Biology subjects

Biswal, S.

Publications and source records attributed to Biswal, S..

12 recordsLinked to original sources

bioRxiv2026

Perinatal exposure to individual and a metal mixture induces persistent and sex-specific alterations to the cardiac transcriptome of offspring

Exposure to heavy metals, such as lead, arsenic, cadmium, and chromium, has been individually linked to cardiac dysfunction during development and into adulthood. Although these metals are commonly encountered as a mixture, few studies have investigated the mixture effects of gestational exposure to these metals on the developing postnatal heart. To this end, we investigated the transcriptomic effects of individual heavy metals (arsenic, cadmium, chromium, and lead) and the combined mixture on female C57BI/6 mice prior to gestation through lactation. RNA was extracted from whole offspring hearts, and total RNA was sent for bulk RNA-sequencing. We found heavy metal exposure altered genes associated with circadian rhythm, cell division and DNA damage repair, and immune signaling. Moreover, we detected changes to the cellular composition of these hearts and an increase in Il2ra expression, indicating an increase in activated natural killer cells. When targeting postnatal heart development and maturation pathways, we found the mixture induced a general upregulation of almost all targeted pathways, which seemed to be driven by co-exposure to all metals instead of one metal driving the mixture phenotype, and revealed a potential functional-energetic mismatch. This study is one of the first to show that perinatal exposure to heavy metals altered circadian rhythm and immune signaling gene expression in a metal- and sex-specific manner, disrupted normal cardiac cellular composition, and upregulated genes associated with postnatal heart maturation.

pharmacology and toxicology↗

bioRxiv2026

A metabolic labelling-based lipid imaging technology establishes VPS13A as a phosphatidylethanolamine lipid transfer protein

The ability to image specific lipid subtypes within cells can have a transformative impact on the study of lipid dynamics and trafficking mechanisms. Herein, we describe a technology for imaging phosphatidylethanolamine (PE) lipids in live mammalian cells that involved screening a library of ethanolamine derivatives to identify an azido compound that efficiently metabolically labels PE. Crucially, this probe evades the cellular methylation machinery specifically labelling PE without forming labelled methylated PE and phosphatidylcholine (PC) lipids. The administration of cyclooctyne dyes to cells metabolically labelled with this probe rendered azido PE lipids fluorescent via strain-promoted click chemistry, enabling imaging. We employed this technology to image PE in various cellular organelles, visualize PE externalization during apoptosis, and discover that the VPS13A protein transports PE from the endoplasmic reticulum to the mitochondria. This technology will facilitate addressing fundamental questions in PE biology and studying dysregulation of PE dynamics and trafficking in disease states.

cell biology↗

bioRxiv2025

Substitution of a valine to glutamic acid in the omega-like loop of MSMEG_6194 of Mycobacterium smegmatis interchanges its activity from DD-carboxypeptidase to beta-lactamase

The genome of Mycobacterium smegmatis encodes numerous penicillin-interacting enzymes, and analysing their functions provides insights into the evolutionary mechanisms behind beta-lactam resistance in mycobacteria. In this study, we characterised one such enzyme, MSMEG_6194, annotated as a putative beta-lactamase. Although MSMEG_6194 shares structural similarity with class A beta-lactamases, it showed no detectable beta-lactamase activity under the tested conditions. Heterologous expression of MSMEG_6194 in Escherichia coli and{Delta} msmeg_6194 deleted strains of M. smegmatis did not confer significant resistance to beta-lactams, and the purified protein failed to hydrolyse nitrocefin either. However, ectopic expression of MSMEG_6194 partly restores the morphological defects in seven PBP-deleted E. coli strains, and the purified enzyme successfully cleaves the terminal D-alanine from a pentapeptide substrate, confirming its DD-carboxypeptidase activity. Structural analysis revealed the absence of a conserved glutamic acid residue in the omega-loop, which is critical for beta-lactamase catalysis in class A beta-lactamase. Substituting this residue (V139E mutant) imparts beta-lactamase activity though significantly reduces DD-carboxypeptidase function. Overall, these findings establish MSMEG_6194 as a DD-carboxypeptidase and demonstrate how a single amino acid change can alter catalytic preference, shedding light on the evolutionary transition from DD-Carboxypeptidases to beta-lactamases in mycobacteria.

