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Tyagi, K.

Publications and source records attributed to Tyagi, K..

13 recordsLinked to original sources

Training-induced alterations in the modulation of human motoneuron discharge patterns with contraction force

Motoneurons adapt to both resistance and endurance training in reduced animal preparations, with adaptations seemingly more apparent in higher threshold neurons, but similar evidence in humans is lacking. Here, we compared the identified motor unit (MU) discharge patterns from decomposed electromyography signals acquired during triangular dorsiflexion contractions up to 70% of maximal voluntary force (MVF) between resistance-trained, endurance-trained, and untrained individuals (n=23 in each group). We then estimated intrinsic motoneuron properties and garnered insight about the proportion of excitatory, inhibitory, and neuromodulatory inputs contributing to motor commands across contraction intensities in each group. Participants also performed a task where a triangular contraction was superimposed onto a sustained one designed to challenge inhibitory control of dendritic persistent inward currents (PICs). Both trained groups demonstrated greater MU discharge rates with greater ascending discharge rate modulation during higher contraction forces ([≥]50% MVF), which were accompanied by more linear MU discharge patterns and greater post-acceleration attenuation slopes of the ascending discharge rates. No differences in discharge rate hysteresis or the discharge rate characteristics during the sombrero tasks between groups, suggesting no differences in neuromodulatory input. Conversely, resistance-compared to endurance-trained individuals exhibited greater acceleration slopes during lower contractions forces ([≤]50% MVF), indicating the possibility of enhanced initial activation of PICs. Collectively, the greater and more linear MU discharge patterns in the trained groups either suggests a more reciprocal (i.e., push-pull) excitation-inhibition coupling during higher contraction forces or enhanced excitatory synaptic input to the motor pool, which might underpin greater force production of trained individuals.

neuroscience↗

Loss-of-Function RUP-Variants Influence Ubiquitin-Proteasome System and Enhance Carotenoid and Folate Levels in Tomato

REPRESSOR OF UV-B PHOTOMORPHOGENESIS (RUP) negatively regulates UV- B signalling, yet its broader physiological roles in crop plants remain largely unexplored. We compared two tomato accessions bearing truncated RUP proteins--rup-1 and rup-2 (rup- variants)--with the cultivar Arka Vikas (AV), which harbours the native RUP protein. Seedlings of rup-variants exhibited enhanced tolerance to supplemental UV-B light. Red ripe (RR) fruits of rup-variants showed significantly elevated carotenoid and folate levels compared to AV. Introgression of rup-variants into AV confirmed that the increased carotenoid accumulation is genetically linked to RUP truncation. Metabolomic profiling of rup-variants revealed a substantial shift in primary metabolic homeostasis, particularly at the breaker stage, marked by a pronounced reduction in sugars and amino acids. Proteomic analyses of rup- variants across ripening stages identified that a significant proportion of differentially expressed proteins belonged to chaperones and ubiquitin-proteasome system (UPS). Upregulation of four key enzymes in the carotenoid biosynthesis pathway likely contributed to increased lycopene content in rup-variants. Elevated folate levels in rup-variants were associated with the upregulation of folate biosynthesis and C1 metabolism enzymes. Despite widespread metabolic reprogramming in rup-variants, hormonal regulatory pathways remained largely unaltered. Our results suggest that RUP modulates metabolic pathways during fruit ripening, and its loss triggers metabolic reprogramming associated with elevated folate/carotenoid levels.

plant biology↗

Metagenomic Profiling of Drinking Water Microbiomes: Insights into Microbial Diversity and Antimicrobial Resistance

