Biology subjects

Mohapatra, A.

Publications and source records attributed to Mohapatra, A..

18 recordsLinked to original sources

bioRxiv2026

The CREB-regulated co-activators 2/3, have a role, in vivo, in osteoblastic gene expression.

Many hormones and substances acting through G-protein coupled receptors and protein kinase A (PKA) activation inhibit the salt-inducible kinases (SIKs) by phosphorylation. SIKs tonically phosphorylate CREB-regulated transcriptional coactivators (CRTC1, 2 and 3), sequestering them in the cytoplasm and, thus, preventing their translocation into the nucleus. Once in the nucleus, CRTCs bind CREB family member transcription factors and enhance their activity. We and others have shown that parathyroid hormone (PTH) activation of PKA and resultant SIK2/3 inhibition allows CRTC2/3 nuclear translocation. One of the major actions of CRTC2/3 in the osteoblast lineage is the regulation of transcription of Rankl, as well as other PTH-controlled genes. However, little is known about the role of these co-activators in the osteoblast lineage in vivo. Here, we have investigated whether there are basal effects in vivo on bone examined at 2 different ages of conditional deletion of these two co-activators in the osteoblast lineage using Col2.3-Cre. We found significant increases in body weight, length, bone mineral density, bone volume/total volume, trabecular thickness and number with decreased trabecular separation in young (2 months old) male mice, all of which dissipated by 6 months of age. Female mice showed minimal changes in the bone phenotype at either age. Nevertheless, there were gene expression changes in bones of both sexes at both ages, and in particular decreases in Rankl, Runx2 and Sost, and accompanying changes in Wnt pathway genes. These effects may explain the changes in the bone phenotype in the young male mice, but it is notable that there is a sexual dimorphism in the action of CRTC2 and CRTC3. Overall, the work supports the data from research in vitro and forms a basis for investigation of the role of these co-activators in PTH action in vivo.

physiology↗

bioRxiv2026

A lipid acyl code-based Dip2-Pkc1 signalling axis maintains mitochondrial integrity in eukaryotes

Organelle membranes employ diverse lipids to relay key signals for efficient coordination of cellular processes. Diacylglycerol (DAG) is a simple yet critical lipid secondary messenger, but the regulatory mechanisms and functional implications for its distribution remain poorly understood. We have recently shown that Protein Kinase C (Pkc1) activation is driven by selective DAGs (C36:0, C36:1), whose levels are governed by Disco-interacting protein 2 (Dip2) (Shambhavi et al., 2025). Here, through genetic, chemical, and lipidomic screens, we show that the absence of Dip2 leads to specific DAG accumulation on the mitochondrial membrane and impacts its morphology, function, and quality control in yeast. Remarkably, the elevated DAGs in{Delta} dip2 promote translocation of Pkc1 to mitochondria via its DAG-binding C1 domain, but not the HR1 domain, suggesting functional partitioning between the regulatory domains. We also show that only specific DAGs, not the bulk DAGs, are required for Pkc1s targeting and inactivating Phospholipase C (Plc1) restores Pkc1 localisation and the associated mitochondrial defects. In addition, we identify that respiratory growth triggers specific DAG (C36:1) accumulation in the mitochondria, thereby promoting Pkc1 recruitment. Furthermore, we establish that the Psi1-Plc1-Dip2 axis is required for survival under respiratory growth conditions. Taken together, our study uncovers a novel, Dip2-mediated, unconventional Pkc1 signalling axis for maintaining mitochondrial homeostasis under nutrient transition and highlights how distinct lipid fingerprints enable precise control over organellar homeostasis.

cell biology↗

bioRxiv2026

The lung tissue environment in Mycobacterium tuberculosis infection determines local monocyte differentiation

