Biology subjects

Mukherjee, K.

Publications and source records attributed to Mukherjee, K..

34 records · Page 2Linked to original sources

bioRxiv2023

ONeSAMP 3.0: Effective Population Size via SNP Data for One Population Sample

O_LIThe genetic effective size (Ne) is arguably one of the most important characteristics of a population as it impacts the rate of loss of genetic diversity. Genetic estimators of (Ne) increasingly popular tools in population and conservation genetic studies. Yet there are very few methods that can estimate the Ne from data from a single population and without extensive information about the genetics of the population, such as a linkage map, or a reference genome of the species of interest. C_LIO_LIWe present ONeSAMP 3.0, an algorithm for estimating Ne from single nucleotide polymorphism (SNP) data collected from a single population sample using Approximate Bayesian Computation and local linear regression. C_LIO_LIWe demonstrate the utility of this approach using simulated Wright-Fisher populations, and empirical data from five endangered Channel Island fox (Urocyon littoralis) populations to evaluate the performance of ONeSAMP 3.0 compared to a commonly used Ne estimator. Our results show that ONeSAMP 3.0 is robust to the number of individual samples and number of loci included in and appears accurate even if the range of true Ne values is large. C_LIO_LIThis method is broadly applicable to natural populations and is flexible enough that future versions could easily include summary statistics appropriate for a suite of biological and sampling conditions. ONeSAMP 3.0 is publicly available under the GNU license at https://github.com/AaronHong1024/ONeSAMP_3 and also available with Bioconda (https://bioconda.github.io/index.html). C_LI

bioinformatics↗

bioRxiv2023

RNA Binding of Syntaxin 5 Synergises Membrane Fusion to Accelerate miRNA Export and Clear Pathogens

Intercellular miRNA exchange acts as a key mechanism to control gene expression post-transcriptionally in mammalian cells. Regulated export of repressive miRNAs allows the expression of inflammatory cytokines in activated macrophages. Intracellular trafficking of miRNAs from endoplasmic reticulum to endosomes is a rate determining step in miRNA export process and plays an important role in controlling cellular miRNA level and inflammatory processes in macrophages. We have identified the SNARE protein Syntaxin5 to show a synchronized expression pattern with miRNA activity loss in activated mammalian macrophage cells. Syntaxin 5 is both necessary and sufficient for macrophage activation and clearance of the intracellular pathogen Leishmania donovani from infected macrophages. Exploring the mechanism of how Syntaxin5 acts as an immunostimulant, we have identified the de novo RNA binding property of this SNARE protein that binds specific miRNAs and facilitates their accumulation in endosomes in a cooperative manner with human ELAV protein HuR to ensure export of miRNAs and allows the expression of miRNA-repressed cytokines. Conversely, in its dual role in miRNA export, this SNARE protein prevents lysosomal targeting of endosomes by enhancing the fusion of miRNA-loaded endosomes with plasma membrane to ensure accelerated release of extracellular vesicles and associated miRNAs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/556844v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@bfabf8org.highwire.dtl.DTLVardef@1b35346org.highwire.dtl.DTLVardef@203a5corg.highwire.dtl.DTLVardef@1d7a15e_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIHuR transfers miRNAs to STX5 for export C_LIO_LISTX5 utilizes its N-terminal disordered domain to bind and target miRNAs to endosomes. C_LIO_LIIn its dual role, STX5 uses the SNARE domain to export miRNA by promoting EV biogenesis and release. C_LIO_LISTX5-mediated miRNA export activates macrophage to clear internalized parasites. C_LI

immunology↗

bioRxiv2023

Biomechanical comparison of plate materials and designs for subcondylar fracture fixation: An in silico assessment

