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Choudhury, B.

Publications and source records attributed to Choudhury, B..

16 recordsLinked to original sources

Structure and function of human NXPE1, a sialic acid O-acetyltransferase

Human genetic studies have identified defects in multiple mechanisms that predispose the risk of developing inflammatory bowel diseases (IBD), which include alterations in adaptive and innate immune responses, epithelial integrity and regulation of the intestinal mucus layer. Despite the importance of intestinal barrier integrity in the pathogenesis of IBD, essentially all current therapies modulate the immune responses. In this study, we determined the high resolution cryo-EM structure of human NXPE1, a IBD associated protein. Based on the structural homology, we identified NXPE1 as an O-acetyltransferase. Since NXPE1 is a pseudo gene in mouse, we generated knockout mouse model that lacked two of the mouse NXPE1 homologs, Nxpe2 and Nxpe4. The O-acetylation of sialic acid on red blood cells was abolished in the double knockout mice, confirming the sialic acid O-acetyltransferase function of NXPE1 family members. These findings underscore the potential of NXPE1 as a novel therapeutic target of the intestinal barrier functions for the treatment of IBD.

immunology↗

Widespread loss of Y expression in the absence of transcriptional dosage compensation in Rumex hastatulus

There is growing interest in the potential role of gene regulatory evolution in the expansion and degeneration of Y chromosomes. Evolutionarily young sex chromosomes, such as those found in the flowering plant Rumex hastatulus, can provide insights into the early stages of this process. Using a new high-quality genome assembly with a well-assembled Y chromosome and a highly replicated transcriptome dataset, we found widespread underexpression of Y genes compared to their homologous counterparts on the X chromosome. We also found evidence for increased expression differences for more distantly diverged gametologs, suggestive of progressive loss of expression of Y linked genes over time. Genes with greater expression loss on the Y chromosome also showed elevated rates of protein evolution, as expected if silencing alleles mask the effects of deleterious mutations on the Y and/or if selective interference drives early degeneration in regulatory sequences. However, in contrast with the predictions of recent models of sex chromosome expansion and degeneration by regulatory evolution, there was no evidence of early dosage compensation. Overall, we conclude that in Rumex Hill-Robertson interference alone may be the main driver of Y chromosome degeneration, although further understanding of the temporal order of regulatory changes could help further untangle cause and effect.

genomics↗

Multi-omic analysis reveals the unique glycan landscape of the blood-brain barrier glycocalyx

The blood-brain barrier (BBB) glycocalyx is the dense layer of glycans and glycoconjugates that coats the luminal surface of the central nervous system (CNS) vasculature. Despite being the first point of contact between the blood and brain, not much is known about the BBB glycocalyx. Here, we performed a multi-omic investigation of the BBB glycocalyx which revealed a unique glycan landscape characterized by enrichment of sialic acid, chondroitin sulfate, and hyaluronan. We found that the BBB glycocalyx was thicker than glycocalyces in the peripheral vasculature and that hyaluronan was the major contributor to its ultrastructure. Using endothelial RNA sequencing, we found potential genetic determinants for these differences, including BBB enrichment of genes involved in sialic acid addition and peripheral enrichment of Tmem2 and Hyal2, the only known cell-surface hyaluronidases. Glycocalyx degradation and increases in vascular permeability are widely associated with inflammation. However, we found that the BBB glycocalyx remains largely unchanged in neuroinflammation during the experimental autoimmune encephalomyelitis (EAE) model of multiple sclerosis and that its degradation is not sufficient to alter BBB permeability in health. Moreover, we showed that CNS endothelial sialic acid removal delays onset of EAE, indicating that BBB glycocalyx sialic acid may contribute to the progression of neuroinflammation. These findings underscore the unique and robust nature of the BBB glycocalyx and provide targets and tools for future studies into its role in health and neuroinflammation.

