scholarly journals Four In Silico Designed and Validated qPCR Assays to Detect and Discriminate Tilletia indica and T. walkeri, Individually or as a Complex

Biology ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1295
Author(s):  
Émilie D. Tremblay ◽  
Julie Carey ◽  
Guillaume J. Bilodeau ◽  
Sarah Hambleton
Keyword(s):  
In Silico ◽  
Single Copy ◽  
Karnal Bunt ◽  
Grass Species ◽  
Tilletia Indica ◽  
Recent Approach ◽  
Highly Sensitive ◽  
Close Relatives ◽  
High Level ◽  
Genomic Regions

Several fungi classified in the genus Tilletia are well-known to infect grass species including wheat (Triticum). Tilletia indica is a highly unwanted wheat pathogen causing Karnal bunt, subject to quarantine regulations in many countries. Historically, suspected Karnal bunt infections were identified by morphology, a labour-intensive process to rule out other tuberculate-spored species that may be found as contaminants in grain shipments, and the closely-related pathogen T. walkeri on ryegrass (Lolium). Molecular biology advances have brought numerous detection tools to discriminate Tilletia congeners (PCR, qPCR, etc.). While those tests may help to identify T. indica more rapidly, they share weaknesses of targeting insufficiently variable markers or lacking sensitivity in a zero-tolerance context. A recent approach used comparative genomics to identify unique regions within target species, and qPCR assays were designed in silico. This study validated four qPCR tests based on single-copy genomic regions and with highly sensitive limits of detection (~200 fg), two to detect T. indica and T. walkeri separately, and two newly designed, targeting both species as a complex. The assays were challenged with reference DNA of the targets, their close relatives, other crop pathogens, the wheat host, and environmental specimens, ensuring a high level of specificity for accurate discrimination.

scholarly journals Expression and in silico characterization of Phenylalanine ammonium lyase against karnal bunt (Tilletia indica) in wheat (Triticum aestivum)

2013 ◽  
Vol 9 (20) ◽  
pp. 1013-1018 ◽  
Author(s):  
Shalini Purwar ◽  
◽  
Shanthy Sundaram ◽  
Sukrat Sinha ◽  
Ankit Gupta ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
In Silico ◽  
Karnal Bunt ◽  
Tilletia Indica ◽  
In Silico Characterization

scholarly journals Mass Spectrometry based Identification and Characterization of 28 kDa protein from Teliospores of Karnal Bunt Pathogen Tilletia Indica

2021 ◽  
Author(s):  
priyanka sharma ◽  
Vishakha Pandey ◽  
Pallavi Mishra ◽  
Sadhna Singh ◽  
veena pande ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
In Silico ◽  
Small Heat Shock Protein ◽  
Protein S ◽  
Karnal Bunt ◽  
Tilletia Indica ◽  
Functional Protein ◽  
Two Dimensional Gel Electrophoresis ◽  
Identification And Characterization

Abstract Background Karnal bunt (KB) of wheat incited by Tilletia indica is an economically important quarantined fungal disease that cause huge economical loss to agricultural productivity. MethodsIn the present investigation, we have characterized the unique immunoreactive determinant present on the teliospore’s wall of Tilletia indica employing proteomic and in-silico approaches. The 28 kDa protein from the teliospore’s walls was eluted from the preparative gels and further subjected to two-dimensional gel electrophoresis. Mass spectrometry was carried out in search of teliosporic protein(s).ResultsProteomic analysis identified and characterized proteins as small Heat shock protein (sHSP20) and Trehalose-6-phosphatase synthase (TPS) in T.indica. In-silico analysis confirmed the function of the identified protein as a sHSP and TPS belonging to stress response and carbohydrate metabolism. These results were further complemented to identify the homologs of proteins by sequence and structure based functional annotation using genome sequence of T. indica. The potential diagnostic protein present in immunoreactive 28 kDa of teliospores wall entities are sHSP and TPS. Conclusion This study is the first to perform finding indicated that proteins sHSP and TPS act as functional protein, involve in the pathogen protection under stress condition. Together these proteins increase our understanding of the transition from vegetative to sporulation process of T. indica by activation of sHSP-TPS, especially in terms of energy metabolism and stimulus responses. Identification of such protein(s) may also provide an opportunity to generate specific immunoprobes for development of rapid immuno-diagnostic assay.