Mandibular subcondylar fractures present challenges in fixation due to high complication rates and the uncertainty in selecting optimal plate design and material. Previous computational studies have primarily relied on simplified models, point loading, and plate-only analyses. This study examines the combined influence of fixation plate design and material properties on fracture stability, with interfragmentary displacement as a key indicator of post-surgical stability. A finite element approach implemented in ANSYS Mechanical APDL v2022 R2, incorporating soft tissues such as the periodontal ligament, was employed to assess fixation stability using five materials - Nitinol, Magnesium alloys, Titanium alloys (Ti-6Al-4V and Ti-29Nb-13Ta-4.6Zr), and Stainless Steel 316L - across four plate designs under ipsilateral and contralateral molar clenching simulated using physiologically-mimetic muscle forces. Results showed a reduction in mandibular strain (up to 4% from around 1635 {micro}{varepsilon} to 1569 {micro}{varepsilon}) with increase in the plate stiffness during ipsilateral clenching, while for contralateral clenching, this trend (up to 5.4% from around 1482 {micro}{varepsilon} to 1402 {micro}{varepsilon}) was observed only for double mini and lambda plates due to enhanced resistance to bending moments from additional screw placement. Among designs, the double mini plate demonstrated the greatest reduction in the interfragmentary gap (by 77% during ipsilateral clenching; by 58% during contralateral clenching) and emerged as the most stable option across materials. Regarding materials, Titanium alloys (TNTZ and Ti-6Al-4V) were mechanically preferable, demonstrating higher safety margins based on factory of safety (FoS) ratios (TNTZ: FoS 5.57 ipsilateral, 3.21 contralateral; Ti-6Al-4V: FoS 5.05 ipsilateral, 2.98 contralateral), indicating reduced risk of yielding under functional loading. These findings underscore the critical interplay between screw configuration, material selection, and loading conditions, offering valuable guidance for implant design optimization.

bioengineering↗

bioRxiv2023

HuR-miRNA complex Activates RAS GTPase RalA to Facilitate Endosome Targeting and Extracellular Export of miRNAs

Extracellular vesicles-mediated exchange of miRNA cargos between diverse types of mammalian cells is a major mechanism of controlling cellular miRNA levels and activity and thus to regulate expression of miRNA-target genes in both donor and recipient cells. Despite tremendous excitement related to extracellular vesicles-associated miRNAs as biomarkers or having therapeutic potential, the mechanism of selective packaging of miRNAs into endosomes and multivesicular bodies for subsequent extracellular export is a poorly studied area due to lack of assay system to study such processes in vitro. We have developed an in vitro assay with endosomes isolated from mammalian macrophage cells to follow miRNA packaging into endocytic organelles. The synthetic miRNAs, used in the assay, get imported inside the isolated endosomes during the in vitro reaction and become protected from RNase in a time and concentration dependent manner. The selective miRNA accumulation inside endosomes requires both ATP and GTP hydrolysis and the miRNA binding protein HuR. The HuR-miRNA complex binds and stimulates the endosomal RalA GTPase to facilitate the import of miRNAs into endosomes and their subsequent export as part of the extracellular vesicles. The endosomal targeting of miRNAs is also very much dependent on endosome maturation process that is controlled by Rab5 protein and ATP. Graphical Abstract{whitebullet} miRNAs get imported to endosomes in vitro and are become protected to RNase {whitebullet}Endosomal miRNA import is sequence specific and requires miRNA exporter protein HuR {whitebullet}HuR-miRNA complex activates RalA GTPases to complete miRNA import. {whitebullet}Rab5 protein and ATP hydrolysis is required for endosome maturation and miRNA import O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/546187v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@217e52org.highwire.dtl.DTLVardef@ec6190org.highwire.dtl.DTLVardef@f972f5org.highwire.dtl.DTLVardef@ea67a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2022

Transposon-derived transcription factors across metazoans

Transposable elements (TE) could serve as sources of new transcription factors (TFs) in plants and some other model species, but such evidence is lacking for most animal lineages. Here, we discovered multiple independent co-options of TEs to generate 788 TFs across Metazoa, including all early-branching animal lineages. Six out of ten super-families of known TEs (ZBED, CENPB, FHY3, HTH-Psq, THAP, and FLYWCH) were recruited as representatives of nine phyla. The most extensive convergent domestication of TE-derived TFs occurred in the hydroid polyps, polychaete worms, cephalopods, oysters, and sea slugs. Phylogenetic reconstructions showed species-specific clustering and lineage-specific expansion; none of the identified TE-derived TFs revealed homologs in their closest neighbors. Together, our study established a framework for categorizing TE-derived TFs and informing the origins of novel genes across phyla.