Infection by Mycobacterium tuberculosis (Mtb) is characterized by pathogen persistence in lung cells derived from blood monocytes. Since monocyte-derived lung subsets differ in their ability to restrict the growth of intracellular Mtb in mice, understanding the ontogeny of these subsets can inform development of host-directed therapies. Circulating monocytes are proposed to be heterogeneous, arising from distinct bone marrow or spleen progenitors that direct local differentiation. However, the role of the Mtb-infected lung environment in this process has not been addressed. We found that infected and uninfected mice had similar bone marrow monopoiesis, resulting in equivalent monocyte differentiation within the infected lung. While pulmonary Mtb infection also induced splenic monopoiesis, we found no impact on lung monocyte differentiation in splenectomized mice. However, when wildtype monocytes were transferred into Mtb-infected Sp140-/- recipients, in which excess Type I interferons and neutrophils alter the lung environment, we observed that donor-derived lung subsets resembled recipient-derived cells. In the lungs of Mtb-infected mice, we identified monocyte-derived lung subsets with unique gene expression, associated with specific spatial distributions and cell neighborhoods. These findings suggest that the local lung environment has a larger influence on the phenotypic diversity of monocyte-derived lung cells than does the peripheral environment.

immunology↗

bioRxiv2026

Tracking vaginal microbiome transitions in bacterial vaginosis for cues of antibiotic resilience

BackgroundBacterial vaginosis (BV) is a common and difficult-to-treat vaginal disorder, with significant implications for reproductive health, particularly in low and middle-income countries. Clinical cure based on symptom resolution or Nugent scores often do not correspond to restoration of healthy vaginal microbiome. Factors underlying treatment failure remain poorly defined, warranting the need for understanding post-treatment microbiome dynamics to improve long-term outcomes. ObjectivesTo delineate longitudinal vaginal bacteriome dynamics, integrating microbial composition, transition patterns, and clinical symptoms in a closely followed cohort of women with BV based on treatment outcome. MethodsVaginal swabs from reproductive-age women (18-45 years) were collected and classified as BV-positive ([≥]7) or healthy ([≤]3) using Nugent scoring. BV cases were treated using single-dose secnidazole and followed for three months. Sociodemographic, clinical, and behavioral data were statistically analyzed across groups. Vaginal microbiome composition was assessed using 16S rRNA sequencing, evaluating taxonomic profiles, alpha and beta diversity, differential abundance, and co-occurrence networks. ResultsAntibiotic treatment reduced overall microbial diversity and shifted community composition toward healthy controls, though relapse samples retained higher diversity of BV-associated taxa such as Sneathia, Dialister, and Gardnerella, while no-relapse and control groups showed higher Lactobacillus abundance. Corynebacterium amycolatum appeared protective, while Mycoplasma and Fusobacterium played symptom-specific roles. Microbial network analysis showed denser and more persistent associations in baseline and relapse groups, with Sneathia remaining a central node. ConclusionShort-term symptom resolution in BV does not correspond to full microbial recovery; necessary for long-term remission. Functional traits of resilient taxa like Sneathia, Fannyhessea and Dialister may confer resilience and enable recolonization, undermining long term treatment efficacy.

microbiology↗

bioRxiv2026

Tensile Expansion Microscopy Applies Mechanical Force to Super-resolve Fixed and Image Live Cellular Samples

