration of the versatility of this platform we present two separate use cases in neurons. In the first application, the presence of luciferin triggers Ca{superscript 2} dependent local illumination that provides activity dependent gene expression by activating a light-sensitive transcription factor. In the second application, neuronal activity-driven Ca{superscript 2} fluctuations via locally generated bioluminescence control neural dynamics through opsin activation in single cells, populations and intact tissue. BLADe can be expanded to couple any signal that bioluminescent enzymes can be engineered to detect with the wide variety of photosensing actuators. This modular strategy of coupling an activity dependent light emitter to a light sensing actuator offers, in principle, a generalizable framework for state dependent cell-autonomous control across biological systems.

neuroscience↗

bioRxiv2023

Wound induced small-peptide mediated signalling cascade regulated by OsPSKR, dictates balance between growth and defense in rice

Wounding is a general stress in plants that results from various pest and pathogenic infections in addition to environment induced mechanical damages. Plants have sophisticated molecular mechanisms to recognize and respond to pests and pathogens. Although several molecules such as phytohormones, peptides and receptors have been attributed to wound responses in dicots, such mechanisms for monocots probably having distinct wound responses are less understood. Here, we show the involvement of two distinct categories of temporally separated, endogenously derived peptides, namely, plant elicitor peptides (PEPs) and phytosulfokine (PSK), that mediate wound responses in rice. These peptides trigger a dynamic signal relay in which a novel receptor kinase named OsPSKR played a major role. OsPSKR perceived PSK ligand, acting in association with a co-receptor OsSERK1, to activate downstream responses in a kinase activity-dependent manner. Perturbation of OsPSKR expression in rice led to compromised development and constitutive autoimmune phenotypes. These results suggested that OsPSKR maintains the trade-off between growth and exaggerated defense responses, both during homeostasis and wounding. Collectively, these findings indicate the presence of a stepwise peptide-mediated signal relay that regulates the transition from defense to growth upon wounding in monocots. One line summaryEndogenous peptide signalling initiated wound responses through a receptor-like kinase OsPSKR to maintain the balance between growth and defense responses.

plant biology↗

bioRxiv2023

A domain-agnostic MR reconstruction framework using a randomly weighted neural network

PurposeTo design a randomly-weighted neural network that performs domain-agnostic MR image reconstruction from undersampled k-space data without the need for ground truth or extensive in-vivo training datasets. The network performance must be similar to the current state-of-the-art algorithms that require large training datasets. MethodsWe propose a Weight Agnostic randomly weighted Network method for MRI reconstruction (termed WAN-MRI) which does not require updating the weights of the neural network but rather chooses the most appropriate connections of the network to reconstruct the data from undersampled k-space measurements. The network architecture has three components, i.e. (1) Dimensionality Reduction Layers comprising of 3d convolutions, ReLu, and batch norm; (2) Reshaping Layer is Fully Connected layer; and (3) Upsampling Layers that resembles the ConvDecoder architecture. The proposed methodology is validated on fastMRI knee and brain datasets. ResultsThe proposed method provides a significant boost in performance for structural similarity index measure (SSIM) and root mean squared error (RMSE) scores on fastMRI knee and brain datasets at an undersampling factor of R=4 and R=8 while trained on fractal and natural images, and fine-tuned with only 20 samples from the fastMRI training k-space dataset. Qualitatively, we see that classical methods such as GRAPPA and SENSE fail to capture the subtle details that are clinically relevant. We either outperform or show comparable performance with several existing deep learning techniques (that require extensive training) like GrappaNET, VariationNET, J-MoDL, and RAKI. ConclusionThe proposed algorithm (WAN-MRI) is agnostic to reconstructing images of different body organs or MRI modalities and provides excellent scores in terms of SSIM, PSNR, and RMSE metrics and generalizes better to out-of-distribution examples. The methodology does not require ground truth data and can be trained using very few undersampled multi-coil k-space training samples.