molecular biology↗

bioRxiv2025

Perinatal Exposure to Metal Mixtures Disrupts Neuronal Function and Behavior

BackgroundEnvironmental exposure to heavy metals such as lead (Pb), arsenic (As), hexavalent chromium [Cr(VI)], and cadmium (Cd), (PACC), is linked to neurodevelopmental disorders. These metals often co-occur in contaminated environments, but their combined effects on brain development remain poorly understood. ObjectiveTo test the hypothesis that perinatal exposure to a mixture of environmentally relevant levels of Pb, As, Cd, and Cr(VI), causes developmental defects in cognition, behavior, and neuronal function. MethodsFemale C57BL/6J mice were exposed to either a single metal or the PACC mixture in drinking water. Exposure began two weeks preconception and continued until weaning at postnatal day 21. Juvenile mice were tested at 4-5 weeks of age in open field (locomotion), novel object recognition (short-term memory), Y-maze (working memory), and elevated plus maze (anxiety-like behavior). A subset of animals underwent Whole-cell patch-clamp recordings in the medial prefrontal cortex (mPFC) and hippocampal CA1 neurons. ResultsPerinatal exposure to PACC metal mixture increased anxiety-like behavior and impaired short-term memory but not locomotion or working memory. Pyramidal neurons in mPFC and hippocampal CA1 displayed increased intrinsic excitability, mPFC neurons also showed elevated amplitude in spontaneous excitatory postsynaptic currents. DiscussionOur findings suggest that perinatal exposure to the PACC metal mixture impairs cognition, increases anxiety-like behavior, and alters neuronal function in specific brain regions of juvenile mice, leading to disruption in neuronal function and behavior later in life. Further studies are needed to provide mechanistic insight into how perinatal heavy metal exposure affects neuronal development. HighlightsO_LIPerinatal exposure to a metal mixture including lead (Pb), arsenic (As), hexavalent chromium (Cr(VI)), and cadmium (Cd), collectively termed PACC metal mixture--impairs cognition and increases anxiety in mice. C_LIO_LINeuronal excitability and synaptic transmission are altered in medial prefrontal cortex after PACC metal mixture exposure. C_LIO_LIPACC mixture exposure decreases short-term memory in both males and females, and increases anxiety in males C_LIO_LIPrincipal component and clustering analyses reveal that PACC mixture exposure and control mice form distinct, nonoverlapping populations in physiological-behavioral space. C_LIO_LIEnvironmentally relevant PACC metal mixtures exert stronger effects than individual metals alone. C_LI

pharmacology and toxicology↗

bioRxiv2025

Early-life Exposure to Arsenic Primes the Offspring to Increased Asthma Risk: Transcriptome and Epigenome Analysis

