Biology subjects

Mitra, S.

Publications and source records attributed to Mitra, S..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts

Animal hosts harbour divergent microbiota, including various Bifidobacterium species and strains, yet their evolutionary relationships, and functional adaptions remain understudied. By integrating taxonomic, genomic and predicted functional annotations, we uncover how Bifidobacterium adapts to host-specific environments, shaped by vertical transmission, dietary influences, and host phylogeny. Our findings reveal that host phylogeny is a major determinant of gut microbiota composition. Distinct microbial networks in mammalian and avian hosts reflect evolutionary adaptations to dietary niches, such as carnivory, and ecological pressures. At a strain-resolved level, we identify strong co-phylogenetic associations between Bifidobacterium strains and their hosts, driven by vertical transmission and dietary selection, underscoring the intricate co-evolutionary dynamics between these microbes and their hosts. Functional analyses highlight striking host-specific metabolic adaptations in Bifidobacterium, particularly in carbohydrate metabolism and oxidative stress responses. In mammals, we observe an enrichment of glycoside hydrolases (GH) tailored to complex carbohydrate-rich diets, including multi-domain GH13_28 -amylases featuring diverse carbohydrate-binding modules (CBM25, CBM26, and the novel CBM74). These adaptations emphasise the ecological flexibility of Bifidobacterium in breaking down -linked glucose polysaccharides, such as resistant starch. Together, our study provides new insights into the evolutionary trajectories and ecological plasticity of Bifidobacterium, revealing how host phylogeny and dietary ecology drive microbial diversity and function. These findings deepen our understanding of host-microbe co-evolution and the critical role of microbiota in shaping animal health and adaptation.

microbiology↗

bioRxiv2024

Inhibition of the extracellular matrix protein fibulin-3 reduces immunosuppressive signaling in tumor stem cells and increases macrophage activation against glioblastoma

Glioblastoma tumors remain a formidable challenge for immune-based treatments because of their molecular heterogeneity, poor immunogenicity, and growth in the largely isolated and immunosuppressive neural environment. As the tumor grows, GBM cells change the composition and architecture of the neural extracellular matrix (ECM), affecting the mobility, survival, and function of immune cells such as tumor-associated microglia and infiltrated macrophages (TAMs). We have previously described the unique expression of the ECM protein EFEMP1/fibulin-3 in GBM compared to normal brain and demonstrated that this secreted protein promotes the growth of the GBM stem cell (GSC) population. Here, we describe a novel immunomodulatory role of fibulin-3 and the immuno-boosting effects of targeting this ECM protein. Mice carrying fibulin-3-deficient intracranial tumors showed increased myeloid infiltration and reduced expression of TAM pro-tumoral markers (Arginase, CD206) compared to controls. The opposite was observed in orthotopic tumors overexpressing fibulin-3. In silico dataset analysis of clinical datasets revealed positive correlation of fibulin-3 with an immunosuppressive signature, which was validated in GSCs and in vivo. We further demonstrated that fibulin-3 regulates the expression of immunosuppressive signals (CSF-1, TGF{beta}) and the innate immune checkpoint CD47 in GSCs via autocrine activation of NF-{kappa}B signaling. Accordingly, immunosuppressive signals were downregulated in GSCs by knockdown of fibulin-3 or inhibition of this protein with an anti-fibulin-3 antibody. Co-culture of GBM cells with syngeneic macrophage lines or primary macrophages in presence of anti-fibulin-3 antibody increased macrophage phagocytosis and antibody-dependent killing of the tumor cells, Furthermore, locoregional delivery of anti-fibulin-3 antibody in mice carrying intracranial GBM increased the infiltration of TAMs expressing pro-inflammatory markers, reducing tumor viability. Our findings show that anti-fibulin-3 approaches, which impact the pericellular ECM surrounding tumor cells and TAMs, can diminish immunosuppression in GBM and boost innate immune responses against the tumor.

cancer biology↗

bioRxiv2024

Choices of regulatory logic class modulate the dynamical regime in random Boolean networks

