Biology subjects

Gupta, Y. K.

Publications and source records attributed to Gupta, Y. K..

10 recordsLinked to original sources

bioRxiv2026

A novel genetically distinct Amdoparvovirus in Sorex araneus in the United Kingdom highlights an unexplored ancestral link

Amdoparvoviruses have historically been documented almost exclusively in carnivores, with recent detections in bats. However, endogenous viral elements in rodent genomes suggest a more ancient and taxonomically broader evolutionary history. Despite this, small mammals have never been systematically surveyed for extant amdoparvovirus infections. In this study, we used whole genome sequencing to screen four different shrew species and wild American mink in the UK, which may act as a reservoir host for amdoparvoviruses. We identified a highly divergent amdoparvovirus in native common shrews (Sorex araneus) from northern England, tentatively named Shrew parvovirus 1(SP 1). Classical amdoparvovirus sequences were also detected in wild American mink (Neogale vison), confirming the presence of known amdoparvovirus strains in UK mustelids. Phylogenetic analysis revealed that the shrew virus, SP 1, forms a distinct clade, suggesting ancient divergence or long-term cryptic circulation in small mammal reservoirs. These findings fundamentally challenge the hypothesis that amdoparvoviruses are carnivore-restricted pathogens and underscore the importance of systematic wildlife surveillance for understanding viral host range evolution and assessing spillover risks.

evolutionary biology↗

bioRxiv2025

Non-invasive brain stimulation protects cognitive impairment in i.c.v.STZ injected rats: role of adult neurogenesis

In Alzheimers like dementia, neurodegeneration and synaptic dysfunction is known to the critical player in explaining the cognitive impairment. Adult neurogenesis, normally a chronic and quite process is explained to have potential in the field of Alzheimers therapy. Previous research on the non-invasive brain stimulation showed that controlling pattern of stimulation externally we can regulate/ entrain neuronal activity, possibly altering the structural changes in the circuit level. However, literature investigating if non-invasive brain stimulation could hold any potential to initiate process of adult neurogenesis are scarce. In the present study, with the use of behavioural, microscopic and biochemical tools we found that extremely low frequency magnetic field at an intensity of 17.96{micro}T with sinusoidal wave of 50Hz for 2hr daily for a period of two week in streptozotocin induced animal model of sporadic Alzheimers disease can cause improvement in spatial and reference memory, influencing their swimming strategy in water maze. Which is caused by stimulation in immature neural pluripotent stem cells, with additional redox balance and mitigation of glial aggravation in brain areas like olfactory bulb, prefrontal cortex and hippocampus. These changes were accompanied by neuroprotection as observed in the granular layer of dentate gyrus. Taken together, present study explains plausible mechanism of action on protection of neurodegeneration in Alzheimers disease through non-invasive brain stimulation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/666022v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@bc7830org.highwire.dtl.DTLVardef@176cc01org.highwire.dtl.DTLVardef@4b869dorg.highwire.dtl.DTLVardef@72e703_HPS_FORMAT_FIGEXP M_FIG Graphical illustration representing external magnetic field causing cognitive improvement eliciting adult neurogenesis in animal model of Alzheimers disease C_FIG

neuroscience↗

bioRxiv2025

The dominant lineage of Phakopsora pachyrhizi in the United States of America does not have a Brazilian origin

O_LIAsian soybean rust (ASR), caused by the obligate biotrophic fungus, Phakopsora pachyrhizi, was first reported in the continental United States of America (USA) in 2004 and over the years has been of concern to soybean production in the USA. The prevailing hypothesis is that P. pachyrhizi spores were introduced into the USA via hurricanes originating from South America, particularly Hurricane Ivan. C_LIO_LITo investigate the genetic diversity and global population structure of P. pachyrhizi, we employed exome-capture based sequencing on 84 field isolates collected from different geographic regions worldwide. We compared the gene-encoding regions from all these field isolates and found that four major haplotypes are prevalent worldwide. Here, we provide genetic evidence supporting multiple incursions that have led to the currently established P. pachyrhizi population of the USA. Phylogenetic analysis of mitochondrial genes further supports this hypothesis. C_LIO_LINotably, we observed limited genetic diversity in P. pachyrhizi populations in Brazil, suggesting a clonal population structure in that country that contrasts to populations from the USA and Africa. C_LIO_LIThis study provides the first comprehensive characterization of P. pachyrhizi population structures defined by genetic evidence from populations across major soybean growing regions. C_LI

evolutionary biology↗

bioRxiv2022

Barley MLA3 recognizes the host-specificity determinant PWL2 from rice blast (M. oryzae)

