Current Issue : April - June Volume : 2019 Issue Number : 2 Articles : 6 Articles
Background: The re-sequencing of C. angulata has revealed many polymorphisms in candidate genes related\nto adaptation to abiotic stress that are not present in C. gigas; these genes, therefore, are probably related to\nthe ability of this oyster to retain high concentrations of toxic heavy metals. There is, in addition, an unresolved\ncontroversy as to whether or not C. angulata and C. gigas are the same species or subspecies. Both oysters have 20\nmetacentric chromosomes of similar size that are morphologically indistinguishable. From a genomic perspective,\nas a result of the great variation and selection for heterozygotes in C. gigas, the assembly of its draft genome was\ndifficult: it is fragmented in more than seven thousand scaffolds.\nResults: In this work sixty BAC sequences of C. gigas downloaded from NCBI were assembled in BAC-contigs and\nassigned to BACs that were used as probes for mFISH in C. angulata and C. gigas. In addition, probes of H3, H4\nhistone, 18S and 5S rDNA genes were also used. Hence we obtained markers identifying 8 out the 10 chromosomes\nconstituting the karyotype. Chromosomes 1 and 9 can be distinguished morphologically. The bioinformatic analysis\ncarried out with the BAC-contigs annotated 88 genes. As a result, genes associated with abiotic adaptation, such as\nmetallothioneins, have been positioned in the genome. The gene ontology analysis has also shown many molecular\nfunctions related to metal ion binding, a phenomenon associated with detoxification processes that are characteristic\nin oysters. Hence the provisional integrated map obtained in this study is a useful complementary tool for the study of\noyster genomes.\nConclusions: In this study 8 out of 10 chromosome pairs of Crassostrea angulata/gigas were identified using BAC\nclones as probes. As a result all chromosomes can now be distinguished. Moreover, FISH showed that H3 and H4\nco-localized in two pairs of chromosomes different that those previously escribed. 88 genes were annotated in\nthe BAC-contigs most of them related with Molecular Functions of protein binding, related to the resistance of\nthe species to abiotic stress. An integrated genetic map anchored to the genome has been obtained in which\nthe BAC-contigs structure were not concordant with the gene structure of the C. gigas scaffolds displayed in the\nGenomicus database....
Background: X chromosome inactivation (XCI) is an important gene regulation mechanism in females to equalize\nthe expression levels of X chromosome between two sexes. Generally, one of two X chromosomes in females is\nrandomly chosen to be inactivated. Nonrandom XCI (XCI skewing) is also observed in females, which has been\nreported to play an important role in many X-linked diseases. However, there is no statistical measure available for\nthe degree of the XCI skewing based on family data in population genetics.\nResults: In this article, we propose a statistical approach to measure the degree of the XCI skewing based on family\ntrios, which is represented by a ratio of two genotypic relative risks in females. The point estimate of the ratio is\nobtained from the maximum likelihood estimates of two genotypic relative risks. When parental genotypes are\nmissing in some family trios, the expectation-conditional-maximization algorithm is adopted to obtain the corresponding\nmaximum likelihood estimates. Further, the confidence interval of the ratio is derived based on the likelihood ratio test.\nSimulation results show that the likelihood-based confidence interval has an accurate coverage probability under the\nsituations considered. Also, we apply our proposed method to the rheumatoid arthritis data from USA for its practical use,\nand find out that a locus, rs2238907, may undergo the XCI skewing against the at-risk allele. But this needs to be further\nconfirmed by molecular genetics.\nConclusions: The proposed statistical measure for the skewness of XCI is applicable to complete family trio data or family\ntrio data with some paternal genotypes missing. The likelihood-based confidence interval has an accurate coverage\nprobability under the situations considered. Therefore, our proposed statistical measure is generally recommended in\npractice for discovering the potential loci which undergo the XCI skewing....