Random Boolean networks (RBNs) have been widely explored as models for understanding complex systems, in particular gene regulatory networks (GRNs). Stability (order) and instability (chaos), critical characteristics of any dynamic system, have naturally been a central focus in RBN research. Several measures have previously been introduced to assess stability, e.g., via damage spreading or via statistical properties of attractors such as their number, lengths or basin sizes. Undoubtedly, network topology plays an important role in shaping the dynamics of RBN. Another key factor influencing the dynamics is the Boolean functions (BFs) assigned to each node. In this work, we conduct a systematic investigation to examine the influence of five different classes of BFs on the dynamics of RBNs. By employing various dynamical stability measures, we show that biologically meaningful BFs consistently drive the dynamics toward the stable regime compared to random BFs. This observation holds across networks with varying size, connectivity, and degree distributions. Additionally, we show that the change in the values of our stability measures with increasing connectivity or size of RBNs is different across the BF classes. For most observables, random BFs change the values significantly, pushing the dynamics toward a more chaotic regime with increasing connectivity or network size. In contrast, biologically meaningful BFs show very minimal fluctuations for most stability measures. These findings emphasize the advantage of restricting to biologically meaningful classes in the reconstruction and modeling of biological systems within Boolean framework.

systems biology↗

bioRxiv2024

Elucidating conformational alteration of human islet amyloid polypeptide by nonsynonymous substitution

Islet amyloid polypeptide (IAPP) is a peptide hormone that serves multiple essential functions, including metabolism and regulating gastric emptying and satiation through amylin receptors. However, mutations in the IAPP, notably in the amyloidogenic segment (20-29 amino acid residues), cause its aggregation and amyloid formation, which leads to {beta}-cell toxicity and death in type 2 diabetes mellitus (T2DM) and protein misfolding disorders (PMDs). The current work aims to elucidate the non-synonymous variants in the IAPP, which may adversely affect its function and rise to T2DM and PMDs. We harnessed in silico non-synonymous single-nucleotide polymorphisms (nsSNPs) assessment and molecular dynamics (MD) simulation to discover the potential deleterious mutants that cause T2DM and PMDs. Firstly, we executed nsSNPs prediction in IAPP using the NCBI dbSNP server, and then, all the predicted nsSNPs were assessed by a total of 26 in silico tools to find out which possessed the most deleterious effect in IAPP. Finally, MD simulation was carried out utilizing the most deleterious nsSNPs to check which significantly alters the conformational dynamics of IAPP. We found a total of 62 nsSNPs, among which the top 4 deleterious nsSNPs (T37P, L45P, G66R, and T69I) were selected based on the deleteriousness predictions by in silico tools and their location in the mature IAPP sequence (34-70 amino acid residues). MD simulations further confirm that three variants (T37P, L45P, and G66R) significantly alter the conformational dynamics of IAPP, suggesting a potential starting point for future research to elucidate the roles of these variants in IAPP aggregation and amyloid formation and their associations with T2DM and PMDs.

biophysics↗

bioRxiv2024

In vivo Treatment of a Severe Vascular Disease via a Bespoke CRISPR-Cas9 Base Editor

Genetic vascular disorders are prevalent diseases that have diverse etiologies and few treatment options. Pathogenic missense mutations in the alpha actin isotype 2 gene (ACTA2) primarily affect smooth muscle cell (SMC) function and cause multisystemic smooth muscle dysfunction syndrome (MSMDS), a genetic vasculopathy that is associated with stroke, aortic dissection, and death in childhood. Here, we explored genome editing to correct the most common MSMDS-causative mutation ACTA2 R179H. In a first-in-kind approach, we performed mutation-specific protein engineering to develop a bespoke CRISPR-Cas9 enzyme with enhanced on-target activity against the R179H sequence. To directly correct the R179H mutation, we screened dozens of configurations of base editors (comprised of Cas9 enzymes, deaminases, and gRNAs) to develop a highly precise corrective A-to-G edit with minimal deleterious bystander editing that is otherwise prevalent when using wild-type SpCas9 base editors. We then created a murine model of MSMDS that exhibits phenotypes consistent with human patients, including vasculopathy and premature death, to explore the in vivo therapeutic potential of this base editing strategy. Delivery of the customized base editor via an engineered SMC-tropic adeno-associated virus (AAV-PR) vector substantially prolonged survival and rescued systemic phenotypes across the lifespan of MSMDS mice, including in the vasculature, aorta, and brain. Together, our optimization of a customized base editor highlights how bespoke CRISPR-Cas enzymes can enhance on-target correction while minimizing bystander edits, culminating in a precise editing approach that may enable a long-lasting treatment for patients with MSMDS.

