Biology subjects

Singh, A. K.

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

At least 55 records · Page 3Linked to original sources

bioRxiv2025

ATLS2021-PA (A Sphingolipid mimetic): Upcoming Host Directed Therapy for Acute and MDR Tuberculosis

Several reports have shown that reduced Sphingolipids content in the lungs largely contributes to the outcome of Tuberculosis diseases. In this context, our pioneer study has advocated that Sphingosine -1 phosphate (a central Sphingolipid metabolite) can help host in limiting Mycobacterium tuberculosis burden in lungs by their virtue of tweaking M1 retuning of infected macrophages. This indicated that S1P may serve as anti-tubercular regimen, however allergic and autoimmune manifestation of S-1P refrain its further use as anti-tubercular Drugs. In view of this limitation, and high demand of developing newer host directed anti tubercular regimen, we explored whether enhancing / boosting Sphingolipids levels via de novo pathways by our patented drugs ATLS2021 and PA would also help host in controlling mycobacterial infection. Our results prudently demonstrated that ATLS2021 was effective in controlling survival of both wild type and MDR strain of TB in various models we tested. Our results further demonstrated the influence of ATLS2021 on NO mediated killing of mycobacteria which indicated one of most possible anti-mycobacterial mechanism of ATLS2021. Additionally, ATLS2021 lowered the IC50 value of Rifampicin for both wild-type and MDR TB by sensitizing the MDR clinical isolate of Mycobacterium tuberculosis to Rifampicin-mediated killing. ATLS2021 induced immunogenic responses in blood derived CD14+ macrophages from both healthy donors as well as MDR-TB patient demonstrating immune adjuvant potential of ATLS2021. Real time PCR data demonstrated that ATLS2021 enhanced the expression of almost all key enzymes involved in the Sphingolipid biosynthesis pathways in the CD14 positive monocytes from healthy donors and MDR TB patients. Taken together these results potentially advocated that ATLS2021 based approach is potentially immunogenic interventions against TB.

pharmacology and toxicology↗

bioRxiv2025

CK2 directly controls CARD9 protein homeostasis

CARD9 is an attractive target for therapeutic intervention because the human genetic data provides strong evidence for the causal role of CARD9 in both protection and susceptibility to autoimmune disease. Expression quantitative trait loci (eQTLs) link higher CARD9 expression to increased disease risk and lower CARD9 expression to protection. Additionally, a rare allele variant leading to a C-terminal truncation of CARD9 (CARD9{Delta}11) and subsequent loss-of-function is also protective for inflammatory bowel disease (IBD). The mechanism of CARD9-driven inflammation through scaffold assembly with BCL10 and MALT1 (CBM complex) suggests a durable inflammatory signal driven by increasing levels of CARD9. Therefore, CARD9 depletion is a desired therapeutic strategy for drug discovery, yet a difficult one due to the nature of CARD9 as an adaptor protein target and the limited number of chemical tools available to engage it. Here, we uncover through a protein homeostasis screen that casein kinase 2 (CK2/CSNK2) inhibition leads to cellular CARD9 depletion. Following up with arrayed CRISPR screening, we identify key casein kinase isoforms/subunits responsible for CARD9 depletion. We find that CK2 directly binds to CARD9 and phosphorylates S424/S425 as well as S483/S484. Orthosteric CK2 inhibition prevents CK2 binding to CARD9 and leads to CARD9 destabilization. We show that the interaction between CK2 and CARD9{Delta}11 is significantly attenuated and not sensitive to CK2-mediated protein stabilization. The CK2-driven CARD9 depletion mechanism is preserved outside of immortalized cell lines and conserved between primary, differentiated mouse and human dendritic cells. Finally, we demonstrate therapeutic proof of concept in vivo using CK2 inhibition to deplete CARD9 in murine whole blood, peritoneum, and colon. Our study expands the scope of cellular consequences dealt by kinase inhibition, offers an unconventional approach for engaging a therapeutically intractable target, and identifies a novel mechanism that could contribute to disease protection conferred by the CARD9{Delta}11 allele.