neuroscience↗

bioRxiv2023

Selection on many loci drove the origin and spread of a key innovation

Key innovations are fundamental to biological diversification, but their genetic architecture is poorly understood. A recent transition from egg-laying to live-bearing in Littorina snails provides the opportunity to study the architecture of an innovation that has evolved repeatedly in animals. Samples do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous genomic regions where all live-bearers carry the same core haplotype. Associated regions show evidence for live-bearer-specific positive selection, and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest live-bearing alleles accumulated gradually, involving selection at different times in the past. Our results suggest that innovation can have a polygenic basis, and that novel functions can evolve gradually, rather than in a single step.

evolutionary biology↗

bioRxiv2023

Effect of Lantana camara ethanolic leaf extract on survival and migration of MDA-MB-231 triple negative breast cancer cell line

IntroductionBreast cancer is a leading cause of cancer-related death worldwide. Lantana camara has been reported to cure a number of ailments, with few studies showing its cytotoxic effects on breast cancer cells. However, the impact of Lantana camara on triple negative breast cancer cells is largely obscure to date. The present study investigated the effect of ethanolic extract of Lantana camara leaves on the triple negative breast cancer cell line, MDA-MB-231. MethodsCytotoxic effect of the extract on the cells was determined by cell survival assay. Cell cycle phase distribution was analysed using flow cytometry. To study the effect on nuclear morphology, nuclear stained cells were visualized using epifluorescence microscopy. The induction of apoptosis and generation of reactive oxygen species was conducted using flow cytometry. Cellular migration was studied by performing wound healing assay. Real-time polymerase chain reaction was done to determine the mRNA levels of some key genes. ResultsLantana camara leaf extract induced cytomorphological changes and growth inhibitory effect on MDA-MB-231 cells in a dose-dependent manner. The extract also induced G0/G1 cell cycle arrest and nuclear condensation. Flow cytometry analysis confirmed cell death by apoptosis. Lantana camara leaf extract also reduced the migration of MDA-MB-231 cells. mRNA expression levels also supported the above observations. ConclusionsThis study demonstrates the efficacy of the extract to induce growth-inhibitory and anti-migratory effects on MDA-MB-231 cells. Our results thus suggest that Lantana camara leaf extract can be considered as a potent source of chemotherapeutic agents for triple negative breast cancer.

cancer biology↗

bioRxiv2023

Defining the contribution of microRNA-specific slicing Argonautes in animals

microRNAs regulate gene expression through interaction with an Argonaute protein family member. While some members of this protein family retain an enzymatic activity capable of cleaving RNA molecules complementary to Argonaute-bound small RNAs, the role of the slicing activity in the canonical microRNA pathway is still unclear in animals. To address the importance of slicing Argonautes in animals, we created Caenorhabditis elegans strains, carrying catalytically dead endogenous ALG-1 and ALG-2, the only two slicing Argonautes essential for the miRNA pathway in this animal model. We observe that the loss of ALG-1 and ALG-2 slicing activity affects overall animal fitness and causes phenotypes, reminiscent of miRNA defects, only when grown and maintained at restrictive temperature. Furthermore, the analysis of global miRNA expression shows that the catalytic activity of ALG-1 and ALG-2 differentially regulate the level of specific subsets of miRNAs in young adults. We also demonstrate that altering the slicing activity of those miRNA-specific Argonautes does not result in any defect in the production of canonical miRNAs. Together, these data support that the slicing activity of miRNA- specific Argonautes function to maintain the levels of a set of miRNAs for optimal viability and fitness in animals particularly exposed to specific growing conditions.

molecular biology↗

bioRxiv2023

SERS nanowire chip and machine learning enabled instant identification and classification of clinically relevant wild-type and antibiotic resistant bacteria at species and strain level

