Biology subjects

Baral, A.

Publications and source records attributed to Baral, A..

12 recordsLinked to original sources

bioRxiv2026

Management of Root-Knot Nematode-Fusarium Wilt Complex with different Bio-management methods in Tomato (Solanum lycopersicum L.) var Srijana

The root-knot nematode-Fusarium complex is a major constraint to protected tomato cultivation in Nepal, particularly on the widely grown Srijana hybrid, which lacks Mi-mediated nematode resistance. The present study was conducted to identify the most effective biocontrol agent, to identify the most effective Solanum rootstock, and to compare the overall efficacy of grafting versus biocontrol agents under polyhouse conditions. For the management of the root knot nematode-Fusarium complex, a pot experiment was set up in a completely randomized design at Pokhara, Kaski. Treatments comprised Trichoderma viride, Pseudomonas fluorescens, their half-dose combination, self-grafted Srijana, and four resistant rootstocks (S. sisymbriifolium, S. melongena, S. torvum, and VNRRs-10), together with nematode-only, Fusarium-only, complex (Nematode + Fusarium), and disease-free controls. Each plant was inoculated with approximately 2,000 nematode eggs, followed by 25 ml of 10^6 spores per ml of Fusarium seven days later to mimic the field complex. Plant growth parameters and nematode infestation data were recorded and analyzed via RStudio v. 2026.04.0. The root knot nematode-Fusarium complex caused significantly greater reductions in vegetative biomass than root knot nematode and Fusarium alone (20.32 gm vs 38.40 gm vs 51.32 gm) at 45 DAT. Single-agent biocontrol gave intermediate protection (T. viride 64.9%; P. fluorescens 47.9% nematode management efficiency), whereas combined T. viride + P. fluorescens treatment produced the highest vegetative biomass but the weakest nematode suppression (320 galls, reproduction factor: 38). Grafting onto S. torvum and S. melongena resulted in the greatest nematode suppression, achieving 97.9% and 93.6% management efficiency, respectively, while S. torvum alongside VNRRs-10 maintained the highest Fusarium suppression (92.5%). Overall resistant rootstocks consistently outperformed biological control in reducing disease severity. These findings indicate that grafting onto resistant solanum rootstocks, particularly S. torvum and S. melongena, was observed as the most effective strategy for managing the root knot nematode-Fusarium complex under protected cultivation, offering a viable chemical-free management option. Keywords: Root-Knot Nematode, Fusarium oxysporum, RKN-Fusarium-complex, Solanum torvum

pathology↗

bioRxiv2026

Mapping the Functional Landscape and Viral Diversity of 2A Peptides

2A peptides are short (~18 to 22 amino acid) sequences utilized by a subset of RNA viruses to process their polyproteins in an unusual co-translational event known as StopGo or ribosome skipping. This process involves ribosome pausing at a conserved C-terminal D(V/I)ExNPGP motif, followed by peptidyl-tRNA hydrolysis of the nascent peptide-tRNAGly, and continued translation from the downstream proline codon. However, how nascent 2A peptide interacts with the ribosomal exit tunnel to promote these event(s) remains poorly understood and the molecular determinants governing 2A mediated StopGo translation remain undefined. Here, we developed a mammalian fluorescence resonance energy transfer (FRET) based high-throughput reporter system to quantitatively measure 2A activity across large libraries of natural and engineered 2A peptides. Systematic mutational analysis of canonical viral 2A peptides from porcine tescovirus and foot-and-mouth disease virus (P2A, F2A) identified key residues required for activity and revealed critical contributions from previously uncharacterized N-terminal residues. Extending this approach to metagenomic viral datasets uncovered conserved sequences governing StopGo efficiency leading to functional ranking of diverse viral 2A peptides in mammalian cells, including identification of a novel subclass that supports high stop-go activity (>99%). Phylogenetic analysis of viral genomes revealed clustering of functional 2A peptides and specific motifs within specific viral lineages branches, suggesting an evolutionary trajectory underlying 2A diversification and optimization. These findings define the sequence and functional landscape of viral 2A peptides and provide mechanistic and evolutionary insights into how nascent peptide ribosome exit tunnel interactions mediate StopGo translation.

biochemistry↗

bioRxiv2026

PanRes: A database of latent and acquired antimicrobial resistance allowing 3D-based protein homology search