immunology↗

bioRxiv2024

Recommendations for Bioinformatics in Clinical Practice

Next Generation Sequencing (NGS) is increasingly used in clinical diagnostics, largely driven by the success and robustness of Whole Genome Sequencing (WGS). Whereas updated guidelines exist for how to interpret and report on variants that are identified from NGS using bioinformatics pipelines, there is a need for standardised bioinformatics practices for diagnostics to ensure clinical consensus, accuracy, reproducibility and comparability of the results. This article presents consensus recommendations developed by 13 clinical bioinformatics units taking part in the Nordic Alliance for Clinical Genomics (NACG), by expert bioinformaticians working in clinical production. The recommendations are based on clinical practice and focus on analysis types, test and validation, standardisation and accreditation, as well as core competencies and technical management required for clinical bioinformatics operations. Key recommendations include adopting the hg38 genome build as the reference and a standard set of recommended analyses, including the use of multiple tools for structural variant (SV) calling and in-house data sets for filtering recurrent calls. Clinical bioinformatics production should operate under the ISO 15189 standard, utilising off-grid clinical-grade high-performance computing systems, standardised file formats, and strict code version control. Containerized software containers or environment management systems are needed to ensure reproducibility. Pipelines should be rigorously documented and tested for accuracy and reproducibility, minimally covering unit, integration, and end-to-end testing. Standard truth sets such as GIAB and SEQC2 for germline and somatic variant calling, respectively, should be supplemented by recall testing of previously validated clinical cases. Data integrity must be verified using file hashing, and sample identity should be checked via sample fingerprinting and genetically inferred identification markers such as sex and relatedness. Finally, clinical bioinformatics teams should encompass diverse skills, including software development, data management, quality assurance, and domain expertise in human genetics. These recommendations provide a consensus framework for standardising bioinformatics practices across clinical WGS applications and can serve as a practical guide to facilities that are new to large-scale sequencing-based diagnostics, or as a reference for those who already run high-volume clinical production using NGS.

bioinformatics↗

bioRxiv2024

High Temperature and Microbiome Conditions Affect Gene Expression in Soybean

Heat stress is increasingly a problem in global agriculture production, both in increasing occurrences and extended durations. Understanding the molecular mechanisms of the soybean heat stress response is essential for breeding heat tolerant soybeans. Plant associated microbiomes are known to mitigate adverse effects from abiotic stress. Soybean heat stress studies have primarily focused on response to short periods of stress, and how soybean responds on a transcriptional level to a soil microbiome is poorly understood. We hypothesize a soil microbiome may help soybean survive long-term heat stress exposure. We used RNA-seq to measure the transcriptional responses in four soybean exposed to two temperature regimes and grown in two soil microbiome conditions. We identified unique responses to temperature based on the soil microbiome conditions and to the different genotypes, with fewer changes across genotypes in response to a soil microbiome. Our findings provide insights on the interaction of soil microbiome with heat stress response in soybean and identify gene targets to further study the soybean heat stress tolerance with applications to develop improved varieties.

