Biology subjects

Kumar, S.

Publications and source records attributed to Kumar, S..

At least 253 records · Page 14Linked to original sources

bioRxiv2024

Retinoic acid breakdown is required for proximodistal positional identity during amphibian limb regeneration

Regenerating limbs retain their proximodistal (PD) positional identity following amputation. This positional identity is genetically encoded by PD patterning genes that instruct blastema cells to regenerate the appropriate PD limb segment. Retinoic acid (RA) is known to specify proximal limb identity, but how RA signaling levels are established in the blastema is unknown. Here, we show that RA breakdown via CYP26B1 is essential for determining RA signaling levels within blastemas. CYP26B1 inhibition molecularly reprograms distal blastemas into a more proximal identity, phenocopying the effects of administering excess RA. We identify Shox as an RA-responsive gene that is differentially expressed between proximally and distally amputated limbs. Ablation of Shox results in shortened limbs with proximal skeletal elements that fail to initiate endochondral ossification. These results suggest that PD positional identity is determined by RA degradation and RA-responsive genes that regulate PD skeletal element formation during limb regeneration.

developmental biology↗

bioRxiv2024

Coralline companions: Exploring microbes in coral ecosystems

Coral reefs exhibit remarkable resilience to natural disturbances but face challenges due to global changes and emerging diseases. In the present study, we recorded a total of 51 ciliates and over 400 bacteria associated with healthy and diseased corals from the Ramsar site Gulf of Mannar Marine National Park, India, based on morphology, silver staining, and Next Generation Sequencing. Our study contributes to the growing understanding of ciliate diversity and provides insights into the dynamics of ciliate-associated coral diseases, towards developing effective biocontrol agents for coral bleaching and conservation strategies to safeguard coral reef ecosystems.

ecology↗

bioRxiv2024

Characterizing microglial signaling dynamics during inflammation using single-cell mass cytometry

Microglia play a critical role in maintaining central nervous system (CNS) homeostasis and display remarkable plasticity in their response to inflammatory stimuli. However, the specific signaling profiles that microglia adopt during such challenges remain incompletely understood. Traditional transcriptomic approaches provide valuable insights, but fail to capture dynamic post-translational changes. In this study, we utilized time-resolved single-cell mass cytometry (CyTOF) to measure distinct signaling pathways activated in microglia upon exposure to bacterial and viral mimetics--lipopolysaccharide (LPS) and polyinosinic-polycytidylic acid (Poly(I:C)), respectively. Furthermore, we evaluated the immunomodulatory role of astrocytes on microglial signaling in mixed cultures. Microglia or mixed cultures derived from neonatal mice were treated with LPS or Poly(I:C) for 48 hrs. Cultures were stained with a panel of 33 metal-conjugated antibodies targeting signaling and identity markers. High-dimensional clustering analysis was used to identify emergent signaling modules. We found that LPS treatment led to more robust early activation of pp38, pERK, pRSK, and pCREB compared to Poly(I:C). Despite these differences, both LPS and Poly(I:C) upregulated the classical activation markers CD40 and CD86 at later time-points. Strikingly, the presence of astrocytes significantly blunted microglial responses to both stimuli, particularly dampening CD40 upregulation. Our studies demonstrate that single-cell mass cytometry effectively captures the dynamic signaling landscape of microglia under pro-inflammatory conditions. This approach may pave the way for targeted therapeutic investigations of various neuroinflammatory disorders. Moreover, our findings underscore the necessity of considering cellular context, such as astrocyte presence, in interpreting microglial behavior during inflammation. Main PointsTime-resolved single cell mass cytometry delineates microglial signaling pathways following LPS or Poly(I:C) treatment. Astrocyte presence led to selective reduction of key microglial signaling nodes along with terminal inflammatory profiles.

neuroscience↗

bioRxiv2024

An anomalous 3'-terminal phosphorothioated mismatch bypass activity and its application as a binary molecular switch