Understanding biophysical phenomena requires techniques that access biologically relevant spatial and temporal scales. Expansion Microscopy (ExM) is a sample preparation approach which achieves super-resolution spatial scales by leveraging osmotic forces in a swellable hydrogel to physically separate structures to distances larger than the diffraction limit of light. Yet, in traditional osmotic ExM only pre- and post- expanded samples can be imaged. Further, fragmentation, hydrogel deformation, and signal loss are common while requiring samples to be chemically fixed. Therefore, there is little control of the expansion, reproducibility can be challenging, and dynamics of biological samples at applicable temporal scales cannot be observed. Here, we develop Tensile Expansion Microscopy (TExM) to mechanically expand fixed and, notably, living cellular samples. Highly-stretchable and tough double network alginate- Ca2+/polyacrylamide hydrogels are expanded by tensile forces applied using an electromechanical iris expansion device during continuous imaging on a fluorescence microscope. We incorporate two-photon polymerized microscale fluorescent fiducial markers to track samples and distortion during expansion. The hydrogels controllably and repeatedly expand up to 3.3x with distortions less than 12 {micro}m across 1.3 mm2. TExM is first applied to fixed NIH 3T3 fibroblast cells with immunohistochemistry-stained microtubules, achieving super-resolutions of 100 nm. Then, TExM is demonstrated with living HeLa cells with internal fluorescent reporters showing increased cell size and cell-to-cell separation under 3.2x linear expansion. Overall, TExM allows for continuous, stepwise, and precise temporal modulation of lateral substrate strain, enabling real time monitoring of dynamics of both fixed and viable live cell processes at higher spatial resolutions. TExM can further investigate broad biophysical questions due to its compatibility with other analytical imaging methods that are sensitive to water or fixatives used in traditional osmotic ExM.

biophysics↗

bioRxiv2026

Chemical interactions in polyethylene glycol-induced condensates lead to an anomalous FRET response from a flexible linker-fluorescent protein crowding sensor

The cellular cytosol is a crowded environment. Biomolecular Forster resonance energy transfer (FRET) sensors have been developed to measure crowding in cytosol mimics comprised of synthetic polymers such as polyethylene glycol (PEG) and Ficoll that impart an excluded volume effect. In the current study, we explore the unsolicited role of PEG in driving the phase separation of a protein crowding sensor, AcGFP1/mCherry-FRET crowding helix 2 (CrH2), into fluorescent puncta. In contrast, a DNA-based crowding sensor (CrD), with an Alexa488/Cy5 FRET pair, does not form puncta under the same crowding conditions. Using fluorescence recovery after photobleaching imaging, we uncover the liquid-like physical properties of the PEG-induced puncta. Two-color fluorescence microscopy imaging reveals crowder-induced inhomogeneity, concentration variations, and partition coefficient across the dilute and dense phases of the liquid puncta, which remain largely underexplored in bulk fluorometry measurements. Thus, the average crowding sensor response may originate from an aqueous biphasic system, reporting an erroneous average response instead of distinct levels of crowdedness. A comparison of excluded volume effects conferred by Ficoll and PEGs of various molecular weight ranges shows the influence of size, concentration, excluded volume, and chemical composition on the CrH2 sensor response. We demonstrate that PEGs enable phase separation and alter sensor response through a mechanism that may be driven by polymer interactions with the flexible hinge region of CrH2. Overall, we determine the biophysical mechanisms underlying PEG-induced condensation of CrH2 and demonstrate a CrD sensor as an alternative that does not undergo phase separation.

biophysics↗

bioRxiv2025

Impaired IFNγ responsiveness of lung monocyte-derived cells limits immunity to Mycobacterium tuberculosis

Lung mononuclear phagocyte (MNP) subsets differ in their ability to restrict Mycobacterium tuberculosis (Mtb) during chronic infection, yet the mechanisms underlying this difference are not well defined. Here, we show that CD11clo monocyte-derived cells (MNC1), the subset of lung cells that is most permissive for Mtb viability during chronic infection, express lower levels of interferon-gamma (IFN{gamma}) signaling proteins, resulting in reduced responses to IFN{gamma} compared to alveolar macrophages (AM) and CD11chi MNC2. Moreover, type I IFN signaling suppresses IFN{gamma}-mediated MHC-II expression, impairing antigen-specific CD4 T cell activation by MNC1 cells. Importantly, prior immunity conferred by contained Mtb infection enhances IFN{gamma} responsiveness of monocyte-derived cells, reducing bacterial burdens in lungs and within MNC subsets. Our findings indicate that heterogeneous IFN{gamma} responsiveness is exploited by Mtb for persistence in vivo. Overcoming or bypassing impaired IFN{gamma} responsiveness may guide the development of more effective TB vaccines and host-directed therapies.

