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PubMed Journals Articles About "Evolution Major Histocompatibility Complex Gene Copy Number" RSS

12:16 EDT 20th June 2019 | BioPortfolio

Evolution Major Histocompatibility Complex Gene Copy Number PubMed articles on BioPortfolio. Our PubMed references draw on over 21 million records from the medical literature. Here you can see the latest Evolution Major Histocompatibility Complex Gene Copy Number articles that have been published worldwide.

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Showing "Evolution major histocompatibility complex gene copy number" PubMed Articles 1–25 of 33,000+

Evolution of copy number at the MHC varies across the avian tree of life.

The evolution of the Major Histocompatibility Complex (MHC) is shaped by frequent gene duplications and deletions, which generate extensive variation in the number of loci (gene copies) between different taxa. Here, we collected estimates of copy number at the MHC for over 250 bird species from 68 families. We found contrasting patterns of copy number evolution between MHC class I and class IIB, which encode receptors for intra- and extra-cellular pathogens, respectively. Across the avian evolutionary tree,...


Genome size-dependent pcna gene copy number in dinoflagellates and molecular evidence of retroposition as a major evolutionary mechanism.

Proliferating cell nuclear antigen (PCNA) plays critical roles in eukaryotic DNA replication and replication-associated processes. It is typically encoded by one or two gene copies (pcna) in eukaryotic genomes. Recently reported higher copy numbers of pcna in some dinoflagellates raised a question of how this gene has uniquely evolved in this phylum. Through real-time PCR quantification, we found a wide range of pcna copy number (2-287 copies) in 11 dinoflagellate species (n=38), and a strong positive corre...

Evolution of major histocompatibility complex gene copy number.

MHC genes, which code for proteins responsible for presenting pathogen-derived antigens to the host immune system, show remarkable copy-number variation both between and within species. However, the evolutionary forces driving this variation are poorly understood. Here, we use computer simulations to investigate whether evolution of the number of MHC variants in the genome can be shaped by the number of pathogen species the host population encounters (pathogen richness). Our model assumed that while increas...


CNValidator: validating somatic copy-number inference.

CNValidator assesses the quality of somatic copy number calls based on coherency of haplotypes across multiple samples from the same individual. It is applicable to any copy number calling algorithm which makes calls independently for each sample. This test is useful in assessing the accuracy of copy number calls, as well as choosing among alternative copy number algorithms or tuning parameter values.

Analysis of copy number variation in the NEDD4L gene potentially implicated in body height in the Japanese population.

Recently it has been recognized that a considerable number of copy number variations (CNVs) are associated with diseases and other complex human traits. In our previous study, we developed a simple quantitative real-time PCR (Q-PCR) method for analysis of CNV copy number, which had the advantage of obviating the need for reference DNA with a known copy number. Using DNA samples obtained from 231 Japanese individuals, we applied this method for analyzing the copy number of a candidate CNV associated with bod...

Effect of gene copy number and chaperone co-expression on recombinant hydrophobin HFBI biosurfactant production in Pichia pastoris.

Hydrophobins are small highly surface-active fungal proteins with potential as biosurfactants in a wide array of applications. However, practical implementation of hydrophobins at large scale has been hindered by low recombinant yields. In this study, the effects of increasing hydrophobin gene copy number and overexpressing endoplasmic reticulum resident chaperone proteins Kar2p, Pdi1p, and Ero1p were explored as a means to enhance recombinant yields of the class II hydrophobin HFBI in the eukaryotic expres...

Genomic copy number variation of the CHKB gene alters gene expression and affects growth traits of Chinese domestic yak (Bos grunniens) breeds.

Copy number variation (CNV) influences the mRNA transcription levels and phenotypic traits through gene dosage, position effects, alteration of downstream pathways, and modulation of the structure and position of chromosomes. A previous study using the read depth approach to genome resequencing analysis revealed CNVs of the choline kinase beta (CHKB) gene in the copy number variable regions (CNVRs) of yak breeds may influence muscle development and therefore the phenotypic traits of yak breeds. Further work...

Genome-based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles.