molecular biology↗

Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals

Bacteroides fragilis is a prominent member of the human gut microbiota, playing crucial roles in maintaining gut homeostasis and host health. Although it primarily functions as a beneficial commensal, B. fragilis can become pathogenic. To determine the genetic basis of its duality, we conducted a comparative genomic analysis of 813 B. fragilis strains, representing both commensal and pathogenic origins. Our findings reveal that pathogenic strains emerge across diverse phylogenetic lineages, due in part to rapid gene exchange and the adaptability of the accessory genome. We identified 16 phylogenetic groups, differentiated by genes associated with capsule composition, interspecies competition, and host interactions. A microbial genome-wide association study identified 44 genes linked to extra-intestinal survival and pathogenicity. These findings reveal how genomic diversity within commensal species can lead to the emergence of pathogenic traits, broadening our understanding of microbial evolution in the gut.

microbiology↗

A sneak peek at the high altitude adaptation of the Ladakh populations

The physiological response to high-altitude stress (for individuals living at 2,400m and above sea level) has been evident. However, recent advances in genomics have allowed us to explore the molecular genetic basis of these adaptive responses and their relationship with physiological responses. In the current study, we focused on thirteen biological parameters to understand the adaptive response to the high altitude of populations living across regions of Sakti, Korzok, Hanle, Aryan and Zanskar valleys of Ladakh and to understand the variation between and across individuals. Interestingly, we found a negative correlation between haemoglobin levels and partial oxygen pressure, thereby testifying to higher haemoglobin levels as an adaptive response in these individuals. The lipid profiles, including cholesterol, triglyceride, LDL and HDL levels, varied significantly across the five regions studied. Notably, individuals from Sakti Valley showed higher LDL (>140) and cholesterol values. These variations in health parameters and lipid profiles may be attributed to diet and altitude adaptations specific to the region. Overall, the study provides valuable insights into the adaptations of highlanders living at different altitudes in the Ladakh region. The findings can have implications for better understanding the molecular mechanism of physiological responses of humans to high-altitude environments.

evolutionary biology↗

LeGenD: determining N-glycoprofiles using an explainable AI-leveraged model with lectin profiling

Glycosylation affects many vital functions of organisms. Therefore, its surveillance is critical from basic science to biotechnology, including biopharmaceutical development and clinical diagnostics. However, conventional glycan structure analysis faces challenges with throughput and cost. Lectins offer an alternative approach for analyzing glycans, but they only provide glycan epitopes and not full glycan structure information. To overcome these limitations, we developed LeGenD, a lectin and AI-based approach to predict N-glycan structures and determine their relative abundance in purified proteins based on lectin-binding patterns. We trained the LeGenD model using 309 glycoprofiles from 10 recombinant proteins, produced in 30 glycoengineered CHO cell lines. Our approach accurately reconstructed experimentally-measured N-glycoprofiles of bovine Fetuin B and IgG from human sera. Explanatory AI analysis with SHapley Additive exPlanations (SHAP) helped identify the critical lectins for glycoprofile predictions. Our LeGenD approach thus presents an alternative approach for N-glycan analysis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/587044v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@11687e4org.highwire.dtl.DTLVardef@33b146org.highwire.dtl.DTLVardef@1bb6bcborg.highwire.dtl.DTLVardef@1a1e47e_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

Mechanism of 2-Fucosyllactose degradation by Human-Associated Akkermansia

Among the first microorganisms to colonize the human gut of breastfed infants are bacteria capable of fermenting human milk oligosaccharides (HMOs). One of the most abundant HMOs, 2-fucosyllactose (2-FL), may specifically drive bacterial colonization of the intestine. Recently, differential growth has been observed across multiple species of Akkermansia on various HMOs including 2FL. In culture, we found growth of two species, A. muciniphila MucT and A. biwaensis CSUN-19, in HMOS corresponded to a decrease in the levels of 2-FL and an increase in lactose, indicating that the first step in 2-FL catabolism is the cleavage of fucose. Using phylogenetic analysis and transcriptional profiling, we found that the number and expression of fucosidase genes from two glycoside hydrolase (GH) families, GH29 and GH95, varies between these two species. During mid-log phase growth, the expression of several GH29 genes was increased by 2-FL in both species, whereas the GH95 genes were induced only in A. muciniphila. We further show that one putative fucosidase and a {beta}-galactosidase from A. biwaensis are involved in the breakdown of 2-FL. Our findings indicate that that plasticity of GHs of human associated Akkermansia sp. enable access to additional growth substrates present in HMOs, including 2-FL. Our work highlights the potential for Akkermansia to influence the development of the gut microbiota early in life and expands the known metabolic capabilities of this important human symbiont. IMPORTANCEAkkermansia are mucin degrading specialists widely distributed in the human population. Akkermansia biwaensis has recently been observed to have enhanced growth relative to other human associated Akkermansia on multiple human milk oligosaccharides (HMOs). However, the mechanisms for enhanced growth are not understood. Here, we characterized the phylogenetic diversity and function of select genes involved in growth of A. biwaensis on 2-fucosyllactose (2-FL), a dominant HMO. Specifically, we demonstrate that two genes in a genomic locus, a putative {beta}-galactosidase and -fucosidase, are likely responsible for the enhanced growth on 2-FL. The functional characterization of A. biwaensis growth on 2-FL delineates the significance of a single genomic locus that may facilitate enhanced colonization and functional activity of select Akkermansia early in life.

