Biology subjects

Tomar, A.

Publications and source records attributed to Tomar, A..

18 recordsLinked to original sources

bioRxiv2026

Computational predictions and evolutionary analysis of LrK10 kinase-related putative PSTOL1 gene homeologs in wheat and orthologs of its wild relatives.

Phosphorus Starvation Tolerance 1 in rice (OsPSTOL1, known as Phosphorus uptake 1, Pup1) is a receptor-like cytoplasmic protein kinase that confers tolerance to phosphorus deficiency. The OsPSTOL1 gene possesses a Ser/Thr kinase and shows high amino-acid sequence similarity with the leaf rust receptor-like kinase (OsLrK10). We hypothesize that the putative wheat TaPSTOL1 and TaLrK10 have a common ancestral origin and that putative TaPSTOL1 diverged recently acquiring new structural modifications and biological functions in the process. In this study, we identified all putative TaPSTOL1 homeologs and examine the evolutionary relationship between TaPSTOL1 and TaLrK10 in Triticum species. Our results indicate that the putative TaPSTOL1 diverged recently without possessing the amino-terminal domain, which is a typical characteristic of TaLrK10. We observed numerous conversions tracts between these two genes and the substitution pattern of randomly selected amino acids indicates that dynamic selection pressures acted on both genes. The putative TaPSTOL1 shows high nucleotide diversity compared to TaLrK10 within Triticum species. Further, a multiple-sequence analysis reveals that the third exon of TaLrK10 appears to have been duplicated and diverged as a putative single-exon based TaPSTOL1 in bread wheat. Overall, our comparative analysis indicates that both TaPSTOL1 and TaLrK10 appears to have diverged from a common ancestor, acquiring distinct structural organizations and biological functions.

genomics↗

bioRxiv2025

Modular to cyclic TCA governs hematopoiesis in Drosophila

TCA cycle is well known for its role in bioenergetics and also a hub for metabolic exchange, here we identify a developmentally programmed, non-uniform TCA architecture that is required for hematopoietic state transitions in the Drosophila lymph gland. Early blood progenitors operate a modular TCA configuration, in which a CS/mAcon1-derived citrate node preserves progenitor identity, while a Gdh/Kdh mediated -ketoglutarate to succinyl-CoA branch, not succinate, supports proliferative potential. As cells exit the progenitor state and initiate lineage commitment, the cells undergo metabolic reorganization and engage a fully cyclic, Pdh- and Idh-dependent oxidative TCA cycle whose cataplerotic activity keeps the levels of TCA metabolites in check as their excess otherwise induces differentiation. Blocking these metabolic transitions disrupts progenitor homeostasis, compromises proliferative competency of transitional progenitors, and distorts balanced differentiation. These findings establish a developmentally regulated alternative to the traditional TCA cycle and reveals that appropriate engagement of modular versus cyclic TCA modes is required for orchestrating hematopoietic fate transitions. This work highlights TCA topology and not flux alone functions as a core determinant of stemness, proliferation, and lineage progression during hematopoiesis. Significance StatementHematopoietic development requires precise metabolic control to maintain progenitors while enabling their transition into differentiated lineages. We show that the Drosophila lymph gland achieves this through a developmentally programmed switch in TCA-cycle configuration where early progenitors rely on a modular TCA architecture that independently sustains identity and proliferation, whereas later stages require a fully cyclic, oxidative TCA mode to maintain homeostasis and balanced differentiation. Disrupting either phase perturbs hematopoietic organization, demonstrating that TCA topology itself regulates cell-state transitions. These findings reveal TCA architecture as the determinant of hematopoietic fate and provides a conceptual framework relevant to hematopoiesis and also stem cell biology.

