Biology subjects

Sharma, S. K.

Publications and source records attributed to Sharma, S. K..

14 recordsLinked to original sources

bioRxiv2026

The RNA helicase KREH2 directly binds the RESC1-RESC2 complex in trypanosomatid mitochondrial RNA editing

Trypanosomatids are medically important single-celled eukaryotic protists with exceptional RNA biology. They display highly unusual RNA biogenesis pathways, notably mitochondrial RNA editing, an essential post-transcriptional process transforming cryptic primary transcripts into functional mRNAs. Large multiprotein assemblies coordinate the RNA editing process, in which small guide RNAs (gRNAs) anneal to the pre-mRNAs and serve as templates for uridine insertion or deletion. Kinetoplast RNA Editing Helicases (KREHs) are important components of the RNA editing process that modifies large portions of pre-mRNA via the sequential annealing and dissociation of multiple gRNAs. However, how KREH helicases interact with components of the editing machinery, and which subunits mediate these interactions, remain unresolved. Here, we examined an association between the DEAH/RHA RNA helicase KREH2 and the RESC1-RESC2 protein heterodimer using proximity labeling and co-immunoprecipitation coupled to quantitative mass spectrometry in vivo. We reconstituted a minimal trimeric KREH2 peptide-RESC1-RESC2 complex in vitro and characterized novel direct binding of a KREH2 peptide to RESC1 using cryo-electron microscopy. These results establish a mechanistic link between the RNA helicase KREH2 and the RESC1-RESC2 module at the 5'-end of gRNAs, providing new avenues for studying the orchestration of RNA remodeling in trypanosomatid mitochondrial RNA editing.

molecular biology↗

bioRxiv2025

Mapping the miRNA Landscape of Gallbladder Cancer: Genome-Wide Insights and Functional Implications

Gallbladder cancer (GBC), the sixth most aggressive gastrointestinal cancer, exhibits complex molecular dysregulation involving microRNAs (miRNAs) that drive tumor progression. This study has comprehensively profiled genome-wide miRNA expression in GBC cells revealing 971 known miRNAs, and 27 novel miRNAs. We identified 388 significantly differentially expressed (DE) miRNAs (191 upregulated and 197 downregulated), providing valuable insights into the various complex molecular mechanisms underlying GBC pathogenesis. These DE miRNAs target key biological processes, including hormone-induced signaling pathways, cell adhesion molecules, apoptosis, ferroptosis, and cancer-associated pathways, particularly those linked to gastric cancer. Profiling of DE miRNAs in GBC cells presents opportunities for novel miRNA-based diagnostic and prognostic approaches in GBC. Notably, among the DE miRNAs, the miR-17[~]92 cluster was significantly suppressed in GBC cells. We also show that miR-17[~]92 cluster targets and destabilizes an S-phase licensing factor Cdt2 (an oncogene) in GBC cells. miR-17[~]92 mediated negative regulation of Cdt2 induces S-phase arrest, leading to checked proliferation and invasive capabilities of GBC cells specifically, without any significant effect on non-cancerous cells, presenting miR-17[~]92 as a potential miRNA therapeutic for GBC. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/679165v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@243970org.highwire.dtl.DTLVardef@36f578org.highwire.dtl.DTLVardef@2dba37org.highwire.dtl.DTLVardef@1c9e1b_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

cancer biology↗

bioRxiv2025

Explainable AI-Driven Diagnosis Model for Early Glaucoma Detection Using Grey-Wolf Optimized Extreme Learning Machine Approach