microbiology↗

Phased assembly of neo-sex chromosomes reveals extensive Y degeneration and rapid genome evolution in Rumex hastatulus

Y chromosomes are thought to undergo progressive degeneration due to stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales and evolutionary forces driving degeneration remain unclear. To investigate the evolution of sex chromosomes on multiple timescales, we generated a high-quality phased genome assembly of the massive older (<10MYA) and neo (<200,000 years) sex chromosomes in the XYY cytotype of the dioecious plant Rumex hastatulus and a hermaphroditic outgroup R. salicifolius. Our assemblies, supported by fluorescence in situ hybridization, confirmed the neo-sex chromosomes were formed by two key events: an X-autosome fusion and a reciprocal translocation between the homologous autosome and the Y chromosome. The enormous sex-linked regions of the X (296 MB) and two Y chromosomes (503 MB) both evolved from large repeat-rich genomic regions with low recombination; however, the complete loss of recombination on the Y still led to over 30% gene loss and major rearrangements. In the older sex-linked region, there has been a significant increase in transposable element abundance, even into and near genes. In the neo sex-linked regions, we observed evidence of extensive rearrangements without gene degeneration and loss. Overall, we inferred significant degeneration during the first 10 million years of Y chromosome evolution but not on very short timescales. Our results indicate that even when sex chromosomes emerge from repetitive regions of already-low recombination, the complete loss of recombination on the Y chromosome still leads to a substantial increase in repetitive element content and gene degeneration.

evolutionary biology↗

Release of extracellular matrix components after human traumatic brain injury

Most research on the evolution of damage after traumatic brain injury (TBI) focuses on cellular effects, but the analysis of human tissue slices and animal research have shown that TBI causes concomitant damage in the extracellular matrix, which can play a significant role in both short-term consequences such as edema, and late effects such as post-traumatic epilepsy (PTE). To test the hypothesis that traumatic brain injury (TBI) in human patients causes disruption of sulfated glycosaminoglycan (sGAG) in the extracellular matrix, we measured levels of these substances in the ventricular cerebrospinal fluid (CSF) in patients with severe TBI in the acute post-injury period, along with concomitant levels in blood and urine. We assessed whether levels corresponded to parenchymal injury load, distance of traumatic brain lesions from the ventricle, presence of polytrauma, or host demographic factors. MethodsSamples of CSF, blood, and urine were obtained within 72 hours of injury in patients who received external ventricular drains as part of their treatment of severe TBI, and levels of chondroitin and heparan sGAGs were measured, along with their disaccharide constituents. Basic demographic information, presence and severity of polytrauma, brain injury load based on imaging findings, and distance of radiologically visible parenchymal injury from the ventricle were analyzed for correlation with total subtype sGAG levels in each patient. ResultsLevels were measured in 14 patients ranging in age from 17-90 years. CSF sGAG levels were variable among patients, and sGAG levels were higher in plasma than in CSF and variable in urine. Patients with polytrauma had non-significantly higher blood sGAG compared to patients with isolated head injury. Subcategories of CSF sGAG levels correlated with distance from the ventricle of parenchymal injury but not with brain injury load, which may reflect rapid metabolism in the parenchyma, contamination by blood, or bulk directional CSF flow from the ventricle to the subarachnoid space. ConclusionThis study is the first to measure sGAG levels in ventricular CSF and also provides the first measurements in patients with TBI. Damage to the extracellular matrix may play a major role in acute and chronic injury sequelae, and these data demonstrate elevation locally of intracranial sGAGS after severe TBI and also suggest rapid local metabolism of these breakdown products. The consequences of extracellular matrix breakdown may provide unique therapeutic and preventive avenues to mitigate post-injury sequelae.