plant biology↗

bioRxiv2024

Genomic and Phenomic Prediction for Soybean Seed Yield, Protein, and Oil

Developments in genomics and phenomics have provided valuable tools for use in cultivar development. Genomic prediction (GP) has been used in commercial soybean [Glycine max L. (Merr.)] breeding programs to predict grain yield and seed composition traits. Phenomic prediction (PP) is a rapidly developing field that holds the potential to be used for the selection of genotypes early in the growing season. The objectives of this study were to compare the use and performance of GP and PP for predicting soybean seed yield, protein content, and oil content. We additionally conducted Genome Wide Association Studies (GWAS) to identify significant SNPs associated with the traits of interest. These SNPs were also used to train the GP models. The GWAS panel of 292 diverse accessions was grown in six environments in replicated trials. Spectral data were collected at three timepoints during the growing season. A GBLUP model was trained on 268 accessions, while three separate machine learning (ML) models were trained on vegetation indices (VIs) and canopy traits. We observed that for PP, Random Forest (RF) algorithm had the highest rank correlation between the predicted and the actual phenotype rank. PP had a higher correlation coefficient than GP for seed yield, while GP had higher correlation coefficients for seed protein and oil contents. VIs with high feature importance were used as covariates in a new GBLUP model, and a new RF model was trained with the inclusion of selected SNPs from the GWAS results. These models did not outperform the original GP and PP models. These results show the capability of using ML for in-season predictions for specific traits in soybean breeding and provide insights on PP and GP inclusions in breeding programs. PLAIN LANGUAGE SUMMARYObtaining DNA information can often be costly for a public breeding program to obtain, which is a barrier of entry for using genomic prediction in these programs to make selections. Phenomic prediction provides an alternative opportunity that does not require the recurring costs of DNA sequencing. This research aimed to compare genomic and phenomic prediction in a diverse panel of soybeans. We found that phenomic prediction had the highest accuracy for seed yield, while genomic prediction was the best model for seed protein and oil. Combining genomic and phenomic data did not improve the predictive ability of the models. Core ideas O_LIIn-season phenomic prediction is able to outperform genomic prediction for seed yield. C_LIO_LIGenomic prediction outperformed in-season phenomic prediction models for seed protein and oil. C_LIO_LIOverlapping spectral indices were identified as the most predictive for seed yield, protein, and oil. C_LIO_LIFusion of genomic and phenomic prediction did not increase the predictive ability of the combined models. C_LI

plant biology↗

bioRxiv2024

Syzygium cumini (L.) Skeels has Thermostable and Selective Anti-Bacillus anthracis Activity

IntroductionGastrointestinal (GI) anthrax caused by Bacillus anthracis remains a neglected disease in many parts of the Americas, Asia, and Africa. The symptoms include dysentery, stomachache, bloating of the stomach, vomiting, fever, chills, etc. Current study evaluated several edible plants traditionally indicated for GI disease/symptoms in the Indian subcontinent for their anti-B. anthracis activity. Materials & MethodsAqueous extracts of plant parts were assessed for anti-B. anthracis activity using standard antimicrobial susceptibility testing assays. Most promising extracts were evaluated for desirable activity under conditions relevant to their usage, including extremes of temperature, pH, presence of bile salt, impact on gut microflora, and interaction with FDA-approved drugs for anthrax treatment. The bioactive components separated by bioactivity-guided thin-layer-chromatography were subjected to GC-MS characterization. ResultsAqueous Syzygium cumini (L.) Skeels or Jamun extract (AJE) was most potent and reduced the viable colony-forming units (CFU) by 6-logs within 2 hours of exposure at [≥]1.9%w/v concentration. It displayed both desirable selectivity towards gut microflora and thermostability (>90% and [~]80% of anti-B. anthracis activity were retained on incubation at 50{degrees}C for 20 days and at 95{degrees}C for 12h, respectively). AJE and FDA-approved antibiotics for anthrax displayed synergy. GC-MS analysis of AJE identified various previously-identified antimicrobials belonging to categories of alkaloids, flavonoids, phenols, etc. ConclusionAJE has potent and selective anti-B. anthracis activity with the desired degree of thermotolerance, compatibility with gut microflora, and recommended antibiotics. Further studies exploring the bioactive components in AJE and their potential application in preventing anthrax and anthrax-like diseases may be undertaken.

microbiology↗

bioRxiv2024

Cryo-EM structures of human GPR155 elucidate its regulatory and transport mechanisms

GPR155 is a polymodal lysosomal membrane "transceptor" comprising both a transporter domain and a GPCR domain, predominantly expressed in brain. GPR155 facilitates cholesterol-dependent mTORC1 signaling and is implicated in neurological disorders like Huntingtons disease. The GPCR domain likely does not bind extracellular ligands canonically, and the functional relationship between GPR155 domains remains unclear. Here, we report the first structures of monomeric human GPR155 and two distinct dimers, revealing an inward-open transporter domain and an inactivated GPCR domain with a unique luminal loop 7 conformation occupying orthosteric pocket. The dimeric assembly is cholesterol-sensitive: at low cholesterol, the transporter domain resembles plant PIN transporters and transports auxin molecules; at high cholesterol, it forms a unique dimer stabilized by cholesterol. Altogether, these findings have implications for uncovering new lysosomal signaling pathways.

