Biology subjects

Verma, A. K.

Publications and source records attributed to Verma, A. K..

34 records · Page 2Linked to original sources

bioRxiv2024

Green Synthesis of Silver and Gold Nanoparticles by Aqueous Artemisia Pallens Extract

We successfully harnessed the potential of Artemisia pallens extracts for the eco-friendly biosynthesis of silver, gold, and silver-gold bimetallic nanoparticles, employing aqueous silver nitrate and chloroauric acid solutions. This innovative approach departs from traditional methods, often involving toxic chemical agents like hydrazine hydrate and sodium borohydride. In the quest for greener protocols, the biological route emerges as a non-toxic, straight-forward, and environmentally sound alternative, opening new avenues for translational research. This article discusses the production of silver, gold, and silver-gold nanoparticles using different species of Artemisia plants. Nanoparticle characterization was carried out using UV-visible spectrophotometry, TEM, XRD, and FTIR techniques. Microwave-assisted synthesis resulted in well-dispersed nanoparticles. In the case of silver nanoparticles, a spherical shape with a size of 6 nm was achieved using the microwave radiation-assisted method, while a size of 20 nm was obtained with UV-assisted synthesis. Gold nanoparticles exhibited diverse shapes, including spherical, triangular, prisms, trapezoids, and hexagonal, with a predominant size of 10 nm. The size range for gold nanoparticles varied from 10 nm to 400 nm.

bioengineering↗

bioRxiv2023

Decoding Prognostic Markers Bioinformatics Insights into PIH1D1 and p53 in Children's Brain Cancer

Genetic alterations in normal brain cells lead to the development of brain tumors (BT). The incidence of newly diagnosed cases is on the rise over time. Understanding the molecular biology of pediatric brain tumors is crucial for advancing novel therapeutic approaches to prevent or effectively manage this disease. The R2TP complex, a conserved co-chaperone from yeast to mammals, including RUVBL1, RUVBL2, PIH1D1, and RPAP3 in humans, plays a crucial role in the assembly and maturation of various multi-subunit complexes. This study evaluates the expression of PIH1D1 and p53 in pediatric brain cancers using The Cancer Genome Atlas (TCGA) data through the UALCAN platform--a novel, user-friendly resource for cancer OMICS data analysis. Our analysis revealed elevated expression levels of PIH1D1 in pediatric brain tumors across all age groups compared to normal tissues, suggesting its potential as an early detection marker and a prognostic indicator. Additionally, P53 emerged as a promising target for brain tumor treatment, warranting exploration for age-specific applications. The Venn Diagram analysis further delineated key genes within the PIH1D1 and P53 networks, providing insights into the genetic landscape of childhood brain cancer. Despite these findings, the study has limitations, primarily relying on bioinformatics databases. Future research will incorporate clinical tissues and cell lines in in vivo and in vitro experiments to unravel the mechanistic roles of PIH1D1 and p53 in brain tumors. This comprehensive approach bridges bioinformatics and clinical exploration, contributing to a holistic understanding of pediatric brain cancer molecular biology and paving the way for targeted therapeutic interventions.

bioinformatics↗

bioRxiv2023

Excessive cortical beta oscillations are associated with slow-wave sleep dysfunction in mild parkinsonism

Increasing evidence associates slow-wave sleep (SWS) dysfunction with neurodegeneration. Using a within-subject design in the nonhuman primate model of Parkinsons disease (PD), we found that reduced SWS quantity in mild parkinsonism was accompanied by elevated beta and reduced delta power during SWS in the motor cortex. Our findings support excessive beta oscillations as a mechanism for SWS dysfunction and will inform development of neuromodulation therapies for enhancing SWS in PD.

neuroscience↗

bioRxiv2023

Interaction studies of Gut metabolite Trimethylene amine Oxide with Bovine Serum Albumin through Spectroscopic, DFT and Molecular Docking Approach