evolutionary biology↗

bioRxiv2022

Biomechanical influence of plate configurations on mandible subcondylar fracture fixation: a finite element study

Mandible subcondylar fractures have very high complication rate, yet there is no consensus in a suitable plate design for optimal patient outcomes. The present study is aimed at understanding the subcondylar fracture fixation by comparing load transfer in intact and reconstructed fractured mandibles with five different plates: single mini, trapezoid, lambda, strut, and double-mini plates under the complete mastication cycle. Under contralateral molar occlusion (LMOL), the single mini plate resulted in the highest strains. On the contrary, during ipsilateral molar clenching (RMOL), the tensile and compressive strain distributions were found to be reversed, with the tensile strains at the posterior border resulting in lesser strain in reconstructed mandible with single mini plate. Owing to the reduced strains in the reconstructed mandibles, the contralateral molar clenching task is preferred during the immediate post-surgery period for patients. Under this contralateral molar clenching, the peak von Mises stresses in the plate decreased with increase in the number of screws. Furthermore, the presence of two arms seems beneficial to neutralise the tensile and compressive strains across load cases. Consequently, double mini and trapezoid plates were found to perform better as compared to single mini plate during the entire mastication cycle for subcondylar fracture fixation.

bioengineering↗

bioRxiv2022

Truncated suPAR simultaneously causes kidney disease and autoimmune diabetes mellitus

Soluble urokinase-type plasminogen activator receptor (suPAR) is a risk factor for kidney diseases. Here we report the presence of C-terminal suPAR fragment, D2D3, in patients with diabetic nephropathy. D2D3-positive human sera inhibited glucose-stimulated insulin release in human islets and were associated with patients requiring insulin therapy. D2D3 transgenic mice presented kidney disease and diabetes marked by decreased levels of insulin and C-peptide, impaired glucose-stimulated insulin secretion, decreased pancreatic {beta}-cell mass, and high fasting glucose. D2D3 fragment dysregulated glucose-induced cytoskeletal dynamics, impaired maturation and trafficking of insulin granules, and inhibited bioenergetics of {beta}-cells in culture. An anti-uPAR antibody restored {beta}-cell function in D2D3 transgenic mice. We show that the D2D3 fragment injures the kidney and pancreas, offering a unique dual therapeutic approach for kidney diseases and insulin-dependent diabetes. SummaryProteolytic suPAR fragment, D2D3, simultaneously injures two organs, the kidney and pancreas, thus causing a dual organ disease.

physiology↗

bioRxiv2021

Leishmania Hijacks microRNA Import-Export Machinery of Infected Macrophage and Survives by Cross-Communicating Host miR-146a to Subjugate HuR and miR-122 in Neighbouring cells

Leishmania donovani, the causative agent of visceral leishmaniasis, infects and resides within tissue macrophage cells of the mammalian host. It is not clear how the parasite infected cells cross-talk with the non-infected cells in the infection niche to regulate the infection process. Interestingly, miRNAs, the regulatory small RNAs of the host, could get trafficked into and out of infected cells as part of extracellular vesicles to ensure exchange of the epigenetic signals and can regulate the expression of their target genes in both donor and recipient cells. Leishmania, for its survival in host macrophage, adopts a dual strategy to regulate the intercellular transport of host miRNAs. The parasite, by preventing mitochondrial function of the host cells, restricts the entry of liver cell derived miR-122 containing extracellular vesicles in infected macrophage to curtail the inflammatory response by miR-122. The parasite reciprocally upregulates the extracellular export of anti-inflammatory miR-146a from the infected cells. The exported miR-146a restricts miR-122 production in liver cells and polarizes neighbouring naive macrophages to the M2 state. miR-146a upregulates IL-10 in neighbouring macrophages where miR-146a dominates the RNA binding and miRNA suppressor protein HuR to inhibit the expression of proinflammatory cytokine mRNAs having HuR-interacting AU-rich elements and polarized the recipient cells to M2 stage. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/459146v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@32e32dorg.highwire.dtl.DTLVardef@e0d3c6org.highwire.dtl.DTLVardef@6f77e6org.highwire.dtl.DTLVardef@289e49_HPS_FORMAT_FIGEXP M_FIG C_FIG Key FindingsO_LILeishmania stops vesicular entry of inflammatory miR-122 in infected cells by causing mitochondrial depolarization C_LIO_LILeishmania secrets miR-146a from infected cells to stop miR-122 production in neighbouring hepatocytes C_LIO_LImiR-146a containing vesicles secreted by infected cells stops inflammatory response in recipient naive macrophage C_LIO_LImiR-146 targets RNA binding protein HuR to stop inflammatory cytokine production C_LI