bioengineering↗

bioRxiv2024

Immunologic and Biophysical Features of the BNT162b2 JN.1- and KP.2-Adapted COVID-19 Vaccines

Vaccines remain a vital public health tool to reduce the burden of COVID-19. COVID-19 vaccines that are more closely matched to circulating SARS-CoV-2 lineages elicit more potent and relevant immune responses that translate to improved real-world vaccine effectiveness. The rise in prevalence of the Omicron JN.1 lineage, and subsequent derivative sublineages such as KP.2 and KP.3, coincided with reduced neutralizing activity and effectiveness of Omicron XBB.1.5-adapted vaccines. Here, we characterized the biophysical and immunologic attributes of BNT162b2 JN.1- and KP.2-adapted mRNA vaccine-encoded spike (S) protein immunogens. Biophysical interrogations of S revealed the structural consequences of hallmark amino acid substitutions and a potential molecular mechanism of immune escape employed by JN.1 and KP.2. The vaccine candidates were evaluated for their immunogenicity when administered as fourth or fifth doses in BNT162b2-experienced mice or as a primary series in naive mice. In both vaccine-experienced and naive settings, JN.1- and KP.2-adapted vaccines conferred improved neutralizing responses over the BNT162b2 XBB.1.5 vaccine against a broad panel of emerging JN.1 sublineages, including the predominant KP.3.1.1 and emerging XEC lineages. Antigenic mapping of neutralizing responses indicated greater antigenic overlap of JN.1- and KP.2-adapted vaccine responses with currently circulating sublineages compared to an XBB.1.5-adapted vaccine. CD4+ and CD8+ T cell responses were generally conserved across all three vaccines. Together, the data support the selection of JN.1- or KP.2-adapted vaccines for the 2024-25 COVID-19 vaccine formula. ONE-SENTENCE SUMMARYThe Omicron JN.1- and KP.2-adapted BNT162b2 mRNA vaccines encoding prefusion S proteins elicit similar preclinical neutralizing antibody responses against circulating JN.1 sublineage pseudoviruses that are more potent than those elicited by past iterations of BNT162b2 licensed vaccines, thus demonstrating the importance of annual strain changes to the COVID-19 vaccine.

immunology↗

bioRxiv2024

Stabilization of HSA32, an aggregation-prone protein, by the protein disaggregase HSP101 plays a critical role in maintaining acquired thermotolerance in Arabidopsis

Heat acclimation confers acquired thermotolerance (AT), and heat-acclimation memory (HAM) is the maintenance of AT for some time. In Arabidopsis and rice, the heat-stress-associated 32-kDa protein (HSA32) and the protein disaggregase heat shock protein101 (HSP101) form a positive feedback loop at the protein level to maintain AT; HSA32 mitigates HSP101 degradation, and HSP101 positively regulates the accumulation of HSA32. Here, we report the underpinning mechanism regarding how HSP101 affects the HSA32 level in Arabidopsis. We found that, without HSP101, nascent HSA32 was rapidly degraded, and the proteasome inhibitor, bortezomib, inhibited the degradation. In response to heat stress, the nascent HSA32-GFP fusion protein was present in liquid condensates and diffused in the cytosol after returning to non-stress temperature. Proximity labeling with HSA32-TurboID identified HSP101 and five other protein chaperones and co-chaperones as the primary interactors. Disturbing the interaction between HSA32 and HSP101 destabilized HSA32 and compromised HAM. HSA32 is predicted as a TIM-barrel protein with three intrinsically disordered regions of high aggregation propensity. Recombinant HSA32 expressed in E. coli was partitioned into insoluble fractions, suggesting that HSA32 is aggregation-prone. Our findings highlight how the interplay between an aggregation-prone protein and a protein disaggregase can maintain plant stress memory.