Trimethyleneamine N-oxide (TMAO); a gut microbiota derived metabolite has been involved in human health and diseases. It is enhanced by insulin resistivity and linked with various metabolic syndromes in human being such as renal, neuro-degenerative, and cardiovascular diseases. The primary mechanism through which TMAOs promotes disease is not clear yet. TMAO with MW= 75.11 g/mol is a small biomolecule hence, it becomes crucial to develop the conjugate of TMAO with BSA for aptamer synthesis. The binding interactions among TMAO and BSA were investigated using spectroscopic methods like UV-Vis, photoluminescence, Fourier transform infrared and circular dichroism. Hydrophilicity/Hydrophobicity of the conjugate was monitored by using contact angle ([O]) measurement. Sodium dodecyl sulphate polyacryl amide gel electrophoresis (SDS-PAGE) confirmed the different ratio of conjugate formation with the help of band size. This interaction study reveals that TMAO bind with BSA on two sites and with high affinity on one site. Docking studies also showed TMAO is involved in non-covalent interaction with bovine serum albumin forming stable docking complex with binding score of -3.6 kcal/mol obtained from the docking simulation. TMAO is involved in interaction with BSA via amino acid residues forming the stable docking complex through hydrogen bond and electrostatic interaction. This kind of interaction study may be helpful in making strategies to break the conjugation between serum albumin and uremic toxin and pave the way for the treatment for CKD and other diseases wherein TMAO is implicated. Also, conjugation of TMAO and BSA studied here may also serve as premise to develop aptamers for the detection of TMAO in the body fluids.

biochemistry↗

bioRxiv2023

Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape

Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human disease remains unexplored. Here, we investigated the impact of non-synonymous mutations in SF3B1 and U2AF1, two splicing factors commonly mutated in cancer, on transcription. We find that the mutations impair RNA Polymerase II (RNAPII) transcription elongation along gene bodies leading to transcription-replication conflicts, replication stress and altered chromatin organization. This elongation defect is linked to disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC complex, which, when modulated, normalize transcription defects and their downstream effects. Our findings shed light on the mechanisms by which oncogenic mutant spliceosomes impact chromatin organization through their effects on RNAPII transcription elongation and present a rationale for targeting the Sin3/HDAC complex as a potential therapeutic strategy. HIGHLIGHTS- Oncogenic mutations in SF3B1 and U2AF1 cause a gene body RNAPII transcription elongation defect - The elongation defect is linked to impaired assembly of early spliceosome complexes and leads to replication stress and changes to chromatin landscape - RNAPII elongation defects in SF3B1K700E are normalized by modulating epigenetic factors but 3 cryptic splicing events are not reversed - Targeting the Sin3/HDAC pathway to normalize RNAPII elongation defect is a potential therapeutic approach in these disorders GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/530019v3_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@dc6d22org.highwire.dtl.DTLVardef@180f36borg.highwire.dtl.DTLVardef@ed341forg.highwire.dtl.DTLVardef@f8dfb2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

Optical tuning of polymer functionalized zinc oxide quantum dots as a selective probe for specific detection of antibiotics

It is crucial to monitor the antibiotic levels in the environment like water, food products in the current scenario as the antibiotic concentration above threshold is harmful for the human health. Excess consumption of antibiotics leads to antibiotic resistance that hinders the control and cure of microbial diseases. So, these challenges motivated to devise an optical nano-senor which can sense the ultra-low concentration of antibiotics. In this proposed research work, emphasis is to develop a method which is simple and selective to analyze the detection and presence of antibiotics in various samples like tape water milk etc. using fluorescent ZnO QDs based nano-sensor. For this, fluorescent and different polymers (polyvinylalcohol - PVA and polyvinylpyrrolidine - PVP) capped ZnO QDs were synthesized using modified sol-gel technique. These were used as fluorescent probe to monitor the presence of antibiotics. The optical characterizations of synthesized QDs were performed using UV-Visible absorption & fluorescence spectroscopic methods while structural characteristics were analyzed by using FTIR, XRD and EDX. Charge on the synthesized QDs were obtained with the help of ZETA potential. Here ten different antibiotics were targeted among, Ciprofloxacin and Moxifloxacin have shown excellent sensing and specificity with PVA-ZnO QDs and PVP-ZnO QDs respectively.

