Biology subjects

Agarwal, S.

Publications and source records attributed to Agarwal, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

DeepUnitMatch: tracking neurons across days in electrophysiology using Deep Neural Networks

To understand neural processes such as learning or memory, we need to track the activity of populations of neurons at the level of single spikes and across days. Here, we leverage deep neural networks to build DeepUnitMatch, a software that reliably tracks individual neurons in high-density electrophysiological recordings across weeks. DeepUnitMatch uses only the spike waveforms of the neurons, and not their spiking patterns, and outperforms current solutions.

neuroscience↗

bioRxiv2025

Genetic elements promote retention of extrachromosomal DNA in cancer cells

Extrachromosomal DNA (ecDNA) is a prevalent and devastating form of oncogene amplification in cancer1,2. Circular megabase-sized ecDNAs lack centromeres and segregate stochastically during cell division3-6 yet persist over many generations. EcDNAs were first observed to hitchhike on mitotic chromosomes into daughter cell nuclei over 40 years ago with unknown mechanism3,7. Here we identify a family of human genomic elements, termed retention elements, that tether episomes to mitotic chromosomes to increase ecDNA transmission to daughter cells. We develop Retain-seq, a genome-scale assay that reveals thousands of human retention elements conferring generational persistence to heterologous episomes. Retention elements comprise a select set of CpG-rich gene promoters and act additively. Live-cell imaging and chromatin conformation capture show that retention elements physically interact with mitotic chromosomes at regions which are mitotically bookmarked by transcription factors and chromatin proteins, intermolecularly recapitulating promoter-enhancer interactions. Multiple retention elements are co-amplified with oncogenes on individual ecDNAs in human cancers and shape their sizes and structures. CpG-rich retention elements are focally hypomethylated; targeted cytosine methylation abrogates retention activity and leads to ecDNA loss, suggesting that methylation-sensitive interactions modulate episomal DNA retention. These results highlight the DNA elements and regulatory logic of mitotic ecDNA retention. Amplifications of retention elements promote the maintenance of oncogenic ecDNA across generations of cancer cells, revealing the principles of episome immortality intrinsic to the human genome.

cancer biology↗

bioRxiv2025

In cellulo DNA assembly for targeted genomic integration and rearrangement in human cells

Although therapeutic genome editing holds great potential to remedy diverse inherited and acquired disorders, targeted installation of medium to large sized genomic modifications in therapeutically relevant cells remains challenging. We have developed an approach that permits DNA sequence assembly and integration in human cells leveraging CRISPR-targeted dual flap synthesis. This method, named prime assembly, allows for RNA-programmable site-specific integration of single- or double-stranded DNA fragments. Unlike homology-directed repair, prime assembly was similarly active in dividing and non-dividing cells. We applied prime assembly to perform targeted exon recoding, transgene integration, and megabase-scale rearrangements, including at therapeutically relevant loci in primary human cells. Prime assembly expands the capabilities of genome engineering by enabling the targeted integration of medium to large sized DNA sequences without relying on double-stranded DNA donors, nuclease-driven double strand breaks, or cell cycle progression.

molecular biology↗

bioRxiv2025

A Temporal Single-Cell Multi-Omics Atlas of Murine Pancreatic Islet Remodeling During Hyperglycaemia Progression