In the Quest for a Stable Triplet State in Small Polyaromatic Hydrocarbons : An In-Silico Tool for Rational Design and Prediction

2019 ◽  
Author(s):  
Madhumita Rano ◽  
Sumanta K Ghosh ◽  
Debashree Ghosh
Keyword(s):  
Triplet State ◽  
Small Molecules ◽  
In Silico ◽  
Qualitative Agreement ◽  
Rational Design ◽  
Polyaromatic Hydrocarbons ◽  
Spin Hamiltonian ◽  
Spin Frustration ◽  
Computationally Efficient ◽  
High Level

<div>Combining the roles of spin frustration and geometry of odd and even numbered rings in polyaromatic hydrocarbons (PAHs), we design small molecules that show exceedingly small singlet-triplet gaps and stable triplet ground states. Furthermore, a computationally efficient protocol with a model spin Hamiltonian is shown to be capable of qualitative agreement with respect to high level multireference calculations and therefore, can be used for fast molecular discovery and screening.</div>

Restriction Fragment Length Polymorphism and Divergence in the Genomic Regions of High and Low Recombination in Self-Fertilizing and Cross-Fertilizing Aegilops Species

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 423-434
Author(s):  
Jan Dvorřák ◽  
Ming-Cheng Luo ◽  
Zu-Li Yang
Keyword(s):  
Related Species ◽  
Gene Diversity ◽  
Single Copy ◽  
Species Variation ◽  
Recombination Rates ◽  
Distal Chromosome ◽  
Phylogenetic Status ◽  
Average Gene ◽  
Genomic Regions ◽  
Chromosome Regions

Abstract RFLP was investigated at 52 single-copy gene loci among six species of Aegilops, including both cross-fertilizing and self-fertilizing species. Average gene diversity (H) was found to correlate with the level of outcrossing. No relationship was found between H and the phylogenetic status of a species. In all six species, the level of RFLP at a locus was a function of the position of the locus on the chromosome and the recombination rate in the neighborhood of the locus. Loci in the proximal chromosome regions, which show greatly reduced recombination rates relative to the distal regions, were significantly less variable than loci in the distal chromosome regions in all six species. Variation in recombination rates was also reflected in the haplotype divergence between closely related species; loci in the chromosome regions with low recombination rates were found to be diverged less than those in the chromosome regions with high recombination rates. This relationship was not found among the more distantly related species.

scholarly journals Investigating regions of shared genetic variation in attention deficit/hyperactivity disorder and major depressive disorder: a GWAS meta-analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Victoria Powell ◽  
Joanna Martin ◽  
Anita Thapar ◽  
Frances Rice ◽  
Richard J. L. Anney
Keyword(s):  
Attention Deficit Hyperactivity Disorder ◽  
Major Depressive Disorder ◽  
Depressive Disorder ◽  
Genetic Correlation ◽  
Attention Deficit ◽  
Meta Analysis ◽  
Major Depressive ◽  
Hyperactivity Disorder ◽  
High Level ◽  
Genomic Regions

AbstractAttention deficit/hyperactivity disorder (ADHD) demonstrates a high level of comorbidity with major depressive disorder (MDD). One possible contributor to this is that the two disorders show high genetic correlation. However, the specific regions of the genome that may be responsible for this overlap are unclear. To identify variants associated with both ADHD and MDD, we performed a meta-analysis of GWAS of ADHD and MDD. All genome wide significant (p < 5 × 10–8) SNPs in the meta-analysis that were also strongly associated (p < 5 × 10–4) independently with each disorder were followed up. These putatively pleiotropic SNPs were tested for additional associations across a broad range of phenotypes. Fourteen linkage disequilibrium-independent SNPs were associated with each disorder separately (p < 5 × 10–4) and in the cross-disorder meta-analysis (p < 5 × 10–8). Nine of these SNPs had not been highlighted previously in either individual GWAS. Evidence supported nine of the fourteen SNPs acting as eQTL and two as brain eQTL. Index SNPs and their genomic regions demonstrated associations with other mental health phenotypes. Through conducting meta-analysis on ADHD and MDD only, our results build upon the previously observed genetic correlation between ADHD and MDD and reveal novel genomic regions that may be implicated in this overlap.