immunology↗

bioRxiv2025

Molecular attributes of intrinsically disordered regions in secretomes influence fungal pathogenesis

Secretory proteins are crucial for establishing fungal infection through biomolecular interactions with the host. Accumulating evidence suggest that intrinsically disordered regions (IDRs) in proteins facilitate molecular interactions. How do IDRs of secretory proteins influence fungal pathogenesis? By analyzing 195,359 secretory proteins of 73 fungal species, we find that IDRs in plant pathogen extracellular non-effectors are enriched for weak polyampholytes and polyelectrolytes. These could adopt beads-on-string conformation effectively promoting assembly of diverse enzymes aiding swift degradation of host cell wall. Both animal pathogen secretory proteins and intracellular plant pathogen effectors show enrichment for strong polyampholytes, potentially aiding phase-separation and organizing intracellular biological matter to hijack or suppress host machinery. Importantly, IDRs of plant pathogen effectors which mimic host IDRs could have emerged through convergent evolution, while those of non-effectors might have evolved de novo. Thus, specific molecular attributes of fungal secretome IDRs can influence initiation, establishment and long-term persistence of infection.

systems biology↗

bioRxiv2025

A Mycobacterium tuberculosis rare variable antigen vaccine reduces lung pathology without affecting bacterial burdens

Mycobacterium tuberculosis is the leading cause of death globally due to a single infectious agent. Currently, no reliable vaccine against pulmonary tuberculosis, the primary adult disease caused by Mtb infection, exists. CD4 T cells are essential in protection against Mtb infection and inducing a protective CD4 T cell response remains the goal of most Mtb vaccines currently in testing. However, most Mtb T cell antigens do not exhibit antigenic variation, suggesting that T cell recognition does not drive selection of escape mutants. We utilized a set of antigens that do exhibit sequence diversity within human T cell epitopes and tested the impact of vaccination with these rare variable antigens (RVMA) using a DNA vaccine platform. We found vaccination with RVMA significantly alters the immune response to Mtb infection in both C57BL/6 and hypersusceptible SP140-/- mice without reducing bacterial burdens. RVMA vaccination of hypersusceptible SP140-/- animals prevented necrosis and altered the lesion composition reducing tissue damage and increasing CD4 T cell distribution. Reductions in pathology were associated with increases in ROR{gamma}t-expressing CD4 T cells and decreases in monocyte-derived cells in the lungs prior to the development of necrotic lesions. These results suggest T cell responses to certain antigens may be involved in preventing pathology without significantly changing bacterial burdens. SignificanceMtb is the leading cause of death worldwide due to an infectious agent, a title it has held for most of human history. Despite significant efforts, an effective vaccine that prevents the morbidity associated with pulmonary tuberculosis, the most prevalent form of adult TB disease, has yet to be developed. A lack of correlates of protection and ideal antigen targets have hampered the development of a subunit vaccine. Mtb is unique in that the CD4 T cell epitope sequences of Mtb are predominantly under purifying selection. Targeting antigens that are an exception to this T cell epitope sequence conservation can inform our understanding of what the most optimal antigens are for inclusion in an effective vaccine against Mtb. Our study describes the effects of a vaccine consisting solely of antigens that exhibit epitope sequence diversity on the outcome of infection and identifies possible benefits to lung pathology. Given the ongoing interest in prevention of disease (POD) vaccines for TB, these results can inform future vaccine design and the search for correlates of protection.

immunology↗

bioRxiv2025

CCR2 recruits monocytes to the lung, while CX3CR1 modulates positioning of monocyte-derived CD11cpos cells in the lymph node during pulmonary tuberculosis