Glaucoma is a prominent threat to vision and ranks as the third leading cause of blindness in India. Early detection is crucial to limit its progression. Retinal image analysis, particularly computer-aided diagnosis (CAD), has gained significant attention due to its potential in effectively screening for and managing glaucoma. Nowadays, Artificial intelligence (AI) has achieved significant progress has been made in medical image analysis across various applications. However, the main challenge hindering the widespread adoption of deep neural models in clinical settings is their lack of interpretability. In response to this need, we propose an enhanced CAD model with four key components: image pre-processing, feature extraction, feature dimensionality reduction, and classification. Utilizing the G1020 and ORIGA datasets, we employ a fast discrete curvelet transform with wrapping (FDCT-WRP) for curve-like feature extraction. A combined feature reduction technique, principal component analysis (PCA) and linear discriminant analysis (LDA), is applied to generate relevant features and reduce the feature dimensionality. Incorporating an improved grey wolf Optimization (IMGWO) with an Extreme Learning Machine (ELM) for classification. Then, IMGWO optimizes parameters, enhancing the efficiency of single-hidden-layer feedforward neural networks. Through a 10 x 5-fold stratified cross-validation (SCV) test on standard datasets, our CAD model demonstrates superior performance. The proposed CAD model achieved better classification result i.e., 93.87% and 95.38% on the G1020 and ORIGA datasets respectively. Additionally, we have proposed a framework named as GlaucoXAI (Glaucoma explainable artificial intelligence), which utilizes seven advanced explanation methods to improve the interpretability of deep learning models for medical experts trust. GlaucoXAI has been employed on glaucoma detection using fundus images. GlaucoXAIs adaptable design could aid ophthalmologists and medical professionals in detection of glaucoma. The experimental results demonstrate that the proposed model surpasses other existing models in classification accuracy, while significantly reducing the number of features.

bioengineering↗

bioRxiv2024

Developmental editing control of mRNA ND7 involves KREH2 helicase-dependent gRNAselection and proposed RNA structure in Trypanosoma brucei

Unknown factors regulate mitochondrial U-insertion/deletion (U-indel) RNA editing in procyclic-form (PCF) and bloodstream-form (BSF) T. brucei. This editing, directed by anti-sense gRNAs, creates canonical protein-encoding mRNAs and may developmentally control respiration. Canonical editing by gRNAs that specify protein-encoding mRNA sequences occurs amid massive non-canonical editing of unclear sources and biological significance. We found PCF-specific repression at a major early checkpoint in mRNA ND7, involving helicase KREH2-dependent opposite modulation of canonical and non-canonical "terminator" gRNA utilization. Terminator-programmed editing derails canonical editing and installs proposed repressive structure in 30% of the ND7 transcriptome. BSF-to-PCF differentiation in vitro recreated this negative control. Remarkably, KREH2-RNAi knockdown relieved repression and increased editing progression by reverting canonical/terminator gRNA utilization. ND7 transcripts lacking early terminator-directed editing in PCF exhibited similar negative editing control along the mRNA sequence, suggesting global modulation of gRNA utilization fidelity. The terminator is a "moonlighting" gRNA also associated with mRNA COX3 canonical editing, so the gRNA transcriptome seems multifunctional. Thus, KREH2 is the first identified repressor in developmental editing control. This and our prior work support a model whereby KREH2 activates or represses editing in a stage and substrate-specific manner. KREH2s novel dual role tunes mitochondrial gene expression in either direction during development.

molecular biology↗

bioRxiv2022

miR-17~92 Suppresses Proliferation and Invasion of Cervical Cancer Cells by Inhibiting Cell Cycle Regulator Cdt2

Cervical cancer (CC) is 4th largest killer of women worldwide when diagnosed in late stages the treatment options are almost negligible. 99% of CC is caused by high risk human papilloma viruses (HR-HPV). Upon integration into human genome the encoded viral proteins mis-regulates various onco-suppressor and checkpoint factors including cell cycle regulators. One such factor is cell cycle S phase licensing factor Cdt2, which has been reported to be highly upregulated in various cancers including CC. HPV proteins also suppress several tumor suppressor miRNAs concluding miR-17-92 cluster. In this study we report that miR-17-92 directly recruits to 3UTR of Cdt2 and downregulates this oncogene which suppresses the proliferation, migration, invasion capabilities of the CC cell lines while normal cells are fine. Suppression of Cdt2 by miR17-92 blocks the cancerous cells in S phase and induces apoptosis eventually leading to their death. Hence, our work for the first time mechanistically shows how miR17-92 could work as tumor suppressor opening up the potential of miR17-92 to be used in developing therapy for cervical cancer treatment.

