Biology subjects

Upadhyay, N.

Publications and source records attributed to Upadhyay, N..

5 recordsLinked to original sources

bioRxiv2026

European taurine vs Indian indicine cattle: a comparative genomic study reveals regions of differentiation during evolution and selection during crossbreeding

Cattle are broadly classified into two subspecies: Bos taurus, adapted to temperate climates, and Bos indicus, adapted to tropical environments. Indicine cattle show better heat tolerance and stronger disease resistance, whereas taurine cattle are known for higher milk yield and better meat quality. Improving milk yield while maintaining resistance to heat stress and infectious diseases is an important objective in cattle breeding. Marker-assisted selection is an effective approach for improving economically important traits, highlighting the need to understand genetic differences between taurine and indicine cattle. However, genome-wide comparisons between European taurine and Indian indicine cattle remain limited. To address this gap, whole-genome sequencing of 48 Indian indicine cattle was performed and combined with publicly available data. This enabled a comparative genomic analysis of 74 Indian indicine and 83 European taurine individuals to identify genes involved in heat tolerance and immune response. Genome-wide analyses using Fst and XP-CLR identified 4,343 and 1,457 differentiated genes, respectively, with 826 genes common to both methods. These genes were mainly associated with immune response, protein stability, and cytoskeletal structure. Strong selection signals were observed in three heat shock protein genes (DNAJC11, DNAJC5, and DNAJB11) and 229 immune-related genes. To examine the inheritance of these genes through crossbreeding, a haplotype-resolved genome assembly was generated for the Indian crossbreed Sunandini, which showed predominantly taurine ancestry (69.13-96.04%), with a smaller indicine contribution (1.22-1.87%). Several genes related to heat tolerance and immune response were inherited exclusively from indicine cattle, highlighting their importance for environmental adaptation and future breeding programs.

genomics↗

bioRxiv2025

Right-Lateralized Maladaptive Topological Reorganization in Hyperthyroidism

Hyperthyroidism (HT) has been associated with cognitive impairments, but the structural connectomic and molecular mechanisms underlying these deficits remain poorly understood. In this study, we investigated large-scale brain network reorganization using structural connectivity derived from diffusion MRI in patients with 30 hyperthyroidism and 28 matched control participants. Subject level connectomes were analyzed to characterize network topology, with a specific focus on hub architecture, nodal alterations, and hemispheric reorganization. To probe molecular underpinnings, we integrated normative neurotransmitter receptor and transporter density maps with network metrics, assessing their correspondence to observed connectomic disruptions. Individuals with hyperthyroidism exhibited increased structural connectivity, particularly in mid- and long-range connections, alongside disrupted network topology. These changes were characterized by reduced modularity, increased characteristic path length and hub reorganization, most prominently in subcortical and right-hemisphere regions. Importantly, network alterations were functionally relevant, as metrics showed significant associations with clinical and cognitive variables, including FT4 levels, BMI, and perceptuomotor performance in the hyperthyroid group. Spatial neuromolecular correspondence analyses further revealed that DAT, 5-HT2A, and NET were closely aligned with topological changes. Moreover, neurotransmitter-weighted within-module degree z-scores moderately predicted TSH levels in HT. Our findings demonstrate that hyperthyroidism is associated with an increase in redundant, spatially extended white matter connections and a marked right-lateralized asymmetry in network organization. Furthermore, serotonergic (5-HT1a) and dopaminergic (DAT) systems consistently contributed to the modulation of intra-modular hubness, suggesting their role in maladaptive structural reorganization that may underlie perceptuomotor dysfunction in hyperthyroidism.

