Abstract
A multitude of factors contribute to complex diseases and can be measured with ‘omics’ methods. Databases facilitate data interpretation for underlying mechanisms. Here, we describe the ...Virtual Metabolic Human (VMH, www.vmh.life) database encapsulating current knowledge of human metabolism within five interlinked resources ‘Human metabolism’, ‘Gut microbiome’, ‘Disease’, ‘Nutrition’, and ‘ReconMaps’. The VMH captures 5180 unique metabolites, 17 730 unique reactions, 3695 human genes, 255 Mendelian diseases, 818 microbes, 632 685 microbial genes and 8790 food items. The VMH’s unique features are (i) the hosting of the metabolic reconstructions of human and gut microbes amenable for metabolic modeling; (ii) seven human metabolic maps for data visualization; (iii) a nutrition designer; (iv) a user-friendly webpage and application-programming interface to access its content; (v) user feedback option for community engagement and (vi) the connection of its entities to 57 other web resources. The VMH represents a novel, interdisciplinary database for data interpretation and hypothesis generation to the biomedical community.
Detection of novel transcripts with deep sequencing has increased the demand for computational algorithms as their identification and validation using in vivo techniques is time-consuming, costly and ...unreliable. Most of these discovered transcripts belong to non-coding RNAs, a large group known for their diverse functional roles but lacks the common taxonomy. Thus, upon the identification of the absence of coding potential in them, it is crucial to recognize their prime functional category. To address this heterogeneity issue, we divide the ncRNAs into three classes and present RNA classifier (RNAC) that categorizes the RNAs into coding, housekeeping, small non-coding and long non-coding classes. RNAC utilizes the alignment-based genomic descriptors to extract statistical, local binary patterns and histogram features and fuse them to construct the classification models with extreme gradient boosting. The experiments are performed on four species, and the performance is assessed on multiclass and conventional binary classification (coding versus no-coding) problems. The proposed approach achieved >93% accuracy on both classification problems and also outperformed other well-known existing methods in coding potential prediction. This validates the usefulness of feature fusion for improved performance on both types of classification problems. Hence, RNAC is a valuable tool for the accurate identification of multiple RNAs .
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Previous studies conducted on the psychological impact of infectious outbreaks have found heavy psychological burdens among general population with more severe affect in the current pandemic. The ...main aim of this study is to examine the level of psychological distress during COVID-19 in Bangladesh and explore factors associated with higher psychological distress.
An internet-based, cross-sectional survey was conducted from March to April 2020 in Bangladesh among adults 18 years old and above using structured online questionnaires distributed through emails and other social media throughout Bangladesh with an overall response rate of 34%. Modified version of the Covid19 peritraumatic distress index (CPDI) was used to measure distress. Univariate and Bivariate analysis was used to estimate prevalence of CPDI symptoms and test for the associations between CPDI and the exposure variables. Logistic regression analyses were used to estimate the odds ratios of our outcome variable by exposure variables.
Overall, 44.3% of respondents were suffering from mild to moderate distress and 9.5% were suffering from severe distress. Female respondents were 2.435 times more likely to suffer from CPDI mild to severe distress than males. As compared to Dhaka and Mymensing region of Bangladesh, odds of distress was 1.945 times more in Chittagong/Sylhet region (p-value = 0.035).
Large proportion of adult population in Bangladesh are experiencing psychological distress, with level of distress varies by different symptoms and predictors. This study suggest the need to develop comprehensive crisis prevention system including epidemiological monitoring, screening, and referral with targeted intervention to reduce psychological distress.
A Zn(
ii
) based one-dimensional (1D) coordination polymer (CP), Zn(
cis
-1,4-chdc)(4-nvp) (
1
) {
cis
-1,4-H
2
chdc =
cis
-1,4-cyclohexanedicarboxylic acid and 4-nvp = 4-(1-naphthylvinyl)pyridine}, ...undergoes a solid-state photochemical 2+2 cycloaddition reaction, accompanied by mechanical motion, wherein crystals show swelling, jumping, splitting and bursting upon UV irradiation, whereas the analogous Cd(
ii
) CP Cd(
cis
-1,4-chdc)(4-nvp) (
2
) does not show any such response under UV light, although it undergoes 2+2 photodimerization. The present study can certainly provide the fundamental understanding for designing smart photoactuating materials.
Two Zn(
ii
)/Cd(
ii
) 1D coordination polymers undergo 2+2 photodimerization, wherein Zn-CP shows mechanical motion and generates a free cyclobutane ligand, while Cd-CP does not.
Expression of eukaryotic genes is largely regulated by non-coding RNAs (ncRNA). Sequence variations in the regulatory RNAs may have critical biological consequences including transcriptional and ...post-transcriptional gene regulation. ncRNA-derived markers thus can be proved useful in molecular breeding, QTL mapping and association studies for trait dissection. In present study, we identified a total of 661 SSRs dwelling in pre-miRNA (15), small nuclear RNA (25) and lncRNA (621). Of these, 46 were validated and 100% amplification success was observed in selected wheat genotypes. A set of 36 ncRNA-SSRs markers was utilized for genetic variability assessment in forty-eight Indian wheat genotypes (which includes bread wheat, durum wheat and relatives). Number of alleles ranged from 1 to 4 with an average of two alleles per SSR locus. Mean PIC, observed heterozygosity and Shannon information index were found to be 0.258, 0.37 and 0.476 which suggests ncRNA-SSRs show higher polymorphism compared to genic SSRs but lower polymorphism compared to genomic SSRs. Thirty-six ncRNA-SSRs showed transferability ranging from 42.1% to 100%. Average genetic dissimilarity among wheat genotypes was found to be 0.29 based on Jaccard’s dissimilarity. This is the first report of ncRNA-SSRs in wheat which will be useful for molecular breeding and genetic improvement of wheat.