Inorganic arsenic (iAs) in drinking water is a global health concern. This study tests whether maternal exposure to iAs in drinking water at the WHO provisional level (10{micro}g/L) increases offspring asthma risk via epigenetic reprogramming. F1 mice prenatally exposed to iAs were analyzed at 5 months for blood transcriptome and methylome changes and challenged with house allergens before lung function testing. Prenatal iAs exposure led to increased airway hyperresponsiveness (AHR) and altered inflammation gene expression and DNA methylation changes. Notably, miR-101c was epigenetically reprogrammed early in development, with persistent downregulation in both target (fetal and adult lungs) and surrogate (amniotic fluid and blood) tissues. These changes correlated with increased allergic AHR and TGF{beta} pathway dysregulation. Findings suggest that maternal iAs exposure primes offspring for asthma risk through epigenetic alterations and may inform risk assessment and biomarker development in affected communities. KEY FINDINGSO_LIIn utero exposure to 10 part per billion (or 10 {micro}g/L, the current WHO and EPA provisional level in drinking water) inorganic arsenic (iAs) increases offspring asthma risk. These results raise concerns about the current safety thresholds for iAs in drinking water (Fig. 1). C_LIO_LITranscriptomic and methylome analyses of blood leukocytes from 5-month-old F1 mice revealed that maternal iAs exposure induces transcriptional changes in genes related to allergic airway responses. Pathway analysis highlighted the involvement of miR-101c and its connection with TGF{beta} downstream targets in regulating extracellular matrix signaling, embryonic development, and inflammatory (Figs. 2 and 3). C_LIO_LITranscriptional changes in col3a1 and miR-101c in blood were strongly correlated with allergen-induced airway hyperresponsiveness (AHR), with similar alterations detected in plasma samples. These findings provide new insights into respiratory health in affected communities and support the development of biomarkers for iAs risk assessment (Figs. 4 and 5). C_LIO_LISeveral gene-specific epigenetic alterations induced by early-life iAs exposure were consistently observed in both surrogate (blood) and target (lung) tissues across developmental stages, offering new panels of easily accessible markers for early detection and monitoring of lung disease risk in offspring. The persistence of these markers over time makes them valuable for predictive modeling and life course studies. (Fig. 6). C_LIO_LIDownregulation of miR-101c was validated in fetal lung and amniotic fluid of the iAs-exposed group, suggesting that epigenetic reprogramming of miR-101c is initiated early in gestation (Fig. 7). These findings help uncover causal pathways linking environmental exposures to asthma pathogenesis. C_LIO_LIDistinct sex-specific patterns in blood transcriptome and methylome alterations in respond to early-life iAs exposure underscore the importance of considering sex as a biological variable in omics research. C_LI O_FIG O_LINKSMALLFIG WIDTH=149 HEIGHT=200 SRC="FIGDIR/small/668223v1_fig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1f5394eorg.highwire.dtl.DTLVardef@855bf8org.highwire.dtl.DTLVardef@1592328org.highwire.dtl.DTLVardef@1133ec4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO Maternal iAs exposure and study design to assess offspring asthma risk. A) Schematic shows the exposure window in which F0 dams received iAs in drinking water from preconception through lactation, followed by collection of F1 progeny for transcriptomic and methylomic analysis. A subset of 5-month-old F1 progenies were assessed for the HDM allergen-induced airway reactivity and airway inflammation. B) Lung resistance was assessed following methacholine (30mg/mL) challenge. C) BAL cells were stained with Diff-Quick, and eosinophil counts are shown. Each datapoint represents a pup from an individual dam; error bars indicate SEM. Five to six dams were used. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/668223v1_fig2.gif" ALT="Figure 2"> View larger version (23K): org.highwire.dtl.DTLVardef@7dc1b1org.highwire.dtl.DTLVardef@378529org.highwire.dtl.DTLVardef@1076fe3org.highwire.dtl.DTLVardef@142d801_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 2.C_FLOATNO Blood transcriptome profiles and predicted canonical pathways and regulatory networks. A) Numbers of differentially expressed genes (DEGs) identified in male and female progeny are illustrated with a Venn diagram. Enriched canonical pathways ranked by the p value are shown. B) Using the set of DEGs common in both sexes, Ingenuity Pathway Analysis (IPA) highlights TGF as a central upstream regulator linking overlapping DEGs related to extracellular matrix signaling (orange), inflammation (yellow), and embryonic development/cell metabolism (blue). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/668223v1_fig3.gif" ALT="Figure 3"> View larger version (23K): org.highwire.dtl.DTLVardef@1732b53org.highwire.dtl.DTLVardef@216332org.highwire.dtl.DTLVardef@1f794d1org.highwire.dtl.DTLVardef@14b62df_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 3.C_FLOATNO Blood methylome analysis and associations between miR-101c and TGF-related differentially expressed genes. A) Number of differentially methylated CpGs (DMCs) identified in male and female progeny are illustrated with a Venn diagram. There are four DMCs overlapping DMCs annotated to miR-101c. B) Expression levels of miR-101c are shown. C) IPA-derived network linking this miRNA to TGF-related DEGs. Each datapoint represents a pup from an individual dam; error bars indicate SEM. Four to five dams were used. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=148 SRC="FIGDIR/small/668223v1_fig4.gif" ALT="Figure 4"> View larger version (38K): org.highwire.dtl.DTLVardef@482e86org.highwire.dtl.DTLVardef@e666bdorg.highwire.dtl.DTLVardef@631538org.highwire.dtl.DTLVardef@10618f6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 4.C_FLOATNO Relationship between iAs-induced blood transcriptional changes and allergen-induced AHR. This figure presents correlation patterns between baseline blood DEGs expression changes prior to HDM challenge and subsequent changes in AHR. Pearson correlation coefficients are depicted using a color gradient to distinguish positive (blue) and negative (peach) associations. * Positive correlation: r>0.8, p<0.05; ^ negative correlation: r<-0.8, p<0.05 C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/668223v1_fig5.gif" ALT="Figure 5"> View larger version (20K): org.highwire.dtl.DTLVardef@150d27eorg.highwire.dtl.DTLVardef@12b4edeorg.highwire.dtl.DTLVardef@4702a8org.highwire.dtl.DTLVardef@1ff9600_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 5.C_FLOATNO Circulating miR-101c levels in progeny exposed to maternal iAs. Plasma levels of miR-101c and COL3A1 protein are shown at different developmental stages. A) Relative expression of miR-101c across F1 progeny at juvenile (3 weeks of age) and adult (5 months of age) prenatally exposed to iAs. B) Levels of COL3A1 protein are shown at juvenile and adult F1 progeny. Each datapoint represents a pup from an individual dam, error bars indicate SEM. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/668223v1_fig6.gif" ALT="Figure 6"> View larger version (46K): org.highwire.dtl.DTLVardef@d0ec76org.highwire.dtl.DTLVardef@5468a2org.highwire.dtl.DTLVardef@1a17e85org.highwire.dtl.DTLVardef@17956ce_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 6.C_FLOATNO Comparison of transcriptional patterns across tissues and developmental stages. Expression changes (FC: fold changes vs. unexposed) of DEGs and miR-101c are compared between blood and lung tissues in both A) juvenile (3 weeks of age) and B) adult (5 months of age) progeny. Blue and orange bars represent FC in blood from male and female progeny, respectively. Black bars represent FC in lung tissues. Solid bars indicate statistically significant changes. C_FIG O_FIG O_LINKSMALLFIG WIDTH=154 HEIGHT=200 SRC="FIGDIR/small/668223v1_fig7.gif" ALT="Figure 7"> View larger version (22K): org.highwire.dtl.DTLVardef@131ef23org.highwire.dtl.DTLVardef@14b0652org.highwire.dtl.DTLVardef@8c1b30org.highwire.dtl.DTLVardef@4cf6d9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 7.C_FLOATNO Fetal lung and amniotic fluid levels of miR-101c. Relative levels of miR-101c are shown in fetal lung tissues and matched amniotic fluid at embryonic day 16. Data illustrate expression patterns in the context of maternal iAs exposure. Each datapoint represents a pup from an individual dam, error bars indicate SEM. C_FIG GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/668223v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@e25f49org.highwire.dtl.DTLVardef@1dddc22org.highwire.dtl.DTLVardef@9f4244org.highwire.dtl.DTLVardef@1b787e9_HPS_FORMAT_FIGEXP M_FIG C_FIG Description: F1 progeny prenatally exposed to iAs were assessed for blood transcriptomic and DNA methylome analysis at 5 months of age. Correlation analysis between transcriptional changes and allergen-induced airway hyperresponsiveness (AHR) was conducted to examine the epigenetic impact of maternal iAs exposure on offspring asthma risk.