plant biology↗

bioRxiv2024

Understanding responses to multi-electrode epiretinal stimulation using a biophysical model

ObjectiveNeural interfaces are designed to evoke specific patterns of electrical activity in populations of neurons by stimulating with many electrodes. However, currents passed simultaneously through multiple electrodes often combine nonlinearly to drive neural responses, making evoked responses difficult to predict and control. This response nonlinearity could arise from the interaction of many excitable sites in each cell, any of which can produce a spike. However, this multi-site activation hypothesis is difficult to verify experimentally. ApproachWe developed a biophysical model to study retinal ganglion cell (RGC) responses to multi-electrode stimulation and validated it using data collected from ex vivo preparations of the macaque retina using a microelectrode array (512 electrodes; 30{micro}m pitch; 10{micro}m diameter). ResultsFirst, the model was validated by using it to reproduce essential empirical findings from single-electrode recording and stimulation, including recorded spike voltage waveforms at multiple locations and sigmoidal responses to injected current. Then, stimulation with two electrodes was modeled to test how the positioning of the electrodes relative to the cell affected the degree of response nonlinearity. Currents passed through pairs of electrodes positioned near the cell body or far from the axon (>40 {micro}m) exhibited approximately linear summation in evoking spikes. Currents passed through pairs of electrodes close to the axon summed linearly when their locations along the axon were similar, and nonlinearly otherwise. Over a range of electrode placements, several distinct, localized spike initiation sites were observed, and the number of these sites covaried with the degree of response nonlinearity. Similar trends were observed for three-electrode stimuli. All of these trends in the simulation were consistent with experimental observations. Significance. These findings support the multi-site activation hypothesis for nonlinear activation of neurons, providing a biophysical interpretation of previous experimental results and potentially enabling more efficient use of multi-electrode stimuli in future neural implants.

bioengineering↗

bioRxiv2024

Activation and regulation of a p38α MAPK by its downstream MAPKAP kinase through feedback phosphorylation and LLPS-driven condensate formation.

MAP kinases (MAPKs) represent a class of evolutionarily conserved stress and extracellular stimuli responsive signaling molecules. p38 group of MAPKs known to be activated by dual-specific upstream MAPK kinases and also by autophosphorylation. They activate MAPK activated protein kinases (MAPKAPKs) in a context dependent manner by specific phosphorylation, and together, they play crucial biological roles. One such pair is PMK3, p38-MAPK and its cognate MAPKAPK, MAK2, downstream of DLK1 (MAPK kinase kinase) and MKK4 (MAPK kinase) in C. elegans. They are implicated in axonal regeneration, degeneration and synaptic pruning in response to neuronal injury. Here, we report that PMK3 and MAK2 engage in a feedback relationship, leading to phosphorylation-mediated activation of both kinases. Interaction of PMK3 with MAK2 through the canonical docking site leads to negligible de novo autophosphorylation of PMK3. Phosphorylation of both Thr and Tyr residues on the TxY-motif necessary for the full activation of PMK3 requires catalytic activity of MAK2 as confirmed by mass spectrometry. Distribution of phosphorylation sites on either kinase when incubated together, and presence of long intrinsically disordered regions in each kinase indicate that PMK3:MAK2 complex is conformationally plastic in nature. MAK2 increases bioavailability of aggregation-prone PMK3 by virtue of its ability to form LLPS-driven condensates in vitro, wherein they retain enzymatic activities and phosphorylate each other. Furthermore, experiments with transgenic C. elegans reveal that MAK2 controls stability of PMK3 and localization of PMK3 puncta in touch neuron. Our observations offer an unreported activation mechanism of a p38-MAPK by its downstream MAPKAPK. Significance StatementMAPK kinases are evolutionarily conserved, and are key players in stress response, cell survival, differentiation, metabolic processes and neuronal response to injury. MAPK pathways are primarily activated through unidirectional flow of phosphorylation-signal MAP3K to MAP2K to MAPK, and in some cases to a downstream MAPKAPK. We found that a C. elegans MAPK (PMK3) can also be activated by its downstream MAPKAPK (MAK2) through feedback phosphorylation that ensures robust activation of PMK3 by MAK2 without requiring the MAP2K. Furthermore, MAK2 increases bioavailability of activation-competent and active PMK3 by preventing its aggregation through LLPS-driven condensate formation in vitro and in the worm neuron. This feedback relationship might ensure rapid activation of such MAPK pathways in response to nervous system injury or stress.