Phosphorothioated (PST) oligonucleotides are increasingly being used in RNA silencing, antisense, and biosensing applications. However, the possibilities and consequences of their desultory interactions with other possible nucleic acids and DNA polymerases inside the cell remain inadequately characterized. In this study, we report the discovery of an unusual terminal mismatch bypass activity involving 3'-PST containing DNA primers and certain strand displacement DNA polymerases. Using rolling circle DNA amplification, we have identified that strand displacement DNA polymerases such as phi29 and BST large fragment (LF) can bypass 3'-terminal PST mismatches upto 1 - 20 nt length. Next, we explore the length and sequence dependence of this unusual attribute, incubation in near-ambient and 60 - 65{degrees}C temperatures, and measures to blockade or modulate this mismatch bypass activity to create a binary fully nucleic acid-based and non-photocontrolled molecular switch (the first of its kind). After proposing possible underlying mechanisms for this activity, we discuss its potential consequences and applications.

biochemistry↗

bioRxiv2024

Integrating Phylogenies with Chronology to Assemble the Tree of Life

Reconstructing the global Tree of Life necessitates computational approaches to integrate numerous molecular phylogenies with limited species overlap into a comprehensive supertree. Our survey of published literature shows that individual phylogenies are frequently restricted to specific taxonomic groups due to the expertise of investigators and molecular evolutionary considerations, resulting in any given species present in a minuscule fraction of phylogenies. We present a novel approach, called the chronological supertree algorithm (Chrono-STA), that can build a supertree of species from such data by using node ages in published molecular phylogenies scaled to time. Chrono-STA builds a supertree of organisms by integrating chronological data from molecular timetrees. It fundamentally differs from existing approaches that generate consensus phylogenies from gene trees with missing taxa, as Chrono-STA does not impute nodal distances, use a guide tree as a backbone, or reduce phylogenies to quartets. Analyses of simulated and empirical datasets show that Chrono-STA can combine taxonomically restricted timetrees with extremely limited species overlap. For such data, approaches that impute missing distances or assemble phylogenetic quartets did not perform well. We conclude that integrating phylogenies via temporal dimension enhances the accuracy of reconstructed supertrees that are also scaled to time.

bioinformatics↗

bioRxiv2024

Differential expression of keratin and keratin associated proteins are linked with hair loss condition in spontaneously mutated inbred mice

Hair loss condition is heritable and is influenced by multifactorial inheritance. In the present study, spontaneously mutated mice showed hair loss phenotype with defect in the first cycle of hair follicle formation leading to cyclic alopecia. These mutant mice follow autosomal recessive inheritance pattern. The transcriptomic profile and differential gene expression analysis of skin tissues by RNA-sequencing at different stages of hair cycle formation was performed. The genes with significant differential genes expression levels in each stage of hair cycle formation were identified and most of these genes were shown to be associated with keratinization process and hair follicle formation. Transcriptome profiling followed by QPCR validation revealed that mRNA levels of Krt16, Alox15, Fetub (upregulated) and Msx2 (downregulated) were significantly differentially expressed in mutant skin tissues during late anagen and catagen stages. Krt6b mRNA and protein levels were significantly higher in the mutant mice during all stages of first hair cycle formation. The present study provides basis for understanding the differential gene expression of hair-related genes, including keratinization-associated proteins and its relevance. These mutant mice can serve as a model for studying hair loss condition that can be further used in the identification, evaluation and treatment strategies for alopecia condition.

genetics↗

bioRxiv2024

Diet-induced obesity mediated through Estrogen-Related Receptor α is independent of intestinal function

Obesity has become an epidemic, prompting advances in therapies targeting this condition. Estrogen-related receptor (ESRRA), a transcription factor, plays pivotal roles in energy metabolism across diverse tissues. Studies have demonstrated that loss of Esrra leads to fat malabsorption and resistance to diet-induced obesity. However, the reliance of these studies on germline Esrra mutants overlooks the tissue-specific implications of ESRRA in diet-induced obesity. Notably, Esrra exhibits high expression in the gastrointestinal (GI) tract relative to other tissues. Given the critical role of the GI tract in dietary lipid metabolism, this study employs mouse genetics and genomics approaches to dissect the specific impact of intestinal ESRRA along with investigating its role in diet-induced obesity. Data TransparencyChIP-seq and RNA-seq data from this publication have been deposited to GEO accession numbers GSE269824 and GSE269825, respectively. Any additional information required to reanalyze the data reported in this paper is available from the corresponding author upon request. Grant SupportThis research was funded by grants from the National Institutes of Health (NIH) to M.P.V. (R01DK121915 and R01DK126446). K.V. was supported by an American Heart Association pre-doctoral fellowship (906006). S.K. was supported by a Rutgers DLS Summer Undergraduate Research Fellowship. A.L. was supported by grants from the NIH grant F31DK137596 and the NIH T32 Biotechnology Training Program (GM135141). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. DisclosuresThe authors declare no competing interests.