Pancreatic islets undergo coordinated cellular remodeling during obesity-induced insulin resistance (IR). However, the associated molecular changes across endocrine and non-endocrine compartments remain largely unexplored. Here, using longitudinal single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) on islets from C57BL/6 mice subjected to high-fat diet (HFD) feeding for 8, 16, and 24 weeks, along with age-matched controls on regular chow, we mapped dynamic changes in islet cell composition and transcriptional states. Beta cells demonstrated pronounced stress-induced reprogramming, with the emergence of proliferative and dysfunctional subsets. Alpha and delta cell fractions declined under HFD, despite increased polyhormonal biosynthesis, suggesting functional rather than numerical adaptation. Immune profiling showed robust expansion of proinflammatory M1 macrophages and upregulation of NF-{kappa}B and chemotaxis pathways, particularly at 16 weeks. Notably, cell-cell communication analyses revealed diet-specific disruption in signaling networks. Under HFD conditions, intercellular communication among beta cells, macrophages, and delta cells was markedly altered, leading to the disruption of key signaling pathways such as the gastric inhibitory polypeptide receptor (GIPR) and major histocompatibility complex-I (MHC-I). Notably, C-C motif chemokine ligand 27A (Ccl27a) expression and chromatin accessibility were significantly altered in a distinct subpopulation of beta cells under HFD condition, indicative of a niche-specific regulatory mechanism. Integration with human islet datasets from obese and type 2 diabetes (T2D) donors confirmed conserved shifts in beta cell identity and immune activation. This study presents a comprehensive high-resolution atlas of islet remodeling under metabolic stress, identifying key communication nodes and transcriptional programs pertinent to T2D pathogenesis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/656754v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@64aee0org.highwire.dtl.DTLVardef@150beborg.highwire.dtl.DTLVardef@1c19c6dorg.highwire.dtl.DTLVardef@4d1a0_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

LOSS OF ROR2 TYROSINE KINASE RECEPTOR IS ASSOCIATED WITH ENDOTHELIAL DYSFUNCTION IN PAH VIA INAPPROPRIATE INTEGRIN BETA 1 ACTIVATION

RationaleEndothelial dysfunction is a key feature of pulmonary arterial hypertension (PAH). We previously identified Wnt7a, a ligand of the Wnt planar cell polarity (PCP) pathway, as essential for pulmonary angiogenesis, with its loss linked to PAH. Given the importance of Wnt/PCP to lung endothelial function and angiogenesis, our goal is to elucidate how Wnt/PCP regulates angiogenic responses in pulmonary microvascular endothelial cells (PMVECs). ROR2, a tyrosine kinase receptor specific to Wnt/PCP, is crucial for cardiovascular development, but its role in PAH is unclear. We hypothesized that ROR2 supports endothelial homeostasis, and its loss would impair angiogenesis, contributing to PAH. MethodsEndothelial-specific ROR2 knockout (ROR2 ECKO) and wild-type (WT) mice were studied under normoxia and chronic hypoxia using echocardiography, hemodynamics, and lung morphometry. PMVECs from healthy and PAH lungs were transfected with ROR2 siRNA/constructs for functional and molecular studies. Focal adhesion (FA) activation and force generation were assessed via FRET-based methods. Bulk and single-cell transcriptomic analyses were performed on siROR2 PMVECs and ROR2 ECKO lungs. ResultsROR2 ECKO mice exhibited worsened pulmonary hypertension, right ventricular remodeling, microvascular loss, and muscularization in hypoxia. Single-cell RNA sequencing of lung endothelial cells showed dysregulation of pathways involved in barrier formation and angiogenesis. Evans blue dye extravasation confirmed reduced endothelial barrier integrity in ROR2 ECKO mice. ROR2-deficient PAH PMVECs displayed increased adhesion, permeability, and FA numbers, with reduced VE-cadherin at cell junctions. Confocal imaging revealed ROR2 localization in FAs, interacting with integrin {beta}1 (ITGB1). FRET analysis showed that ITGB1 remained in an active, adhesion-promoting state in ROR2-deficient cells. Restoring ROR2 in PAH PMVECs normalized adhesion, barrier function, and FA abundance. Transcriptomic analysis identified Rab12 as a key mediator of ROR2-ITGB1 crosstalk, with Rab12 knockdown mimicking ROR2 deficiency in PMVECs. ConclusionsROR2 regulates pulmonary angiogenesis by maintaining endothelial barrier integrity and facilitating integrin recycling. Restoring ROR2 signaling could be a potential therapeutic approach for PAH.