Antimicrobial resistance databases are central to genomic surveillance, but resistance determinants remain distributed across resources with different scopes, structures, and annotations. We developed PanRes, a curated resistance database of 11,717 genes integrating acquired and latent determinants of antibiotic, biocide, and metal resistance within a unified ontology. We predicted representative protein structures and clustered them by structural similarity, grouping proteins into 598 structurally conserved clusters coherent despite sequence divergence. Their structure-guided alignments were used to build Hidden Markov Models (HMMs) for remote homology search. In wastewater metagenomes from seven European cities, PanRes 3D-based HMMs expanded detection beyond high-confidence BLAST, with 35.2% of retained hits identified only by the HMMs and generally showing greater divergence from known proteins. For beta-lactamases, several proteins retained beta-lactamase-like folds and catalytic geometry despite weak sequence similarity. PanRes is available through an interactive web platform (https://panres.rambio.dk/), a structure-informed resource for exploring the whole resistome.

bioinformatics↗

bioRxiv2026

Elevating Neuronal CYLD Causes Frontotemporal Dementia (FTD)-Relevant Behavioral and Physiological Deficits

Frontotemporal dementia (FTD), a leading form of presenile dementia disrupting behavior, language and/or movement, is linked to mutations of a number of genes, including CYLD that encodes a Lys63 (K63) deubiquitinating enzyme. Among several CYLD variants found in FTD patients, a gain-of-function missense mutant, M719V, has been proposed to be pathogenic, but its pathogenicity in vivo and the underlying mechanism remain unknown. Here, we have developed transgenic mice that express either wildtype (WT) or M719V-CYLD in neurons throughout the mouse brain using adeno-associated virus (AAV) mediated somatic brain transgenesis. We show that somatic M719V-CYLD transgenic mice display profound FTD-associated behavioral impairments, including risk-taking, reduced social interaction, and loss of empathy that emerge from early stages and worsen with aging. Furthermore, M719V-CYLD mice also show significant early neurophysiological impairments in the prefrontal cortex (PFC), including depolarized resting membrane potential, decreased synaptic transmission, and reduced neuronal excitability. Surprisingly, however, M719V-CYLD mouse brain exhibits elevated autophagy activity and decreased Akt-mTOR signaling without overt neuronal cell loss or microgliosis even at 12 months of age. Most M719V-CYLD-associated cellular and behavioral phenotypes are also recapitulated but to a lesser extent in WT-CYLD mice, suggesting CYLD activation is responsible for the observed neural circuit deficits and the M719V mutation is gain-of-function in nature. Our results uncover important roles of neuronal CYLD in PFC function and social behaviors and establish a unique animal model to investigate pathogenic mechanisms of FTD, in particular its social behavioral deficits, at molecular, cellular, synaptic and circuit levels.

neuroscience↗

bioRxiv2026

Calibrating for absolute microbiome abundances without spike-ins

Metagenomics is a widely used approach in microbiome research. However, a major limitation of metagenomic datasets is their compositional nature, which prevents direct quantification of absolute abundances and complicates cross-sample comparisons. Existing strategies for absolute quantification typically require additional experiments or spike-in controls. Here, we introduce the MetaGenome Calibrator (MGCalibrator), a new tool that enables spike-in free, absolute abundance estimation based on routine DNA concentration measurements. We validated the accuracy of absolute abundances obtained with MGCalibrator against qPCR for 5 targets. Our results show a strong correlation with qPCR data, indicating that MGCalibrator enables qPCR-like trend analyses. For Bacteroides dorei, the estimated abundances were highly similar between the two methods (r2 = 0.98, y = 1.00x). For other targets like crAssphage or the bacterial 16S rRNA gene, qPCR values were underrepresented by a factor of 7 or overrepresented by a factor of 4. Benchmarking with synthetic microbiome data demonstrated that our method accurately determines copy numbers in sequencing datasets, and application to whole-cell mock community samples produced expected values based on known extraction biases. In an extraction-bias-free experiment, MGCalibrator accurately quantified genome copy numbers within a twofold range in 98% of cases and determined 16S rRNA gene copies within 1.6-fold or less. Finally, we applied MGCalibrator to track temporal trends in antibiotic resistance genes (ARGs) in wastewater treatment plants in two Dutch provincial capitals. We observed an overall increase in ARGs--such as sul2 in Utrecht and qnrS5 in Houtrust--likely driven by rising bacterial loads. Our findings demonstrate that MGCalibrator provides robust calibration of metagenomic data, paving the way for metagenomics to play a central role in future surveillance by enabling trend analysis across thousands of genetic targets, similar to the capabilities of qPCR for individual genes. The source code and documentation for MGCalibrator are available at github.com/NimroddeWit/MGCalibrator.