developmental biology↗

bioRxiv2025

Epithelial and stromal remodeling in murine Crohn's disease-like ileitis

Background and AimsInflammatory bowel disease is characterized by progressive epithelial, immune, and stromal dysfunction. Human datasets yield important insights yet are inherently descriptive, requiring animal models for in vivo mechanistic interrogation. The SAMP1/YitFc (SAMP) mouse model develops spontaneous Crohns disease (CD)-like ileitis while allowing controlled manipulation of pathophysiologic pathways. To understand cell-specific disease-associated transcriptional changes, we defined the single-nucleus transcriptomes of inflamed SAMP ilea using single-nucleus RNA-sequencing (snRNA-seq). MethodsWe performed whole-ileum snRNA-seq on SAMP (n=4) and control AKR/J (n=3) mice using the gut-optimized CitraPrep protocol, generating 58,349 high-quality nuclei across epithelial, immune, and stromal lineages. We corroborated SAMP-associated changes with immunofluorescent staining, Western blotting, spatial transcriptomic, and human single-cell RNA-sequencing data. ResultsWe observed a primary type 2 immune phenotype in SAMP compared to AKR mice, but most transcriptional changes occurred in stromal and epithelial, not immune, cells. Stromal remodeling included increased fibroblast-derived Igf1. In SAMP epithelium, expansion of tuft cells and emergence of SAMP-specific Pcsk6+ crypt enterocytes were observed and confirmed in human CD patients. Finally, we identified cross-compartmental changes in cell-cell signaling, including enterocyte-to-type 3 innate lymphoid cell (ILC3) communication and enhanced global Igf1 signaling. These features recapitulate known, as well as novel, characteristics of CD and extend our understanding of disease-associated multicellular networks. ConclusionThis atlas of ileitis-prone SAMP mice provides a high-resolution resource for dissecting conserved and novel mechanisms of inflammation and tissue remodeling. Herein, we uncover disease-associated transcriptional changes conserved in human CD, presenting a translational platform for future mechanistic and therapeutic studies.

molecular biology↗

bioRxiv2025

Improving retention time of Indocyanine Green for in vivo two-photon microscopy using liposomal encapsulation

We propose a technique for improving the retention time of Indocyanine Green (ICG), an FDA-approved, widely available, near infrared (NIR) probe for in vivo imaging of the cerebrovascular structure in rodents. We present a synthesis process for liposomal nanoparticles that, when used to encapsulate ICG, significantly increase the circulation time of the vascular label. Further, we conduct in vivo imaging experiments with unencapsuated (free) ICG and liposomal ICG (L-ICG) and compare the retention of ICG in the vascular network. Our work tackles one of the most fundamental limitations in using ICG i.e. rapid clearance, for the purpose of two-photon microscopy.

neuroscience↗

bioRxiv2025

Protometabolically generated NADH mediates material properties of aqueous dispersions to coacervate microdroplets

Macromolecular assembly between biomolecules dictates the material state of aqueous dispersions like the cytoplasm. The formation of protein precipitates, fibres, or liquid droplets have been associated with the regulation of biochemical function and disease. However, the effect of small molecules and metabolites on tuning phase behaviour remains underexplored. Here we use the protometabolic reduction of NAD+ to NADH by pyruvate to study the effect of NADH production on the phase properties of polyarginine in bicarbonate buffer. Our results show that reduction of NAD+ in the presence of polyarginine can tune the material properties of the dispersion between precipitates, homogeneous solution and liquid droplets depending on the buffer concentration. In-situ droplet formation results in 2-3 times higher reaction rate and NADH yield, compared to homogeneous solution. Our results demonstrate how small molecules can significantly impact material properties in aqueous dispersions and the positive effect of heterogeneous dispersions on primitive metabolic reactions. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/642830v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@19261c8org.highwire.dtl.DTLVardef@151aae5org.highwire.dtl.DTLVardef@aaa110org.highwire.dtl.DTLVardef@342e16_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2024

Sub-chronic elevation in ambient temperature drives alterations to the sperm epigenome and accelerates early embryonic development in mice