Infection by Mycobacterium tuberculosis (Mtb) continues to cause more than 1 million deaths annually, due to pathogen persistence in lung macrophages and dendritic cells derived from blood monocytes. While accumulation of monocyte-derived cells in the Mtb-infected lung partially depends on the chemokine receptor CCR2, the other chemoattractant receptors regulating trafficking remain undefined. We used mice expressing knock-in/knockout reporter alleles of Ccr2 and Cx3cr1 to interrogate their expression and function in monocyte-derived populations of the lungs and draining mediastinal lymph nodes during Mtb infection. CCR2 and CX3CR1 expression varied across monocyte-derived subsets stratified by cell surface Ly6C expression in both organs. We found that expression of CCR2 predicted dependence of monocyte-derived cells on the receptor for lung and lymph node accumulation. CCR2-deficient mice were also observed to have worsened lung and lymph node Mtb burden. While CX3CR1 deficiency, alone or in combination with CCR2 deficiency, did not affect cell frequencies or lung Mtb control, its absence was associated with altered positioning of monocyte-derived dendritic cells in mediastinal lymph nodes. We found that combined loss of Ccr2 and Cx3cr1 also worsened Mtb control in the mediastinal lymph node, suggesting a rationale for the persistent expression of CX3CR1 among monocyte-derived cells in pulmonary tuberculosis. IMPORTANCEMycobacterium tuberculosis is the respiratory pathogen responsible for the deadliest infectious disease worldwide. Susceptible humans exhibit ineffective immune responses, in which infected phagocytes are not able to eliminate the pathogen. Since recruited monocyte-derived cells serve as reservoirs for persistent infection, understanding how these phagocytes accumulate in the lung and why they are unable to eliminate Mtb can inform development of therapies that can synergize with antimicrobials to achieve faster and more durable Mtb elimination. Monocyte-derived cells express the chemokine receptors CCR2 and CX3CR1, but the role of the latter in Mtb infection remains poorly defined. The significance of our study is in elucidating the roles of these receptors in the trafficking of monocyte-derived cells in the infected lung and mediastinal lymph node. These data shed light on the host response in tuberculosis and in other pulmonary infections.

immunology↗

bioRxiv2024

A phosphorylation signal activates genome-wide transcriptional control by BfmR, the global regulator of Acinetobacter resistance and virulence.

The nosocomial pathogen Acinetobacter baumannii is a major threat to human health. The sensor kinase-response regulator system, BfmS-BfmR, is essential to multidrug resistance and virulence in the bacterium and represents a potential antimicrobial target. Important questions remain about how the system controls resistance and pathogenesis. Although BfmR knockout alters expression of >1000 genes, its direct regulon is undefined. Moreover, how phosphorylation controls the regulator is unclear. Here, we address these problems by combining mutagenesis, ChIP-seq, and in vitro phosphorylation to study the functions of phospho-BfmR. We show that phosphorylation is required for BfmR-mediated gene regulation, antibiotic resistance, and sepsis development in vivo. Consistent with activating the protein, phosphorylation induces dimerization and target DNA affinity. Integrated analysis of genome-wide binding and transcriptional profiles of BfmR led to additional key findings: (1) Phosphorylation dramatically expands the number of genomic sites BfmR binds; (2) DNA recognition involves a direct repeat motif widespread across promoters; (3) BfmR directly regulates 303 genes as activator (eg, capsule, peptidoglycan, and outer membrane biogenesis) or repressor (pilus biogenesis); (4) BfmR controls several non-coding sRNAs. These studies reveal the centrality of a phosphorylation signal in driving A. baumannii disease and disentangle the extensive pathogenic gene-regulatory network under its control.

microbiology↗

bioRxiv2024

Prior exposure to malaria decreases SARS-CoV-2 mediated mortality in K18-hACE2 mice without influencing viral load in lungs