microbiology↗

bioRxiv2026

Aurora kinase A is a synthetic lethal target in FANCA-deficient cancers

Loss-of-function genomic alterations in FANCA occur across multiple cancer types, yet no molecularly tailored therapies have successfully exploited this potential vulnerability. Using complementary unbiased approaches, including a genome-wide CRISPR/Cas9 loss-of-function screen and a high-throughput drug screen in isogenic cancer cell-based models, we identified Aurora kinase A (AURKA) as a reproducible synthetic lethal target of FANCA-deficient cancers. Inhibition of AURKA induced chromosomal instability, micronucleation, and early G2/M arrest selectively in FANCA-deficient cells, consistent with an increased reliance on mitotic checkpoint control. Mechanistically, FANCA deficiency is associated with an elevated AURKA expression at both the transcriptomic and protein levels, and with an upregulation of mitotic spindle and G2/M checkpoint gene signatures. Analysis of large-scale cancer genomics datasets, including over 650,000 clinically sequenced tumors, confirms that FANCA is the most frequently altered Fanconi anemia pathway gene across cancers, and that Fanconi anemia-defective tumors exhibit an increased tumor mutational burden and genomic instability. Collectively, our findings point to AURKA inhibition as a promising precision treatment strategy in FANCA-deficient cancers and provide a rationale to further explore this strategy in the clinic.

cancer biology↗

bioRxiv2024

Deficiency of actin depolymerizing factors ADF/Cfl1 in microglia decreases motility and impairs memory

Microglia are highly motile cells that play a crucial role in the central nervous system in health and disease. Here we show that actin depolymerizing factors ADF and Cofilin1 (Cfl1) are key factors of microglia integrity and function. We found a profound morphological phenotype in absence of ADF and Cfl1 in microglia. In vivo two-photon imaging of microglia with ADF/Cfl1-KO revealed reduced microglial fine processes motility and impaired microglia migration towards a laser-induced lesion. We found increased accumulation of stabilized F-actin and altered microtubule dynamics in ADF/Cfl1-KO microglia, indicating that ADF/Cfl1 are necessary for microglial cytoskeleton dynamics. Interestingly, microglial ADF/Cfl1-deficiency decreased learning and memory, suggesting that impaired microglial cytoskeleton dynamics affect neuronal functions relevant for cognition. Our results reveal a fundamental role of ADF/Cfl1 in microglia function and underscore the importance of these innate immune cells for higher cognitive functions.

neuroscience↗

bioRxiv2021

Opposing roles of p38α phosphorylation and arginine methylation in driving TDP-43 proteinopathy.

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder typically characterized by insoluble inclusions of hyperphosphorylated TDP-43. The mechanisms underlying toxic TDP-43 accumulation are not understood. Persistent activation of p38 mitogen-activated protein kinase (MAPK) is implicated in ALS. However, it is unclear how p38 MAPK affects TDP-43 proteinopathy. Here, we demonstrate that inhibition of p38 MAPK reduces pathological TDP-43 phosphorylation, aggregation, cytoplasmic mislocalization, and neurotoxicity. We establish that p38 MAPK phosphorylates TDP-43 at pathological serine 409/410 (S409/S410) and serine 292 (S292), which reduces TDP-43 liquid-liquid phase separation (LLPS) but allows pathological TDP-43 aggregation. Moreover, we show that protein arginine methyltransferase 1 methylates TDP-43 at R293. Importantly, S292 phosphorylation reduces R293 methylation, and R293 methylation reduces S409/S410 phosphorylation. R293 methylation permits TDP-43 LLPS and reduces pathological TDP-43 aggregation. Thus, strategies to reduce p38-mediated TDP-43 phosphorylation and promote R293 methylation could have therapeutic utility for ALS and related TDP-43 proteinopathies.

molecular biology↗

bioRxiv2020

In-silico development of a method for the selection of optimal enzymes using L-asparaginase II against Acute Lymphoblastic Leukemia as an example.

