In addition to circadian rhythms, circadian genes play pivotal roles in myriad signaling pathways. Consequently, their dysregulation contributes to the onset and progression of various ...diseases.Identifying SNPs in clock genes offers an exciting avenue to predict the predisposition of an individual to different pathologies/variations in phenotype.Experimental models and human trials have confirmed that SNPs in core circadian genes are associated with pathologies.Given the inherent complexity of diseases, that are often polygenic traits influenced by gene–environment interactions, robust statistical approaches utilizing large and diverse sample sizes is crucial when identifying disease-linked SNPs. Furthermore, recognizing the key role of population stratification in minimizing confounding effects ensures the reliability of associations between SNPs and diseases.
Circadian rhythms, ~24 h cycles of physiological and behavioral processes, can be synchronized by external signals (e.g., light) and persist even in their absence. Consequently, dysregulation of circadian rhythms adversely affects the well-being of the organism. This timekeeping system is generated and sustained by a genetically encoded endogenous mechanism composed of interlocking transcriptional/translational feedback loops that generate rhythmic expression of core clock genes. Genome-wide association studies (GWAS) and forward genetic studies show that SNPs in clock genes influence gene regulation and correlate with the risk of developing various conditions. We discuss genetic variations in core clock genes that are associated with various phenotypes, their implications for human health, and stress the need for thorough studies in this domain of circadian regulation.
Circadian rhythms, ~24 h cycles of physiological and behavioral processes, can be synchronized by external signals (e.g., light) and persist even in their absence. Consequently, dysregulation of circadian rhythms adversely affects the well-being of the organism. This timekeeping system is generated and sustained by a genetically encoded endogenous mechanism composed of interlocking transcriptional/translational feedback loops that generate rhythmic expression of core clock genes. Genome-wide association studies (GWAS) and forward genetic studies show that SNPs in clock genes influence gene regulation and correlate with the risk of developing various conditions. We discuss genetic variations in core clock genes that are associated with various phenotypes, their implications for human health, and stress the need for thorough studies in this domain of circadian regulation.
Exploiting root system variations related to drought stress adaptation using quantitative genetics and genomics approaches has potential in developing resilient varieties of cereal crops.
Abstract
...Cereals are important crops worldwide that help meet food demands and nutritional needs. In recent years, cereal production has been challenged globally by frequent droughts and hot spells. A plant’s root is the most relevant organ for the plant adaptation to stress conditions, playing pivotal roles in anchorage and the acquisition of soil-based resources. Thus, dissecting root system variations and trait selection for enhancing yield and sustainability under drought stress conditions should aid in future global food security. This review highlights the variations in root system attributes and their interplay with shoot architecture features to face water scarcity and maintain thus yield of major cereal crops. Further, we compile the root-related drought responsive quantitative trait loci/genes in cereal crops including their interspecies relationships using microsynteny to facilitate comparative genomic analyses. We then discuss the potential of an integrated strategy combining genomics and phenomics at genetic and epigenetic levels to explore natural genetic diversity as a basis for knowledge-based genome editing. Finally, we present an outline to establish innovative breeding leads for the rapid and optimized selection of root traits necessary to develop resilient crop varieties.
Background. Trichophyton species are considered the most frequent causative and considerable agents in infection concerns. Objective. The existing training designed to conduct the sequencing analysis ...of nucleotides of ITS1-5.8S-ITS2 for Trichophyton mentagrophytes. Methods. The isolation and identification of pathogenic fungi, Trichophyton mentagrophytes from clinical specimens was done based on the standard morphological and molecular methods. The genomic DNA of fungal isolates were extracted and purified to amplify with primers of 18S rRNA gene for detection and sequencing the nitrogenous bases to define the genetic variation among clinical isolates of Trichophyton mentagrophytes in compared with strains recorded in NCBI GenBank. Results. Eight isolates of Trichophyton mentagrophytes were isolated and identified from clinical specimen of dermatophytosis. The DNA sequencing analysis showed the presence of some genetic variation in nitrogenous bases between the local isolates and that recorded in locus of world NCBI GenBank. Multiple Alignment sequence using NCBI BLAST revealed the recoding a new mutant isolate among the local isolates based on DNA homology percent. Conclusion. The present results proved the successful the use of molecular methods in diagnosis the fungal isolates of Trichophyton mentagrophytes especially the sequencing analysis to find the genetically bases of these isolates.
While in some countries, the possession of psychoactive substances leads to prison sentences or execution, other countries, like Portugal, follow an avenue leading to a drug-tolerant culture. ...However, there is a lack of empirical data on Portuguese populations to measure the drug-use trend. The present study uses multidisciplinary approaches to explore the prevalence of alcohol and drug consumption on a Portuguese student population (N = 81, ages ranged from 17 to 40 years), associating it with psychological and genetic factors. The results show a prevalence of cannabis consumption higher than what is reported by the EMCDDA, and suggests that carriers of the minor allele of 5-HTTLPR have a higher propensity for addiction.