biochemistry↗

bioRxiv2024

Low Kit expression identifies Hematopoietic Stem Cell subsets with enhanced lymphoid potential in mice and humans

Hematopoietic stem cells (HSCs) with multilineage potential are critical for effective T cell reconstitution and restoration of the adaptive immune system after allogeneic Hematopoietic Cell Transplantation (allo-HCT). The Kitlo subset of HSCs is enriched for multipotential precursors,1, 2 but their T-cell lineage potential has not been well-characterized. We therefore studied the thymic reconstituting and T-cell potential of Kitlo HSCs. Using a preclinical allo-HCT model, we demonstrate that Kitlo HSCs support better thymic recovery, and T-cell reconstitution resulting in improved T cell responses to infection post-HCT. Furthermore, Kitlo HSCs with augmented BM lymphopoiesis mitigate age-associated thymic alterations, thus enhancing T-cell recovery in middle-aged hosts. We find the frequency of the Kitlo subset declines with age, providing one explanation for the reduced frequency of T-competent HSCs and reduced T-lymphopoietic potential in BM precursors of aged mice.3, 4, 5 Chromatin profiling revealed that Kitlo HSCs exhibit higher activity of lymphoid-specifying transcription factors (TFs), including Zbtb1. Deletion of Zbtb1 in Kitlo HSCs diminished their T-cell potential, while reinstating Zbtb1 in megakaryocytic-biased Kithi HSCs rescued T-cell potential, in vitro and in vivo. Finally, we discover an analogous Kitlo HSC subset with enhanced lymphoid potential in human bone marrow. Our results demonstrate that Kitlo HSCs with enhanced lymphoid potential have a distinct underlying epigenetic program.

immunology↗

bioRxiv2024

RNA/DNA Binding Protein TDP43 Regulates DNA Mismatch Repair Genes with Implications for Genome Stability

TDP43 is an RNA/DNA binding protein increasingly recognized for its role in neurodegenerative conditions, including amyotrophic lateral sclerosis and frontotemporal dementia (FTD). As characterized by its aberrant nuclear export and cytoplasmic aggregation, TDP43 proteinopathy is a hallmark feature in over 95% of ALS/FTD cases, leading to the formation of detrimental cytosolic aggregates and a reduction in nuclear functionality within neurons. Building on our prior work linking TDP43 proteinopathy to the accumulation of DNA double-strand breaks (DSBs) in neurons, the present investigation uncovers a novel regulatory relationship between TDP43 and DNA mismatch repair (MMR) gene expressions. Here, we show that TDP43 depletion or overexpression directly affects the expression of key MMR genes. Alterations include MLH1, MSH2, MSH3, MSH6, and PMS2 levels across various primary cell lines, independent of their proliferative status. Our results specifically establish that TDP43 selectively influences the expression of MLH1 and MSH6 by influencing their alternative transcript splicing patterns and stability. We furthermore find aberrant MMR gene expression is linked to TDP43 proteinopathy in two distinct ALS mouse models and post-mortem brain and spinal cord tissues of ALS patients. Notably, MMR depletion resulted in the partial rescue of TDP43 proteinopathy-induced DNA damage and signaling. Moreover, bioinformatics analysis of the TCGA cancer database reveals significant associations between TDP43 expression, MMR gene expression, and mutational burden across multiple cancers. Collectively, our findings implicate TDP43 as a critical regulator of the MMR pathway and unveil its broad impact on the etiology of both neurodegenerative and neoplastic pathologies.