Forecasted increases in the prevalence and severity of extreme weather events accompanying changes in climatic behavior pose potential risk to the reproductive capacity of humans and animals of ecological and agricultural significance. While several studies have revealed that heat stress induced by challenges such as testicular insulation can elicit a marked negative effect on the male reproductive system, and particularly the production of spermatozoa, less is known about the immediate impact on male reproductive function following sub-chronic whole-body exposure to elevated ambient temperature. To address this knowledge gap, we exposed unrestrained male mice to heat stress conditions that emulate a heat wave (daily cycle of 8_h at 35{degrees}C followed by 16 h at 25{degrees}C) for a period of seven days. Neither the testes or epididymides of heat exposed male mice exhibited evidence of gross histological change, and similarly, spermatozoa of exposed males retained their functionality and ability to support embryonic development. However, the embryos generated from heat exposed spermatozoa experienced pronounced changes in gene expression linked to acceleration of early embryo development, aberrant blastocyst hatching and increased fetal weight. Such changes were causally associated with an altered sperm small non-coding RNA (sncRNA) profile, such that these developmental phenotypes were recapitulated by microinjection of wild-type embryos sired by control spermatozoa with RNAs extracted from heat exposed spermatozoa. Such data highlight that even a relatively modest excursion in ambient temperature can affect male reproductive function and identify the sperm sncRNA profile as a particular point of vulnerability to this imposed environmental stress. Significance StatementThe fidelity of sperm production underpins successful reproduction yet is highly vulnerable to various forms of environmental challenge, including heat stress. Despite this knowledge, we lack a complete understanding of the immediate impact on male reproduction of whole-body exposure to elevated ambient temperatures such as those encountered during a heatwave. By experimentally emulating heatwave conditions, we demonstrate that the spermatozoa of exposed male mice accumulate changes in their small RNA profile that are causally linked to pronounced changes in embryonic gene expression, accelerated pre-implantation development, aberrant blastocyst hatching, and increased fetal weight. Such data highlight that even a relatively modest alteration in ambient temperature can affect male reproductive function, demonstrating the acute sensitivity of sperm small RNAs to environmental stress.

cell biology↗

bioRxiv2024

Non-Degenerate Two-Photon Imaging of Deep Rodent Cortex using Indocyanine Green in the water absorption window

We present a novel approach for deep vascular imaging in rodent cortex at excitation wavelengths susceptible to water absorption using two-photon microscopy with photons of dissimilar wavelengths. We demonstrate that non-degenerate two-photon excitation (ND-2PE) enables imaging in the water absorption window from 1400-1550 nm using two synchronized excitation sources at 1300 nm and 1600 nm that straddle the absorption window. We explore the brightness spectra of indocyanine green (ICG) and assess its suitability for imaging in the water absorption window. Further, we demonstrate in vivo imaging of the rodent cortex vascular structure up to 1.2 mm using ND-2PE. Lastly, a comparative analysis of ND-2PE at 1435 nm and single-wavelength, two-photon imaging at 1300 nm and 1435 nm is presented. Our work extends the excitation range for fluorescent dyes to include water absorption regimes and underscores the feasibility of deep two-photon imaging at these wavelengths.

neuroscience↗

bioRxiv2023

Wide-field Intensity Fluctuation Imaging

The temporal intensity fluctuations contain important information about the light source and light-medium interaction and are typically characterized by the intensity autocorrelation function, g2({tau}). The measurement of g2({tau}) is a central topic in many optical sensing applications, ranging from stellar intensity interferometer in astrophysics, to fluorescence correlation spectroscopy in biomedical sciences and blood flow measurement with dynamic light scattering. Currently, g2({tau}) at a single point is readily accessible through high-frequency sampling of the intensity signal. However, two-dimensional widefield measurement of g2({tau}) is still limited by camera frame rates. We propose and demonstrate a 2-pulse within-exposure modulation approach to break through the camera frame rate limit and obtain the quasi g2({tau}) map in wide field with cameras of only ordinary frame rates. HighlightsO_LIThe quasi intensity autocorrelation function can be measured at almost arbitrary time lags C_LIO_LICameras of ordinary frame rates are sufficient for the measurement C_LIO_LIIllumination within the camera exposure is modulated by an acoustic optical modulator using two short pulses C_LI