scholarly journals Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Marie-Anne Cambon-Bonavita ◽  
Johanne Aubé ◽  
Valérie Cueff-Gauchard ◽  
Julie Reveillaud
Keyword(s):  
Hydrothermal Vents ◽  
Carbon Fixation ◽  
Iron Sulfide ◽  
Hydrogen Oxidation ◽  
Niche Partitioning ◽  
Sulfur Oxidation ◽  
Single Copy ◽  
Trophic Levels ◽  
Rimicaris Exoculata ◽  
Close Relatives

Abstract Background Free-living and symbiotic chemosynthetic microbial communities support primary production and higher trophic levels in deep-sea hydrothermal vents. The shrimp Rimicaris exoculata, which dominates animal communities along the Mid-Atlantic Ridge, houses a complex bacterial community in its enlarged cephalothorax. The dominant bacteria present are from the taxonomic groups Campylobacteria, Desulfobulbia (formerly Deltaproteobacteria), Alphaproteobacteria, Gammaproteobacteria, and some recently discovered iron oxyhydroxide-coated Zetaproteobacteria. This epibiotic consortium uses iron, sulfide, methane, and hydrogen as energy sources. Here, we generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic communities to reconstruct and investigate symbiotic genomes. We collected specimens from three geochemically contrasted vent fields, TAG, Rainbow, and Snake Pit, to unravel the specificity, variability, and adaptation of Rimicaris–microbe associations. Results Our data enabled us to reconstruct 49 metagenome-assembled genomes (MAGs) from the TAG and Rainbow vent fields, including 16 with more than 90% completion and less than 5% contamination based on single copy core genes. These MAGs belonged to the dominant Campylobacteria, Desulfobulbia, Thiotrichaceae, and some novel candidate phyla radiation (CPR) lineages. In addition, most importantly, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (average nucleotide identity ANI < 77% with the closest relative Ghiorsea bivora isolated from TAG, and 88% with each other), suggesting potential novel species. Genes for Calvin-Benson Bassham (CBB) carbon fixation, iron, and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts co-existing in a single shrimp at both the basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further examination of the seeming functional redundancy among these epibionts revealed important differences. Conclusion These data highlight microniche partitioning in the Rimicaris holobiont and support recent studies showing that functional diversity enables multiple symbiont strains to coexist in animals colonizing hydrothermal vents.

scholarly journals Induction of MAP Kinase Homologues during Growth and Morphogenetic Development of Karnal Bunt (Tilletia indica) under the Influence of Host Factor(s) from Wheat Spikes

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Atul K. Gupta ◽  
J. M. Seneviratne ◽  
G. K. Joshi ◽  
Anil Kumar
Keyword(s):  
Map Kinase ◽  
Map Kinases ◽  
Fungal Growth ◽  
Host Factor ◽  
Host Factors ◽  
Karnal Bunt ◽  
Dependent Manner ◽  
Tilletia Indica ◽  
Mitogen Activated Protein

Signaling pathways that activate different mitogen-activated protein kinases (MAPKs) in response to certain environmental conditions, play important role in mating type switching (Fus3) and pathogenicity (Pmk1) in many fungi. In order to determine the roles of such regulatory genes inTilletia indica, the causal pathogen of Karnal bunt (KB) of wheat, semi-quantitative and quantitative RT-PCR was carried out to isolate and determine the expression of MAP kinase homologues during fungal growth and development underin vitroculture. Maximum expression of TiFus3 and TiPmk1 genes were observed at 14th and 21st days of culture and decreased thereafter. To investigate whether the fungus alters the expression levels of same kinases upon interaction with plants, cultures were treated with 1% of host factors (extracted from S-2 stage of wheat spikes). Such treatment induced the expression of MAPks in time dependent manner compared to the absence of host factors. These results suggest that host factor(s) provide certain signal(s) which activate TiFus3 and TiPmk1 during morphogenetic development ofT. indica. The results also provides a clue about the role of host factors in enhancing the disease potential due to induction of MAP kinases involved in fungal development and pathogenecity.

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