cancer biology↗

bioRxiv2022

mulEEG: A Multi-View Representation Learning on EEG Signals

Modeling effective representations using multiple views that positively influence each other is challenging, and the existing methods perform poorly on Electroencephalogram (EEG) signals for sleepstaging tasks. In this paper, we propose a novel multi-view self-supervised method (mulEEG) for unsupervised EEG representation learning. Our method attempts to effectively utilize the complementary information available in multiple views to learn better representations. We introduce diverse loss that further encourages complementary information across multiple views. Our method with no access to labels, beats the supervised training while outperforming multi-view baseline methods on transfer learning experiments carried out on sleep-staging tasks. We posit that our method was able to learn better representations by using complementary multi-views.{dagger}

neuroscience↗

bioRxiv2022

miR-34a negatively regulates cell cycle factor Cdt2/DTL in HPV infected Cervical Cancer Cells

MicroRNAs have emerged as an important factor in regulating cell cycle and various other cellular processes. Aberration in microRNAs has been linked with development of several cancers and other diseases but still very little is known about the mechanism behind their function in regulating cellular processes. 99% of cervical cancer is caused by the infection of high-risk HPVs (HR HPVs) which suppresses multiple tumor suppressors and checkpoint factors of the host cell. It also stabilizes oncogenic proteins, one of them is Cdt2/DTL which promotes cell transformation and proliferation. In this study, we have reported that in cervical cancer cell lines miR-34a by targeting HPV E6 protein, regulates Cdt2/DTL protein level and leads to its destabilization. Destabilization of Cdt2 stabilizes onco-suppressor proteins like p21 and Set8 in these cell lines. We have also shown that the overexpression of miR-34a suppresses cell proliferation, invasion and migration capabilities of HPV positive cervical cancer cells which was reverted by overexpression of either HPV E6 or Cdt2 genes. This is the first-ever report to show that miR-34a regulates cell cycle factor Cdt2 by suppressing viral E6 protein level, which opens up the scope of exploring miR-34a as a specific therapy for cervical cancer treatment. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/486030v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@723381org.highwire.dtl.DTLVardef@1937614org.highwire.dtl.DTLVardef@2d1ce1org.highwire.dtl.DTLVardef@1c31bc5_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2021

Are members of the Anopheles fluviatilis complex conspecific?

Anopheles fluviatilis sensu lato, a primary malaria vector in India, was identified to be comprised of four cryptic species, provisionally designated as species S, T, U and V. However, Kumar et al. (Mol Ecol Resour, 2013;13:354-61) considered all of the then known three members of this species complex (S, T and U) conspecific. The specific status of species S and T was refuted based on the lack of sufficient barcode gap in mitochondrial-CO1 and the perceived presence of heterozygotes in populations as detected through one of the two species-specific PCR assays employed for the cryptic species identification. The existence of species U was refuted claiming that earlier investigations have already refuted their existence. This conclusion is concerning because of the differential public health implications of members of the Fluviatilis Complex. Here we discuss problems associated with the CO1-based barcode approach for delimitation of cryptic species, the perceived heterozygosity between species S and T based on a species-specific PCR assay, and interpretation of published reports. We demonstrated that fixed differences do exist in the ITS2-rDNA sequence of species S and T with no evidence of heterozygotes in sympatric populations and, that the observed heterozygosity by Kumar et al. in the ITS2-based species diagnostic PCR is due to the high mispriming tendency of the T-specific primer with species S. We infer that mitochondrial DNA-based barcoding gap, an arbitrary threshold recommended for species delimitation, alone, is inadequate to delimit the members of An. fluviatilis complex.

molecular biology↗

bioRxiv2020

Complete mitogenome of endemic Plum-headed parakeet Psittacula cyanocephala - characterization and phylogenetic analysis