bioengineering↗

bioRxiv2023

Enteric glial hub cells coordinate intestinal motility

The enteric nervous system is a complex network of neurons and glia within the gut that coordinate gut motility. By optimizing single nucleus RNA-sequencing methods and spatial transcriptomics, we generated maps of the mouse duodenum and identified distinct molecular classes of enteric glia across the intestine with unique morphological and spatial identities. Here we show enteric glial functional specialization, with one myenteric subtype directly sensing force and expressing the mechanosensory ion channel PIEZO2. Genetic reduction of PIEZO2 in enteric glial populations enriched for this mechanosensory subtype led to defects in gastrointestinal motility. These results provide insight into the multifaceted functions of distinct enteric glial cell subtypes in maintaining gut health, and emphasize the importance of considering subtype-specific roles of enteric glia in a wide range of diseases and disorders.

neuroscience↗

bioRxiv2023

Pulse train gating to improve signal generation for in vivo two-photon fluorescence microscopy

SignificanceTwo-photon microscopy is used routinely for in vivo imaging of neural and vascular structure and function in rodents with a high resolution. Image quality, however, often degrades in deeper portions of the cerebral cortex. Strategies to improve deep imaging are therefore needed. We introduce such a strategy using gates of high repetition rate ultrafast pulse trains to increase signal level. AimWe investigate how signal generation, signal-to-noise ratio (SNR), and signal-to-background ratio (SBR) improve with pulse gating while imaging in vivo mouse cerebral vasculature. ApproachAn electro-optic modulator is used with a high-power (6 W) 80 MHz repetition rate ytterbium fiber amplifier to create gates of pulses at a 1 MHz repetition rate. We first measure signal generation from a Texas Red solution in a cuvette to characterize the system with no gating and at a 50%, 25%, and 12.5% duty cycle. We then compare signal generation, SNR, and SBR when imaging Texas Red-labeled vasculature using these conditions. ResultsWe find up to a 6.73-fold increase in fluorescent signal from a cuvette when using a 12.5% duty cycle pulse gating excitation pattern as opposed to a constant 80 MHz pulse train. We verify similar increases for in vivo imaging to that observed in cuvette testing. For deep imaging we find pulse gating to result in a 2.95-fold increase in SNR and a 1.37-fold increase in SBR on average when imaging mouse cortical vasculature at depths ranging from 950 m to 1050 m. ConclusionsWe demonstrate that a pulse gating strategy can either be used to limit heating when imaging superficial brain regions or used to increase signal generation in deep regions. These findings should encourage others to adopt similar pulse gating excitation schemes for imaging neural structure through two-photon microscopy.

neuroscience↗

bioRxiv2022

A deep learning approach for improving two-photon vascular imaging speeds

A potential method for tracking neurovascular disease progression over time in preclinical models is multiphoton fluorescence microscopy (MPM), which can image cerebral vasculature with capillary-level resolution. However, obtaining high-quality, three-dimensional images with a traditional point scanning MPM is time-consuming and limits sample sizes for chronic studies. Here, we present a convolutional neural network-based algorithm for fast upscaling of low-resolution or sparsely sampled images and combine it with a segmentation-less vectorization process for 3D reconstruction and statistical analysis of vascular network structure. In doing so, we also demonstrate that the use of semi-synthetic training data can replace the expensive and arduous process of acquiring low- and high-resolution training pairs without compromising vectorization outcomes, and thus open the possibility of utilizing such approaches for other MPM tasks where collecting training data is challenging. We applied our approach to large field of view images and show that our method generalizes across imaging depths, disease states and other differences in neurovasculature. Our pre-trained models and lightweight architecture can be used to reduce MPM imaging time by up to fourfold without any changes in underlying hardware, thereby enabling deployability across a range of settings.