L-Asparaginase II (asnB), a periplasmic protein, commercially extracted from E. coli and Erwinia, is often used to treat Acute Lymphoblastic Leukemia. L-Asparaginase is an enzyme that converts L-asparagine to aspartic acid and ammonia. Cancer cells are dependent on asparagine from other sources for growth and when these cells are deprived of asparagine by the action of the enzyme the cancer cells selectively die. Questions remain as to whether asnB from E. coli and Erwinia is the best asparaginase as they have many side-effects. asnB with the lowest Michaelis constant (Km) (most potent), and with the lowest immunogenicity is considered the most optimal enzyme. In this paper asnB sequence of E. coli was used to search for homologous proteins in different bacterial and archaeal phyla and a maximum likelihood phylogenetic tree was constructed. The sequences that are most distant from E. coli and Erwinia were considered best candidates in terms of immunogenicity and were chosen for further processing. The structures of these proteins were built by homology modeling and asparagine was docked with these proteins to calculate the binding energy. asnBs from Streptomyces griseus, Streptomyces venezuelae and Streptomyces collinus were found to have the highest binding energy i.e. -5.3 kcal/mol, -5.2 kcal/mol, and -5.3 kcal/mol respectively (Higher than the E.coli and Erwinia asnBs) and were predicted to have the lowest Kms as we found that there is an inverse relationship between binding energy and Km. Besides predicting the most optimal asparaginase, this technique can also be used to predict the most optimal enzymes where the substrate is known and the structure of one of the homologs is solved.

bioinformatics↗

bioRxiv2020

TGN/EE SNARE protein SYP61 is ubiquitinated and required for carbon/nitrogen-nutrient responses in Arabidopsis

Ubiquitination is a post-translational modification with reversible attachment of the small protein ubiquitin, which is involved in numerous cellular processes including membrane trafficking. For example, ubiquitination of cargo proteins is known to regulate their subcellular dynamics, and plays important roles in plant growth and stress adaptation. However, the regulatory mechanism of the trafficking machinery components remains elusive. Here, we report Arabidopsis trans-Golgi network/early endosome (TGN/EE) localized soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) protein SYP61 as a novel ubiquitination target of a membrane localized ubiquitin ligase ATL31. SYP61 is a key component of membrane trafficking in Arabidopsis. SYP61 was ubiquitinated with K63-linked chain by ATL31 in vitro and in plants. The knockdown mutants of SYP61 were hypersensitive to the disrupted carbon (C)/nitrogen (N)-nutrient stress, suggesting its critical role in plant homeostasis in response to nutrients. We also found the ubiquitination status of SYP61 is affected by C/N-nutrient availability. These results provided possibility that ubiquitination of SNARE protein has important role in plant physiology.

plant biology↗

bioRxiv2020

External mechanical cues reveal core molecular pathway behind tissue bending in plants

Tissue folding is a central building block of plant and animal morphogenesis. In dicotyledonous plants, hypocotyl folds to form hook after seedling germination that protects their aerial stem cell niche during emergence from soil. Auxin response factors and auxin transport are classically thought to play a key role in this process. Here we show that the microtubule-severing enzyme katanin contributes to hook formation. However, by exposing hypocotyls to external mechanical cues mimicking the natural soil environment, we reveal that auxin response factors ARF7/ARF19, auxin influx carriers, and katanin are dispensable for apical hook formation, indicating that these factors primarily play the role of catalyzers of tissue bending in the absence of external mechanical cues. Instead, our results reveal the key roles of the non-canonical TMK-mediated auxin pathway, PIN efflux carriers and cellulose microfibrils as components of the core pathway behind hook formation in presence or absence of external mechanical cues.

plant biology↗

bioRxiv2019

Label-free characterization of Amyloid-β-plaques and associated lipids in brain tissues using stimulated Raman scattering microscopy

The brains of patients with neurodegenerative diseases such as Alzheimers Disease (AD) often exhibit pathological alterations that involve abnormal aggregations of proteins and lipids. Here, we demonstrate that high-resolution, label-free, chemically-specific imaging using Stimulated Raman Scattering Microscopy (SRS) provides novel insights into the biophysical properties and biochemical composition of such pathological structures. In brain slices of a mouse model of AD, SRS reveals large numbers of Amyloid-{beta} plaques that commonly form a characteristic, three-dimensional core-shell structure, with a fibrillar proteinaceous core surrounded by a halo-like shell of lipid-rich deposits. SRS spectroscopic imaging allows for a clean, label-free visualization of the misfolded ({beta}-sheet) Amyloid-{beta} content in the plaque core. Surrounding lipid-rich deposits are found to contain comparatively high concentrations of membrane lipids (sphingomyelin, phosphatidylcholine), but lower levels of cholesterol than healthy white matter structures. Overall, the SRS spectra of plaque-associated lipids closely resemble those of nearby neurites, with the notable difference of a higher degree of lipid unsaturation compared to healthy brain structures. We hypothesize that plaque-associated lipid deposits may result from neuritic dystrophy associated with AD, and that the observed increased levels of unsaturation could help identify the kinds of pathological alterations taking place. Taken together, our results highlight the potential of Stimulated Raman Scattering microscopy to contribute to a deeper understanding of neurodegenerative diseases.

neuroscience↗