cell biology↗

bioRxiv2025

CES1 DEFICIENCY IS ASSOCIATED WITH METABOLIC REPROGRAMING AND ENDOTHELIAL DYSFUNCTION IN PULMONARY ARTERIAL HYPERTENSION

BackgroundPulmonary arterial hypertension (PAH) is a progressive disease characterized by pulmonary microvascular loss and obliterative remodeling, driven by metabolic reprogramming, oxidative stress, and endothelial dysfunction. While BMPR2 mutations contribute to metabolic shifts in pulmonary microvascular endothelial cells (PMVECs), their low penetrance suggests additional genetic modifiers play a role. A genetic screen of PAH PMVECs identified carboxylesterase 1 (CES1)--an endoplasmic reticulum (ER) enzyme involved in lipid metabolism and detoxification--as a candidate regulator of endothelial metabolism and angiogenesis. We hypothesize that CES1 loss promotes endothelial dysfunction via metabolic reprogramming, lipotoxicity, and oxidative stress. MethodsPAH and healthy PMVECs and lung tissues were obtained from transplant donors and commercial sources. CES1 expression was modulated in PMVECs using siRNA knockdown and plasmid overexpression. Mitochondrial and ER function were assessed via confocal microscopy and proteomics. CES1 heterozygous knockout (HET KO) and endothelial-specific knockout (ECKO) mice were exposed to normoxia or hypoxia, with lung tissues analyzed by single-cell RNA sequencing (scRNA-seq) and histopathology. ResultsCES1 expression was significantly reduced in PAH PMVECs and vascular lesions. CES1-deficient PMVECs exhibited increased apoptosis, reactive oxygen species (ROS) production, mitochondrial fragmentation, ER stress, and impaired angiogenesis. Confocal imaging and metabolic studies revealed lipid droplet accumulation, reduced fatty acid oxidation, and a glycolytic shift-- phenotypes reversed by CES1 restoration. Mechanistically, CES1 transcription was induced by BMPR2 via NRF2 activation, a key regulator of redox and metabolic homeostasis. In vivo, CES1-deficient mice developed severe pulmonary hypertension (PH) under hypoxia, with extensive vascular remodeling, right ventricular dysfunction, and dysregulated angiogenesis and lipid metabolism pathways, as confirmed by lung scRNA-seq. ConclusionsCES1 is essential for pulmonary endothelial homeostasis and serves as a critical modifier of BMPR2 signaling. Given the limited efficacy of current PAH therapies in reversing endothelial dysfunction and small-vessel loss, restoring CES1 expression represents a promising therapeutic strategy.

biochemistry↗

bioRxiv2025

Benchmarking overlapping community detection methods for applications in human connectomics

Brain networks exhibit non-trivial modular organization, with groups of densely connected areas participating in specialized functions. Traditional community detection algorithms assign each node to one module, but this representation cannot capture integrative, multi-functional nodes that span multiple communities. Despite the increasing availability of overlapping community detection algorithms (OCDAs) to capture such integrative nodes, there is no objective procedure for selecting the most appropriate method and its parameters for a given problem. Here we overcome this limitation by introducing a datadriven method for selecting an OCDA and its parameters from performance on a tailored ensemble of generated benchmark networks, assessing 22 unique algorithms and parameter settings. Applied to the human structural connectome, we find that the Order Statistics Local Optimization Method (OSLOM) best identifies ground-truth overlapping structure in the benchmark ensemble and yields a seven-network decomposition of the human cortex. These modules are bridged by fifteen overlapping regions that generally sit at the apex of the putative cortical hierarchy--suggesting integrative, higher-order function-- with network participation increasing along the cortical hierarchy, a finding not supported using a non-overlapping modular decomposition. This data-driven approach to selecting OCDAs is applicable across domains, opening new avenues to detecting and quantifying informative structures in complex real-world networks.

neuroscience↗

bioRxiv2025

6-thio-2-deoxyguanosine inhibits telomere elongation by inducing a non-productive stalled telomerase complex