Psittacula cyanocephala is a parakeet endemic to the Indian sub-continent, widespread in the illegal bird trade. Previous studies on Psittacula parakeets have highlighted taxonomic ambiguities, warranting further studies to resolve such issues. Since the mitochondrial genome provides useful information about a species concerning its evolution and phylogenetics, we sequenced the complete mitogenome of P. cyanocephala using NGS, validated 38.86% of the mitogenome using Sanger Sequencing and compared it with other available whole mitogenomes of Psittacula. The complete mitogenome of the species was 16814 bp in length with 54.08% AT composition. P. cyanocephala mitogenome comprises of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. P. cyanocephala mitogenome organization was consistent with other Psittacula mitogenomes. Comparative codon usage analysis indicated the role of natural selection on Psittacula mitogenomes. Strong purifying selection pressure was observed maximum on nad1 and nad4l genes. The mitochondrial control region of all Psittacula species displayed the ancestral avian CR gene order. Phylogenetic analyses revealed the Psittacula genus as paraphyletic nature, containing at least 4 groups of species within the same genus, suggesting its taxonomic reconsideration. Our results provide useful information for developing forensic tests to control the illegal trade of the species, scientific basis for phylogenetic revision of genus Psittacula.

evolutionary biology↗

bioRxiv2020

Emergence and expansion of highly infectious spike:D614G mutant SARS-CoV-2 in central India

COVID 19 has emerged as global pandemic with largest damage to the economy and human psyche. The genomic signature deciphered during the ongoing pandemic period is valuable to understand the virus evolutionary patterns and spread across the globe. Increased availability of genome information of circulating strain in our country will enable to generate selective details in virulent and non virulent markers to prophylaxis and therapeutic interventions. The first case of SARS CoV-2 was detected in Chambal region of Madhya Pradesh state in mid of March 2020 followed by multiple introduction events and expansion of COVID-19 cases within 3 months in this region. We analyzed around 5000 COVID -19 suspected samples referred to Defence Research and Development Establishment, Gwalior, Madhya Pradesh. A total of 136 cases were found positive over a span of three months period this includes virus introduction to region and further spread. Whole genome sequences employing Oxford nanopore technology were deciphered for 26 SARS-CoV-2 circulating in 10 different districts in Madhya Pradesh State of India. The region witnessed index cases with multiple travel history responsible for introduction of COVID-19 followed by remarkable expansion of virus. The genome wide substitutions including in important viral proteins were observed. The detailed phylogenetic analysis revealed the circulating SARS-CoV-2 clustered in multiple clades A2a, A4 and B. The cluster wise segregation was observed suggesting multiple introduction links and evolution of virus in the region. This is the first comprehensive details of whole genome sequence analysis from central India region, which will add genome wide knowledge towards diagnostic and therapeutic interventions.

molecular biology↗

bioRxiv2020

Complexity in SARS-CoV-2 genome data: Price theory of mutant isolates

SARS-CoV-2 is a highly virulent and deadly RNA virus causing the Covid-19 pandemic and several deaths across the world. The pandemic is so fast that any concrete theory of sudden widespread of this disease is still not known. In this work, we studied and analyzed a large number of publicly available SARS-CoV-2 genomes across the world using the multifractal approach. The mutation events in the isolates obey the Markov process and exhibit very high mutational rates, which occur in six specific genes and highest in orf1ab gene, leading to virulent nature. f () analysis indicated that the isolates are highly asymmetric (left-skewed), revealing the richness of complexity and dominance by large fluctuations in genome structure organization. The values of Hq and Dq are found to be significantly large, showing heterogeneous genome structure self-organization, strong positive correlation in organizing the isolates, and quite sensitive to fluctuations in and around it. We then present multiple-isolates hosts-virus interaction models, and derived Price equation for the model. The phase plane analysis of the model showed asymptotic stability type bifurcation. The competition among the mutant isolates drives the trade-off of the dominant mutant isolates, otherwise confined to the present hosts.