Key message
TaPTST1, a wheat homolog of AtPTST1 containing CBM can interact with GBSSI and regulate starch metabolism in wheat endosperm.
In cereal endosperm, native starch comprising amylose and ...amylopectin is synthesized by the coordinated activities of several pathway enzymes. Amylose in starch influences its physio-chemical properties resulting in several human health benefits. The
G
ranule-
B
ound
S
tarch
S
ynthase I (GBSSI) is the most abundant starch-associated protein. GBSSI lacks dedicated Carbohydrate-binding module (CBM). Previously,
P
rotein
T
argeting
To
S
tarch 1 (PTST1) was identified as a crucial protein for the localization of GBSSI to the starch granules in
Arabidopsis
. The function of its homologous protein in the wheat endosperm is not known. In this study, TaPTST1, an AtPTST1 homolog, containing a CBM and a coiled-coil domain was identified in wheat. Protein-coding nucleotide sequence of TaPTST1 from Indian wheat variety ‘C 306’ was cloned and characterized. Homology modelling and molecular docking suggested the potential interaction of TaPTST1 with glucans and GBSSI. The
TaPTST1
expression was higher in wheat grain than the other tissues, suggesting a grain-specific function. In vitro binding assays demonstrated different binding affinities of TaPTST1 for native starch, amylose, and amylopectin. Furthermore, the immunoaffinity pull-down assay revealed that TaPTST1 directly interacts with GBSSI, and the interaction is mediated by a coiled-coil domain. The direct protein–protein interaction was further confirmed by bimolecular fluorescence complementation assay (BiFC) in planta. Based on our findings we postulate a functional role for TaPTST1 in starch metabolism by targeting GBSSI to starch granules in wheat endosperm.
•bZIP transcription factors-based SSR markers developed in wheat.•Cross-species transferability of the new SSR markers.•Tri nucleotide SSRs were most abundant.
Assessment of existing diversity is the ...key for germplasm conservation and crop improvement. Wheat (Triticum aestivum L.) is among the most important cereal crop and consumed by two billion world’s populations. DNA-based markers are predominantly used for diversity characterization because they are easy to develop and not influenced by environment. Among them microsatellites (simple sequence repeats, SSRs) are most suitable due to their genome-wide distribution, hypervariability and reproducibility for their applications in diversity, genetic improvement, and molecular breeding. bZIP transcription factors play major roles in plants in light and stress signalling, seed development, and defence. A total of 846 SSRs were identified from 370 wheat cDNA sequences and a sub-set of 35 polymorphic TabZIPMS (TriticumaestivumbZIP MicroSatellites) was used for diversity and genetic structure analysis of 92 Indian wheat varieties and related species. 114 SSR variants ranging from 2 to 5 per SSR locus were detected for 35 SSRs in the varieties. Average polymorphic information content (PIC) and observed heterozygosity was found to be 0.135 and 0.838, respectively. Thirty-four SSRs showed cross-transferability into different related species. Combined Bayesian model and Jaccard’s similarity based genetic clustering analysis revealed two clusters of 80 bread wheat varieties and one separate cluster of related species. In this study, a total 35 novel bZIP-derived SSRs were identified in a set 370 bZIP genes and shown high polymorphism and cross-species transferability in wheat. The findings provide resources for future utilization in genetic resource conservation, trait introgression, breeding and varietal development.
Resistant starch (RS) also known as healthy starch has shown several health benefits. Enhancing the RS through genetic modification approaches has huge commercial importance. Regulatory RNA like long ...non-coding RNA (lncRNA) plays an important role in gene regulation. In this study, we mined 63 transcriptome datasets of wheat belonging to 35 genotypes representing two seed developmental stages. Contrasting expression of a subset of
lncRNAs in RS mutant lines compared to parent wheat variety ‘C 306’ signifies their probable role in RS biosynthesis. Further, lncRNA- TCONS_00130663 showed strong positive correlation (r2 = 1) with LYPL gene and strong negative correlation with SBEIIb (r2 = −0.94). We found TCONS_00130663 as positive regulator of LYPL gene through interaction with miR1128. Based on relative expression, in silico interaction and DSC analysis we hypothesize the dual role of TCONS_00130663 in RS type 2 and type 5. The study provides a useful resource for functional mechanism of lncRNAs.
•443 lncRNA were identified in wheat grain through in-silico prediction.•Contrasting expression of lncRNAs signifies their role in resistant starch (RS) biosynthesis.•TCONS_00130663 interacting with mir-1128 possibly regulates LYPL gene for lipid biosynthesis.•Strong correlation of TCONS_00130663 with SBEIIb and LYPL suggesting its possible role in RS2 and RS5 formation
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