genomics↗

bioRxiv2025

Comprehensive Transcriptomic and Epigenomic Insights into Environmental Toxicant Exposures: The TaRGET II Resource

Environmental exposures to toxic chemicals can profoundly alter the transcriptome and epigenome in both humans and animals, contributing to disease development across the lifespan. To elucidate how early-life exposure to toxicants exerts such persistent effects, the Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription II (TaRGET II) Consortium generated a landmark resource comprising 2,564 epigenomes and 1,043 transcriptomes from longitudinal studies in mice. All data are publicly available through the TaRGET II data portal and the WashU Epigenome Browser. This resource from target (liver, brain, lung, heart) and surrogate (blood) tissues at weaning (3 weeks) and two adult time-points (5 and 10 months) characterized the molecular response to arsenic (As), lead (Pb), bisphenol-A (BPA), di-2-ethylhexyl phthalate(DEHP), tributyltin (TBT), tetrachlorodibenzo-p-dioxin (TCDD), and particulate matter with a diameter of <2.5m (PM2.5). The findings revealed persistent, toxicant-specific, sex-dependent epigenomic and transcriptomic perturbations, resulting in disrupted expression of 14,908 genes, altered chromatin accessibility at 87,409 regulatory elements, DNA methylation changes at 113,186 genomic regions, and chromatin state switching of histone modifications. The resulting high-resolution map of how environmental exposures reprogram the epigenome and transcriptome is broadly accessible via ToxiTaRGET database, offering unparalleled opportunities for the scientific community to investigate the molecular underpinnings of environmental toxicant exposures and their contributions to disease pathogenesis.

pharmacology and toxicology↗

bioRxiv2025

Early-Life Environmental Exposures Reprogram Epigenomic Aging to Alter Gene Expression Trajectories