Plant nucleotide-binding leucine-rich repeat immune receptors (NLRs) directly or indirectly recognize pathogen-secreted effector molecules to initiate plant defense. Recognition of multiple pathogens by a single NLR is rare and usually occurs via monitoring for changes to host proteins; few characterized NLRs have been shown to recognize multiple effectors. The barley NLR Mla has undergone functional diversification and Mla alleles recognize host-adapted isolates of barley powdery mildew (Blumeria graminis f. sp. hordei; Bgh). Here, we show that Mla3 also confers resistance to rice blast (Magnaporthe oryzae) in a dosage dependent manner. Using a forward genetic screen, we discovered that the recognized effector from M. oryzae is PWL2, a host range determinant factor that prevents M. oryzae from infecting weeping lovegrass (Eragrostis curvula). Mla3 has therefore convergently evolved the capacity to recognize effectors from diverse pathogens.

plant biology↗

bioRxiv2022

The soybean rust pathogen Phakopsora pachyrhizi displays transposable element proliferation that correlates with broad host-range adaptation on legumes

Asian soybean rust, caused by Phakopsora pachyrhizi, is one of the worlds most economically damaging agricultural diseases. Despite P. pachyrhizis impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. We simultaneously sequenced three P. pachyrhizi genomes uncovering a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. The proliferation of TEs within the genome occurred in several bursts and correlates with the radiation and speciation of the legumes. We present data of clear de-repression of TEs that mirrors expression of virulence-related candidate effectors. We can see a unique expansion in amino acid metabolism for this fungus. Our data shows that TEs play a dominant role in P. pachyrhizis genome and have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity of the genome.

microbiology↗

bioRxiv2022

Cognitive dysfunction and anxiety resulted from synaptic downscaling, hippocampal atrophy and ventricular enlargement in i.c.v. streptozotocin injected male Wistar rats

Insulin-resistant brain state is proposed to be the early sign of Alzheimers disease(AD), which can be studied in intracerebroventricular streptozotocin (ICV-STZ) rodent model. ICV-STZ is reported to induce sporadic AD with the majority of the disease hallmarks as phenotype. On the other hand, Available experimental evidence has used varying doses of STZ (<1 to 3mg/kg) and studied its effect for different study durations, ranging from 14-270 days. Though these studies suggest 3mg/kg of ICV-STZ to be the optimum dose for progressive pathogenesis, the reason for such is elusive. Here we sought to investigate the mechanism of action of 3mg/kg ICV-STZ on cognitive and non-cognitive aspects at a follow-up interval of two weeks for two months. On 60th day, we examined layer thickness, cell density, ventricular volume, spine density, protein expression related to brain metabolism and mitochondrial function by histological examination. Findings suggest progressive loss of spatial, episodic, avoidance memory with increase in anxiety in a span of two month. Furthermore, hippocampal neurodegeneration, ventricular enlargement, diffused amyloid plaque deposition, loss of spine in dentate gyrus and imbalance in energy homeostasis was found on 60th day post injection. Interestingly, AD rats showed a uniform fraction of time spent in four quadrants of water maze with change in strategy when they were exposed to height. Our findings reveal that ICV-STZ injection at a dose of 3mg/kg can cause cognitive and neuropsychiatric abnormalities due to structural loss both at neuronal as well as synaptic level, which is tightly associated with change in neuronal metabolism.

neuroscience↗

bioRxiv2022

RNA binding to human METTL3-METTL14 restricts N6-deoxyadenosine methylation of DNA in vitro