biochemistry↗

bioRxiv2024

A guanidine-based coronavirus replication inhibitor which targets the nsp15 endoribonuclease and combines a direct antiviral effect with subtle boosting of interferon

The approval of COVID-19 vaccines and antiviral drugs has been crucial to end the global health crisis caused by SARS-CoV-2. However, to prepare for future outbreaks from drug-resistant variants and novel zoonotic coronaviruses (CoVs), additional therapeutics with a distinct antiviral mechanism are needed. Here, we report a novel guanidine-substituted diphenylurea compound that suppresses CoV replication by interfering with the uridine-specific endoribonuclease (EndoU) activity of the viral non-structural protein-15 (nsp15). This compound, designated EPB-113, exhibits strong and selective cell culture activity against human coronavirus 229E (HCoV-229E) and also suppresses the replication of SARS-CoV-2. Viruses, selected under EPB-113 pressure, carried resistance sites at or near the catalytic His250 residue of the nsp15-EndoU domain. Although the best-known function of EndoU is to avoid induction of type I interferon (IFN-I) by lowering the levels of viral dsRNA, EPB-113 was found to mainly act via an IFN-independent mechanism, situated during viral RNA synthesis. Using a combination of biophysical and enzymatic assays with the recombinant nsp15 proteins from HCoV-229E and SARS-CoV-2, we discovered that EPB-113 enhances the EndoU cleavage activity of hexameric nsp15, while reducing its thermal stability. This mechanism explains why the virus escapes EPB-113 by acquiring catalytic site mutations which impair compound binding to nsp15 and abolish the EndoU activity. Since the EPB-113-resistant mutant viruses induce high levels of IFN-I and its effectors, they proved unable to replicate in human macrophages and were readily outcompeted by the wild-type virus upon co-infection of human fibroblast cells. Our findings suggest that antiviral targeting of nsp15 can be achieved with a molecule that induces a conformational change in this protein, resulting in higher EndoU activity and impairment of viral RNA synthesis. Based on the appealing mechanism and resistance profile of EPB-113, we conclude that nsp15 is a challenging but highly relevant drug target. Author summaryDespite major achievements in ending the global COVID-19 crisis through vaccines and antiviral drugs, SARS-CoV-2 infection remains a serious health threat for vulnerable individuals, such as elderly and immunocompromised patients. These populations could benefit from innovative treatments that target the virus from multiple angles. In this study, we focus on the nsp15 endoribonuclease (EndoU), a poorly understood coronavirus protein that aids in viral evasion from the host innate immune response and is also assumed to regulate viral RNA synthesis. Our research centers around a newly identified, first-in-class inhibitor of coronavirus nsp15, designated EPB-113. Although nsp15 is best-known for its function in interferon evasion, EPB-113 mainly acts via an interferon-independent mechanism that is situated during viral RNA synthesis. When incubated with nsp15 protein, EPB-113 induces a structural change and enhances its EndoU enzyme activity. EPB-113 selects for escape mutants that carry substitutions in the core of EndoU, leading to a severe replication defect. Hence, our study introduces a novel drug concept to disturb the multifunctional nsp15 protein and suppress coronavirus replication on multiple fronts.

microbiology↗

bioRxiv2024

Interruption of glucagon signaling augments islet non-alpha cell proliferation in SLC7A2- and mTOR-dependent manners