To understand how early-life environmental exposures shape health and disease risk across the lifecourse, the TaRGET II Consortium exposed mice to diverse toxicants from pre-conception through weaning, and followed individual animals into adulthood, generating over 800 epigenomic and transcriptomic profiles. These profiles revealed that early-life exposures induced persistent epigenomic reprogramming and significantly disrupted the adult transcriptome. Notably, despite their diverse mechanisms of action, the exposure signatures of the xenoestrogen BPA, obesogen TBT, dioxin TCDD, and air pollutant PM2.5, were all largely comprised of genes normally differentially expressed during liver aging. Epigenetic histone modifications at enhancers--and, to a lesser extent, promoters--emerged as key targets for this reprogramming. Despite differing mechanisms of action, these four toxicants imparted similar "fingerprints" on the adult liver, characterized by direction-and cell type-specific polarization of the transcriptome. Hepatocyte genes that typically increase with age, particularly those in metabolic pathways, were downregulated, while conversely, non-parenchymal cell genes that typically decrease with age, such as those involved in extracellular matrix production, were upregulated. A similar signature of anti-correlation with programmed aging aging was also found in the transcriptome of patients with liver disease and hepatocellular carcinoma (HCC), and was effective at distinguishing healthy from diseased human livers. These findings demonstrate that the plasticity of epigenomic aging is vulnerable to early-life environmental exposures, which can reprogram the epigenome with lasting impacts on the transcriptome, and disease risk, later in life.

genomics↗

bioRxiv2024

Acinetobacter baumannii DacC influences cell shape, biofilm formation, and physiological fitness by manifesting DD-carboxypeptidase and β-lactamase dual-enzyme activities

With the growing threat of drug-resistant Acinetobacter baumannii, there is an urgent need to comprehensively understand the physiology of this nosocomial pathogen. As penicillin-binding proteins are attractive targets for antibacterial therapy, herein we have tried to explore the physiological roles of two putative DD-carboxypeptidases, viz., dacC and dacD in A. baumannii. Surprisingly, the deletion of dacC resulted in a reduced growth rate, loss of rod-shaped morphology, reduction in biofilm-forming ability, and enhanced susceptibility towards {beta}-lactams, whereas, the deletion of dacD had no such effect. Interestingly, ectopic expression of dacC restored the lost phenotypes. The double deletion mutant in which both dacC and dacD were absent showed properties similar to the dacC single knockout. On the other hand, cell-shape reverting efficiency in septuple PBP deleted E. coli and in vitro enzyme kinetics assessments reveal that dacD is a stronger DD-CPase as compared to dacC. The expression of dacC was in the log phase whereas dacD expression takes place in the stationary phase. In summary, we conclude that dacC encodes a dual enzyme, possessing activities of DD-CPase and {beta}-lactamase, which significantly affects the physiology of A. baumannii in various ways whereas dacD encodes a strong DD-CPase and plays a role in cell morphology, though it exerts negligible impact on other physiological aspects like intrinsic antibiotic resistance or biofilm formation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/603720v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@18820c9org.highwire.dtl.DTLVardef@208baeorg.highwire.dtl.DTLVardef@b2673eorg.highwire.dtl.DTLVardef@983aae_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Subchronic exposure to ambient PM2.5 impairs novelty recognition and spatial memory

Air pollution remains a great challenge for public health, with the detrimental effects of air pollution on cardiovascular, rhinosinusitis, and pulmonary health increasingly well understood. Recent epidemiological associations point to the adverse effects of air pollution on cognitive decline and neurodegenerative diseases. Mouse models of subchronic exposure to PM2.5 (ambient air particulate matter < 2.5 {micro}m) provide an opportunity to demonstrate the causality of target diseases. Here, we subchronically exposed mice to concentrated ambient PM2.5 for 7 weeks (5 days/week; 8h/day) and assessed its effect on behavior using standard tests measuring cognition or anxiety-like behaviors. Average daily PM2.5 concentration was 200 {micro}g/m3 in the PM2.5 group and 10 {micro}g/m3 in the filtered air group. The novel object recognition (NOR) test was used to assess the effect of PM2.5 exposure on recognition memory. The increase in exploration time for a novel object versus a familiarized object was lower for PM2.5-exposed mice (42% increase) compared to the filtered air (FA) control group (110% increase). In addition, the calculated discrimination index for novel object recognition was significantly higher in FA mice (67 %) compared to PM2.5 exposed mice (57.3%). The object location test (OLT) was used to examine the effect of PM2.5 exposure on spatial memory. In contrast to the FA-exposed control mice, the PM2.5 exposed mice exhibited no significant increase in their exploration time between novel location versus familiarized location indicating their deficit in spatial memory. Furthermore, the discrimination index for novel location was significantly higher in FA mice (62.6%) compared to PM2.5 exposed mice (51%). Overall, our results demonstrate that subchronic exposure to higher levels of PM2.5 in mice causes impairment of novelty recognition and spatial memory.