biochemistry↗

bioRxiv2024

Co-existence of plasmid-mediated blaNDM-1 and blaNDM-5 in Escherichia coli sequence type 167 and ST101 and their discrimination through restriction digestion

The concurrent presence of multiple New Delhi metallo-{beta}-lactamase (blaNDM) variants within an isolate often goes undetected without the use of next-generation sequencing. This study detects and characterizes dual blaNDM-variants in Escherichia coli through Sanger and whole-genome sequencing. Additionally, a rapid identification method utilizing restriction digestion was designed for detecting variants carrying M154L mutation. Antibiotic susceptibility, minimal inhibitory concentration for meropenem and ertapenem, PCR and Sanger sequencing of blaNDM along with genome sequencing using Ilumina and Nanopore technology were conducted. Transmissibility and replicon types of blaNDM-harbouring plasmids were evaluated. Restriction digestion using restriction enzyme, BtsCI was developed to distinguish between blaNDM-1 and variants possessing M154L mutations. Two isolates belonging to phylogroups A; ST167 and B1; ST101 and resistant to meropenem and ertapenem ([≥]16mg/L) were recovered from the blood of a neonate and the rectal swab of a pregnant woman respectively. blaNDM was detected by PCR, and Sanger sequences of blaNDM showed two peaks at 262 (G & T) and 460 (A & C) nucleotide positions indicative of more than one blaNDM variant. Hybrid assembly confirmed co-existence of blaNDM-1 and blaNDM-5 in each isolate. blaNDM-1 was located on IncY (ST167) and IncHI1A/HI1B (ST101), while blaNDM-5 was on a IncFIA/FII (ST167) and IncC (ST101) plasmids. Digestion with BtsC1 could discriminate blaNDM-1 and blaNDM-5. Co-existence of multiple blaNDMS, blaNDM-1 and blaNDM-5 in epidemic clones of E. coli is concerning. Restriction digestion method and Sanger sequencing can facilitate quick identification of dual blaNDM variants in single isolate. ImportanceThe global dissemination of antimicrobial resistance genes is a serious concern. One such gene, blaNDM, has spread all across the globe via plasmids. blaNDM confers resistance against all {beta}-lactam antibiotics except monobactams. Most of the earlier literature reported presence of single blaNDM variants. However, this study reports the prevalence of dual blaNDM variants (blaNDM-1 and blaNDM-5) located on two separate plasmids identified in two distinct E. coli epidemic clones ST167 and ST101; isolated from a septicaemic neonate and a pregnant mother respectively. blaNDM-5 differs from blaNDM-1 due to presence of two point mutations i.e., V88L and M154L. This study detected dual blaNDM-variants through Sanger sequences and further validated through hybrid-genome assembly. Detection of multiple blaNDM-variants in a single isolate remains difficult until genome sequencing or southern blotting are carried out. Hence, a simple restriction digestion method was devised for rapid screening of dual blaNDM-variants containing M154L mutation.

microbiology↗

bioRxiv2024

Post-GWAS functional analyses of CNTNAP5 suggests its role in glaucomatous neurodegeneration