neuroscience↗

B3GALT6 Promotes Dormant Breast Cancer Cell Survival and Recurrence by Enabling Heparan Sulfate-Mediated FGF Signaling

Breast cancer mortality results primarily from incurable recurrent tumors seeded by dormant, therapy-refractory residual tumor cells (RTCs). Understanding the mechanisms enabling dormant RTC survival is therefore essential for improving patient outcomes. We derived a dormancy-associated RTC signature that mirrors the transcriptional response to neoadjuvant chemotherapy in patients and is enriched for extracellular matrix-related pathways. In vivo CRISPR-Cas9 screening of dormancy-associated candidate genes identified the galactosyltransferase B3GALT6 as a functional regulator of RTC fitness. B3GALT6 covalently attaches glycosaminoglycans (GAGs) to proteins to generate proteoglycans and its germline loss-of-function causes skeletal dysplasias. We determined that B3GALT6-mediated biosynthesis of the GAG heparan sulfate predicts poor patient outcomes, promotes tumor recurrence by enhancing dormant RTC survival in multiple contexts, and does so via a B3GALT6-heparan sulfate/HS6ST1-heparan 6-O-sulfation/FGF1-FGFR2 signaling axis. These findings identify a role for B3GALT6 in cancer and suggest targeting FGF signaling as a novel approach to preventing recurrence by eradicating dormant RTCs.

cancer biology↗

Distributed Compact Plasma Reactor Sterilization for Planetary Protection in Space Missions

This paper presents a proof-of-concept study establishing effectiveness of the Active Plasma Sterilizer (APS) for sterilization in planetary protection. The APS uses Compact Portable Plasma Reactors (CPPRs) to produce surface dielectric barrier discharge, a type of cold plasma, using ambient air to generate and distribute reactive species like ozone used for decontamination. Sterilization tests were performed with pathogenic bacteria (Escherichia coli and Bacillus subtilis) on materials (Aluminum, Polycarbonate, Kevlar and Orthofabric) relevant to space missions. Results show that the APS can achieve 4 to 5 log reductions of pathogenic bacteria on four selected materials, simultaneously at 11 points within 30 minutes, using power of 13.2 {+/-} 2.22 W. Spatial sterilization data shows the APS can uniformly sterilize several areas of a contaminated surface within 30 minutes. Ozone penetration through Kevlar and Orthofabric layers was achieved using the CPPR with no external agent assisting penetration. Preliminary material compatibility tests with SEM analysis of the APS exposed materials showed no significant material damage. Thus, this study shows the potential of the APS as a light-weight sustainable sterilization technology for planetary protection with advantages of uniform spatial decontamination, low processing temperatures, low exposure times, material compatibility and the ability to disinfect porous surfaces.

microbiology↗

Avian and Human Influenza Viruses Exhibit Distinct Glycoconjugate Receptor Specificities in Human Lung Cells