Monitoring microbial components in drinking water is as essential as tracking its chemical composition. Although traditional culture-based methods provide valuable insight into microbial morphology and behaviour, their scope is restricted to culturable species. With the advent of high-throughput sequencing, we can now detect a wider range of microbes in any ecosystem, along with efficient insights into their functional potential and metabolic capabilities. In this study, metagenomic analyses were performed to fully understand the microbiome of drinking water supplied through public distribution systems in an Indian city. Our findings identified bacteria from the phyla Pseudomonadota, Planctomycetota, Bacteroidota, and Actinomycetota, consistent with previous studies of drinking water microbiomes of other countries. At the species level, Afipia carboxidovorans, Klebsiella pneumoniae, Pseudomonas aeruginosa, Sphingopyxis macrogoltabida, and Variovorax paradoxus were identified as members of the core microbiome. It was observed that the temperature of the water samples, even as little as a 5{o}C increase, influenced the composition and diversity of the microbial communities. No significant correlation was detected between the abundance of microbial species and the metal concentration in the sample. In addition, we traced the distribution of antibiotic resistance genes (ARGs), finding widespread resistance to aminoglycosides, tetracyclines, and macrolides in samples. In particular, ARGs such as adeF and ermR, which are known to be associated with multidrug resistance, were detected. Although this study did not directly assess the pathogenicity or mobility of these genes, their presence in potable water raises potential public health concerns due to the possibility of horizontal gene transfer (HGT) in environmental settings. Therefore, continuous monitoring of antibiotic resistance genes (ARGs) is imperative to accurately evaluate long-term risks and to guide evidence-based water quality management strategies. In summary, this study provides a comprehensive metagenomic overview of drinking water microbiota, ARGs, and water quality, offering a foundation for future surveillance and risk mitigation strategies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/636216v3_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@819c0org.highwire.dtl.DTLVardef@1d29372org.highwire.dtl.DTLVardef@1ce3cf9org.highwire.dtl.DTLVardef@1050997_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

New Record of Four Thrips Species Infesting Flower Buds of Magnolia champaca in India

The golden-flowered, highly fragrant local variety of Magnolia champaca, known as Sonchafa, is very popular loose flower crop in Maharashtra and adjoining states of India. In response to the rising thrips problems in Sonchafa (M. champaca) fields leading to significant economic losses, we looked into the thrips species composition infesting the plant in the Western Maharashtra region of India. Four thrips species were newly recorded as pests, including Psephenothrips machili (Moulton), Thrips florum Schmutz, Thrips hawaiiensis (Morgan) and Thrips orientalis (Bagnall). Among these, P. machili was identified as the dominant species, responsible for 63% to 71% of bud damage across various fields. This study also marks the first report of an anthophilous host association of P. machili with M. champaca, causing significant economic damage. The observed damage symptoms include, the typical distortion of flower tissues and buds, black spots on buds were ascribed to P. machili. The other three species were found in groups and caused silvery streaks on early-stage buds. The diagnostic characteristics of all the reported species are provided here, accompanied by photomicrographs.

zoology↗

Whole Genome Sequencing and Assembly of the House Sparrow, Passer domesticus

The common house sparrow, Passer domesticus is a small bird belonging to the family Passeridae. Here, we provide high-quality whole genome sequence data along with assembly for the house sparrow. The final genome assembly was assembled using a Shovill/SPAdes/MASURCA/BUSCO workflow, consisting of contigs spanning 268193 bases and coalescing around a 922 MB sized reference genome. We employed rigorous statistical thresholds to check the coverage, as the Passer genome showed considerable similarity to Gallus gallus (chicken) and Taeniopygia guttata (Zebra finch) genomes, also providing a functional annotation. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian, and vertebrate evolution. SignificanceAvian evolution has been of great interest in the context of extinction. Annotating the genomes such as passerines would be of significant interest as we could understand the behavior/foraging traits and further explore their evolutionary landscape. In this work, we provide a full genome sequence of Indian house sparrow, viz. Passer domesticus which will serve as a useful resource in understanding the adaptability, evolution, geography, allee effects and circadian rhythms.

evolutionary biology↗

Reduced γ-glutamyl hydrolase activity likely contributes to high folate levels in Periyakulam-1 tomato