genetics↗

bioRxiv2024

FUSION: A web-based application for in-depth exploration of multi-omics data with brightfield histology

Spatial -OMICS technologies facilitate the interrogation of molecular profiles in the context of the underlying histopathology and tissue microenvironment. Paired analysis of histopathology and molecular data can provide pathologists with otherwise unobtainable insights into biological mechanisms. To connect the disparate molecular and histopathologic features into a single workspace, we developed FUSION (Functional Unit State IdentificatiON in WSIs [Whole Slide Images]), a web-based tool that provides users with a broad array of visualization and analytical tools including deep learning-based algorithms for in-depth interrogation of spatial -OMICS datasets and their associated high-resolution histology images. FUSION enables end-to-end analysis of functional tissue units (FTUs), automatically aggregating underlying molecular data to provide a histopathology-based medium for analyzing healthy and altered cell states and driving new discoveries using "pathomic" features. We demonstrate FUSION using 10x Visium spatial transcriptomics (ST) data from both formalin-fixed paraffin embedded (FFPE) and frozen prepared datasets consisting of healthy and diseased tissue. Through several use-cases, we demonstrate how users can identify spatial linkages between quantitative pathomics, qualitative image characteristics, and spatial --omics

pathology↗

bioRxiv2024

Chromosome-level genome assembly of autotetraploid Selenicereus megalanthus and gaining genomic insights into the evolution of trait patterning in diploid and polyploid pitaya species

Yellow pitaya (Selenicereus megalanthus, 2n=4x=44) breeding remains severely hindered due to lacking a reference genome. Here we report yellow pitayas high-quality chromosome-level genome assembly and link the phenotypic trait with genomic data, based on Hi-C, ATAC, and RNA-seq data of specific tissues. We declared yellow pitaya as an autotetraploid with a 7.16 Gb genome size (harboring 27,246 high confidence genes) and majorly evolved from diploid ancestors, which remains unknown. Beyond generating the genome assembly, we explored the 3D chromatin organization which revealed insights into the genome, compartments A (648 and 519), compartments B (728 and 1064), topologically associated domains-TADs (3376 and 2031), and varying numbers of structural variations (SVs) in diploid and polyploid pitaya species, respectively. Overall, TAD boundaries were enriched with the motifs of AP2, WRKY18/60/75, MYB63/116, PHL2, and GATA8 in both pitaya species. By linking the open chromatin genomic structure to function, we identified the major changes in betalains biosynthesis pathway in diploid and polyploid pitaya. Moreover, the higher genetic expression of SmeADH1 [Chr11, Compartment A (135400000 - 135500000), genes inside the TAD region (135480000 - 135520000)], and lower expression of HuDOPA [Chr11, Compartment A (87100000 - 87200000), genes inside the TAD region (87160000-87200000)] acts as a key regulator of yellow and red color on the pericarp of polyploid and diploid pitaya, respectively. In addition, higher expression of HuCYP76AD1 genes in diploid pitaya and lower expression of SmeCYP76AD1 in polyploid pitaya potentially created the difference in the oxidase process that led to the production of betacyanin and betaxanthin, respectively. Furthermore, our results revealed not only the type of motifs that play a potential role in trait patterning but we also further uncovered that motif count in TAD-boundaries may impact the gene expression within the TAD regions of diploid and polyploid pitaya. Our valuable genomic resource and comparison of 3D euchromatin architecture of diploid and polyploid pitaya species will not only aid in the advancement of molecular breeding efforts but also offer insights into the organization of genomes, SVs, compartmentalization (A and B), and TADs, which have the potential to strengthen the idea of TADs-based trait improvement to achieve global food security.