Primary angle closure glaucoma (PACG) affects more than 20 million people worldwide, with an increased prevalence in south-east Asia. In a prior haplotype-based GWAS, we identified a novel CNTNAP5 genic region, significantly associated with PACG. In the current study, we have extended our perception of CNTNAP5 involvement in glaucomatous neurodegeneration in a zebrafish model, through investigating phenotypic consequences pertinent to retinal degeneration upon knockdown of cntnap5 by translation-blocking morpholinos. While cntnap5 knockdown was successfully validated using an antibody, immunofluorescence followed by western blot analyses in cntnap5-morphant (MO) zebrafish revealed increased expression of acetylated tubulin indicative of perturbed cytoarchitecture of retinal layers. Moreover, significant loss of Nissl substance is observed in the neuro-retinal layers of cntnap5-MO zebrafish eye, indicating neurodegeneration. Additionally, in spontaneous movement behavioural analysis, cntnap5-MO zebrafish have a significantly lower average distance traversed in light phase compared to mismatch-controls, whereas no significant difference was observed in the dark phase, corroborating with vision loss in the cntnap5-MO zebrafish. This study provides the first direct functional evidence of a putative role of CNTNAP5 in visual neurodegeneration.

genetics↗

bioRxiv2024

Sex-specific fear acquisition following early life stress is linked to amygdala glutamate metabolism

Early life stress (ELS) adversely affects physiological and behavioral outcomes, increasing the vulnerability to stress-related disorders, such as post-traumatic stress disorder (PTSD). PTSD prevalence is significantly higher in women and is partially mediated by genetic risk variants. Understanding how sex influences the interaction of PTSD risk genes, such as FKBP5, with trauma-related behaviors is crucial for uncovering PTSDs neurobiological pathways. The development of in-depth behavioral analysis tools using unsupervised behavioral classification is thereby a crucial tool to increase the understanding of the behavioral outcomes related to stress-induced fear memory formation. The current study investigates the sex-specific effects of ELS exposure by using the limited bedding and nesting (LBN) paradigm. The LBN exposure disrupted different facets of the hypothalamic-pituitary-adrenal (HPA) axis in a sex-specific manner directly after stress and at adult age. Moreover, freezing was altered by LBN exposure in both the acquisition and the retrieval of fear in a sex-dependent manner. Unsupervised behavioral analysis revealed a higher active fear response after LBN exposure during fear acquisition in females, but not in males. The regulation of the HPA axis is closely intertwined with cellular metabolism and core regulatory cascades. To investigate the impact of LBN exposure on tissue-specific metabolism, a metabolomic pathway analysis in the basolateral amygdala revealed a specific sex- and stress-dependent effect on purine, pyrimidine, and glutamate metabolism. The present study highlights the intricate interplay between metabolic pathways and the neurobiological substrates implicated in fear memory formation and stress regulation. Overall, these findings highlight the importance of considering sex-specific metabolic alterations in understanding the neurobiological mechanisms underlying stress-related disorders and offer potential avenues for targeted interventions.

animal behavior and cognition↗

bioRxiv2023

ABI3 regulates ABI1 function to control cell length in primary root elongation zone

Post-embryonic primary root growth is effectively an interplay of several hormone signalling pathways. Here, we show that the ABA-responsive transcription factor ABI3, controls primary root growth through regulation of JA signalling molecule JAZ1 along with ABA responsive factor ABI1. In absence of ABI3, primary root elongation zone is shortened with significantly reduced cell length. Expression analyses and ChIP based assays indicate that ABI3 negatively regulates JAZ1 expression by occupying its upstream regulatory sequence and enriching repressive histone modification mark H3K27 trimethylation, thereby occluding RNAPII occupancy. Previous studies have shown that JAZ1 interacts with ABI1, the protein phosphatase 2C, that works during ABA signalling. Our results indicate that in absence of ABI3, when JAZ1 expression levels are high, ABI1 protein shows increased stability, compared to when JAZ1 is absent, or ABI3 is overexpressed. Consequently, in abi3 mutant, due to higher stability of ABI1, reduced phosphorylation of plasma membrane H+ATPase (AHA2) occurs. HPTS staining further indicated that, abi3 root cell apoplasts show reduced protonation, compared to wild type and ABI3 overexpressing seedlings. Such impeded proton extrusion, negatively affects cell length in primary root elongation zone. ABI3 therefore controls cell elongation in primary root by affecting ABI1-dependent protonation of root cell apoplasts. In summary, ABI3 controls expression of JAZ1 and in turn modulates function of ABI1 to regulate cell length in the elongation zone during primary root growth.