Dermatophytes are species with slight genetic variation, and are yet several uncertainties about the differences among species. This study aims to isolate and diagnose the Trichophyton interdigitale ...by molecular technique and to reveal the phylogenetic distance and similarity of the Iraqi isolates to other isolates from the globe, in addition, to submit the obtained sequences to the NCBI database. This study included 86 with multiple lesions on different parts of the body. The results showed different variations within the ITS gene between the isolates. It was concluded that Trichophyton interdigitale in Iraqi isolates had two types of substitution variations (Transition and Transversion) different than global isolates. Moreover, it appeared according to the phylogenetic tree, the similarity was 97% with isolates from the Czech Republic and Japan, whereas 98% with the isolates from France and Germany.
Keywords. Dermatophytes, genetic variations, ITS gene, multiple lessons
Schizophrenia (SZ) onset and treatment outcome have important genetic components, however individual genes do not have strong effects on SZ phenotype. Therefore, it is important to use the ...pathway‐based approach and study metabolic and signaling pathways, such as dopaminergic and serotonergic. Serotonin pathway has an important role in brain signaling, nevertheless, its role in SZ is not as thoroughly examined as that of dopamine pathway. In this study, we reviewed serotonin pathway genes and genetic variations associated with SZ, including variations at DNA, RNA, and epigenetic level. We obtained 30 serotonin pathway genes from Kyoto encyclopedia of genes and genomes and used these genes for the literature review. We extracted 20 protein coding serotonin pathway genes with genetic variations associated with SZ onset, development, and treatment from 31 research papers. Genes associated with SZ are present on all levels of serotonin pathway: serotonin synthesis, transport, receptor binding, intracellular signaling, and reuptake; however, regulatory genes are poorly researched. We summarized common challenges of genetic association studies and presented some solutions. The analysis of reported serotonin pathway‐SZ associations revealed lack of information about certain serotonin pathway genes potentially associated with SZ. Furthermore, it is becoming clear that interactions among serotonin pathway genes and their regulators may bring further knowledge about their involvement in SZ.
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•The DeepSAV predictor of SAV functional impact was updated and improved.•The diversity of multiple sequence alignment is an important factor in DeepSAV performance.•DBSAV provides ...DeepSAV scores for human SAVs and GTS scores for human genes.•DBSAV is a valuable resource for mechanistic interpretation of human SAVs.
Deleterious single amino acid variation (SAV) is one of the leading causes of human diseases. Evaluating the functional impact of SAVs is crucial for diagnosis of genetic disorders. We previously developed a deep convolutional neural network predictor, DeepSAV, to evaluate the deleterious effects of SAVs on protein function based on various sequence, structural, and functional properties. DeepSAV scores of rare SAVs observed in the human population are aggregated into a gene-level score called GTS (Gene Tolerance of rare SAVs) that reflects a gene's tolerance to deleterious missense mutations and serves as a useful tool to study gene-disease associations. In this study, we aim to enhance the performance of DeepSAV by using expanded datasets of pathogenic and benign variants, more features, and neural network optimization. We found that multiple sequence alignments built from vertebrate-level orthologs yield better prediction results compared to those built from mammalian-level orthologs. For multiple sequence alignments built from BLAST searches, optimal performance was achieved with a sequence identify cutoff of 50% to remove distant homologs. The new version of DeepSAV exhibits the best performance among standalone predictors of deleterious effects of SAVs. We developed the DBSAV database (http://prodata.swmed.edu/DBSAV) that reports GTS scores of human genes and DeepSAV scores of SAVs in the human proteome, including pathogenic and benign SAVs, population-level SAVs, and all possible SAVs by single nucleotide variations. This database serves as a useful resource for research of human SAVs and their relationships with protein functions and human diseases.
The objective of the present study was to estimate the correlation coefficients and assess agro-morphological variability of single cross hybrids of maize. This study was conducted at research field ...of National Maize Research Program, Rampur, Chitwan, Nepal during the winter season from October 6, 2015 to March 5, 2016. Fourteen single cross maize hybrids were evaluated to study correlation and agro-morphological traits. Single cross hybrid namely RML-98 / RL-105 (6229 kg ha-1) significantly produced the highest yield, followed by RM1-4 / NML-2 (6073 kg ha-1), RML-95 / RL-105 (5904 kg ha-1) and RML-5/RL-105 (5528 kg ha-1). Cob length was strongly correlated with cob diameter (0.885), number of kernels per row (0.812), number of kernel rows per cob (0.951), test weight (0.870) and grain yield (0.916). Similarly, cob diameter was strongly correlated with number of kernels per row (0.870), number of kernel rows per cob (0.934), test weight (0.922) and grain yield (0.946). The number of kernels per row was strongly correlated with number of kernel rows per cob (0.915), test weight (0.781) and grain yield (0.847). The number of kernel rows per cob was strongly correlated with test weight (0.902) and grain yield (0.942). Similarly, test weight was strongly correlated with grain yield (0.968). The grain yield of the evaluated hybrids was significantly positively correlated with yield attributing traits. There was considerable variability among the hybrids evaluated for growth, grain yield, and traits indicating the presence of variation. Therefore, the results of this study suggest that farmers should grow maize hybrids RML-98 / RL-105, RM1-4 /NML-2, RML-95 / RL-105 and RML-5/RL-105 to achieve higher maize production.
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