plant biology↗

bioRxiv2024

Native mass spectrometry of membrane protein-lipid interactions in different detergent environments

Native mass spectrometry (MS) is revealing the role of specific lipids in modulating membrane protein structure and function. Membrane proteins solubilized in detergents are often introduced into the mass spectrometer; however, commonly used detergents for structural studies, such as dodecylmaltoside, tend to generate highly charged ions, leading to protein unfolding, thereby diminishing their utility for characterizing protein-lipid interactions. Thus, there is a critical need to develop approaches to investigate protein-lipid interactions in different detergents. Here, we demonstrate how charge-reducing molecules, such as spermine and trimethylamine-N-oxide, enable characterization of lipid binding to the bacterial water channel (AqpZ) and ammonia channel (AmtB) in complex with regulatory protein GlnK in different detergent environments. We find protein-lipid interactions are not only protein-dependent but can also be influenced by the detergent and type of charge-reducing molecule. AqpZ-lipid interactions are enhanced in LDAO (n-dodecyl-N,N-dimethylamine-N-oxide), whereas the interaction of AmtB-GlnK with lipids is comparable among different detergents. A fluorescent lipid binding assay also shows detergent dependence for AqpZ-lipid interactions, consistent with results from native MS. Taken together, native MS will play a pivotal role in establishing optimal experimental parameters that will be invaluable for various applications, such as drug discovery, as well as biochemical and structural investigations.

biochemistry↗

bioRxiv2024

De Novo Design of Integrin α5β1 Modulating Proteins for Regenerative Medicine

Integrin 5{beta}1 is crucial for cell attachment and migration in development and tissue regeneration, and 5{beta}1 binding proteins could have considerable utility in regenerative medicine and next-generation therapeutics. We use computational protein design to create de novo 5{beta}1-specific modulating miniprotein binders, called NeoNectins, that bind to and stabilize the open state of 5{beta}1. When immobilized onto titanium surfaces and throughout 3D hydrogels, the NeoNectins outperform native fibronectin and RGD peptide in enhancing cell attachment and spreading, and NeoNectin-grafted titanium implants outperformed fibronectin and RGD-grafted implants in animal models in promoting tissue integration and bone growth. NeoNectins should be broadly applicable for tissue engineering and biomedicine. One-Sentence SummaryA de novo-designed fibronectin substitute, NeoNectin, is specific for integrin 5{beta}1 and can be incorporated into biomaterials for regenerative medicine.

bioengineering↗

bioRxiv2024

Revealing heterogeneity in dementia using data-driven unsupervised clustering of cognitive profiles

Dementia is characterized by a decline in memory and thinking that is significant enough to impair function in activities of daily living. Patients seen in dementia specialty clinics are highly heterogenous with a variety of different symptoms that progress at different rates. Recent research has focused on finding data-driven subtypes for revealing new insights into dementias underlying heterogeneity, compared to analyzing the entire cohort as a single homogeneous group. However, current studies on dementia subtyping have the following limitations: (i) focusing on AD-related dementia only and not examining heterogeneity within dementia as a whole, (ii) using only cross-sectional baseline visit information for clustering and (iii) predominantly relying on expensive imaging biomarkers as features for clustering. In this study, we seek to overcome such limitations, using a data-driven unsupervised clustering algorithm named SillyPutty, in combination with hierarchical clustering on cognitive assessment scores to estimate subtypes within a real-world clinical dementia cohort. We use a longitudinal patient data set for our clustering analysis, instead of relying only on baseline visits, allowing us to explore the ongoing temporal relationship between subtypes and disease progression over time. Results showed that subtypes with very mild or mild dementia were more heterogenous in their cognitive profiles and risk of disease progression.

neuroscience↗

bioRxiv2024

Reversible kink instability drives ultrafast jumping in nematodes and soft robots