BackgroundEpidemiological evidence for decreased prevalence and/or mortality due to SARS-CoV-2 infections in countries endemic for malaria have been reported. However, such associational studies in human population are limited by known and several unknown confounding factors. The current study, the first of its kind, was designed to seek experimental evidence to test the hypothesis if prior exposure to Plasmodial infections cross-protect against SARS-CoV-2 challenge infection in a murine model, K-18 human ACE2 transgenic mice. MethodsMice that had recovered from Plasmodium chabaudi infection 40 days earlier were challenged with a virulent strain of SARS-CoV-2 and viral load in lungs as well as mortality were scored and compared with K18 hACE2 mice that had not experienced prior malaria. ResultsThe viral load in lungs 6 days post challenge were comparable in malaria recovered mice and controls suggesting no significant generation of anti-viral immunity. However, mice with prior malaria exposure were significantly protected against SARS-CoV-2 induced mortality. Significant differences were observed in several host immune responses between the two groups when cytokines, chemokines and transcription factors were quantified in lungs. The plasma levels of several cytokines and chemokines were also significantly different between the two groups. ConclusionThe results of the study suggest that prior exposure to malaria protects mice against viral induced mortality in K18 hACE2 transgenic mice challenged with a virulent isolate of SARS- CoV-2 in the absence of demonstrable host immunity inhibiting viral growth in lungs.

immunology↗

bioRxiv2023

Alpha-synuclein expression in neuron modulates the Japanese encephalitis virus infection

Japanese encephalitis virus (JEV) stands as a prominent vector-borne zoonotic pathogen, displaying neurotropism and eliciting Parkinsons disease (PD)-like symptoms among most symptomatic survivors. A characteristic feature of PD is aggregation of mutated -synuclein (-syn) that damages the dopaminergic neurons. Considering this link between JEV-induced PD-like symptoms and -syn pathogenesis, we explored the role of -syn in JEV infectivity in neuronal cells. Our investigation revealed significant increase in endogenous -syn expression in JEV-infected cells. Additionally, treatment with exogenous -syn (Exo-syn) led to a substantial reduction in JEV replication, suggesting its anti-JEV effect. Furthermore, Exo-syn treatment led to the upregulation of superoxide dismutase 1 (SOD1) and reduction in reactive oxygen species (ROS). The results were validated by endogenous -syn-silencing, that decreased SOD1 level and raised ROS level in neuronal cells. Similarly, the SOD1 inhibition via LCS-1 also intensified ROS and JEV infection. Overall, our results suggest that -syn exerts an anti-JEV effect by regulating protein involved in oxidative stress inside neuronal cells. This study contributes valuable insights into the interplay between -syn expression and JEV infectivity, shedding light on avenues to further investigate the potential role of -syn in JEV pathogenesis. ImportanceJapanese encephalitis virus (JEV) poses significant threat particularly to children. Despite extensive research efforts, the development of effective treatments against JEV has been impeded. One of the major setbacks is a lack of comprehensive understanding of neurotropism. The study focuses on alpha synuclein (-syn), a neuronal protein, and aims to determine its role in JEV pathogenesis. Present study reveals that host cell upregulates -syn in response of JEV infection. -syn restrains JEV propagation by modulating superoxide dismutase 1 (SOD1) expression which further blocks JEV-induced ROS generation. Endogenous -syn silencing led to decrease in SOD1 expression and increased viral titer. -syn plays crucial role in counteracting oxidative stress through SOD1, which is essential for limiting JEV replication. This study provides broader implications for antiviral strategies and its possible role in neurodegenerative diseases; however, there is still much to explore, particularly regarding its aggregation kinetics in JEV infection.