The world health organization considers antimicrobial resistance (AMR) to be a critical global public health problem. Conventional culture-based methods that are used to detect and identify bacterial infection are slow. Thus, there is a growing need for the development of robust, cost-effective, and fast diagnostic solutions for the identification of pathogens. Surface-enhanced Raman spectroscopy (SERS) can be used to identify target analytes with sensitivity down to the single-molecule level. Here, we developed a SERS chip by optimizing the entire fabrication pipeline of the metal-assisted chemical etching (MACE) method. The MACE approach offers a large-scale, densely packed silver (Ag) nanostructure on top of silicon nanowires (Si-NWs) with a large aspect ratio that significantly enhances the Raman signal due to localised surface plasmonic enhancement. The optimised SERS chips exhibited sensitivity down to 10-12 M concentration of R6G molecule and detected reproducible Raman spectra of bacteria down to a concentration of 100 colony forming units (CFU)/ml, which is a thousand times lower than the clinical threshold of bacterial infections like UTI (105 CFU/ml). A Siamese neural network model was used to classify SERS Raman spectra from bacteria specimens. The trained model identified 12 different bacterial species, including those which are causative agents for tuberculosis and urinary tract infection (UTI). Next, the SERS chips and another Siamese neural network model were used to differentiate antibiotic-resistant strains from susceptible strains of E. coli. The enhancement offered by SERS chip enabled acquisitions of Raman spectra of bacteria directly in the synthetic urine by spiking the sample with only 103 CFU/ml E. coli. Thus, the present study lays the ground for the identification and quantification of bacteria on SERS chips, thereby offering a potential future use for rapid, reproducible, label-free, and low limit detection of clinical pathogens.

biophysics↗

bioRxiv2023

UFMTrack: Under-Flow Migration Tracker enabling analysis of the entire multi-step immune cell extravasation cascade across the blood-brain barrier in microfluidic devices

The endothelial blood-brain barrier (BBB) strictly controls immune cell trafficking into the central nervous system (CNS). In neuroinflammatory diseases such as multiple sclerosis, this tight control is, however, disturbed, leading to immune cell infiltration into the CNS. The development of in vitro models of the BBB combined with microfluidic devices has advanced our understanding of the cellular and molecular mechanisms mediating the multi-step T-cell extravasation across the BBB. A major bottleneck of these in vitro studies is the absence of a robust and automated pipeline suitable for analyzing and quantifying the sequential interaction steps of different immune cell subsets with the BBB under physiological flow in vitro. Here we present the Under-Flow Migration Tracker (UFMTrack) framework for studying immune cell interactions with endothelial monolayers under physiological flow. We then showcase a pipeline built based on it to study the entire multi-step extravasation cascade of immune cells across brain microvascular endothelial cells under physiological flow in vitro. UFMTrack achieves 90% track reconstruction efficiency and allows for scaling due to the reduction of the analysis cost and by eliminating experimenter bias. This allowed for an in-depth analysis of all behavioral regimes involved in the multi-step immune cell extravasation cascade. The study summarizes how UFMTrack can be employed to delineate the interactions of CD4+ and CD8+ T cells with the BBB under physiological flow. We also demonstrate its applicability to the other BBB models, showcasing broader applicability of the developed framework to a range of immune cell-endothelial monolayer interaction studies. The UFMTrack framework along with the generated datasets is publicly available in the corresponding repositories. Author summaryImmune cells continuously travel through our body to perform immune surveillance. They travel within blood vessels at a very high speed and slow down upon reaching their target organ by the sequential interaction with different adhesion and signaling molecules on the vascular endothelial cells. The study of molecular mechanisms mediating this multi-step extravasation of immune cells has been significantly advanced by in vitro cultures of microvascular endothelial cell monolayers. The dynamic interaction of the immune cells with endothelial monolayers can be imaged over time in vitro in microfluidic devices under physiological flow. The 2-dimensional structure of the endothelial monolayer allows for reliable visualization of the extravasation process required for the study of the molecular mechanisms involved. The manual analysis of the acquired imaging data is time- consuming and prone to experimenter error. Analysis automation is, however, hampered by the similar appearance of the unlabeled immune and endothelial cells and by the flow causing rapid immune cell displacement. Here we introduce UFMTrack, the under-flow migration tracker framework allowing for automated analysis of immune cell interactions with microvascular endothelial cells under flow in vitro. UFMTrack performs comparably to the manual analysis of an experienced researcher, eliminates experimenters bias, and improves the accuracy of the immune cell tracking. Taken together, UFMTrack sets the stage for scalability of in vitro live cell imaging studies of immune cell extravasation.