bioengineering↗

bioRxiv2022

Interpreting ICT: from Blood Flow to Vascular Network

The inverse correlation time (ICT) is a key quantity in laser speckle contrast imaging (LSCI) measurements. Traditionally, ICT is regarded as a metric of blood flow, such as speed or perfusion. However, we highlight that ICT not only contains important information about blood flow, but also reflects the underlying structure of the vascular network. In the past, ICT has been found to be correlated with vessel diameter. Here, we further report that ICT exhibits a different sensitivity to blood flow depending on vessel orientation. Specifically, ICT is more sensitive to blood flow speed changes in vessels descending from or arising to the tissue surface, compared with those laying parallel to the surface. Those findings shift our understanding of ICT from purely blood flow to a combination of blood flow and vascular network structure. We also develop theories to facilitate the study of vascular networks impact on ICT.

bioengineering↗

bioRxiv2021

An evaluation of resonant scanning as a high-speed imaging technique for two-photon imaging of cortical vasculature

We demonstrate a simple, low-cost two-photon microscope design with both galvo-galvo and resonant-galvo scanning capabilities. We quantify and compare the signal-to-noise ratios and imaging speeds of the galvo-galvo and resonant-galvo scanning modes when used for murine neurovascular imaging. The two scanning modes perform as expected under shot-noise limited detection and are found to achieve comparable signal-to-noise ratios. Resonant-galvo scanning is capable of reaching desired signal-to-noise ratios using less acquisition time when higher excitation power can be used. Given equal excitation power and total pixel dwell time between the two methods, galvo-galvo scanning outperforms resonant-galvo scanning in image quality when detection deviates from being shot-noise limited.

neuroscience↗

bioRxiv2021

Differential impact of acute and chronic stress on CA1 spatial coding and gamma oscillations

Chronic and acute stress differentially affect behaviour, as well as the structural integrity of the hippocampus, a key brain region involved in cognition and memory. However, it remains unclear if and how the facilitatory effects of acute stress on hippocampal information coding are disrupted as the stress becomes chronic. To examine this, we compared the impact of acute and chronic stress on neural activity in the CA1 subregion of male mice subjected to a chronic immobilization stress paradigm. We observed that following first exposure to stress (acute stress), the spatial information encoded in the hippocampus sharpened and the neurons became increasingly tuned to the underlying theta oscillation in the local field potential (LFP). However, following repeated exposure to same stress (chronic stress), spatial tuning was poorer and the power of both the slow-gamma (30-50 Hz) and fast-gamma (55-90 Hz) oscillations, which correlate with excitatory inputs into the region, decreased. These results support the idea that acute and chronic stress differentially affect neural computations carried out by hippocampal circuits and suggest that acute stress may improve cognitive processing.

neuroscience↗

bioRxiv2021

Blood progenitor redox homeostasis through GABA control of TCA cycle in Drosophila hematopoiesis

The importance of reactive oxygen species (ROS) in myeloid cell development and function is well-established. However, a comprehensive understanding of metabolic states controlling ROS levels during hematopoiesis remains elusive. Myeloid-like blood progenitor cells of the Drosophila larvae reside in a specialized hematopoietic organ called the lymph gland. We find that these progenitors in homeostasis, utilize TCA to generate ROS. Excessive activation of TCA however raises ROS levels causing them to precociously differentiate and leads to retardation of lymph gland size. Thus, to maintain ROS homeostasis, progenitor cells utilize systemically derived GABA. GABA internalization and catabolism via inhibiting hydroxy prolyl hydroxylase (Hph) activity, promotes pyruvate dehydrogenase kinase enzyme activity (PDK). PDK controls inhibitory phosphorylation of pyruvate dehydrogenase (PDH), the rate-limiting enzyme, connecting pyruvate to TCA cycle and OXPHOS. Thus, by regulating PDK, GABA regulates progenitor TCA activity and ROS levels. In addition to this, GABA-catabolism/Hph axis via Hif/Sima drives a glycolytic state in progenitor cells. The dual control established by GABA on PDK and Sima maintains progenitor cell metabolism and sustains ROS homeostasis necessary for their development. Taken together, our study demonstrates the metabolic underpinnings of GABA in myeloid ROS regulation and their development, the relevance of which may be broadly conserved.