Tomato cultivars show wide variation in nutraceutical folate in ripe fruits, yet the loci regulating folate levels in fruits remain unexplored. To decipher regulatory points, we compared two contrasting tomato cultivars: Periyakulam-1 (PKM-1) with high folate and Arka Vikas (AV) with low folate. The progression of ripening in PKM-1 was nearly similar to AV but had substantially lower ethylene emission. In parallel, the levels of phytohormones salicylic acid, ABA, and jasmonic acid were substantially lower than AV. The fruits of PKM-1 were also metabolically distinct from AV, with upregulation of several amino acids. Consistent with higher {degrees}Brix levels, the red ripe fruits also showed upregulation of sugars and sugar-derived metabolites. In parallel with higher folate, PKM-1 fruits also had higher carotenoid levels, especially lycopene and {beta}-carotene. Transcript levels of genes encoding folate biosynthesis did not show a perceptible difference in relative expression. The proteome analysis showed upregulation of carotenoid sequestration and folate metabolism-related proteins in PKM-1. The deglutamylation pathway mediated by {gamma}-glutamyl hydrolase (GGH) was substantially reduced in PKM-1 at the red-ripe stage. The red-ripe fruits had reduced transcript levels of GGHs and lower GGH activity than AV. Conversely, the percent polyglutamylation of folate was much higher in PKM-1. Our analysis indicates the regulation of GGH activity as a potential target to elevate folate levels in tomato fruits.

plant biology↗

Genome duplication and transposon mediated gene alteration shapes the pathogenicity of Rhizoctonia solani AG1-IA

Rhizoctonia solani AG1-IA is a polyphagous basidiomycete fungal pathogen that causes sheath blight disease in rice. In a high-quality genome assembly-based analysis, we report a recent whole genome duplication in R. solani AG1-IA. Duplicated syntenic gene blocks showed presence of district clusters of transposable elements (TEs), which introduced disruption in the continuity of synteny and caused alterations in gene structures. Genome duplication followed by TE-mediated gene structure alterations caused neofunctionalization of genes associated with pathogenicity, as experimentally shown by variation in expression patterns and their involvement during plant colonization. High throughput genome sequencing of forty-two rice field isolates of R. solani AG1-IA from different agro-climatic zones of India profiled the population genetic structure of the Indian isolates and classified those into three distinct groups and a subgroup of admixture, emphasizing exchange of genetic material under field conditions. Genetic diversity analysis of this population predicted the regions that are that are targets for diversifying and purifying selections. Experimental evidence showed that the genes undergoing diversifying and purifying selections were essential for pathogenicity. Together, our data and the analysis revealed profound impact of genome duplication and the transposable elements on genomic diversity and evolution that shaped the pathogenicity of R. solani AG1- IA.

evolutionary biology↗

Seeing the unseen: A trifoliate (MYB117) mutant allele fortifies folate and carotenoids in tomato fruits

Micronutrient deficiency also termed hidden hunger affects a large segment of the human population, particularly in developing and underdeveloped nations. Tomato the second most consumed vegetable crop in the world after potato can serve as a sustainable source to alleviate micronutrient deficiency. In tomato, the mutations in the R2R3-MYB117 transcription factor elicit trifoliate leaves and initiate axillary meristems; however, its effect on fruit metabolome remains unexplored. The fruits of a new trifoliate (tf) allele (tf-5) were firmer, had higher {degrees}Brix, folate, and carotenoids. The transcriptome, proteome, and metabolome profiling of tf-5 reflected a broad-spectrum change in homeostasis. The tf-5 allele enhanced the fruit firmness by suppressing cell wall softening-related proteins. The tf-5 fruit displayed a substantial increase in aminome, particularly {gamma}-aminobutyric acid, with a parallel reduction in aminoacyl t-RNA synthases. The increased lipoxygenases proteins and transcripts seemingly elevated jasmonic acid. In addition, increased abscisic acid hydrolases transcripts coupled with reduced precursor supply lowered abscisic acid. The upregulation of carotenoids was mediated by modulation of methylerythreitol and plastoquinone pathways along with an increase in carotenoids isomerization proteins. The upregulation of folate in tf-5 was connoted by the increase in precursor p-aminobenzoic acid and transcripts of several folate biosynthesis pathway genes. The reduction in pterin-6-carboxylate and {gamma}-glutamyl hydrolase activity indicated that the diminished folate degradation also enriched folate levels. Our study delineates that introgression of the tf-5 can be used for the {gamma}-aminobutyric acid, carotenoids, and folate fortification of tomato. One-sentence summaryA tomato trifoliate allele encoding a truncated MYB117 transcription factor alters cellular homeostasis and fortifies {gamma}-aminobutyric acid, folate, and carotenoids in tomato fruits.