Most cancers upregulate the telomere lengthening enzyme telomerase to achieve unlimited cell division. How chemotherapeutic nucleoside 6-thio-2-deoxyguanosine (6-thio-dG) targets telomerase to inhibit telomere maintenance in cancer cells and tumors was unclear. Here, we demonstrate that telomerase insertion of 6-thio-dGTP prevents synthesis of additional telomeric repeats but does not disrupt telomerase binding to telomeres. Specifically, 6-thio-dG inhibits telomere extension after telomerase translocates along its product DNA to reposition the template, inducing a non-productive complex rather than enzyme dissociation. Furthermore, we provide direct evidence that 6-thio-dG treatment inhibits telomere synthesis by telomerase in cancer cells. In agreement, telomerase-expressing cancer cells harboring critically short telomeres are more sensitive to 6-thio-dG and show a greater induction of telomere losses compared to cancer cells with long telomere reserves. Our studies reveal that telomere length and telomerase status determine 6-thio-dG sensitivity and uncover the molecular mechanism by which 6-thio-dG selectively inhibits telomerase synthesis of telomeric DNA.

cancer biology↗

bioRxiv2025

Comparison of embolic effects between permanent and novel resorbable microspheres in a porcine renal artery embolization model for TAE

PurposeThis study evaluated porcine renal artery embolization using resorbable alginate microspheres versus permanent microspheres (Embozene), assessing vessel recanalization, local/systemic foreign body reactions, and potential complications. Materials and MethodsTwelve Yorkshire swine (3 female, 9 male) underwent unilateral kidney arterial embolization with either Embozene or resorbable microspheres. Angiography was performed to confirm embolization. Vessel recanalization for was determined through angiography. The effect of embolization was evaluated by assessment of serum chemistry markers and by renal histopathology at 1, 3, 7 and 28 days post-procedure. ResultsEmbolization procedures with both embolic agents were performed with 100% technical success. Hematology, coagulation factors and serum chemistry were largely unremarkable throughout the study period of 28 days. Alginate resorbable alginate microspheres facilitated compete recanalization and revascularisation within the initial 24hr observation window, while the permanent microsphere remained present at all evaluated time points. No inflammation was observed with resorbable microsphere whereas Embozene-induced inflammation was minimal to mild. Vascular histopathologic alteration with resorbable microspheres was limited and resolved by 24 hours, whereas Embozene caused sustained injury extending alteration to the internal elastic lamina, tunica media or adventitia. ConclusionAlginate resorbable microsphere demonstrated effective temporary embolization with a recanalization time of around 24 hours together with complete renal tissue recovery, no systemic impact, and minimal local reaction compared to Embozene. The findings suggest that embolization using resorbable microspheres is safe and may be suitable for use where temporary embolization of vessels is required.

bioengineering↗

bioRxiv2025

Resorbable alginate embolic microsphere for Musculoskeletal embolization applications

Resorbable embolic agents can be used for musculoskeletal (MSK) pain relief applications using a Transarterial Embolisation (TAE) technique. However, inconsistent particle size and shape, degradation rates, and unpredictable resorption and excretion of the breakdown products, limit their widespread clinical adoption. The present study reports self-degradable, rehydratable, freeze-dried, resorbable Ca2+-crosslinked alginate microspheres as a novel vascular embolic agent. The alginate lyase enzyme was incorporated into the alginate microspheres to achieve a controlled degradation rate under physiological conditions. Whilst the feasibility of alginate microspheres as embolic agents has been demonstrated, this is the first study where the controlled release is achieved in physiological conditions. To incorporate the alginate lyase enzyme in the alginate matrix, its activity was reversibly inhibited by preparing an alginate lyase-alginate-excipient mixture in a pH 3.6-3.9 buffered solution. An electrostatic encapsulator enabled the scalable preparation of microspheres of size 210 {+/-} 8 {micro}m at room temperature. The results showed that freeze-dried microspheres regained their shape and size within two minutes after reconstitution with saline, along with active alginate lyase. The reperfusion time of alginate microspheres was evaluated using digital subtraction angiography (DSA) and compared with imipenem and celestine (IMP-CS)in a porcine renal arterial embolisation model. It was observed that most of the blood vessels reperfused within 130-210 minutes, and complete vascular blush was recovered within 24 hours. Embolization with resorbable alginate microspheres induced recoverable ischemic necrosis in the targeted renal arteries. This unique feature of resorbable alginate microspheres in inducing ischemic necrosis, potentially in pain-propagating neovessels, makes it an ideal candidate embolic agent for treating MSK-associated pain using the TAE technique.