IAV utilize sialic acid (Sia) containing cell surface glycoconjugates for host cell infection, and IAV strains from different host species show preferences for structurally distinct Sia at the termini of glycoconjugates. Various types of cell surface glycoconjugates (N-glycans, O-glycans, glycolipids) display significant diversity in both structure and carbohydrate composition. To define the types of glycoconjugates that facilitate IAV infection, we utilized the CRISPR/Cas9 technique to truncate different types of glycoconjugates, either individually or in combination, by targeting glycosyltransferases essential to glycan biosynthesis in a human lung epithelial cell line. Our studies show that both human and avian IAV strains do not display strict preferences for a specific type of glycoconjugate. Interestingly, truncation of all three types of glycoconjugates significantly decreased the replication of human IAV strains, yet did not impact the replication of avian IAV strains. Taken together, our studies demonstrate that avian IAV strains utilize a broader repertoire of glycoconjugates for host cell infection as compared to human IAV strains. Author SummaryIt is well known that influenza A viruses (IAV) initiate host cell infection by binding to sialic acid, a sugar molecule present at the ends of various sugar chains called glycoconjugates. These glycoconjugates can vary in chain length, structure, and composition. However, it remains unknown if IAV strains preferentially bind to sialic acid on specific glycoconjugates for host cell infection. Here, we utilized CRISPR gene editing to abolish sialic acid on different glycoconjugate types in human lung cells, and evaluated human versus avian IAV infections. Our studies show that both human and avian IAV strains can infect human lung cells by utilizing any of the three major sialic acid-containing glycoconjugate types, specifically N-glycans, O-glycans, and glycolipids. Interestingly, simultaneous elimination of sialic acid on all three glycoconjugate types in human lung cells dramatically decreased human IAV infection, yet had little effect on avian IAV infection. Our studies indicate that avian IAV strains can utilize a wide variety of glycoconjugates for infection, whereas human IAV strains display restrictions in glycoconjugate type usage. These novel studies show distinct differences in host glycoconjugate preferences between human and avian IAV strains.

microbiology↗

Utilization efficiency of human milk oligosaccharides by human-associated Akkermansia is strain-dependent

Akkermansia muciniphila are mucin degrading bacteria found in the human gut and are often associated with positive human health. However, despite being detected as early as one month of age, little is known about the role of Akkermansia in the infant gut. Human milk oligosaccharides (HMOs) are abundant components of human milk and are structurally similar to the oligosaccharides that comprise mucin, the preferred growth substrate of human-associated Akkermansia. A limited subset of intestinal bacteria has been shown to grow well on HMOs and mucin. We therefore examined the ability of genomically diverse strains of Akkermansia to grow on HMOs. First, we screened 85 genomes representing the four known Akkermansia phylogroups to examine their metabolic potential to degrade HMOs. Furthermore, we examined the ability of representative isolates to grow on individual HMOs in a mucin background and analyzed the resulting metabolites. All Akkermansia genomes were equipped with an array of glycoside hydrolases associated with HMO-deconstruction. Representative strains were all able to grow on HMOs with varying efficiency and growth yield. Strain CSUN-19 belonging to the AmIV phylogroup, grew to the highest level in the presence of fucosylated and sialylated HMOs. This activity may be partially related to the increased copy numbers and/or the enzyme activities of the -fucosidases, -sialidases, and {beta}-galactosidases. Utilization of HMOs by strains of Akkermansia suggests that ingestion of HMOs by an infant may enrich for these potentially beneficial bacteria. Further studies are required to realize this opportunity and deliver long-lasting metabolic benefits to the human host. ImportanceHuman milk oligosaccharides (HMOs) are utilized by a limited subset of bacteria in the infant gut. Akkermansia are detected in infants as young as one month of age and are thought to contribute to the HMO deconstruction capacity of the infant. Here, using phylogenomics, we examined the genomic capacity of different Akkermansia phylogroups to potentially deconstruct HMOs. Furthermore, we experimentally showed that strains from all the currently known phylogroups of Akkermansia can deconstruct all the major types of HMOs, albeit with different utilization efficiencies. This study thus examines Akkermansia-HMO interactions that can potentially influence the gut microbial ecology during the first 1,000 days of life - a critical phase for the development of the gut microbiome and infant health. This study will be of interest to a wide range of scientists from microbiologists, glycochemists/glycobiologists, to functional food developers investigating Akkermansia as probiotics or functional foods containing milk oligosaccharides as prebiotics.

microbiology↗

THAP1 Modulates Oligodendrocyte Maturationby Regulating ECM Degradation in Lysosomes