immunology↗

bioRxiv2021

Finding Overlapping Rmaps via Gaussian Mixture Model Clustering

Optical mapping is a method for creating high resolution restriction maps of an entire genome. Optical mapping has been largely automated, and first produces single molecule restriction maps, called Rmaps, which are assembled to generate genome wide optical maps. Since the location and orientation of each Rmap is unknown, the first problem in the analysis of this data is finding related Rmaps, i.e., pairs of Rmaps that share the same orientation and have significant overlap in their genomic location. Although heuristics for identifying related Rmaps exist, they all require quantization of the data which leads to a loss in the precision. In this paper, we propose a Gaussian mixture modelling clustering based method, which we refer to as OMO_SCPLOWCLUSTC_SCPLOW, that finds overlapping Rmaps without quantization. Using both simulated and real datasets, we show that OMO_SCPLOWCLUSTC_SCPLOW substantially improves the precision (from 48.3% to 73.3%) over the state-of-the art methods while also reducing CPU time and memory consumption. Further, we integrated OMO_SCPLOWCLUSTC_SCPLOW into the error correction methods (Elmeri and O_SCPLOWCC_SCPLOWOMO_SCPLOWETC_SCPLOW) to demonstrate the increase in the performance of these methods. When OMO_SCPLOWCLUSTC_SCPLOW was combined with O_SCPLOWCC_SCPLOWOMO_SCPLOWETC_SCPLOW to error correct Rmap data generated from human DNA, it was able to error correct close to 3x more Rmaps, and reduced the CPU time by more than 35x. Our software is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/OMclust

bioinformatics↗

bioRxiv2021

Complete loss of CASK causes severe ataxia through cerebellar degeneration in human and mouse

Heterozygous loss of X-linked genes like CASK and MeCP2 (Rett syndrome) causes neurodevelopmental disorders (NDD) in girls, while in boys such loss leads to profound encephalopathy. The cellular basis for these disorders remains unknown. CASK is presumed to work through the Tbr1-reelin pathway in neuronal migration during brain development. Here we report our clinical and histopathological analysis of a deceased 2-month-old boy with a CASK-null mutation. We demonstrate that although smaller in size, the CASK-null human brain exhibits normal lamination without defective neuronal differentiation, migration, or axonal guidance, excluding the role of reelin in CASK-linked pathology. The disproportionately hypoplastic cerebellum in humans without CASK expression is associated with cerebellar astrogliosis, a marker for neuronal loss. Cerebellum-specific deletion in mouse confirms a post-developmental degeneration of cerebellar granular neurons that results in a small cerebellum. Mechanistically, cerebellar hypoplasia in CASK mutation thus results from neurodegeneration rather that developmental defects. Zygosity-pathology correlation suggests that NDDs like CASK mutation and Rett syndrome are pathologically neurodegenerative; however, random X-chromosome inactivation in the typical heterozygous mutant girls results in 50% of cells expressing the functional gene, resulting in a non-progressive pathology, whereas complete loss of the only allele in boys leads to unconstrained degeneration and encephalopathy. One sentence summary of studyCASK loss causes cerebellar degeneration. The authors have declared that no conflict of interest exists.