bioengineering↗

bioRxiv2025

A third type of PETase from the marine Halopseudomonas lineage

The enzymatic degradation of polyethylene terephthalate (PET) offers a sustainable solution for PET recycling. Over the past two decades, more than 100 PETases have been characterized, primarily exhibiting similar sequences and structures. Here, we report new PET-degrading /{beta} hydrolases, including HaloPETase1 from the marine Halopseudomonas lineage, thereby extending the narrow sequence space by novel features at the active site. The crystal structure of HaloPETase1 was determined to a resolution of 1.16 [A], revealing a unique active site architecture and a lack of the canonical {pi}-stacking clamp found in PETases so far. Further, variations in active site composition and loop structures were observed. Additionally, we found five more enzymes from the same lineage, two of which have a high similarity to type IIa bacterial PETases, while the other three resemble HaloPETase1. All these enzymes exhibited high salt tolerance ranging from 2.5 to 5 M NaCl leading to higher total product releases upon PET degradation at 40 or 50 {degrees}C. Based on these findings, we propose an extension of the existing PETase classification system to include type III PETases.

biochemistry↗

bioRxiv2024

Unveiling theranostic potential: Insights into cell-free microRNA-protein interactions

MicroRNAs (miRNAs) belong to a short endogenous class of non-coding RNAs which have been well studied for their crucial role in regulating cellular homeostasis. Their role in modulation of diverse biological pathways by intracellular or extracellular communication and interaction with DNA, RNA or protein, projects them or their targets as promising biomarkers and therapeutic agents. However, studying specific interactions in the extracellular or cell-free environment for drug discovery or biomarker establishment is resource-intensive. In this study, we derive a computational approach based on available experimental data to decipher patterns in miRNA-protein interactions in the cell-free milieu. We characterized the miRNA-protein interactome (miRPin, https://www.mirna.in/miRPin) and identified consensus sequences governing these interactions. The study establishes the role of multiple miRNAs and protein interactions present in cell-free environments leading to pathological conditions, viz., role of proteins like METTL3 and AGO2 etc. and miRNAs like hsa-miR-484 and hsa-miR-30 families, hsa-mir-126-5p etc. in association with multiple miRNAs in different cancer types, cardiovascular diseases, and neurological disorders. The findings outlined in the study may facilitate new avenues of therapeutic discovery leading to the understanding of cellular mechanisms underlying therapy relapse and drug resistance. By addressing these interactions in an extracellular environment may further gain insight into regulating disease initiation and progression, overcoming challenges related to drug efficacy and drug delivery in the presence of bilayer membranes with drug efflux pumps.

bioinformatics↗

bioRxiv2024

SurFlex Microscopy: Measuring Flexibility of Surface-Tethered Biomolecules

The flexibility of tethered molecules, such as those bound to biological membranes, is an important property that can influence molecular height, mobility, and accessibility. However, quantifying the flexibility of surface-tethered biomolecules in aqueous environments has been difficult due to a lack of experimental tools. Here we introduce SurFlex microscopy, a method based on fluorescence anisotropy that exploits the relationship between the conformational dynamics of a tethered molecule and the rotational diffusion of an attached fluorophore to extract information about molecular flexibility. By analyzing the polarization state of photons emitted after polarized excitation, we quantify apparent molecular flexibilities that include effects of tethering, self-interactions and buffer conditions. We first demonstrate the capabilities of SurFlex microscopy by measuring the flexibility of bilayer-tethered single-stranded DNA (ssDNA) of different lengths and nucleotide sequences. We find that sequence significantly impacts ssDNA flexibility, consistent with theoretical estimates, with weak intramolecular interactions in random sequences leading to higher apparent stiffness. Interestingly, we show that a pathological DNA sequence linked to Huntingtons disease exhibits unusual flexibility despite intramolecular interactions. We next extend SurFlex microscopy to live cells by measuring surface glycoprotein flexibility on red blood cells using fluorescent lectins. We show that trypsinization decreases glycan fluctuations, demonstrating that modifications to the cell surface can alter the flexibility of remaining surface molecules. SurFlex microscopy provides a new tool for quantifying molecular flexibility that can be used to study the role of tethered surface molecules in fundamental biological processes. Significance statementBiomolecules immobilized on one end play crucial roles in diverse cellular processes, from cell-cell signaling through surface receptors to the formation of DNA secondary structures. However, measuring biomolecular flexibility on surfaces has remained challenging. Here we present SurFlex microscopy, a technique that uses fluorescence anisotropy to quantify the flexibility of surface-anchored molecules. By analyzing the rotational dynamics of fluorophores attached to the ends of fluctuating biomolecules, SurFlex microscopy can be used to quantify persistence length. We demonstrate its capabilities by measuring sequence-dependent flexibility of DNA and crowding-dependent changes in glycan flexibility on native cell surfaces. This method opens new avenues for understanding how biomolecular flexibility influences key biological processes, such as those at cell surfaces during cell-cell contact formation and subsequent signaling.