biophysics↗

bioRxiv2022

Iron Chelation Improves Ineffective Erythropoiesis and Iron Overload in Myelodysplastic Syndrome Mice

Myelodysplastic syndrome (MDS) is a heterogeneous group of bone marrow stem cell disorders characterized by ineffective hematopoiesis and cytopenias, most commonly anemia. Red cell transfusion therapy for anemia in MDS results in iron overload, correlating with reduced overall survival. Whether treatment of iron overload benefits MDS patients remains controversial. We evaluate underlying iron-related pathophysiology and the effect of iron chelation using deferiprone on erythropoiesis in NUP98-HOXD13 transgenic mice, a highly penetrant well-established MDS mouse model. Our results characterize an iron overload phenotype with aberrant erythropoiesis in these mice which was reversed by deferiprone-treatment. Serum erythropoietin level decreased while erythroblast erythropoietin receptor expression increased in deferiprone-treated MDS mice. We demonstrate, for the first time, normalized expression of the iron chaperones Pcbp1 and Nco4 and increased ferritin stores in late stage erythroblasts from deferiprone-treated MDS mice, evidence of aberrant iron trafficking in MDS erythroblasts. Importantly, erythroblast ferritin is increased in response to deferiprone, correlating with decreased erythroblast ROS. Finally, we confirmed increased expression of genes involved in iron uptake, sensing, and trafficking in stem and progenitor cells from MDS patients. Taken together, our findings provide evidence that erythroblast-specific iron metabolism is a novel potential therapeutic target to reverse ineffective erythropoiesis in MDS. BRIEF SUMMARYIneffective erythropoiesis in MDS mice correlates with aberrant iron trafficking within bone marrow erythroblasts, consistent with findings in MDS patient progenitors, reversed after iron chelation.

pathology↗

bioRxiv2022

Dynamic in vivo mapping of the methylproteome using a chemoenzymatic approach

Dynamic protein post-translation methylation is essential for cellular function, highlighted by the essential role of methylation in transcriptional regulation and its aberrant dysregulation in diseases including cancer. This underscores the importance of cataloging the cellular methylproteome. However, comprehensive analysis of the methylproteome remains elusive due to limitations in current enrichment and analysis pipelines. Here, we employ an L-Methionine analogue, ProSeMet, that is chemoenzymatically converted to the SAM analogue ProSeAM in cells and in vivo to tag proteins with a biorthogonal alkyne that can be directly detected via LC-MS/MS, or functionalized for subsequent selective enrichment and LC-MS/MS identification. Without enrichment, we identify lysine mono-, di-, and trimethylation, histidine methylation, and arginine methylation with site specific resolution on proteins including heat shock protein HSPA8, for which methylation is implicated in human disease. With enrichment, we identify 486 proteins known to be methylated and 221 proteins with novel methylation sites encompassing diverse cellular functions. Systemic ProSeMet delivery in mice pseudomethylates proteins across organ systems with blood-brain barrier penetrance and identifies site-specific pseudomethylation in vivo with LC-MS/MS. Leveraging these pipelines to define the cellular methylproteome may have broad applications for understanding the methylproteome in the context of disease.

biochemistry↗

bioRxiv2022

Experimental and In Silico interaction studies of Alpha Amylase-Silver nanoparticle: a nano-bio-conjugate

In the current work, biosynthesis of silver nanoparticle (Ag NPs) and interaction study between alpha amylase and Ag NPs/nanocluster has been performed via wet-lab as well as in silico approach. We have synthesized Ag NPs using alpha amylase enzyme which reduces the silver nitrate precursor forming the stable Ag NPs. UV-Visible spectroscopy and fluorescence spectroscopies were performed for optical characterization of Ag NPs. UV-Vis spectra showed the wide absorption band centered around 475 nm due to surface plasmon resonance. We have also observed gradual decrease in fluorescence intensity with the increase in incubation time. Also, shift in {lambda}max of the emission spectra was recorded which clearly suggested the formation of nano-bio-conjugate. Circular dichroism spectra show the initial decrease in the ellipticity, when we added the silver nitrate, but after incubating for different time, there are no major changes in secondary structure of protein. In computational study we have modelled ground state configuration of (Ag)24 nanocluster using in silico approach. Further docking of the modelled optimized nanocluster with alpha amylase was performed and found that Ag-nanocluster showing non-covalent interaction with alpha amylase and forming stable docking complex.