ObjectiveDysregulated glucagon secretion and inadequate functional beta cell mass are hallmark features of diabetes. While glucagon receptor (GCGR) antagonism ameliorates hyperglycemia and elicits beta cell regeneration in pre-clinical models of diabetes, it also promotes alpha and delta cell hyperplasia. We sought to investigate the mechanism by which loss of glucagon action impacts pancreatic islet non-alpha cells, and the relevance of these observations in a human islet context. MethodsWe used zebrafish, rodents, and transplanted human islets comprising six different models of interrupted glucagon signaling to examine their impact on delta and beta cell proliferation and mass. We also used models with global deficiency of the cationic amino acid transporter, SLC7A2, and mTORC1 inhibition via rapamycin, to determine whether amino acid-dependent nutrient sensing was required for islet non-alpha cell growth. ResultsInhibition of glucagon signaling stimulated delta cell proliferation in mouse and transplanted human islets, and in mouse islets. This was rapamycin-sensitive and required SLC7A2. Likewise, gcgr deficiency augmented beta cell proliferation via SLC7A2- and mTORC1-dependent mechanisms in zebrafish and promoted cell cycle engagement in rodent beta cells but was insufficient to drive a significant increase in beta cell mass in mice. ConclusionOur findings demonstrate that interruption of glucagon signaling augments islet non-alpha cell proliferation in zebrafish, rodents, and transplanted human islets in a manner requiring SLC7A2 and mTORC1 activation. An increase in delta cell mass may be leveraged for future beta cell regeneration therapies relying upon delta cell reprogramming.

cell biology↗

bioRxiv2024

Exploring Probiotic Potential: A Comparative Genomics and In Silico Assessment of Genes within the Genus Geobacillus

The pursuit of new probiotic targets has seen a surge, aided by next-generation sequencing, facilitating a thorough exploration of bacterial traits. The genus Geobacillus stands out as a promising target for uncovering its potential as a probiotic. The study explored the genetic attributes of the genus Geobacillus for their resilience to gastrointestinal conditions, nutrient production, and immunomodulatory compound creation, revealing potential probiotic traits. Additionally, the research undertook predictive analyses of genomic elements such as prophages, CRISPR-Cas systems, insertion sequences, genomic islands, antibiotic resistance genes, and CAZymes. These evaluations aimed to assess the safety aspects associated with the genus Geobacillus. A comparative genomic analysis was also carried out using 18 validly published genomes of the genus Geobacillus and a few other genomes of Lactobacillus and Bifidobacterium were taken as control. Genes associated with probiotic traits like adhesion, stress tolerance (acid/bile, osmotic, oxidative), immune modulation, and molecular chaperones were uniformly detected in the Geobacillus genus. Notably, mobile genetic elements such as plasmids, prophages, and insertion sequences were absent, as were virulence factors, toxins, and Antibiotic resistance genes. Additionally, CRISPR-Cas systems and CAZymes were present. The pan-genome encompassed 25,284 protein-coding genes with translation. Comparative genomic analysis revealed an open pan-genome for Geobacillus. Pan-genome exhibited variability, particularly in genes linked to environmental interaction and secondary metabolite synthesis. In conclusion, Geobacillus appears potentially safe and well-suited for the gut habitat. However, further in vitro studies are essential to add to the knowledge of the probiotic potential of Geobacillus species. ImportanceThis comprehensive study highlights the significant probiotic potential and genetic makeup of the Geobacillus genus, shedding light on its unique attributes in adapting to extreme environmental conditions. Understanding the probiotic properties of Geobacillus is crucial amidst growing concerns over antibiotic resistance, offering promising alternatives for combating pathogenic microbes. Additionally, exploring the genetic diversity and adaptive mechanisms of Geobacillus through genomic and metagenomic approaches provides valuable insights into its biotechnological applications and evolutionary history. By employing in-silico methods and comparative analyses with established probiotic genera, this study contributes to elucidating the probiotic characteristics of Geobacillus, paving the way for further research in harnessing its beneficial traits for various applications in health, biotechnology, and environmental remediation.

microbiology↗

bioRxiv2024

UPF1 is required for gene expression in mitochondria and for the elimination of paternal mtDNA