immunology↗

bioRxiv2022

Anti-Biofilm Potential of Nanonized Eugenol against Pseudomonas aeruginosa

This study dealt with nanonization of eugenol, a major phytochemical present in basil leaf, which has pharmacological potential as an anti-bacterial agent. Eugenol nanoparticle (ENP) was synthesized by simple ultrasonic cavitation method through emulsification of hydrophobic eugenol into hydrophilic gelatin. Thus, the nanonization process made the water-insoluble eugenol to water-soluble nano-eugenol, making the nano-form bioavailable. The average size of the ENPs was 20-30 nm. Entrapment efficiency of eugenol within gelatin cap was about 80% of the eugenol, that was used as precursor in the nanonization reaction. In vitro release of eugenol from gelatin cap was slow and sustained over a period of five days. The ENP had higher anti-biofilm potency than eugenol for both formation and eradication of biofilm, formed by clinically relevant pathogen Pseudomonas aeruginosa. Minimal biofilm inhibitory concentration and minimal biofilm eradication concentration of ENPs were 2.0 and 4.0 mM respectively. In addition, the measurement of P. aeruginosa biofilm biomass, biofilm pellicle formation, biofilm thickness, amount of biofilm-forming extra-polymeric substance, cell surface hydrophobicity, cell swarming and twitching efficiencies, cellular morphology and biofilm formation in catheter demonstrated that the anti-biofilm efficacy of nano-eugenol was 30-40% higher than that of bulk eugenol. Thus, ENP can be used as a potential drug against pneumonia, a chronic infection in lung caused by P. aeruginosa, which is difficult to treat with antibiotics, due to natural intrinsic resistance of biofilm-formed cells to most antibiotics. The overall actions of ENP have been presented in the figure 1. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/521144v1_fig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@12445e2org.highwire.dtl.DTLVardef@6813aforg.highwire.dtl.DTLVardef@e4779borg.highwire.dtl.DTLVardef@1688a9a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Graphical abstract showing overall anti-biofilm action of ENP that is capable to inhibit each and every step of biofilm formation. ENP also carries the potential to destroy EPS and kill the biofilm residing cells by membrane disruption. Bacterial colonization has been found to be prevented significantly on ENP-coated catheter. C_FIG HighlightsO_LINano-formulation of eugenol, an important phytochemical, by ultrasonic cavitation method, which was simple, time-saving, low-cost and eco-friendly. C_LIO_LINanonization made water-insoluble eugenol into water-soluble form with enhanced therapeutic efficacy. C_LIO_LIThe eugenol nanoparticle (ENP) could inhibit formation of biofilm as well as facilitate eradication of pre-formed biofilm of P. aeruginosa. C_LIO_LIBiofilm formation was found to be prevented significantly on ENP-coated catheter. C_LIO_LINano-eugenol may be used as a potential drug against bacterial diseases, caused by pseudomonal biofilm, which are difficult to treat by antibiotics. C_LIO_LINano-formulated eugenol may also be used as an effective anti-fouling agent for biomedical devices like contact lens, pace-maker, materials for organ transplantation etc. to prevent bacterial colonization. C_LI

microbiology↗

bioRxiv2022

e-cone and d-cone singularities drive submucosal collagen fiber remodeling in intestinal anastomotic surgery

Following resection of a diseased segment of intestine, a reconnection (anastomotic) geometry is chosen to reduce postoperative stress and optimize outcomes. As proper healing of an intestinal anastomosis is strongly affected by its mechanobiology, much attention has been devoted to the conical structures formed along the suture lines, where stress-focusing is expected. However, geometric considerations reveal that in addition to the obvious loci of stress-focusing, additional remote locations of stress-focusing may form. We identify conical structures that inevitably form within regions of otherwise uninterrupted tissue. In this work we use geometric analysis, finite element modeling (FEM), and in-vivo experiments to investigate these emergent stress-focusing structures, their mechanical stresses, and the resulting submucosal collagen fiber re-orientation, as these naturally arise in the side-to-side small bowel anastomosis (SBA), the most common configuration performed in patients. FEM predicts the appearance of remote high-stress regions. Allowing for tissue remodeling, our simulations also predict an increased dispersion of submucosal collagen fibers in these regions. In-vivo experiments performed on ten-week-old male C57BL/6 mice assigned the creation of side-to-side SBA or sham-laparotomy corroborate this result. Anastomoses were analyzed at sacrifice on post-operative day (POD) 14 and 88 with histologic-sectioning, staining, high magnification imaging, and submucosal collagen fiber orientation ({kappa}) mapping. The mean and variance of{kappa} , a measure of collagen fiber dispersion, at POD-14 far from the anastomosis show similar values to those obtained for sham-operated mice, while the FEM-predicted loci of stress-focusing display statistically significant higher values. The values at POD-88 at all loci show no statistically-significant difference, and agree with those of the sham-operated mice at POD-14.