biophysics↗

bioRxiv2022

REM Sleep Movements in Parkinson's Disease: Is the Basal Ganglia Engaged?

To elucidate the role of the basal ganglia during REM sleep movements in Parkinsons disease (PD) we recorded pallidal neural activity from four PD patients. Unlike desynchronization commonly observed during wakeful movements, beta oscillations (13-35 Hz) synchronized during REM sleep movements; furthermore, high-frequency oscillations (150-350 Hz) synchronized during movement irrespective of sleep-wake states. Our results demonstrate differential engagement of the basal ganglia during REM sleep and awake movements.

neuroscience↗

bioRxiv2021

Abolished miR158 activity leads to 21-nucleotide tertiary phasiRNA biogenesis that targets NHX2 in Arabidopsis thaliana

Small RNAs including microRNAs (miRNAs) are short 20-24-nucleotide non-coding RNAs. They are key regulators of gene expression in plants and other organisms. Some small RNAs, mostly 22-nucleotide long trigger biogenesis of secondary small interfering RNAs (siRNAs). Those siRNAs having distinctive phased configuration are known as phased siRNAs (phasiRNAs) and act either in cis or trans enhancing silencing cascade. Here, we report natural variants of MIR158 having deletions or insertions led to negligible or reduced expression of miR158. The deletion/insertion events affected processing of primary transcript of miR158 to precursor and to mature miR158. We show that miR158 targets a pseudo-pentatricopeptide gene and its abolished activity led to 21-nucleotide tertiary phasiRNA generation from its target. The biogenesis of these phasiRNAS is triggered by TAS2 derived two siRNAs. Accordingly, small RNA analyses of these natural variants, mutants and over-expression lines of MIR158 or its target exhibited enhanced or reduced phasiRNA biogenesis. Finally, we functionally validated the highest expressed tertiary phasiRNA that targets NHX2 thereby regulating transpiration and stomatal conductance. Overall, we deciphered a new module of small RNA network, miRNA-TAS-siRNA-pseudogene-tertiary phasiRNA-NHX2, suggesting an additional layer of gene regulation and larger role of pseudogene in plants.

plant biology↗

bioRxiv2020

A Novel Class of Azoles with potent Anti-Leishmanial activity

ObjectivesTo investigate the anti-leishmanial activity of novel azole compounds against Leishmania donovani, which causes deadly visceral leishmaniasis disease. MethodsA focused azole-based library was screened both against promastigotes and amastigotes forms of L. donovani strains in flat-bottomed 96-well tissue-culture plates and J774A.1 macrophages infected with L. donovani. The comprehensive screening azole-based library against L. donovani strains provided novel hits, which can serve as a good starting point to initiate hit to lead optimization campaign. ResultsHits identified from azole-based library exhibited potent in vitro activity against promastigotes and amastigotes of L. donovani. ConclusionsThese potent novel azole hits could be a good starting point to carry out for further medicinal chemistry exploration for anti-leishmania program.

microbiology↗

bioRxiv2020

Identification of subfunctionalized aggregate-remodeling J-domain proteins in plants