UPF1 is a conserved RNA helicase in eukaryotes typically defined by its role in nonsense-mediated mRNA decay (NMD). This study presents ChIP-seq evidence indicating an RNA-dependent interaction of UPF1 with mtDNA, consistent with an RNA-mediated association. Mitochondrial localisation was observed as discrete foci throughout the mitochondrial network, frequently in proximity to nucleoids, as confirmed microscopically by immunostaining and GFP tagging of UPF1 in different fly tissues and S2 cells. Depletion of UPF1, but not depletion of the other core NMD factors UPF2 or UPF3, in salivary glands results in smaller mitochondria and, unexpectedly, increased respiratory activity. This increase is observed specifically in salivary glands and correlates with elevated expression of nuclear genes involved in respiratory chain assembly and mitochondrial translation. Changes in mtDNA-encoded gene expression are also observed upon the depletion of UPF1. These findings indicate that UPF1 operates in mitochondria and, independently of canonical NMD, is linked to mitochondrial gene expression and may coordinate nuclear and mitochondrial gene expression in a tissue-specific manner.

cell biology↗

bioRxiv2024

Genetic Dissection of Heat Stress Tolerance in Soybean through Genome-Wide Association Studies and the Use of Genomic Prediction to Enhance Breeding Applications

Rising temperatures and associated heat stress pose an increasing threat to soybean [Glycine max L. (Merr.)] productivity. Due to a limited choice of mitigation strategies, the primary arsenal in crop protection comes from improved genetic stress tolerance. Despite this current and looming threat to soybean production, limited studies have examined the genetics of heat stress tolerance. There is a need to conduct large-scale germplasm screening and genetic studies, including genome-wide association mapping and genomic prediction, to identify genomic regions and useful markers associated with heat tolerance traits that can be utilized in soybean breeding programs. We screened a diverse panel of 450 soybean accessions from MG 0-IV to dissect the genetic architecture of physiological and growth-related traits under optimal and heat stress temperatures and study trait relationships and predictive ability. The genetic architecture information of the response to heat revealed in this study provides insights into the genetics of heat stress tolerance. Thirty-seven significant SNPs were detected, with 20 unique SNPs detected in optimal, 16 detected in heat stress, and a single SNP detected for a heat tolerance index. Only one significant SNP was identified across temperature treatments indicating a genetic divergence in soybean responses to temperature. The genomic prediction worked well for biomass traits, but physiological traits associated with heat stress had poor model accuracy. Through our phenotyping efforts, we identified heat tolerant soybean accessions. The identification of heat tolerant accessions and significant SNPs are useful in heat tolerant variety development through marker-assisted and genomic selection. Core ideasO_LISoybean exhibit phenotypic diversity in response to heat stress. C_LIO_LILarge scale phenotypic screening identified heat tolerant accessions. C_LIO_LIPreviously unreported QTL and SNP associated with biomass and physiological parameters under heat stress are reported. C_LIO_LIGenomic prediction shows promise in abiotic stress breeding applications. C_LI

genomics↗

bioRxiv2024

The Northern Colours: Isolation and Characterisation of 4 Pigment-Producing Bacteria from the Arctic

Due to the adverse effects of synthetic colours on human health and the environment, there is a rapid shift towards the use of colours from natural sources like plants and microorganisms. Many pigment-producing microorganisms are identified and isolated from extreme environments like glaciers, ice cores, marine surface waters, etc. In this study, we have isolated 4 distinct pigment-producing bacterial strains from an Arctic stone sample collected from the vicinity of the Indian Research Station Himadri (78{degrees}55'N 11{degrees}56'E), located at the International Arctic Research Base, Ny[A]lesund, Svalbard, Norway. Pigment production was optimised by identifying the right growth medium, temperature, pH, and incubation period. The morphological, cultural, and biochemical characteristics were identified using several experiments like Gram Staining, Catalase Test, Oxydative-Fermentative Test, etc. The objective of this study is to identify novel bacterial strains capable of producing distinct pigments for pharmaceutical and industrial applications.

microbiology↗

bioRxiv2024

Nitrogen Management on Improving Resilience of Flood-Tolerant (Sub1) Rice Varieties in Flood-Prone Rainfed Lowlands