bioengineering↗

bioRxiv2022

Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype

Macaques provide the most widely used nonhuman primate models for studying immunology and pathogenesis of human diseases. While the macaque major histocompatibility complex (MHC) region shares most features with the human leukocyte antigen (HLA) region, macaques have an expanded repertoire of MHC class I genes. Although a chimera of two rhesus macaque MHC haplotypes was first published in 2004, the structural diversity of MHC genomic organization in macaques remains poorly understood due to a lack of adequate genomic reference sequences. We used ultra-long Oxford Nanopore and high-accuracy PacBio HiFi sequences to fully assemble the [~]5.2 Mb M3 haplotype of an MHC-homozygous, Mauritian-origin cynomolgus macaque (Macaca fascicularis). The MHC homozygosity allowed us to assemble a single MHC haplotype unambiguously and avoid chimeric assemblies that hampered previous efforts to characterize this exceptionally complex genomic region in macaques. The high quality of this new assembly is exemplified by the identification of an extended cluster of six Mafa-AG genes that contains a recent duplication with a remarkably similar [~]48.5 kb block of sequence. The MHC class II region of this M3 haplotype is similar to the previously sequenced rhesus macaque haplotype and HLA class II haplotypes. The MHC class I region, in contrast, contains 13 MHC-B genes, four MHC-A genes, and three MHC-E genes (versus 19 MHC-B, two MHC-A, and one MHC-E in the previously sequenced haplotype). These results provide an unambiguously assembled single contiguous cynomolgus macaque MHC haplotype with fully curated gene annotations that will inform infectious disease and transplantation research.

genomics↗

bioRxiv2022

C-4-Modified Isotetrones Prevent Biofilm Growth and Persister Cell Resuscitation in Mycobacterium smegmatis

Hyperphosphorylated guanosine nucleotide (p)ppGpp, synthesized by Rel proteins, regulates the stringent response pathway responsible for biofilm growth and persister cell formation in the stationary phase of mycobacteria. The discovery of vitamin C as a potent inhibitor of Rel protein activities raises the prospect of such a tetrone lactone to prevent biofilm growth and persister cell formation. The closely related isotetrone lactone derivatives are identified in the present study as potent inhibitors of the above processes in a mycobacterium. Isotetrone lactone derivatives are synthesized from appropriate -ketocarboxylic acids, derived from the a-amino acids. Aldol condensation with formaldehyde, followed by the lactone formation, completes synthesis of isotetrone derivatives, possessing varied substituents at C-4 carbon, in good yields. A series of biochemical evaluations of biofilm growth and persister cell formation in M. smegmatis is conducted. Among the derivatives, isotetrone possessing phenyl substituent at C-4 carbon completely inhibit the biofilm formation at 400 g mL-1 concentration, 84 h of post-exposure, followed by a moderate inhibition by the isotetrone possessing p-hydroxyphenyl substituent. Whereas, the latter isotetrone inhibits the growth of cells at 400 g mL-1 f.c. when monitored for 2 weeks, under PBS starvation condition. Isotetrones also potentiate the inhibition of antibiotic tolerant regrowth of cells by ciprofloxacin antibiotic (0.75 g mL-1) and thus act as bio-enhancers. The combination is shown to significantly arrest the emergence of ciprofloxacin-resistant genetic mutants. The observations suggest that isotetrones in combination with ciprofloxacin are therapeutically superior when administered together. Systematic molecular dynamics studies show that isotetrone derivative binds to Rel protein more efficiently than vitamin C and the binding is aided by hydrogen bonding, van der Waals and electrostatic interactions at a binding site possessing serine, threonine, lysine and arginine residues. The present study establishes that the identified isotetrone derivatives (i) act as inhibitors of M. smegmatis biofilm growth and (ii) arrest the re-emergence of recalcitrant persister cells when administered together with ciprofloxacin antibiotic. Results of this study establish that isotetrones as new chemical entities that interfere with stringent response pathways in a mycobacterium under stress and permit overcoming the multidrug-resistant persister cell emergence in the bacterium.