plant biology↗

The new kid on the block: A dominant-negative mutation of phototropin1 enhances carotenoid content in tomato fruits

Phototropins, the UVA-blue light photoreceptors, endow plants to detect the direction of light and optimize photosynthesis by regulating chloroplasts positioning and stomatal gas exchange. Little is known about their functions in other developmental responses. A tomato Non-phototropic seedling1 (Nps1) mutant, bearing an Arg495His substitution in the vicinity of LOV2 domain in phototropin1, dominant-negatively blocks phot1 and phot2 responses. The fruits of Nps1 mutant were enriched in carotenoids, particularly lycopene, than its parent, Ailsa Craig. Contrarily, CRISPR/CAS9-edited loss of function phototropin1 mutants displayed subdued carotenoids than the parent. The enrichment of carotenoids in Nps1 fruits is genetically linked with the mutation and exerted in a dominant-negative fashion. Nps1 also altered volatile profiles with high levels of lycopene-derived 6-methyl 5-hepten2-one. The transcript levels of several MEP and carotenogenesis pathways genes were upregulated in Nps1. Nps1 fruits showed altered hormonal profiles with subdued ethylene emission and reduced respiration. Proteome profiles showed a causal link between higher carotenogenesis and increased levels of protein protection machinery, which may stabilize proteins contributing to MEP and carotenogenesis pathways. Given the enhancement of carotenoid content by Nps1 in a dominant-negative fashion, it offers a potential tool for high lycopene-bearing hybrid tomatoes. One-sentence summaryA dominant-negative phototropin1 mutation enhances carotenoid levels, alters metabolite homeostasis, and protein quality control machinery in tomato fruits.

plant biology↗

The complete mitochondrial genome of endangered Assam Roofed Turtle, Pangshura sylhetensis (Testudines: Geoemydidae): Genomic features and Phylogeny

Assam Roofed Turtle, Pangshura sylhetensis is an endangered and least studied species endemic to India and Bangladesh. The genomic feature of P. sylhetensis mitogenome is still anonymous to the scientific community. The present study decodes the first complete mitochondrial genome of P. sylhetensis (16,568 bp) by using next-generation sequencing. This de novo assembly encodes 13 Protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). Most of the genes were encoded on the majority strand, except NADH dehydrogenase subunit 6 (nad6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for Cytochrome oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 5 (nad5) with GTG. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for serine (trnS1) with lack of conventional DHU arm and loop. Both, Bayesian and Maximum-likelihood topologies showed distinct clustering of all the Testudines species with their respective taxonomic ranks and congruent with the previous phylogenetic hypotheses (Pangshura and Batagur sister taxa). Nevertheless, the mitogenomic phylogeny with other amniotes corroborated the sister relationship of Testudines with Archosaurians (Birds and Crocodilians). Additionally, the mitochondrial Gene Order (GO) analysis indicated that, most of the Testudines species showed plesiomorphy with typical vertebrate GO.

genomics↗

The first complete mitochondrial genome of marigold pest thrips, Neohydatothrips samayunkur (Sericothripinae) and comparative analysis

The complete mitogenomes in order Thysanoptera is limited to subfamily Thripinae heretofore. In the present study, we sequenced the first mitochondrial genome of Neohydatothrips samayunkur (15,295 bp), a member of subfamily Sericothripinae. The genome was characterized by 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three control regions (CRs). This mitogenome had two overlapping regions of 4 bp and twenty four intergenic spacers accounting for 165 bp. All the tRNA had typical cloverleaf secondary structures, except for trnV and trnS which lacked DHU stem and loop. The mitogenomes of N. samayunkur was highly rearranged with many unique features as compared to other thrips mitogenomes, atp6 and nad1 were terminated with TAG and TGA stop codons respectively; location of trnL2, trnA, trnC, and trnV was rearranged; and the first control region (CR1) was upstream of nad6. The phylogenetic analysis of 13 PCGs implementing maximum likelihood and Bayesian inference showed the clustering of N. samayunkur with Scirtothrips dorsalis supporting the Scirtothrips genus-group and Sericothripinae morphology based relationships. Generation of more mitogenomes from different hierarchical level in the order Thysanoptera is required to understand the gene rearrangements, phylogeny and evolutionary relationships.