biophysics↗

bioRxiv2024

PRMT5-mediated histone methylation regulates alternative splicing via MECP2-PTBP1 to promote EMT in breast cancer hypoxia

Tumor hypoxia induced alterations in the epigenetic landscape and alternative splicing influence cellular adaptations. PRMT5 is a type II protein arginine methyltransferase that regulates several tumorigenic events in many cancer types. However, the regulation of PRMT5 and its direct implication on aberrant alternative splicing under hypoxia remains unexplored. In this study, we observed hypoxia induced upregulation of PRMT5 via the CCCTC binding factor, CTCF. Further, PRMT5-mediated symmetric arginine dimethylation H4R3me2s and H3R8me2s directly regulated the alternative splicing of Transcription Factor 3 (TCF3). Under hypoxia, PRMT5-mediated histone dimethylation at the intronic conserved region (ICR) present between TCF3 exon 18a and exon 18b recruits DNA methyltransferase 3A (DNMT3A), resulting in DNA methylation. DNA methylation at the TCF3-ICR is recognized and bound by Methyl CpG binding protein (MECP2) resulting in RNA-Pol II pausing, promoting the recruitment of the negative splicing factor PTBP1 to the splicing locus of TCF3 mRNA. PTBP1 promotes the exclusion of exon 18a which results in the production of the pro-invasive TCF3-18B (E47) isoform which promotes EMT and invasion of breast cancer cells under hypoxia. Collectively, our results indicate PRMT5-mediated symmetric arginine dimethylation of histones regulates alternative splicing of TCF3 gene thereby enhancing EMT and invasion in breast cancer hypoxia.

cancer biology↗

bioRxiv2024

Protein recruitment to dynamic DNA-RNA host condensates

We describe the design and characterization of artificial nucleic acid condensates that are engineered to recruit and locally concentrate proteins of interest in vitro. These condensates emerge from the programmed interactions of nanostructured motifs assembling from three DNA strands and one RNA strand that can include an aptamer domain for the recruitment of a target protein. Because condensates are designed to form regardless of the presence of target protein, they function as "host" compartments. As a model protein we consider streptavidin (SA) due to its widespread use in binding assays, thus the host condensates presented here could find immediate use for the physical separation of a variety of biotin-tagged components. In addition to demonstrating protein recruitment, we describe two approaches to control the onset of condensation and protein recruitment. The first approach uses UV irradiation, a physical stimulus that bypasses the need for exchanging molecular inputs and is particularly convenient to control condensation in emulsion droplets. The second approach uses RNA transcription, a ubiquitous biochemical reaction that is central to the development of the next generation of living materials. We finally show that the combination of RNA transcription and degradation leads to an autonomous dissipative system in which host condensates and protein recruitment occur transiently, and that the host condensate size as well as the timescale of the transient can be controlled by the level of RNA degrading enzyme. For Table of Contents Only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/597281v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1f6dc00org.highwire.dtl.DTLVardef@1e5a9eforg.highwire.dtl.DTLVardef@f7c247org.highwire.dtl.DTLVardef@1f3c3d0_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2024