Flash flood causing submergence adversely affects rice production in vast areas of rainfed lowlands of South and Southeast Asia. Introgression at the Sub1 locus by molecularly assisted backcrossing incorporated tolerance into varieties traditional/modern high-yielding varieties and has released some varieties for commercial planting by Indian farmers. In the present study, we investigated the application of fractional N to further improve the survival and productivity potential of two Sub1 introgression varieties, Sambha Mahsuri-Sub1, and BR11-Sub1.Thirty days (d) old seedlings were transplanted, and 28-d after transplanting i.e. 58 days old seedlings were completely submerged for 18-d. Full doses of phosphorus and potassium were applied as a basal, while nitrogen was applied in split doses. Plant survival was recorded at 0, 5 and 20 days after de-submergence (AS) to study the recovery dynamics of cultivar Sub1. Results evidently established that varieties with higher biomass, tiller number, total chlorophyll and soluble sugars concentrations before flooding have higher survival rates after water drainage. They also had faster growth and better recovery, which was reflected in yield characteristics and grain yield. The 20-day and 40- day AS N application replenished flood-disturbed soil N pools, resulting in higher N uptake and N-use efficiency. These results may contribute to better nitrogen fertilization programs for rice crops and improve stress tolerance in newly developed tolerant rice varieties. It is evident from perusal of results that treatment T2 i.e.1/4 N applied as a basal and rest of residual N applied in three split doses respectively after de-submergence on days 5, 20 and 40 resulted in higher survival thanT1 and T3 respectively minimising mortality rate. This method of nitrogen fertilization (T2) also significantly affected plant-1 stem biomass, plant-1 tiller number, total chlorophyll, and soluble sugar concentrations before and after flooding. Based on these findings we proposed that application of lower dose of N (30kg/ha) as basal and rest amount of N in three split doses along with P and K (40kg/ha) in the field might be exploited to improve submergence tolerance and to obtain higher yield under flood prone ecosystem due to higher survival after de submergence corresponding to less post oxidative damage through proper N management during before and post submergence period.

plant biology↗

bioRxiv2024

Leveraging Soil Mapping and Machine Learning to Improve Spatial Adjustments in Plant Breeding Trials

Spatial adjustments are used to improve the estimate of plot seed yield across crops and geographies. Moving mean and P-Spline are examples of spatial adjustment methods used in plant breeding trials to deal with field heterogeneity. Within trial spatial variability primarily comes from soil feature gradients, such as nutrients, but study of the importance of various soil factors including nutrients is lacking. We analyzed plant breeding progeny row and preliminary yield trial data of a public soybean breeding program across three years consisting of 43,545 plots. We compared several spatial adjustment methods: unadjusted (as a control), moving means adjustment, P-spline adjustment, and a machine learning based method called XGBoost. XGBoost modeled soil features at (a) local field scale for each generation and per year, and (b) all inclusive field scale spanning all generations and years. We report the usefulness of spatial adjustments at both progeny row and preliminary yield trial stages of field testing, and additionally provide ways to utilize interpretability insights of soil features in spatial adjustments. These results empower breeders to further refine selection criteria to make more accurate selections, and furthermore include soil variables to select for macro- and micro-nutrients stress tolerance.

plant biology↗

bioRxiv2024

Epigenetic Modulation to perturb the SYNGAP1 Intellectual Disability (ID) that ameliorates synaptic and behavioural deficits

Sporadic heterozygous mutations in SYNGAP1 affects social and emotional behaviour that are often observed in intellectual disability (ID) and autism spectrum disorder (ASD). Although neurophysiological deficits have been extensively studied, the epigenetic landscape of SYNGAP1 mutation-mediated intellectual disability is unexplored. Here, we have surprisingly found that the p300/CBP specific acetylation marks of histones are significantly repressed in the adolescent hippocampus of Syngap1+/- mouse. To establish the causal relationship of Syngap1+/- phenotype and the altered histone acetylation signature we have treated 2-4 months old Syngap1+/- mouse with glucose-derived carbon nanosphere (CSP) conjugated potent small molecule activator (TTK21) of p300/CBP lysine acetyltransferase (CSP-TTK21). The enhancement of the p300/CBP specific acetylation marks of histones by CSP-TTK21 restored deficits in spine density, synaptic function, and social preferences of Syngap1+/- mouse that is very closely comparable to wild type littermates. The hippocampal RNA-Seq analysis of the treated mice revealed that the expression of many critical genes related to the ID/ASD reversed due to the treatment of the specific small molecule activator. This study could be the first demonstration of the reversal of autistic behaviour and neural wiring upon the modulation of altered epigenetic modification (s).