Hsp70s and J-domain proteins (JDPs) are among the most critical components of the cellular protein quality control machinery, playing crucial roles in preventing and solubilizing cytotoxic protein aggregates. Bacteria, yeast and plants additionally have large, multimeric Hsp100-class disaggregases which, allow the resolubilization of otherwise "dead-end" aggregates, including amyloids. JDPs interact with aggregated proteins and specify the aggregate remodeling activities of Hsp70s and Hsp100s. Plants have a complex network of cytosolic Hsp70s and JDPs, however the aggregate remodeling properties of plant JDPs are not well understood. Here we identify evolutionary-conserved Class II JDPs in the model plant Arabidopsis thaliana with distinct aggregate remodeling functionalities. We identify eight plant orthologs of the yeast protein, Sis1, the principal JDP responsible for directing the yeast chaperone machinery for remodeling protein aggregates. Expression patterns vary dramatically among the eight paralogous proteins under a variety of stress conditions, indicating their subfunctionalization to address distinct stressors. Consistent with a role in solubilizing cytotoxic protein aggregates, six of these plant JDPs associate with heat-induced protein aggregates in vivo as well as colocalize with plant Hsp101 to distinct heat-induced protein aggregate centers. Finally, we show that these six JDPs can differentially remodel multiple model protein aggregates in yeast confirming their involvement in aggregate resolubilization. These results demonstrate that compared to complex metazoans, plants have a robust network of JDPs involved in aggregate remodeling activities with the capacity to process a variety of protein aggregate conformers.

molecular biology↗

bioRxiv2020

K18-hACE2 Mice for Studies of COVID-19 Treatments and Pathogenesis Including Anosmia

The ongoing COVID-19 pandemic is associated with substantial morbidity and mortality. While much has been learned in the first months of the pandemic, many features of COVID-19 pathogenesis remain to be determined. For example, anosmia is a common presentation and many patients with this finding show no or only minor respiratory signs. Studies in animals experimentally infected with SARS-CoV-2, the cause of COVID-19, provide opportunities to study aspects of the disease not easily investigated in human patients. COVID-19 severity ranges from asymptomatic to lethal. Most experimental infections provide insights into mild disease. Here, using K18-hACE2 mice that we originally developed for SARS studies, we show that infection with SARS-CoV-2 causes severe disease in the lung, and in some mice, the brain. Evidence of thrombosis and vasculitis was detected in mice with severe pneumonia. Further, we show that infusion of convalescent plasma (CP) from a recovered COVID-19 patient provided protection against lethal disease. Mice developed anosmia at early times after infection. Notably, while treatment with CP prevented significant clinical disease, it did not prevent anosmia. Thus K18-hACE2 mice provide a useful model for studying the pathological underpinnings of both mild and lethal COVID-19 and for assessing therapeutic interventions.

microbiology↗

bioRxiv2018

Macrophage-induced rifampin tolerance across Mycobacterium tuberculosis lineages is Rv1258c-dependent

The Mycobacterium tuberculosis (Mtb) Lineage 4 strains CDC1551 and H37Rv develop tolerance to multiple antibiotics upon macrophage residence. Genetic mutation of the efflux pump Rv1258c in CDC1551 abolishes rifampin tolerance but not isoniazid tolerance. Here we show that clinical isolates from the other predominant Mtb lineages developed macrophage-induced isoniazid tolerance. Furthermore, all lineages developed rifampin tolerance except Lineage 2 Beijing strains, which are natural Rv1258c mutants. Thus macrophage-induced antibiotic tolerance is featured across the majority of Mtb lineages. Our findings further link Rv1258c to rifampin tolerance among clinical isolates.

microbiology↗

bioRxiv2017

Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Patients with Celiac Disease and Controls

Recent studies on celiac disease (CeD) have shown the role of gut microbiota alterations in CeD pathogenesis. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific taxa between pre-diseases and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to faecal samples indicating larger disruption of microbiota at disease site. Increased abundance of specific Helicobacter ASVs were observed in duodenum of CeD when compared to FDR (p < 0.01). In case of fecal samples CeD microbiome and Actinomyces. In addition, predicted functional metagenome showed reduced ability of gluten that ecosystem level diversity measures (except in the duodenum) were not significantly different is characterized by reduced abundance of beneficial taxa such as Akkermansia, Ruminococcus degradation by CeD faecal microbiota in comparison to FDRs and controls.

microbiology↗