Ribosomal DNA (rDNA) copy number variation (CNV) has major physiological implications for all organisms, but how it varies for fungi, an ecologically ubiquitous and important group of microorganisms, has yet to be systemically investigated. Here, we examine rDNA CNV using an in silico read depth approach for 91 fungal taxa with sequenced genomes and assess copy number conservation across phylogenetic scales and ecological lifestyles. rDNA copy number varied considerably across fungi, ranging from an estimat...

Genome-Wide Identification and Analysis of High-Copy-Number LTR Retrotransposons in Asian Pears.

A large proportion of the genome of 'Suli' pear () contains long terminal repeat retrotransposons (LTR-RTs), which suggests that LTR-RTs have played important roles in the evolution of . Further analysis of retrotransposons, particularly of high-copy-number LTR-RTs in different species, will provide new insights into the evolutionary history of . A total of 4912 putative LTR-RTs classified into 198 subfamilies were identified in the 'Suli' pear genome. Six Asian pear accessions, including cultivars and wild...

Associations of CYP24A1 Copy Number Variation with Vitamin D Deficiency and Insulin Secretion.

Vitamin D plays an important role in insulin secretion. As the enzyme that initiates degradation of the active metabolite of vitamin D (1,25-(OH)2D), 24-hydroxylase encoded by CYP24A1 may be associated with insulin secretion. In this study, we aimed at investigating the association between copy number of CYP24A1 and the concentration of insulin. 1528 rural people in Henan Province of China were included. The copy number of CYP24A1 and the concentrations of serum 25(OH)D3 and insulin were determined. Associa...

Killer meiotic drive and dynamic evolution of the wtf gene family.

Natural selection works best when the two alleles in a diploid organism are transmitted to offspring at equal frequencies. Despite this, selfish loci known as meiotic drivers that bias their own transmission into gametes are found throughout eukaryotes. Drive is thought to be a powerful evolutionary force, but empirical evolutionary analyses of drive systems are limited by low numbers of identified meiotic drive genes. Here, we analyze the evolution of the wtf gene family of Schizosaccharomyces pombe that c...

Pair analysis and custom array CGH can detect a small copy number variation in COQ6 gene.

Recently, comprehensive genetic approaches for steroid-resistant nephrotic syndrome (SRNS) using next-generation sequencing (NGS) have been established, but causative gene mutations could not be detected in almost 70% of SRNS patients. Main reason for the low variant detection rate is that most of them are SRNS caused not by genetic but by immunological factors. But some of them are probably because of the difficulty of detecting copy number variations (CNVs) in causative genes by NGS.

Age-dependent copy number variations of TP53 tumour suppressor gene associated with altered phosphorylation status of p53 protein in sporadic schwannomas.

Point mutations of TP53 tumour suppressor are very rare in schwannomas. We aim to characterize the frequency of exonic copy-number changes of the gene in the tumour and to examine the association between TP53 alterations, phosphorylation status of p53 protein and clinical phenotypes.

Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant-parasitic nematode Meloidogyne incognita.

Adaptation to changing environmental conditions represents a challenge to parthenogenetic organisms and until now, how phenotypic variants are generated in clones in response to the selection pressure of their environment remains poorly known. The obligatory parthenogenetic root-knot nematode species Meloidogyne incognita has a worldwide distribution and is the most devastating plant-parasitic nematode. Despite its asexual reproduction, this species exhibits an unexpected capacity of adaptation to environme...

Genome-Wide Copy Number Variation Detection Using NGS: Data Analysis and Interpretation.

Copy number variants (CNVs) and copy neutral loss of heterozygosity (CN-LOH) represent important types of genomic abnormalities in cancer. Genomic DNA microarray serves as the current gold standard method for detecting genome-wide CNVs and CN-LOH. However, as next-generation sequencing (NGS) is widely used to detect gene variants in clinical testing, the ability of NGS to detect CNVs and CN-LOH has also been demonstrated. This chapter describes a protocol for detecting genome-wide large somatic CNVs and CN-...

ACE: Absolute Copy number Estimation from low-coverage whole-genome sequencing data.

Chromosomal copy number aberrations can be efficiently detected and quantified using low-coverage whole-genome sequencing (lcWGS), but analysis is hampered by the lack of knowledge on absolute DNA copy numbers and tumor purity. Here we describe an analytical tool for Absolute Copy number Estimation, ACE, which scales relative copy number signals from chromosomal segments to optimally fit absolute copy numbers, without the need for additional genetic information, such as SNP data. In doing so, ACE derives an...