Methyltransferase like-3 (METTL3) and METTL14 complex transfers a methyl group from S-adenosyl-L-methionine to N6 amino group of adenosine bases in RNA (m6A) and DNA (m6dA). Emerging evidence highlights a role of METTL3-METTL14 in the chromatin context, especially in processes where DNA and RNA are held in close proximity. However, a mechanistic framework about specificity for substrate RNA/DNA and their interrelationship remain unclear. By systematically studying methylation activity and binding affinity to a number of DNA and RNA oligos with different propensities to form inter- or intra-molecular duplexes or single-stranded molecules in vitro, we uncover an inverse relationship for substrate binding and methylation and show that METTL3-METTL14 preferentially catalyzes the formation of m6dA in single-stranded DNA (ssDNA), despite weaker binding affinity to DNA. In contrast, it binds structured RNAs with high affinity, but methylates the target adenosine in RNA (m6A) much less efficiently than it does in ssDNA. We also show that METTL3-METTL14-mediated methylation of DNA is largely regulated by structured RNA elements prevalent in long noncoding and other cellular RNAs.

biochemistry↗

bioRxiv2021

Conserved secreted effectors determine endophytic growth and multi-host plant compatibility in a vascular wilt fungus

Fungal interactions with plant roots, either beneficial or detrimental, have a major impact on agriculture and ecosystems. The soil inhabiting ascomycete Fusarium oxysporum (Fo) constitutes a species complex of worldwide distribution causing vascular wilt in more than a hundred different crops. Individual isolates of the fungus exhibit host-specific pathogenicity, determined by proteinaceous effectors termed secreted in xylem (SIX). However, such isolates can also colonize roots of non-host plants asymptomatically as endophytes, or even protect them against pathogenic isolates. The molecular determinants of multi-host plant colonization are currently unknown. Here, we identified a set of fungal effectors termed ERCs (Early Root Compatibility effectors), which are secreted during early biotrophic growth of Fo on both host and non-host plants. In contrast to the strain-specific SIX effectors, which are encoded on accessory genomic regions, ERCs are encoded on core regions and are found across the entire Fo species complex as well as in other phytopathogens, suggesting a conserved role in fungus-plant associations. Targeted deletion of ERC genes in a pathogenic Fo isolate resulted in reduced virulence on the host plant and rapid activation of plant immune responses, while in a non-pathogenic isolate it led to impaired root colonization and loss of biocontrol ability. Strikingly, some ERCs also contribute to Fo infection on the non-vascular land plant Marchantia polymorpha. Our results reveal an evolutionarily conserved mechanism for multi-host colonization by root infecting fungi.

plant biology↗

bioRxiv2021

A metal ion orients mRNA to ensure accurate 2'-O ribosyl methylation of the first nucleotide of the SARS-CoV-2 genome

The SARS-CoV-2 nsp16/nsp10 enzyme complex modifies the 2-OH of the first transcribed nucleotide of the viral mRNA by covalently attaching a methyl group to it. The 2-O methylation of the first nucleotide converts the status of mRNA cap from Cap-0 to Cap-1, and thus, helps the virus evade immune surveillance in the host cell. Here, we report two structures of nsp16/nsp10 representing pre- and post-release states of the RNA product (Cap-1). We observe overall widening of the enzyme upon product formation, and an inward twisting motion in the substrate binding region upon product release. These conformational changes reset the enzyme for the next round of catalysis. The structures also identify a unique binding mode and the importance of a divalent metal ion for 2-O methylation. We also describe underlying structural basis for the perturbed enzymatic activity of a clinical variant of SARS-CoV-2, and a previous SARS-CoV outbreak strain.

biochemistry↗

bioRxiv2020

Structural Basis of RNA Cap Modification by SARS-CoV-2 Coronavirus

The novel severe acute respiratory syndrome coronoavirus-2 (SARS-CoV-2), the causative agent of COVID-19 illness, has caused over 2 million infections worldwide in four months. In SARS coronaviruses, the non-structural protein 16 (nsp16) methylates the 5-end of virally encoded mRNAs to mimic cellular mRNAs, thus protecting the virus from host innate immune restriction. We report here the high-resolution structure of a ternary complex of full-length nsp16 and nsp10 of SARS-CoV-2 in the presence of cognate RNA substrate and a methyl donor, S-adenosyl methionine. The nsp16/nsp10 heterodimer was captured in the act of 2-O methylation of the ribose sugar of the first nucleotide of SARS-CoV-2 mRNA. We reveal large conformational changes associated with substrate binding as the enzyme transitions from a binary to a ternary state. This structure provides new mechanistic insights into the 2-O methylation of the viral mRNA cap. We also discovered a distantly located ligand-binding site unique to SARS-CoV-2 that may serve as an alternative target site for antiviral development.

biophysics↗