neuroscience↗

bioRxiv2020

EKLF/KLF1 expression defines a unique macrophage subset during mouse erythropoiesis

Erythroblastic islands are a specialized niche that contain a central macrophage surrounded by erythroid cells at various stages of maturation. However, identifying the precise genetic and transcriptional control mechanisms in the island macrophage remains difficult due to macrophage heterogeneity. Using unbiased global sequencing and directed genetic approaches focused on early mammalian development, we find that fetal liver macrophage exhibit a unique expression signature that differentiates them from erythroid and adult macrophage cells. The importance of EKLF/KLF1 in this identity is shown by expression analyses in EKLF-/- and in EKLF-marked macrophage cells. Single cell sequence analysis simplifies heterogeneity and identifies clusters of genes important for EKLF-dependent macrophage function and novel cell surface biomarkers. Remarkably, this singular set of macrophage island cells appears transiently during embryogenesis. Together these studies provide a detailed perspective on the importance of EKLF in establishment of the dynamic gene expression network within erythroblastic islands in the developing embryo and provide the means for their efficient isolation.

developmental biology↗

bioRxiv2020

Lipid Droplets Promote Phase Separation of Ago2 to Accelerate Dicer1 Loss and Decelerate miRNA Activity in Lipid Exposed Hepatic Cells

miR-122 is a liver specific miRNA that plays an important role in controlling metabolic homeostasis in mammalian liver cells. Interestingly, miR-122 on exposure to lipotoxic stress is reduced in liver cells. To fight stress, miRNA processor Dicer1 is depleted to cause reduced miR-122 production and the lowering of miRNA level ensures a better stress response in hepatocytes under lipotoxic stress. Interestingly, lipid droplets, formed in the liver cells on exposure to high fat, ensure cytoplasmic phase separation of Ago2 and prevent interaction of Ago2 with Dicer1. Lipid droplets bind miRNA and enhance miRNA-Ago2 uncoupling and Ago2 phase separation. Loss of interaction between Ago2 and Dicer1 eventually facilitates export and lowering of cellular Dicer1, a process also dependent on the endosomal maturation controller protein Alix, thereby ceasing pre-miRNA processing by Dicer1 in lipid exposed cells. Depletion of lipid droplets by downregulation of Perilipins with siRNAs resulted in a rescue of cellular Dicer1 level and Ago2-Dicer1 interaction. This is a novel mechanism that liver cells adopt to restrict cellular miRNA levels under stress condition. Thus, lipid droplets prevent cell death upon exposure to high fat by reducing intra and extracellular pool of miR-122 in hepatic tissue.

cell biology↗

bioRxiv2020

Robust expression of LINE-1 retrotransposon encoded proteins in oral squamous cell carcinoma

Retrotransposons are sequences which transpose within genomes using RNA as an intermediate. Long INterpersed Element-1 (LINE1 or L1) is the only active retrotransposon occupying around 17% of the human genome with an estimated 500,000 copies. An active L1 encodes two proteins (L1ORF1p and L1ORF2p); both of which are critical in the process of retrotransposition. In-order to propagate to the nextgeneration, L1s remain active in germ tissues and at an early stage of development. Surprisingly, by some unknown mechanism, L1 also shows activity in certain parts of the normal brain and many cancers. L1 activity is generally determined by assaying L1ORF1p because of its high expression and availability of the antibody. However, due to its lowerexpression and the unavailability of a robust antibody, detection of L1ORF2p has been limited. L1ORF2p is the crucial protein in the process of retrotransposition as it provides endonuclease and reverse transcriptase (RT) activity. Here, we report a novel human L1ORF2p antibody generated using an 80-amino-acid stretch from the RT domain, which is highly conserved among different species. The antibody detects significant L1ORF2p expression in murine germ tissues and human oral squamous cell carcinoma (OSCC) samples. This particular cancer is prevalent in India due to excessive use of tobacco. Here, using our in-house antibodies against L1 proteins, we show that more than fifty percent of samples are positive for L1 proteins. Overall, we reported a novel L1ORF2p antibody that detects L1 activity in germ tissues and OSCC

cancer biology↗

bioRxiv2020

GW182 Proteins Restrict Extracellular Vesicle Mediated Selective Export of Used miRNAs In Mammalian Cancer Cells