microbiology↗

bioRxiv2022

Reductive Enzyme Cascades for Valorization of PET Deconstruction Products

To better incentivize the collection of plastic wastes, new chemical transformations must be developed that add value to plastic deconstruction products. Polyethylene terephthalate (PET) is a common plastic whose deconstruction through chemical or biological means has received much attention. However, a limited number of alternative products have been formed from PET deconstruction, and only a small share could serve as building blocks for alternative materials or therapeutics. Here, we demonstrate the production of useful mono-amine and diamine building blocks from known PET deconstruction products. We achieve this by designing one-pot biocatalytic transformations that are informed by the substrate specificity of an {omega}-transaminase and diverse carboxylic acid reductases (CAR) towards PET deconstruction products. We first establish that an {omega}-transaminase from Chromobacterium violaceum (cvTA) can efficiently catalyze amine transfer to potential PET-derived aldehydes to form the mono-amine para-(aminomethyl)benzoic acid (pAMBA) or the diamine para-xylylenediamine (pXYL). We then identified CAR orthologs that could perform the bifunctional reduction of TPA to terephthalaldehyde (TPAL) or the reduction of mono-(2-hydroxyethyl) terephthalic acid (MHET) to its corresponding aldehyde. After characterizing 17 CARs in vitro, we show that the CAR from Segniliparus rotundus (srCAR) had the highest observed activity on TPA. Given these newly elucidated substrate specificity results, we designed modular enzyme cascades based on coupling srCAR and cvTA in one-pot with enzymatic co-factor regeneration. When we supply TPA, we achieve a 69 {+/-} 1% yield of pXYL, which is useful as a building block for materials. When we instead supply MHET and subsequently perform base-catalyzed ester hydrolysis, we achieve 70 {+/-} 8% yield of pAMBA, which is useful for therapeutic applications and as a pharmaceutical building block. This work expands the breadth of products derived from PET deconstruction and lays the groundwork for eventual valorization of waste PET to higher-value chemicals and materials. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/520786v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1bb7386org.highwire.dtl.DTLVardef@19d8c55org.highwire.dtl.DTLVardef@68569eorg.highwire.dtl.DTLVardef@ed398_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2021

Evolution of reduced mate-harming tendency of males in Drosophila melanogaster populations selected for faster life history

Detrimental effect of males on female, often termed mate harm, is a hallmark of sexual conflict. Allowed to evolve unchecked, mate harming traits are predicted to bring down average fitness of a population, unless mitigated by the evolution of resistance in females. In addition, life history may also modulate sexual conflict, but the mechanism is not clearly understood. Here we investigated the evolution of mate harm in a set of experimentally evolved laboratory populations of Drosophila melanogaster wherein a faster aging has evolved in response to >1000 generations of selection for faster development and early reproduction. We quantified mortality and fecundity of Oregon R females held with evolved (ACO) and ancestral males (CO) to show that the evolved males are significantly less detrimental to their mates. We compared our results from the ACO males with that from a phenocopied version of the ancestral regime (CCO) to show that only part of the observed difference in mate harm can be attributed to the evolved difference in body size. We further show that the reduction in mate harming ability evolved despite an increase in courtship activity, especially early in life. We discuss the causative role of an evolved reproductive schedule and altered breeding ecology. Significance statementSexually antagonistic male effects can significantly bring down female fitness. Along with female counter evolution of resistance traits, life history has been conjectured to impose constrains on the evolution of such harming ability in males. Here, we report the evolution of mate harming ability in males of a set of five replicate Drosophila melanogaster populations that evolved smaller size and faster aging as a result of >1000 generations of experimental evolution for faster development and early reproduction. We show that in spite of ample scope of sexual selection, the faster aging males have evolved reduced mate harming ability despite being more active in courting their mates. To the best of our knowledge, this is one of the first clear evidences demonstrating the causal relationship between evolution of life history and reduction in sexual antagonism in a population.

evolutionary biology↗

bioRxiv2021

Generation of transducible version of a recombinant human HAND2 transcription factor from Escherichia coli