Entomopathogenic nematodes (EPNs) exhibit a bending-elastic instability, or kink, before becoming airborne, a feature hypothesized but not proven to enhance jumping performance. Here, we provide the evidence that this kink is crucial for improving launch performance. We demonstrate that EPNs actively modulate their aspect ratio, forming a liquid-latched closed loop over a slow timescale O(1 s), then rapidly open it O (10 {micro}s), achieving heights of 20 body lengths (BL) and generating [~] 104 W/Kg of power. Using jumping nematodes, a bio-inspired Soft Jumping Model (SoftJM), and computational simulations, we explore the mechanisms and implications of this kink. EPNs control their takeoff direction by adjusting their head position and center of mass, a mechanism verified through phase maps of jump directions in simulations and SoftJM experiments. Our findings reveal that the reversible kink instability at the point of highest curvature on the ventral side enhances energy storage using the nematodes limited muscular force. We investigated the impact of aspect ratio on kink instability and jumping performance using SoftJM, and quantified EPN cuticle stiffness with AFM, comparing it with C. elegans. This led to a stiffness-modified SoftJM design with a carbon fiber backbone, achieving jumps of [~]25 BL. Our study reveals how harnessing kink instabilities, a typical failure mode, enables bidirectional jumps in soft robots on complex substrates like sand, offering a novel approach for designing limbless robots for controlled jumping, locomotion, and even planetary exploration.

biophysics↗

bioRxiv2024

Elucidating key determinants of engineered scFv antibody in MMP-9 binding using high throughput screening and machine learning

An imbalance in matrix metalloproteinase-9 (MMP-9) regulation can lead to numerous diseases, including neurological disorders, cancer, and pre-term labor. Engineering single-chain antibody fragments (scFvs) Targeting MMP-9 to develop novel therapeutics for such diseases is desirable. We screened a synthetic scFv antibody library displayed on the yeast surface for binding improvement to MMP-9 using FACS (fluorescent-activated cell sorting). The scFv antibody clones isolated after FACS showed improvement in binding to MMP-9 compared to the endogenous inhibitor. To understand molecular determinants of binding between engineered scFv antibody variants and MMP-9, next-generation DNA sequencing, and computational protein structure analysis were used. Additionally, a deep-learning language model was trained on the synthetic library to predict the binding of scFv variants using their CDR-H3 sequences.

bioengineering↗

bioRxiv2024

Preclinical study of the human recombinant Erythropoietin (GBPD002) compared with Eprex

Erythropoietin (EPO) is a glycoprotein that an essential growth factor for erythroid progenitors at the bone marrow, which appears in blood as a response to hypoxia. It is produced mainly by the kidneys; and its biosynthesis and release are stimulated by the reduction of tissue oxygenation and/or the reduction of the mass of erythrocytes. Here, we report the results of the preclinical evaluation of the safety of GBPD002 a recombinant human erythropoietin (rhEPO) developed by the Globe Biotech Limited, Bangladesh, through a comparative study of acute toxicity with Eprex(R), a commercial homologue from Janssen, UK. The product was administered subcutaneously into Wistar rats, at 500 lU/kg of therapeutic dose (TD) and 3 times of TD for the single dose toxicity study on 14 consecutive days and 125 UL/kg, 250 UL/kg, 500 UL/kg, 750 UL/kg, 1000 UL/kg, 1250 UL/kg and 1500 UL/kg of GBPD002 and Eprex(R) on 7 consecutive days respectively for the repeated dose toxicity study. Hematological and biochemical parameters were measured for all test subjects before first dose injection and the day after last dose injection of the both studies. Necropsy and histopathology of representative subjects from each group were also observed to find any pathological significance like degeneration or cellular necrosis in internal organs such as kidney, liver, lung and spleen of any rat under experiment. Both GBPD002 and Eprex(R) comparative toxicology studies revealed similar pharmacologically driven mechanisms of toxicity, which is statistically insignificant (p >0.05). Though hematology parameter values stayed within the normal range during the assay period but the high count of hemoglobin and high hematocrit (P<0.05), together with the decrease in white blood cell, confirm the therapeutic effect of Erythropoietin in both studies. Moreover, in both studies, the initial and final values of aspartate aminotransferase, alanine aminotransferase and blood urea nitrogen were also found similar (p >0.05) for both GBPD002 and Eprex(R) in the study. The study clearly established that the toxicological profile of "GBPD002" and Eprex(R), administered subcutaneously, were similar and related to the known pharmacology of erythropoietin alfa; hereby, demonstrating the proof of totality and no residual uncertainty between "GBPD002" and Eprex(R). Therefore, "GBPD002" and Eprex(R) shall be administered interchangeably in relevant indications.