microbiology↗

bioRxiv2022

Cinemeducation improves early clinical exposure to Inborn Errors of Metabolism

BackgroundCinemeducation has been shown to be an effective tool to help the students develop humanistic skills. However, there is a dearth of studies to find out if this can also be utilized to improve the interest and satisfaction of students learning about rare diseases such as the Inborn Errors of Metabolism. The aim was to introduce cinemeducation as part of early clinical exposure in teaching the inborn errors of metabolism for first-year MBBS students in the Department of Biochemistry. The Objectives were 1) to develop, validate and assess the feasibility of structured modules on Cinemeducation in teaching the Inborn Errors of Metabolism, 2) to study the impact of Cinemeducation on the satisfaction, interest, and academic performance of first-year MBBS students and 3) to study the perception of students and faculty towards Cinemeducation MethodsThis was a quasi-experimental, cross-over study involving 100 MBBS students in the Department of Biochemistry, AIIMS Kalyani. Movie clips prepared from Lorenzos Oil (for Lipid metabolism) and Extraordinary Measures (for Lysosomal Storage Disease) and corresponding paper-based cases; questionnaires and feedback forms were validated by expert group review. Analysis of quantitative data was performed in GraphPad, MS Excel and MAXQDA2022 software. Findings, Discussions and ConclusionsStudents academic performance was found to be improved in the groups where the Extraordinary Measures movie was used for Cinemeducation. Both learners and facilitators were satisfied with Cinemeducation. Cinemeducation was effectively introduced for teaching Inborn Errors of Metabolism in the Department of Biochemistry.

scientific communication and education↗

bioRxiv2022

Phylophenomic and Phylogenomic analysis for Ovis aries reveals distinct identity of newly reported breed

Domestication and phylogenetics for Ovis aries is an important species to study, since there exists enormous biodiversity in terms of habitat and utility of sheep. The present study aimed at identification of the biodiversity existing within sheep breeds reared in different agroclimatic zones of the state West Bengal (Garole, Birbhum, Bonpala and Chotanagpuri) through phylogenetic analysis of phenotypic traits as growth and biomorphometric traits through principal component analysis, factor analysis, genetic correlation, multivariate cluster analysis through Hierarchial classification and k-means cluster analysis. Confirmation of the phylophenomic studies were later on carried out with phylogenomic analysis with microsatellite markers for sheep. Birbhum sheep from dry arid region of West Bengal is reported as the newly reported breed of sheep with distinct genetic identity.

genetics↗

bioRxiv2022

Molecular phylogenetic analysis for Ovis aries with whole mitochondrial genome sequencing

Domestication of Ovis aries has taken place time immorial across the different geographical regions across the globe. Biodiversity among the sheep population has been interesting to study by a group of researchers based on mitochondrial genes like Cytochrome B, D loop. The current study is a novel attempt to understand the molecular phylogenomics among Ovis aries through all the 37 genes of mitochondria. We have analyzed complete mitochondrial genome sequencing for sheep breeds for West Bengal as Garole, Chotanagpuri, Bonpala and Birbhum sheep. Phylogenetic analysis reveals genetic similarity between Garole and Chotanagpuri brred of sheep, where as Birbhum and Bonpala were found to be genetically distinct. Phylogenomics in a global prospect reveal three lineages, Lineage A comprise of sheep from West Bengal grouped with Tibetan sheep. Lineage B consists of sheep population across the other parts including Europe (France, Denmark), Africa and Syro-Arabian desert, whereas Lineage C emerged as smaller outgroup.