Mechanisms controlling myelination during CNS maturation play a pivotal role in the development and refinement of CNS circuits. The transcription factor THAP1 is essential for timing the inception of myelination during CNS maturation through a cell-autonomous role in the oligodendrocyte lineage. Here, we demonstrate that THAP1 modulates ECM composition by regulating glycosaminoglycan (GAG) catabolism within oligodendrocyte progenitor cells (OPCs). Thap1-/- OPCs accumulate and secrete excess GAGs, inhibiting their maturation through an auto-inhibitory mechanism. THAP1 controls GAG metabolism by binding to and regulating the GusB gene encoding {beta}-glucuronidase, a GAG-catabolic lysosomal enzyme. Applying GAG-degrading enzymes or overexpressing {beta}-glucuronidase rescues Thap1-/- OL maturation deficits in vitro and in vivo. Our studies establish lysosomal GAG catabolism within OPCs as a critical mechanism regulating oligodendrocyte development.

neuroscience↗

Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations

Microbiota-accessible carbohydrates (MACs) are powerful modulators of microbiota composition and function. These substrates are often derived from diet, such as complex polysaccharides from plants or human milk oligosaccharides (HMOs) during breastfeeding. Host-derived mucus glycans on gut-secreted mucin proteins may serve as a continuous endogenous source of MACs for resident microbes; here we investigate the potential role of purified, orally-administered mucus glycans in maintaining a healthy microbial community. In this study, we liberated and purified O-linked glycans from porcine gastric mucin and assessed their efficacy in shaping the recovery of a perturbed microbiota in a mouse model. We found that porcine mucin glycans (PMGs) and HMOs enrich for taxonomically similar resident microbes. We demonstrate that PMGs aid recovery of the microbiota after antibiotic treatment, suppress C. difficile abundance, delay the onset of diet-induced obesity, and increase relative abundance of resident Akkermansia muciniphila. In silico analysis revealed that genes associated with mucus utilization are abundant and diverse in prevalent gut commensals and rare in enteric pathogens, consistent with these glycan-degrading capabilities being selected for during host development and throughout evolution of the host-microbe relationship. Importantly, we identify mucus glycans as a novel class of prebiotic compounds that can be used to mitigate perturbations to the microbiota and provide benefits to host physiology.

microbiology↗

Down-regulated GDF9 and BMP15 mRNAs are the important determining factors for the unexplained female infertility cases advised for assisted reproductive technology

BackgroundIn India, the potential risk factors influencing female infertility are not well-characterized. Hence, this study was initially aimed to determine the multi-factor risk-predictive models for the infertile females from different Indian ethnics. Afterwards, when treatment was performed for correcting the abnormal demographic and clinical parameters obtained from our initial findings, some of the patients were observed to be treatment-non-responsive. This further recommended assessing the expression pattern of GDF9 and BMP15 mRNAs in those unexplained infertile females. MethodologyThis study included 470 Primary, 209 Secondary infertile and 419 age-matched Healthy females, where baseline demographic and clinicopathological factors were assessed. Additionally, from the treatment-non-responsive patients, laparoscopy and trans-vaginal ultrasound-guided collection of ovarian follicular fluid were done for studying the expression pattern of GDF9 and BMP15 mRNAs using q-PCR. Principal FindingsMid-education level, no contraception usage and duration of infertility for >2 years were the critical risk factors for female infertility (OR>>1; p<0.05), whereas elevated platelet count showed ~10-fold more risk of having secondary infertility and high ESR showed 3.33-fold increased threat of primary infertility. Besides, abnormal MCV, LH/FSH ratio, mild-anaemia and hypothyroidism were the best risk-predictive multi-factor model. After correcting these abnormal clinical factors, 6.8% of the patients were treatment-non-responsive, where elevated ESR, hypothyroidism and anaemia remained uncorrected. Interestingly, in those unexplained cases, GDF9 and BMP15 mRNAs were significantly down-regulated (2-4 fold) irrespective of age groups. Additionally, for predicting female infertility, the cut-off for the expression level of GDF9 and BMP15 mRNAs were estimated -2.09 and -2.75, respectively, with a relatively high sensitivity ([&ge;]62.5%) and specificity (75%). ConclusionsGDF9 and BMP15 mRNAs may be considered as molecular markers for predicting female infertility. Their down-regulation along with hypothyroidism and anaemia probably led to the treatment-non-responsiveness, thus, those patients may be advised to assisted reproductive technology with supplementation of exogenous GDF9 and/or BMP15.

epidemiology↗