HW_TEST, a program for comprehensive HARDY-WEINBERG equilibrium testing
This article deals with a Windows ( © Microsoft Inc.) executable, user-friendly program that tests the hypothesis of Hardy-Weinberg (HW) proportions from autosomal multiallelic data using different methods that include parametric, nonparametric and exact bootstrap tests, the latter obtained through computer simulations. The program c an be obtained free of charge directly from the internet repository https://github.com/Lemes-RenanB/HardyWeinbergTesting. (Source: Genetics and Molecular Biology)
Source: Genetics and Molecular Biology - May 11, 2020 Category: Genetics & Stem Cells Source Type: research
Comparison of the heterochromatin and telomeric sequences distribuition in chromosomes of 11 species of Amazonian marsupials (Didelphimorphia; Didelphidae)
Abstract In recent decades the diploid numbers recorded in the New World marsupials have been widely discussed in the context of the processes of karyotype evolution in these mammals. While Interstitial Telomeric Sequences (ITS) have long been interpreted as remnants of chromosomal fusion, the biological role of these features, together with their intraspecific variation, has raised a number of questions. In the present study, we analyzed the karyotype of 11 species of Amazonian didelphids, comparing the distribution of the heterochromatin with that of the telomeric signals, and found that, in six species, the ITS coincide...
Source: Genetics and Molecular Biology - May 11, 2020 Category: Genetics & Stem Cells Source Type: research
BAP1 functions as a tumor promoter in prostate cancer cells through EMT regulation
Abstract BRCA1-associated protein 1 (BAP1) is a deubiquitinating enzyme that has long been considered to be a tumor suppressor in various tumors, including renal cell carcinoma, uveal melanoma, mesothelioma, and cutaneous melanoma. However, the involvement of BAP1 in the progression of prostate cancer has not been studied until recently. Herein, we investigated the tumor promoting function of BAP1 in the context of prostate cancer. Analysis of The Cancer Genome Atlas (TCGA) data set showed that prostate cancer patients express high levels of BAP1 mRNA. High BAP1 expression is inversely correlated with disease-free survival...
Source: Genetics and Molecular Biology - May 8, 2020 Category: Genetics & Stem Cells Source Type: research
Methodological differences can affect sequencing depth with a possible impact on the accuracy of genetic diagnosis
In this study, we aimed to analyze the pattern of sequencing depth in variants from whole-exome sequencing data in the 1000 Genomes project phase 3, focusing on the variants present in the ClinVar database that were predicted to affect protein-coding regions. We demonstrate that the distribution of the sequencing depth varies across different sequencing centers (pair-wise comparison, p< 0.001). Most importantly, we found that the distribution pattern of sequencing depth is specific to each facility, making it possible to correctly assign 96.9% of the samples to their sequencing center. Thus, indicating the presence of a...
Source: Genetics and Molecular Biology - April 27, 2020 Category: Genetics & Stem Cells Source Type: research
Transcriptomics analysis of Psidium cattleyanum Sabine (Myrtaceae) unveil potential genes involved in fruit pigmentation
This study reveals stimulating data for the understanding of the pathways and mechanisms involved in the maturation and colouring of P. cattleyanum fruits and suggests that the ANS and UFGT genes are key factors involved in the synthase and pigmentation accumulation in red fruits. (Source: Genetics and Molecular Biology)
Source: Genetics and Molecular Biology - April 27, 2020 Category: Genetics & Stem Cells Source Type: research
A comparison between SOLiD 5500XLand Ion Torrent PGM-derived miRNA expression profiles in two breast cell lines
Abstract Next-generation sequencing (NGS) platforms allow the analysis of hundreds of millions of molecules in a single sequencing run, revolutionizing many research areas. NGS-based microRNA studies enable expression quantification in unprecedented scale without the limitations of closed-platforms. Yet, whereas a massive amount of data produced by these platforms is available, comparisons of quantification/discovery capabilities between platforms are still lacking. Here we compare two NGS-platforms: SOLiD and PGM, by evaluating their microRNA identification/quantification capabilities using two breast-derived cell-lines. ...
Source: Genetics and Molecular Biology - April 27, 2020 Category: Genetics & Stem Cells Source Type: research
Combined use of mitochondrial and nuclear genetic markers further reveal immature marine turtle hybrids along the South Western Atlantic
Abstract Marine turtle hybridization is usually sporadic and involves reports of only a few individuals; however, Brazilian populations have high hybridization rates. Here we investigated the presence of hybrids in morphologically identified immature hawksbills (Eretmochelys imbricata) along the South Western Atlantic (SWA). We sequenced one mitochondrial (D-Loop) and three nuclear DNA (RAG1, RAG2, and CMOS) markers to better understand the patterns and characteristics of hybrids. We identified 22 hybrids (n = 270), 11 of them at the extreme South of the SWA. Uruguay had the highest hybrid frequency in the SWA (~37.5%) fol...
Source: Genetics and Molecular Biology - April 27, 2020 Category: Genetics & Stem Cells Source Type: research
Phylogenetic niche conservatism and plant diversification in South American subtropical grasslands along multiple climatic dimensions
Abstract Phylogenetic niche conservatism can be investigated at multiple scales on an explicit geographical context. Haplotype-based comparative analyses of lineages occupying the same region, and thus subjected to similar environmental factors, allow decoupling shared evolutionary and ecological patterns, as well as multiple dimensions of adaptive diversification. Here we aimed to assess the role of environmental drivers on diversification of subtropical grassland, based on haplotypic diversity of two plant genera. We sampled two closely related and co-distributed grassland plant genera, Petunia and Calibrachoa, across th...