MicroRNAs are small regulatory RNAs of relatively long half-life in non-proliferative human cells. However, in cancer cells the half-lives of miRNAs are comparatively short. To understand the mechanism of rapid miRNA turn over in cancer cells, we explored the effect of "usage" of specific miRNAs for translation repression of their targets on the abundance of that miRNA. We have noted an accelerated extracellular vesicle mediated export of "used" miRNAs in mammalian cells and the miRNA-export process get retarded by Ago2 interacting protein GW182B. The GW182 group of proteins are localized to GW182 Bodies or RNA Processing Bodies in mammalian cells and GW182B dependent retardation of miRNA export depends on GW-body integrity and is independent of HuR mediated auxiliary pathway of miRNA export. Our data thus support existence of a HuR independent pathway of miRNA export in human cells that can be targeted to increase cellular miRNA levels in cancer cells to induce senescence. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/294488v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1d6e30dorg.highwire.dtl.DTLVardef@d4ab06org.highwire.dtl.DTLVardef@282ad4org.highwire.dtl.DTLVardef@113ef76_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LIUsage of miRNA is proportional with its export and turnover C_LIO_LIGW182 proteins cause phase separation of Ago2 to P-bodies and restrict miRNA export via extracellular vesicles (EVs) C_LIO_LIHuR driven auxiliary path of miRNA export is independent of GW182 controlled main path of miRNA exclusion C_LI

molecular biology↗

bioRxiv2020

A Highly Sensitive Fluorogenic Assay for the Detection of Nephrotoxin-Induced Oxidative Stress in Live Cells and Renal Tissue

A common manifestation of drug toxicity is kidney injury or nephrotoxicity. Nephrotoxicity frequently leads to termination of clinical trials and drug withdrawals, which jeopardize biomedical progress. Efficient preclinical screening platforms capable of detecting mild signs of kidney damage, which may elicit considerable toxic response in vivo, are essential. A common manifestation of chemical toxicity is oxidative modification of cellular biomolecules. Therefore, we have developed a facile biomolecule carbonyl detection assay that well surpasses the sensitivity of the standard assays in identifying modest forms of renal injury. Using a novel fluorogenic sensor, TFCH, we have demonstrated the applicability of the assay in live kidney cells and in renal tissue. This robust assay can help inform preclinical decisions to recall unsafe drug candidates. Application of this assay in identifying and analyzing diverse pathologies is envisioned.

biochemistry↗

bioRxiv2018

Error Correcting Optical Mapping Data

Optical mapping is a unique system that is capable of producing high-resolution, high-throughput genomic map data that gives information about the structure of a genome [21]. Recently it has been used for scaffolding contigs and assembly validation for large-scale sequencing projects, including the maize [32], goat [6], and amborella [4] genomes. However, a major impediment in the use of this data is the variety and quantity of errors in the raw optical mapping data, which are called Rmaps. The challenges associated with using Rmap data are analogous to dealing with insertions and deletions in the alignment of long reads. Moreover, they are arguably harder to tackle since the data is numerical and susceptible to inaccuracy. We develop cOMet to error correct Rmap data, which to the best of our knowledge is the only optical mapping error correction method. Our experimental results demonstrate that cOMet has high prevision and corrects 82.49% of insertion errors and 77.38% of deletion errors in Rmap data generated from the E. coli K-12 reference genome. Out of the deletion errors corrected, 98.26% are true errors. Similarly, out of the insertion errors corrected, 82.19% are true errors. It also successfully scales to large genomes, improving the quality of 78% and 99% of the Rmaps in the plum and goat genomes, respectively. Lastly, we show the utility of error correction by demonstrating how it improves the assembly of Rmap data. Error corrected Rmap data results in an assembly that is more contiguous, and covers a larger fraction of the genome.

bioinformatics↗