neuroscience↗

bioRxiv2024

Beyond the CTCT: Remote Structural Changes After VIM-MRgFUS in Essential Tremor

IntroductionEssential tremor (ET) is a progressive disorder characterized by altered network connectivity between the cerebellum, thalamus, and cortical regions. Magnetic Resonance-guided Focused Ultrasound (MRgFUS) of the ventral intermediate nucleus (VIM) is an effective, minimally invasive treatment for ET. Increasing clinical use in ET facilitates research on structural changes after thalamic lesions. MethodsForty-six patients with medication-resistant ET underwent unilateral VIM-MRgFUS. Voxel-based morphometry was applied to investigate Gray Matter Volume (GMV) changes over a time span of 6 months in the whole brain and the thalamus in particular to investigate local and distant effects. ResultsClinically, contralateral tremor significantly decreased by 68 % at 6 months following MRgFUS. In addition to local changes in thalamic nuclei (VIM, ventral lateral posterior, centromedian thalamus and pulvinar), VBM revealed remote GMV decreases in the ipsilesional insula and the anterior cingulate cortex as well as the contralesional middle occipital gyrus. Increased GMV was found in both temporal gyri. There was no significant correlation between regional GMV declines and tremor improvement. However, temporal volume increases were associated with improved motor-related functional abilities and quality of life outcomes. ConclusionOur findings implicate distributed structural changes following unilateral VIM-MRgFUS. Structural losses could reflect Wallerian degeneration of VIM output neurons or plasticity due to decreased sensory input following tremor improvement.

neuroscience↗

bioRxiv2023

Fractional Amplitude of Low-Frequency Fluctuations Associated with Endocannabinoid, {micro}-Opioid and Dopamine Receptor Distributions in the Central Nervous System after High-Intensity Exercise Bouts

Dopaminergic, opiod and endocannabinoid neurotransmission are thought to play an important role in the neurobiology of acute exercise and, in particular, in mediating positive affective responses and reward processes. Recent evidence indicates that changes in fractional amplitude of low-frequency fluctuations (zfALFF) in resting-state functional MRI (rs-fMRI) may reflect changes in specific neurotransmitter systems as tested by means of spatial correlation analyses. Here, we tested for this relationship at different exercise intensities in twenty young healthy trained athletes performing low-intensity (LIIE), high-intensity (HIIE) interval exercises and a control condition on three separate days. Positive And Negative Affect Schedule (PANAS) scores and rs-fMRI were acquired before and after each of the three experimental conditions. Respective zfALFF changes were analysed using a repeated measures ANOVAs. We explored spatial cross-correlations between pre-to-post zfALFF changes in each condition with available neurotransmitter maps using the JuSpace toolbox, and performed additional analyses for the main systems of interest (dopaminergic, opiod, endocannabinoid), focusing on specific brain networks related to reward and emotion. Elevated PANAS Positive Affect was observed after LIIE and HIIE but not in the control condition. HIIE compared to the control condition resulted in differential zfALFF decreases in precuneus, orbitofrontal cortex, thalamus, and cerebellum, whereas differential zfALFF increases were identified in hypothalamus, pituitary, and periaqueductal gray. The spatial alteration patterns in zfALFF were positively associated with dopaminergic and -opioidergic receptor distributions within the reward network. These findings provide new insight into the neurobiology of exercise supporting the importance of reward-related neurotransmission during high-intensity physical activity. KeypointsO_LIPositive mood changes, indexed as elevated PANAS Positive Affect, were identified after high- and low-intensity exercise bouts, supporting previous accounts on mood-improving effects of physical activity. C_LIO_LIHigh-intensity exercise was found to be associated with distributed changes in fractional amplitude of low-frequency fluctuations, indicating enduring neural activity changes after anaerobic exercise bouts. C_LIO_LIResults of spatial cross-correlations with representative PET neurotransmitter distribution maps suggest involvement of endocannabinoid, dopaminergic, and opioidergic neurotransmission after high-intensity exercise. C_LIO_LIUtilizing spatial cross-correlations of changes in fractional amplitude of low-frequency fluctuations and representative PET neurotransmitter distribution maps, despite being an indirect metric, provides an innovative methodological framework for human exercise research, as it allows for non-invasive testing of acute exercise-related changes multiple neurotransmitter. C_LI

neuroscience↗

bioRxiv2019

Visible light-triggered NO generation from Naphthalimide-based probe for photoreceptor-mediated plant root growth regulation

An efficient visible light-triggered nitric oxide (NO) releasing fluorescent molecule is designed and synthesized by coupling 2,6-dimethyl nitrobenzene moiety at the peri-position of 1, 8-naphthalimide through an alkene bond. The NO-releasing ability is investigated in details using various spectroscopic techniques, and the photoproduct was also characterized. Further, the photo-generated NO has been employed to examine the effect of photoreceptor-mediated NO uptake on plant root growth regulation.

plant biology↗