Source: Genetics and Molecular Biology - April 27, 2020 Category: Genetics & Stem Cells Source Type: research
Genetic diversity in populations of African mahogany (Khaya grandioliola C. DC.) introduced in Brazil
Abstract Given its high-valued wood, the African mahogany (Khaya grandifoliola) has been envisaged as a renewable source of tropical hardwoods in Brazil. However, there are concerns about the hypothesized low diversity among the few K. grandifoliola germplasm sources introduced in the country. Using eight microsatellite markers, we evaluated the genetic diversity and divergence among 53 superior trees selected from three provenances of K. grandifoliola located in the state of Para. These populations are among the oldest plantations (>15 years) in Brazil and, therefore, the country's main seed sources. The average number...
Source: Genetics and Molecular Biology - April 27, 2020 Category: Genetics & Stem Cells Source Type: research
Comparative analysis of the complete chloroplast genomes from six Neotropical species of Myrteae (Myrtaceae)
In this study, we report the sequencing and de novo assembly of the complete chloroplast (cp) genomes of six Myrteae species: Eugenia brasiliensis, E. pyriformis, E. nitida, Myrcianthes pungens, Plinia edulis and Psidium cattleianum. We characterized genome structure, gene content, and identified SSRs to detect variation within Neotropical Myrteae. The six newly sequenced plastomes exhibit a typical quadripartite structure, gene content and organization highly conserved among Myrtaceae species. Some differences in genome length, protein-coding genes and non-coding regions were found. Besides, IR boundaries present structur...
Source: Genetics and Molecular Biology - April 23, 2020 Category: Genetics & Stem Cells Source Type: research
Comparative transcriptome analysis of the hippocampus from sleep-deprived and Alzheimer’s disease mice
Abstract We did a comparative analysis of the gene expression profiles of the hippocampus from sleep deprivation and Alzheimer ’ s disease (AD) mice. Differentially expressed genes (DEGs) were identified by comparing the transcriptome profiles of the hippocampus of sleep deprivation or AD mouse models to matched controls. The common DEGs between sleep deprivation and AD were identified by the overlapping analysis, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The results showed that a total of 16 common DEGs showed similar change patterns in both sleep deprivation mice and AD...
Source: Genetics and Molecular Biology - April 23, 2020 Category: Genetics & Stem Cells Source Type: research
CRZ1 regulator and calcium cooperatively modulate holocellulases gene expression in Trichoderma reesei QM6a
Abstract Trichoderma reesei is the main filamentous fungus used in industry to produce cellulases. Here we investigated the role of CRZ1 and Ca2+signaling in the fungus T. reesei QM6a concerning holocellulases production. For this, we first searched for potential CRZ1 binding sites in promoter regions of key genes coding holocellulases, as well as transcriptional regulators and sugar and calcium transporters. Using a nearly constructed T. reeseiAcrz1 strain, we demonstrated that most of the genes expected to be regulated by CRZ1 were affected in the mutant strain induced with sugarcane bagasse (SCB) and cellulose. In parti...
Source: Genetics and Molecular Biology - April 23, 2020 Category: Genetics & Stem Cells Source Type: research
Chromosome comparison among five species of Neotropical cichlids of Cichlasoma and Gymnogeophagus (Perciformes)
Abstract The genera Cichlasoma and Gymnogeophagus belong to the subfamily Cichlinae, the only one in Neotropical cichlids. Cichlasoma dimerus, C. paranaense, C. portalegrense, Gymnogeophagus rhabdotus, and G. lacustris were collected at different points in the Paranapanema and Paraguay basins and the Lagoon of Patos hydrographic system. In addition to conventional analysis, CMA3 fluorochrome staining, and FISH with 18S rDNA probe were performed. All species had a diploid number equal to 48, with interand intraspecific differences in karyotype formulae. All species presented a single AgNOR site, except G. rhabdotus and the ...
Source: Genetics and Molecular Biology - April 23, 2020 Category: Genetics & Stem Cells Source Type: research
Extinction and emergence of genomic haplotypes during the evolution of Avian coronavirus in chicken embryos
Abstract Avian coronavirus (AvCoV) is ubiquitously present on poultry as a multitude of virus lineages. Studies on AvCoV phenotypic traits are dependent on the isolation of field strains in chicken embryonated eggs, but the mutant spectrum on each isolate is not considered. This manuscript reports the previously unknown HTS (high throughput sequencing)-based complete genome haplotyping of AvCoV isolates after passages of two field strains in chicken embryonated eggs. For the first and third passages of strain 23/2013, virus loads were 6.699 log copies/ μ L and 6 log copies/ μ L and, for 38/2013, 5.699 log copies/ μ L an...
Source: Genetics and Molecular Biology - April 23, 2020 Category: Genetics & Stem Cells Source Type: research
Cancer-related worry and risk perception in Brazilian individuals seeking genetic counseling for hereditary breast cancer
In conclusion, the results of this study indicate that cancer-related worry and cancer risk perception are significant aspects of morbidity in individuals seeking CGC, whether they are cancer-affected or unaffected. CGC has an important role in health education and cancer prevention for its potential of promoting an accurate perception of the risk. (Source: Genetics and Molecular Biology)
Source: Genetics and Molecular Biology - April 23, 2020 Category: Genetics & Stem Cells Source Type: research