plant biology↗

bioRxiv2023

Fusobacterium nucleatum present in the saliva of oral cancer subjects can activate niche defense of oral squamous cell carcinoma

Oral cancer is a subset of head and neck cancer (HNC), has a high incidence rate in this malignancy group. Cancer Stem Cells (CSCs) are population of the heterogeneous malignant cells present within oral tumor microenvironment. CSCs stemness permits them to control several signaling pathways and so play a role in cancer progression and relapse. A number of studies have recently demonstrated the presence of specific oral bacteria populations and their lipopolysaccharides (LPS) in the tumor microenvironment. The precise mechanism of action in the initiation, progression, and relapse of oral cancer by the oral bacteria are yet to be determined. We previously reported pathogenic bacterial internalization in CSCs. Based on the findings; we have developed an in-vitro model to investigate how oral microbiota may integrate into the tumor microenvironments CSC population and control its activity. Notably, we found that live bacteria and their LPS, mostly Fusobacterium nucleatum isolated from clinical subjects, were capable of invading CSCs in the in-vitro experimental design setup. Post the host-pathogen interaction; it enabled the activation of a niche modulatory tumor stemness defense (TSD) phenotype in the CSCs. These aggressive CSCs with the TSD phenotype have been found to have a critical role in the progression and relapse of oral cancer.

cancer biology↗

bioRxiv2023

Preponderance of generalized chain functions in reconstructed Boolean models of biological networks

Boolean networks (BNs) have been extensively used to model the dynamics of gene regulatory networks (GRNs) that underlie cellular decisions. The dynamics of BNs depend on the network architecture and regulatory logic rules (or Boolean functions (BFs)) associated with nodes, both of which have been shown to be far from random in large-scale studies of reconstructed Boolean models. At the level of the BFs, nested canalyzing functions (NCFs) have been shown to be strongly enriched in such GRN models. The central question we address here is whether that enrichment is due to certain sub-types of NCFs. To answer this, we build on one sub-type of NCFs, the chain functions (or chain-0 functions) proposed by Gat-Viks and Shamir. First, we propose 2 other sub-types of NCFs, namely, the class of chain-1 functions which is the dual of the class of chain-0 functions, and generalized chain functions, the union of the chain-0 and chain-1 types. Next, we find that the fraction of NCFs that are chain-0 functions decays exponentially with the number of inputs, and exhibits a fractal-like behaviour as a function of the bias for a fixed number of inputs. Moreover, we explain several of these observations analytically. Then, by analyzing 5990 BFs extracted from a large dataset of reconstructed Boolean models, and 2 other datasets, we find that generalized chain functions are significantly enriched within the NCFs. Lastly, we illustrate the severe restriction imposed by generalized chain functions compared to NCFs for 3 biological models and perform model selection on them using known relative stability constraints.

systems biology↗

bioRxiv2023

Gestures Of Hunger: Uncovering Intentional Gestural Communication In Free-Ranging Hanuman Langurs

Contrary to previous beliefs, intentional gestural communication (IGC) is not exclusive to the hominoid lineage but is also present in other non-human primates. Here, we report the presence of IGC among free-ranging Hanuman langur troop in Dakshineswar, West Bengal, India. These langurs exhibit a food-requesting behaviour wherein they use several gestures to communicate with the humans nearby. Moreover, they can also assess the recipients mental state and persistently check if the signal (food request) has been received, waiting until they receive the desired food item. We have identified eight begging gestures used by langurs of all ages, except infants. The most common gesture is by holding cloth (BGc), but provocation-initiated begging (BGpi) and begging by embracing legs (BGe) efficiently direct these events to its success. The frequency of successful begging events is higher in the evening due to increased human interactions. Our findings suggest that ontogenetic ritualization might be at play here among these troop members as this gestural communication has been learned through imitation and reinforced by the reward of receiving food. Moreover, these successful begging events serve as an effective foraging strategy for urban-adapted langurs, allowing them to acquire high-calorie processed food items within a human-modified urban ecosystem.

animal behavior and cognition↗