genomics↗

bioRxiv2022

Molecular evolution and characterization of domestic duck (Anas platyrynchos) and Goose (Anser indicus) with reference to its wild relatives through whole mitochondrial genome sequencing

It is important to study the evolution and domestication of the domesticated duck (Anas platyrynchos) population from the wide range of wild relatives of Anas spp. Whole mitochondrial genome sequencing was attempted for Anas platyrynchos (Bengal duck) and Anser indicus (goose) from same geographical region. The study deals with the Molecular evolution of domestic duck based on mitochondrial gene due to its sequence variability, and to find out the phylogenetic relationships among Anas platyrynchos and its wild relatives. In this study we have used 45 wild species of Anas spp to study the mitochondrial genes and phylogenomics. Our result signifies that duck species were effectively discriminated with respect to mitochondrial genes, which could then be used for an appropriate genetic conservation program for the wild duck and domestic duck breeds. The DNA sequences from any unknown sample of the mitochondrial gene may be determined and can compare with those on a DNA database and can do blast for phylogenetic analysis of unknown wild duck, which gives its future scope. In silico analysis for 3D structure for Anas platyrynchos with the closest relative as Anas poecilorhyncha (Indian spot-billed duck) was attempted. Anas platyrynchos was also compared with Anser indicus. Therefore, this experiment was conducted to investigate the genetic diversity of West Bengal wild ducks with reference to its wild relatives based on mitochondrial gene.

genomics↗

bioRxiv2022

Whole mitochondrial genome sequencing- a novel approach for studying Phylogenomics for Anas platyrynchos

The evolution of duck and its distribution across the globe has been an interesting aspect. Domestication of duck and its evolution was also important to analyze if domesticated duck has migrated to other region of the globe or separate domestication process has occurred in particular region of the world. Mitochondrial genes as D-loop or cytochrome B had been used for studying evolution or molecular phylogeny. In current study, we aim to study phylogenomics for Anas platyrynchos across the globe. Whole mitochondrial genome sequencing for Bengal duck (indigenous duck from West Bengal, India) was performed on illumina platform and gene sequences were analyzed for all 37 mitochondrial genes. Variabilities were observed at nucleotide sequence, but absent in amino acid sequence and corresponding 3D structure of polypeptides coded by mitochondrial genes. We observed Anas platyrynchos from Eurasia (europe and Asia) were clustered together indicating common origin. Extensive variabilities were observed among the chinese duck population. The duck population from US was outgrouped. These ducks might have migrated from China and later bred with wild ducks to evolve as new breed or strain in US.

genomics↗

bioRxiv2022

Genomics for reproduction in Anas platyrynchos-a novel report

Anas platyrynchos (ducks) are reared mostly for egg, which are very nutritious, that fetch better prices, however duck meat possess rich nutrient content. They possess the unique characteristics of disease resistance to the common avian diseases, even asymptomatic to avian influenza, with a scopeto evolve as one of the best poultry species The major limitation encountered is the lowered average egg production as well as higher age at first egg (an indicator for sexual maturity) for the indigenous ducks compared to that of exotic ones. In this current study, we attempt to explore the genes responsible for duck reproduction in terms of sexual maturity,egg production and fertility of the ducks. We had compared the genomic constitution for the Bengal duck with highest egg production with that of non-layer (infertile or sexually immature) ducks. We characterized the genes in indigenous ducks from ovarian tissues, identified important domains for characterized genes for the first time, and studied differential mRNA expression profiling for these genes with respect to layer and non-layer groups. Upregulation was observed for ESR2, DIAPH2, KMT2E, ASCF2 genes for Bengal duck in highest egg producing duck in comparison to non-layer duck, whereas downregulation was observed for KSR1, A2M, BMPR1B, ACVR1. In the next step, we explored the association with the genes which were actually responsible for egg production. Thus, duck may be utilized as a model for studying the molecular aspect of reproduction. Genes upregulated may be utilized for knock in of gene, whereas down regulated genes may be knocked out or knocked down through gene editing technologies for the improvement of reproductive performance of the duck in future. Molecular biomarkers may be developed with these genes for early selection of better reproducing ducks at day of hatch or even earlier.

genomics↗