Distribution and association study in copy number variation of KCNJ12 gene across four Chinese cattle populations.

Copy number variation is a large genome variation which usually happens in the noncoding-region, and it may occur at the locus associated with the functional gene to further influence the phenotype. Potassium inwardly-rectifying channel, subfamily J 12 (KCNJ12) gene expressed widely in cardiomyocytes and neurons, plays an important role in tumor therapy and muscle movement regulation. In this study, we detected the distribution of CNVs for KCNJ12 gene in 404 individuals belonging to four Chinese cattle bree...

Whole-Genome Single Nucleotide Polymorphism Microarray for Copy Number and Loss of Heterozygosity Analysis in Tumors.

The basis of cancer biology is built upon two fundamental processes that result in uncontrolled cell proliferation and tumor formation: loss of tumor suppressor gene function and gain of oncogene function. Somatic DNA copy number variants (CNVs), which generally range in size from kilobases to entire chromosomes, facilitate gains and losses of chromosomal material incorporating oncogenes and tumor suppressor genes, respectively. In fact, many cancer types are characterized by DNA copy number changes and rel...

Studying Copy Number Variations in Cell-Free DNA: The Example of AR in Prostate Cancer.

Serum and plasma cell-free DNA (cfDNA) has been shown as an informative noninvasive source of biomarkers for different diseases, including cancer. Starting from the hypothesis that the gain of androgen receptor (AR) gene is a frequent aberration in advanced prostate cancer patients, we analyzed it in cfDNA as a potential predictive biomarker of specific treatments. Here we report a general protocol that may be considered to analyze gene copy number variations in serum or plasma fluids.

Seasons of change: Mechanisms of genome evolution in human fungal pathogens.

Fungi are a diverse kingdom of organisms capable of thriving in various niches across the world including those in close association with multicellular eukaryotes. Fungal pathogens that contribute to human disease reside both within the host as commensal organisms of the microbiota and the environment. Their niche of origin dictates how infection initiates but also places specific selective pressures on the fungal pathogen that contributes to its genome organization and genetic repertoire. Recent efforts to...

Development and interlaboratory evaluation of a NIST Reference Material RM 8366 for EGFR and MET gene copy number measurements.

Background The National Institute of Standards and Technology (NIST) Reference Material RM 8366 was developed to improve the quality of gene copy measurements of EGFR (epidermal growth factor receptor) and MET (proto-oncogene, receptor tyrosine kinase), important targets for cancer diagnostics and treatment. The reference material is composed of genomic DNA prepared from six human cancer cell lines with different levels of amplification of the target genes. Methods The reference values for the ratios of the...

Segregational drift and the interplay between plasmid copy number and evolvability.

The ubiquity of plasmids in all prokaryotic phyla and habitats and their ability to transfer between cells marks them as prominent constituents of prokaryotic genomes. Many plasmids are found in their host cell in multiple copies. This leads to an increased mutational supply of plasmid-encoded genes and genetically heterogeneous plasmid genomes. Nonetheless, the segregation of plasmid copies into daughter cells during cell division is considered to occur in the absence of selection on the plasmid alleles. W...

Copy number loss in is common among Finnish and Norwegian patients with iNPH.

To evaluate the role of the copy number loss in in a Caucasian population.

Involvement of increased p53 expression in the decrease of mitochondrial DNA copy number and increase of SUV of FDG-PET scan in esophageal squamous cell carcinoma.

We appraised Warburg effect through analysis of mitochondrial DNA (mtDNA) copy number and maximum standard uptake value (SUV) of F-fluorodeoxyglucose positron emission tomography (FDG-PET) scan and their alterations in esophageal squamous cell carcinoma (ESCC). Later T-status and longer longitudinal tumor length was associated with lower mtDNA copy number (p 

An interaction-based model for neuropsychiatric features of copy-number variants.

Variably expressive copy-number variants (CNVs) are characterized by extensive phenotypic heterogeneity of neuropsychiatric phenotypes. Approaches to identify single causative genes for these phenotypes within each CNV have not been successful. Here, we posit using multiple lines of evidence, including pathogenicity metrics, functional assays of model organisms, and gene expression data, that multiple genes within each CNV region are likely responsible for the observed phenotypes. We propose that candidate ...


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