systems biology↗

bioRxiv2020

Comprehensive bioinformatic analysis of newly sequenced Turdoides affinis mitogenome reveals the persistence of translational efficiency and dominance of NADH dehydrogenase complex-I in electron transport system over Leiothrichidae family

Mitochondrial genome provides useful information about species with respect to its evolution and phylogenetics. We have taken the advantage of high throughput next-generation sequencing technique to sequence the complete mitogenome of Yellow-billed babbler (Turdoides affinis), a species endemic to Peninsular India and Sri Lanka. Both, reference-based and de-novo assemblies of mitogenome were performed and observed that de-novo assembled mitogenome was most appropriate. The complete mitogenome of yellow-billed babbler (assembled de-novo) was 17,671 bp in length with 53.2% AT composition. Thirteen protein-coding genes along with 2 rRNAs and 22 tRNAs were detected along with duplicated control regions. The arrangement pattern of these genes was found conserved among Leiothrichidae family mitogenomes. Downstream bioinformatics analysis revealed the effect of translational efficiency and purifying selection pressure over all the thirteen protein-coding genes in yellow-billed babbler mitogenome. Moreover, genetic distance and variation analysis indicated the dominance of NADH dehydrogenase complex-I in the electron transport system of T. affinis. Evolutionary analysis revealed the conserved nature of all the protein-coding genes across Leiothrichidae family mitogenomes. Our limited phylogenetics results suggest that T. affinis is closer to Garrulax.

genomics↗

bioRxiv2019

Organization in complex brain networks: energy distributions and phase shift

The Hamiltonian function of a network, derived from the intrinsic distributions of nodes and edges, magnified by resolution parameter has information on the distribution of energy in the network. In brain networks, the Hamiltonian function follows hierarchical features reflecting a power-law behavior which can be a signature of self-organization. Further, the transition of three distinct phases driven by resolution parameter is observed which could correspond to various important brain states. This resolution parameter could thus reflect a key parameter that controls and balances the energy distribution in the brain network.

neuroscience↗

bioRxiv2017

Newly identified relatives of botulinum neurotoxins shed light on their molecular evolution

The evolution of bacterial toxins is a central question to understanding the origins of human pathogens and infectious disease. Through genomic data mining, we traced the evolution of the deadliest known toxin family, clostridial neurotoxins, comprised of tetanus and botulinum neurotoxins (BoNT). We identified numerous uncharacterized lineages of BoNT-related genes in environmental species outside of Clostridium, revealing insights into their molecular ancestry. Phylogenetic analysis pinpointed a sister lineage of BoNT-like toxins in the gram-negative organism, Chryseobacterium piperi, that exhibit distant homology at the sequence level but preserve overall domain architecture. Resequencing and assembly of the C. piperi genome confirmed the presence of BoNT-like proteins encoded within two toxin-rich gene clusters. A C. piperi BoNT-like protein was validated as a novel toxin that induced necrotic cell death in human kidney cells. Mutagenesis of the putative active site abolished toxicity and indicated a zinc metalloprotease-dependent mechanism. The C. piperi toxin did not cleave common SNARE substrates of BoNTs, indicating that BoNTs have diverged from related families in substrate specificity. The new lineages of BoNT-like toxins identified by computational methods represent evolutionary missing links, and suggest an origin of clostridial neurotoxins from ancestral toxins present in environmental bacteria.\n\nSignificance statementThe origins of bacterial toxins that cause human disease is a key question in our understanding of pathogen evolution. To explore this question, we searched genomes for evolutionary relatives of the deadliest biological toxins known to science, botulinum neurotoxins. Genomic and phylogenetic analysis revealed a group of toxins in the Chryseobacterium piperi genome that are a sister lineage to botulinum toxins. Genome sequencing of this organism confirmed the presence of toxin-rich gene clusters, and a predicted C. piperi toxin was shown to induce necrotic cell death in human cells. These newly predicted toxins are missing links in our understanding of botulinum neurotoxin evolution, revealing its origins from an ancestral family of toxins that may be widespread in the environment.

bioinformatics↗