Biological activities and metabolic profile of endophytic Bacillus haynesii from Momordica charantia

Endophytes share a complex intimate relationship due to which they are capable of synthesizing metabolites that are either similar or derivative of host bioactive compounds. Such endophytes especially from medicinal plants can be prospected for commercial-scale production of the therapeutic compound. Thus, the study evaluates the antioxidant and anti-inflammatory potential of Momordica charantia fruit endophyte Bacillus haynesii R2MCFF61, and determines its metabolite profile through LC-Q-TOF-MS for the bioactive compounds produced. B. haynesii R2MCFF61 showed significant antioxidant and anti-inflammatory potential with increased DPPH scavenging activity in the standard compound and inhibition of protein denaturation respectively. The metabolic profile of this endophyte showed 23 compounds, mostly consisting of metabolites from lipid, phenylpropanoid and triterpenoid pathways. B. haynesii R2MCFF61 showed production of cucurbitane-triterpenoids namely Momordicoside K, 19-dimethoxycucurbita-5(10),6,22(E),24-tetraen-3{beta}-ol and 23(E)-7{beta}-methoxycucurbita-5,23,25-trien-3{beta}-ol. These compounds are mainly produced by M. charantia fruit and their production by its endophyte is reported for the first time. Thus, these results indicate the promising therapeutic potential of B. haynesii R2MCFF61 which can be utilized as a low-cost sustainable source of these bioactive compounds.

microbiology↗

bioRxiv2024

Exploiting gene expression profiles of circulating extracellular vesicles for breast cancer detection

BackgroundLiquid biopsy-based biomarkers offer several advantages since they are minimally invasive, can be useful in longitudinal monitoring of the disease and have higher patient compliance. We hypothesize that RNA content of circulating EVs differs in breast cancer patients and healthy women. EV RNAs may provide an opportunity to diagnose, detect subtypes and metastatic states. Experimental DesignRNA-seq analysis and qRT-PCR from matched tumor biopsy, circulating EVs from breast cancer patients (EV-C) and healthy donors (EV-H) was performed to find genes that discriminate between these groups. ResultsEV-C to EV-H comparison yielded 320 DEGs (adjusted p value [≤]0.05) enriched for cancer related pathways like Myc, Reactive oxygen species, and Angiogenesis. Allograft rejection and Interferon pathway genes were over-represented in the cancer group. Top 6 genes were validated by qRT-PCR in a validation cohort. 5 genes consistently and correctly classified cancer and healthy groups. An independent set of 374 and 640 DEGs could segregate ER positive/ER negative and non-metastatic versus metastatic samples, respectively. EVs from metastatic samples had higher variability in gene expression patterns whereas those from non-metastatic samples showed better correlation. Ability of 4 genes to classify metastases state was explored. ConclusionWe report five EV RNAs that can be used to diagnose breast cancer in a subtype independent manner. Initial analysis indicates that EV RNA content differs based on subtype specificity and metastasis status.

cancer biology↗

bioRxiv2024

The kinetics and optimality of influenza A virus locomotion

Influenza A viruses (IAVs) must navigate through a dense extracellular mucus to infect airway epithelial cells. The mucous layer, composed of glycosylated biopolymers (mucins), presents sialic acid that binds to ligands on the viral envelope and can be irreversibly cleaved by viral enzymes. It was recently discovered that filamentous IAVs exhibit directed persistent motion along their long axis on sialic acid-coated surfaces. This study demonstrates through stochastic simulations and mean-field theory, how IAVs harness a burnt-bridge Brownian ratchet mechanism for directed persistent translational motion. Importantly, our analysis reveals that equilibrium features of the system primarily control the dynamics, even out-of-equilibrium, and that ligand asymmetry allows for more robust directed transport. We show viruses occupy the optimal parameter range ( Goldilocks zone) for efficient mucous transport, possibly due to the evolutionary adaptation of enzyme kinetics. Our findings suggest novel therapeutic targets and provide insight into possible mechanisms of zoonotic transmission.

biophysics↗