Transcription factor HAND2 has a significant role in vascularization, angiogenesis, and cardiac neural crest development. Also, it is one of the key cardiac factors crucial for the enhanced derivation of functional and mature myocytes from non-myocyte cells. Here, we report the generation of the recombinant human HAND2 fusion protein from the heterologous system. First, we cloned the full-length human HAND2 gene (only protein-coding sequence) after codon optimization along with the fusion tags (for cell penetration, nuclear translocation, and affinity purification) into the expression vector. We then transformed and expressed it in Escherichia coli (E. coli) strain, BL21(DE3). Next, the effect (in terms of expression) of tagging of fusion tags with this recombinant protein at two different terminals was also investigated. Notably, using affinity chromatography, we established the one-step homogeneous purification of human recombinant HAND2 protein; and through circular dichroism spectroscopy, we established that this purified protein had retained its secondary structure. Furthermore, we show that this purified human protein could transduce the human cells and translocate to its nucleus. Prospectively, the purified recombinant HAND2 protein can potentially be a safe and effective molecular tool in the direct cardiac reprogramming process and other biological applications.

bioengineering↗

bioRxiv2019

High fat diet worsens pathology and impairment in an Alzheimers mouse model, but not by synergistically decreasing cerebral blood flow

Obesity is linked to increased risk for and severity of Alzheimers disease (AD). Cerebral blood flow (CBF) reductions are an early feature of AD and are also linked to obesity. We showed that non-flowing capillaries, caused by adhered neutrophils, underlie the CBF reduction in mouse models of AD. Because obesity could exacerbate the vascular inflammation likely underlying this neutrophil adhesion, we tested links between obesity and AD by feeding APP/PS1 mice a high fat diet (Hfd) and evaluating behavioral, physiological, and pathological changes. We found trends toward poorer memory performance in APP/PS1 mice fed a Hfd, impaired social interactions with either APP/PS1 genotype or a Hfd, and synergistic impairment of sensory-motor function in APP/PS1 mice fed a Hfd. The Hfd led to increases in amyloid-beta monomers and plaques in APP/PS1 mice, as well as increased brain inflammation. These results agree with previous reports showing obesity exacerbates AD-related pathology and symptoms in mice. We used a crowd-sourced, citizen science approach to analyze imaging data to determine the impact of the APP/PS1 genotype and a Hfd capillary stalling and CBF. Surprisingly, we did not see an increase in the number of non-flowing capillaries or a worsening of the CBF deficit in APP/PS1 mice fed a Hfd as compared to controls, suggesting capillary stalling is not a mechanistic link between a Hfd and increased severity of AD in mice. Reducing capillary stalling by blocking neutrophil adhesion improved CBF and short-term memory function in APP/PS1 mice, even when fed a Hfd. Significance statementObesity, especially in mid-life, has been linked to increased risk for and severity of Alzheimers disease. Here, we show that blocking adhesion of white blood cells leads to increases in brain blood flow that improve cognitive function, regardless of whether mice are obese or not.

neuroscience↗

bioRxiv2018

Discovery of Large Disjoint Motif in Biological Network using Dynamic Expansion Tree

Network motifs play an important role in structural analysis of biological networks. Identification of such network motifs leads to many important applications, such as: understanding the modularity and the large-scale structure of biological networks, classification of networks into super-families etc. However, identification of network motifs is challenging as it involved graph isomorphism which is computationally hard problem. Though this problem has been studied extensively in the literature using different computational approaches, we are far from encouraging results. Motivated by the challenges involved in this field we have proposed an efficient and scalable Motif discovery algorithm using a Dynamic Expansion Tree (MDET). In this algorithm embeddings corresponding to child node of expansion tree are obtained from the embeddings of parent node, either by adding a vertex with time complexity O(n) or by adding an edge with time complexity O(1) without involving any isomorphic check. The growth of Dynamic Expansion Tree (DET) depends on availability of patterns in the target network. DET reduces space complexity significantly and the memory limitation of static expansion tree can overcome. The proposed algorithm has been tested on Protein Protein Interaction (PPI) network obtained from MINT database. It is able to identify large motifs faster than most of the existing motif discovery algorithms.

bioinformatics↗