neuroscience↗

bioRxiv2023

Conserved Cardiovascular Network: Bioinformatics Insights into Genes and Pathways for Establishing Caenorhabditis elegans as an Animal Model for Cardiovascular Diseases.

Cardiovascular disease (CVD) is a collective term for disorders of the heart and blood vessels. The molecular events and biochemical pathways associated with CVD are difficult to study in clinical settings on patients and in vitro conditions. Animal models play a pivotal and indispensable role in cardiovascular disease (CVD) research. Caenorhabditis elegans, a nematode species, has emerged as a prominent experimental organism widely utilised in various biomedical research fields. However, the specific number of CVD-related genes and pathways within the C. elegans genome remains undisclosed to date, limiting its in-depth utilisation for investigations. In the present study, we conducted a comprehensive analysis of genes and pathways related to CVD within the genomes of humans and C. elegans through a systematic bioinformatic approach. A total of 1113 genes in C. elegans orthologous to the most significant CVD-related genes in humans were identified, and the GO terms and pathways were compared to study the pathways that are conserved between the two species. In order to infer the functions of CVD-related orthologous genes in C. elegans, a PPI network was constructed. Orthologous gene PPI network analysis results reveal the hubs and important KRs: pmk-1, daf-21, gpb-1, crh-1, enpl-1, eef-1G, acdh-8, hif-1, pmk-2, andaha-1 in C. elegans. Modules were identified for determining the role of the orthologous genes at various levels in the created network. We also identified 9 commonly enriched pathways between humans and C. elegans linked with CVDs that include autophagy (animal), the ErbB signalling pathway, the FoxO signalling pathway, the MAPK signalling pathway, ABC transporters, the biosynthesis of unsaturated fatty acids, fatty acid metabolism, glutathione metabolism, and metabolic pathways. This study provides the first systematic genomic approach to explore the CVD-associated genes and pathways that are present in C. elegans, supporting the use of C. elegans as a prominent animal model organism for cardiovascular diseases.

bioinformatics↗

bioRxiv2023

Activated PI3Kδ specifically perturbs mouse Treg homeostasis and function leading to immune dysregulation

Foxp3+ regulatory T cells (Treg) are required for maintaining immune tolerance and preventing systemic autoimmunity. PI3K{delta} is required for normal Treg development and function. However, the impacts of dysregulated PI3K{delta} signaling on Treg function remain incompletely understood. Here, we used a conditional mouse model of activated PI3K{delta} syndrome (APDS) to investigate the role of altered PI3K{delta} signaling specifically within the Treg compartment. Aged mice expressing a PIK3CD gain-of-function mutation (aPIK3CD) specifically within the Treg compartment exhibited weight loss and evidence for chronic inflammation as demonstrated by increased memory/effector CD4+ and CD8+ T cells with enhanced IFN-{gamma} secretion, spontaneous germinal center responses and production of broad-spectrum autoantibodies. Intriguingly, aPIK3CD facilitated Treg precursor development within the thymus and an increase in peripheral Treg numbers. Peripheral Treg, however, exhibited an altered phenotype including increased PD1 expression and reduced competitive fitness. Consistent with these findings, Treg specific-aPIK3CD mice mounted an elevated humoral response following immunization with a T-cell dependent antigen, that correlated with a decrease in follicular Treg. Taken together, these findings demonstrate that an optimal threshold of PI3K{delta} activity is critical for Treg homeostasis and function, suggesting that PI3K{delta} signaling in Treg might be therapeutically targeted to either augment or inhibit immune responses.

immunology↗