pharmacology and toxicology↗

bioRxiv2024

Microarray Integrated Spatial Transcriptomics (MIST) for Affordable, Robust, and Comprehensive Digital Pathology

10X Visium, a popular Spatial transcriptomics (ST) method, faces limited adoption due to its high cost and restricted sample usage per slide. To address these issues, we propose Microarray Integrated Spatial Transcriptomics (MIST), combining conventional tissue microarray (TMA) with Visium, using laser-cutting and 3D printing to enhance slide throughput. Our design facilitates independent replication and customization in individual labs to suit specific experimental needs. We provide a step-by-step guide from designing TMAs to the library preparation step. We demonstrate MISTs cost-effectiveness and technical benefits over Visium and GeoMx Nanostring. We also introduce AnnotateMap, a novel computational tool for efficient analysis of multiple ROIs processed through MIST.

bioinformatics↗

bioRxiv2024

In Vivo Simvastatin and Brain Radiation in a Model of HER2+ Inflammatory Breast Cancer Brain Metastasis

PurposeInhibiting HMG-CoA reductase with simvastatin prevents breast cancer metastases in preclinical models and radiosensitizes monolayer and stem-like IBC cell lines in vitro. Given the extensive use of simvastatin worldwide and its expected penetration into the brain, we examined whether regulating cholesterol with simvastatin affected IBC3 HER2+ brain metastases. Methods and MaterialsBreast cancer cell lines KPL4 and MDA-IBC3 were examined in vitro for DNA repair after radiation with or without statin treatment. Brain metastasis endpoints were examined in the MDA-IBC3 brain metastasis model after ex vivo exposure to lipoproteins and after tail vein injections with and without whole-brain radiotherapy (WBR) and oral statin exposure. ResultsEx vivo preculture of MDA-IBC3 cells with very low-density lipoprotein (vLDL) enhanced the growth of colonized lesions in the brain in vivo compared with control or high-density lipoprotein (HDL), and concurrent oral simvastatin/ WBR reduced the incidence of micrometastatic lesions evaluated 10 days after WBR. However, statin, with or without WBR, did not reduce the incidence, burden, or number of macrometastatic brain lesions evaluated 5 weeks after WBR. ConclusionsAlthough a role for cholesterol biosynthesis is demonstrated in DNA repair and response to whole brain radiation in this model, durable in vivo efficacy of concurrent whole brain irradiation and oral statin was not demonstrated.

cancer biology↗

bioRxiv2024

The role of Tyr34 in proton-coupled electron transfer of human manganese superoxide dismutase

Human manganese superoxide dismutase (MnSOD) plays a crucial role in controlling levels of reactive oxygen species (ROS) by converting superoxide (O2*-) to molecular oxygen (O2) and hydrogen peroxide (H2O2) with proton-coupled electron transfers (PCETs). The reactivity of human MnSOD is determined by the state of a key catalytic residue, Tyr34, that becomes post-translationally inactivated by nitration in various diseases associated with mitochondrial dysfunction. We previously reported that Tyr34 has an unusual pKa due to its proximity to the Mn metal and undergoes cyclic deprotonation and protonation events to promote the electron transfers of MnSOD. To shed light on the role of Tyr34 MnSOD catalysis, we performed neutron diffraction, X-ray spectroscopy, and quantum chemistry calculations of Tyr34Phe MnSOD in various enzymatic states. The data identifies the contributions of Tyr34 in MnSOD activity that support mitochondrial function and presents a thorough characterization of how a single tyrosine modulates PCET catalysis.

biochemistry↗