developmental biology↗

bioRxiv2020

Stress enhances hippocampal neuronal synchrony and prolongs sharp-wave ripples

Chronic stress affects hippocampal function at multiple levels of neural organization. However, much of this understanding is derived from postmortem analyses of molecular, morphological, physiological and behavioral changes at fixed time points. Neural signatures of an ongoing stressful experience in the intact brain of awake animals and their links to later hippocampal dysfunction remain poorly understood. Here we used in vivo tetrode recordings to analyze the dynamic impact of 10 days of immobilization stress on neuronal activity in area CA1 of mice. Unexpectedly, there was a net decrease in pyramidal cell activity in stressed animals. Although these results suggest a lack of stress-induced hyperexcitability, more detailed analysis revealed that a greater fraction of spikes occurred specifically during sharp-wave ripples, resulting in an increase in neuronal synchrony. After repeated stress some of these alterations were visible during rest even in the absence of stress. These findings offer new insights into stress-induced alterations in ripple-spike interactions and mechanisms through which chronic stress may interfere with subsequent information processing.

neuroscience↗

bioRxiv2019

Darwinian selection analysis of the two-component system PmrAB indicates there could be lingering delay in emergence of colistin resistance in Acinetobacter baumannii

Investigations on the selection pressure acting on point mutations in PmrAB two-component system may provide insights into the future of colistin therapy in Acinetobacter baumannii, since mutations in pmrAB are implicated in colistin resistance. We performed adaptive selection analysis of pmrAB and compared with the available data on colistin resistant strains. We analysed PmrAB sequences in 3113 draft genomes of A. baumannii obtained from RefSeq database. Adaptive selection analysis was performed by two widely used programs namely, HyPhy and PAML. In addition, to examine the reliability of the approach, the same analysis was performed on gyrA of Escherichia coli and Salmonella enterica, since adaptive mutations on gyrA confer quinolone resistance. Mutations that had caused colistin resistance were found to be neither adaptive nor polymorphic, rather they occur at sites that are either under neutral or purifying selection. Strong negative evolutionary selection pressure is also observed at sites throughout both PmrA and PmrB. Sites with high levels of polymorphisms in PmrAB were found to be under neutral selection. Notably, there was no sign of positive selection. Some of them are rather deleterious. These conditions might be maintaining the incidence of colistin resistance in A. baumannii under check. Therefore, in the context of colistin resistance, natural selection plays only a minor role and we assert that in future, A. baumannii may not be able to sustain and successfully disseminate colistin resistance. Therefore, at present the concerns raised about continuing the usage of colistin for the treatment against A. baumannii infections appears to be unnecessary.

microbiology↗

bioRxiv2019

In-vivo targeted tagging of RNA isolates cell specific transcriptional responses to environmental stimuli and identifies liver-to-adipose RNA transfer

Bio-fluids contain various circulating cell-free RNA transcripts (ccfRNAs). The composition of these ccfRNAs varies between bio-fluids and constitute tantalizing biomarker candidates for several pathologies. ccfRNAs have also been demonstrated as mediators of cellular communication, yet little is known about their function in physiological and developmental settings and most works are limited to in-vitro studies. Here, we have developed iTAG-RNA, a novel method for the unbiased tagging of RNA transcripts in mice in-vivo. We used this method to isolate hepatocytes and kidney proximal epithelial cells-specific transcriptional response to a dietary challenge without interfering with the tissue architecture, and to identify multiple hepatocyte-secreted ccfRNAs in plasma. We also identified transfer of these hepatic derived ccfRNAs to adipose tissue, where they likely serve as a buffering mechanism to maintain cholesterol and lipid homeostasis. Our findings directly demonstrate in-vivo transfer of RNAs between tissues and highlight its implications for endocrine signaling and homeostasis.

molecular biology↗