pharmacology and toxicology↗

bioRxiv2021

Nrf2 Regulates β-cell Mass by Suppressing Cell Death and Promoting Proliferation

Finding therapies that can protect and expand functional {beta}-cell mass is a major goal of diabetes research. Here we generated {beta}-cell-specific conditional knockout and gain-of-function mouse models and used human islet transplant experiments to examine how manipulating Nrf2 levels affects {beta}-cell survival, proliferation and mass. Depletion of Nrf2 in {beta}-cells resulted in decreased glucose-stimulated {beta}-cell proliferation ex vivo and decreased adaptive {beta}-cell proliferation and {beta}-cell mass expansion after a high fat diet in vivo. Nrf2 protects {beta}-cells from apoptosis after a high fat diet. Nrf2 loss-of-function decreases Pdx1 abundance and insulin content. Activating Nrf2 in a {beta}-cell-specific manner increases {beta}-cell proliferation and {beta}-cell mass. Human islets transplanted under the kidney capsule of immunocompromised mice and treated systemically with CDDO-Me, an Nrf2 activator, display increased {beta}-cell proliferation. Thus, Nrf2 regulates {beta}-cell mass and is an exciting therapeutic target for expanding {beta}-cell mass in diabetes.

physiology↗

bioRxiv2020

Heterozygous deletion of SYNGAP enzymatic domains in rats causes selective learning, social and seizure phenotypes

Pathogenic variants in SYNGAP1 are one of the most common genetic causes of nonsyndromic intellectual disability (ID) and are considered a risk for autism spectrum disorder (ASD). SYNGAP1 encodes a synaptic GTPase activating protein that modulates the intrinsic GTPase activity of several small G-proteins and is implicated in regulating the composition of the postsynaptic density. By targeting the deletion of exons encoding the calcium/lipid binding (C2) and GTPase activating protein (GAP) domains, we generated a novel rat model to study SYNGAP related pathophysiology. We find that rats heterozygous for the C2/GAP domain deletion (Syngap+/{Delta}-GAP) exhibit reduced exploration and fear extinction, altered social behaviour, and spontaneous seizures, while homozygous mutants die within days after birth. This new rat model reveals that the enzymatic domains of SYNGAP are essential for normal brain function and provide an important new model system in the study of both ID/ASD and epilepsy.

neuroscience↗

bioRxiv2020

Insights into the Binding Mechanism of Ascorbic Acid and Violaxanthin with Violaxanthin De-Epoxidase (VDE) and Chlorophycean Violaxanthin De-Epoxidase (CVDE) Enzymes: Docking, Molecular Dynamics, and Free Energy Analysis

Photosynthetic organisms have evolved to work under low and high lights in photoprotection, acting as a scavenger of reactive oxygen species. The light dependent xanthophyll cycle involved in this process is performed by a key enzyme (present in the thylakoid lumen) Violaxanthin De-Epoxidase (VDE) in the presence of violaxanthin and ascorbic acid substrates. Phylogenetically, VDE is found to be connected with an ancestral enzyme Chlorophycean Violaxanthin De-Epoxidase (CVDE) present in the green algae on the stromal side of the thylakoid membrane. However, the structure and functions of CVDE were not known. In search of functional similarities involving this cycle, the structure, binding conformation, stability, and interaction mechanism of CVDE are explored with the two substrates in comparison to VDE. The structure of CVDE was determined by homology modeling and validated. In-silico docking (of first-principles-optimized substrates) revealed it has a larger catalytic domain than VDE. A thorough analysis of the binding affinity and stability of four enzyme-substrate complexes are performed by computing free energies and its decomposition, the root-mean-square deviation (RMSD) and fluctuation (RMSF), the radius of gyration, salt-bridge and hydrogen bonding interactions in molecular dynamics. Based on these, violaxanthin interacts with CVDE to the similar extent as that of VDE, hence its role is expected to be the same for both the enzymes. On the contrary, ascorbic acid has a weaker interaction with CVDE than VDE. As these interactions drive epoxidation or de-epoxidation process in the xanthophyll cycle, it immediately discerns that either ascorbic acid does not take part in de-epoxidation or this process requires a different cofactor because of the weaker interaction of ascorbic acid with CVDE in comparison to VDE.

plant biology↗