genomics↗

Sequencing and characterization of the complete mitochondrial genome of Critically Endangered Black Soft-shell Turtle (Nilssonia nigricans)

The complete mitochondrial genome (16796 bp) of an endangered freshwater turtle, Nilssonia nigricans was firstly sequenced and annotated. The mitogenome was encoded by 37 genes and a major non-coding Control Region (CR). The mitogenome was A+T biased (62.16%) and spread with six overlapping and 19 intergenic spacer regions. The initiation codons were exceptionally changed as ATA, ATT, and ATC in three Protein-coding genes (PCGs) and a single base (A, T, and C) incomplete termination codons in nine PCGs. The Relative synonymous codon usage (RSCU) value was consistent among all the studied species; exception with significant reduction of Serine (S) frequency in N. nigricans, N. formosa, and R. swinhoei. The secondary structure of N. nigricans showed a lack of conventional dihydrouridine (DHU) arm in trnS (GCT), as well as formed a small loop structure in the acceptor stem of both trnR (TCG) and trnH (GTG). The mitogenome of N. nigricans also revealed two unique tandem repeats (ATTAT)8, and (TATTA)20 in CR. Further, the average Ka/Ks values of 13 PCGs were indicating a strong natural selection in the studied Trionychidae species. The constructed Maximum Likelihood (ML) phylogeny by PCGs shows cohesive clustering of N. nigricans with N. formosa. The resulted phylogeny illustrated the similar topology by all studied species from different taxonomic ranks and supported the previous taxonomic classification. Moreover, further taxon sampling from different taxonomic hierarchy, and their mitogenomics study is vital to reconcile the Testudines phylogeny and assure their evolutionary relationship.

genomics↗

The complete mitochondrial genome of Melon thrips, Thrips palmi (Thripinae) and comparative analysis: A vector for Tospoviruses

The melon thrips, Thrips palmi is a serious pest and vector for plant viruses on a wide range of economically important crops. DNA barcoding evidenced the presence of cryptic diversity in T. palmi and that warrants exhaustive molecular data. Our present study is on decoding the first complete mitochondrial genome of T. palmi (15,333 bp) through NGS technology. The mitogenome contains 37 genes, including 13 PCGs, two rRNAs, 22 tRNAs, and two control regions. The comparative analyses were conducted for gene arrangements, nucleotide composition, codon usage and phylogenetic relationship with other thrips mitogenomes. The nucleotide composition was 78.29% AT, and 21.72% GC with positive AT skewness (0.09) and negative GC skewness (-0.06). The ATN initiation codons were observed in 12 PCGs except cox1 with unique start codon (TTG). The RSCU analysis revealed Phe, Leu, Ile, Tyr, Asn, Lys and Met were the most frequently used amino acids in all PCGs. The codon CGG (Arg) was absent in T. palmi as compared to other thrips mitogenomes. The Ka/Ks ratio ranges from 0.078 in cox1 to 0.913 in atp8. We observed the typical cloverleaf secondary structure in most of the tRNA genes with a few exceptions; absence of DHU stem and loop in trnV and trnS, absence of DHU loop in trnE, lack of T-arm and loop in trnN. The position of trnS1 (between cox3 and CR2) is unique in T. palmi among all the studied thrips mitogenomes. The mitogenome contained 24 intergenic spacer regions and 12 overlapping regions. The CR2 is 63.77% similar to CR1, indicating a possible duplication and translocation in control region. Both the ML and BI phylogenetic trees revealed the close relationships of Thrips with Scirtothrips as compared to Frankliniella. Thus, more mitogenomes on the diverse thrips species is required to understand the in-depth phylogenetic and evolutionary relationships.

genomics↗