Birt-Hogg-Dub´e syndrome is a genetic disorder characterized by skin fibrofolliculomas, cystic lung disease, and\nbilateral renal tumors. It has also been implicated in the formation of tumors in other organs, particularly thyroid and colon.\nThis case presents a young female presenting with only cystic lung disease and kidney tumors, identified as having a never before\nidentified heterozygous mutation in the folliculin (FLCN) gene which is the likely cause of her syndrome. Case Presentation. A 34-\nyear-old female was found to have bilateral renal masses, 2.4 cm on the right and 7.6 cm on the left, as well asmultiple, small cysts in\nthe lungs. Chest imaging further characterized the lung cysts as being basilar predominant with the largest measuring 1.6cm.The\nleft kidney mass was resected with a partial nephrectomy with final pathologic diagnosis of an oncocytoma. Genetic testing was\nundertaken as she did not have characteristic skin findings. A previously undescribed mutation in the FLCN gene (c.780-2A>G)\nwas identified with no matches in the human genetic mutation database (HGMD). Review of that database identified over 160\nseparate mutations in the FLCN gene. Extensive history did not identify any family members who had similar disease processes\nsuggesting that this could be a spontaneous mutation in the proband. Conclusions. This case highlights that the traditional view of\nBirt-Hogg-Dube syndrome as having a strong familial component may be incorrect and that spontaneous mutation may be more\ncommon than previously thought. Also notable is the fact that this patient had no characteristically described fibrofolliculomas\nthat traditionally are the hallmark of the condition. This case suggests that genetic testing should be obtained in all suspected cases\nof Birt-Hogg-Dube syndrome as the patient may not present with the typical skin findings and may also present with no family\nhistory consistent with this disorder....
The aim of this study was to determine the clinical, serological, and genetic features of anti-Jo-1 positive antisynthetase patients\nfollowed by aHungarian single centre to identify prognostic markers,which can predict disease phenotypes and disease progression.\nIt was a retrospective study using clinical database of 49 anti-Jo-1 positive patients. 100% of patients exhibited myositis, 73%\ninterstitial lung disease, 88% arthritis, 65% Raynaudâ??s phenomenon, 43% fever, 33% mechanicâ??s hand, and 12% dysphagia.We could\ndetect significant correlation between anti-Jo-1 titer and the CK and CRP levels at disease onset and during disease course. HLA\nDRB1*03 positivity was present in 68.96% of patients, where the CK level at diagnosis was significantly lower compared to the\nHLA DRB1*03 negative patients. HLA DQA1*0501-DQB1*0201 haplotype was found in 58.62% of patients, but no significant\ncorrelation was found regarding any clinical or laboratory features. Higher CRP, ESR level, RF positivity, and the presence of fever\nor vasculitic skin lesions at the time of diagnosis indicated a higher steroid demand and the administration of higher number of\nimmunosuppressants during the follow-up within anti-Jo-1 positive patients.The organ involvement of the disease was not different\nin HLA-DRB1*0301 positive or negative patients who were positive to the anti-Jo-1 antibody; however, initial CK level was lower\nin HLA-DRB1*0301 positive patients. Distinct laboratory and clinical parameters at diagnosis could be considered as prognostic\nmarkers....
We analyzed variations in 90 mitochondrial DNA (mtDNA) D-loop and heat shock protein 70 (HSP70) gene sequences from\nfour populations of domesticated helmeted Guinea fowls (70 individuals) and 1 population of wild helmeted Guinea fowls (20\nindividuals) in Kenya in order to get information about their origin, genetic diversity, and traits associated with heat stress. 90\nsequences were assigned to 25 distinct mtDNA and 4 HSP70 haplotypes. Most mtDNA haplotypes of the domesticated helmeted\nGuinea fowls were grouped into two main haplogroups, HgA and HgB. The wild population grouped into distinct mtDNA\nhaplogroups. Two mtDNA haplotypes dominated across all populations of domesticated helmeted Guinea fowls: Hap2 and Hap4,\nwhile the dominant HSP70 haplotype found in all populations was CGC. Higher haplotype diversities were generally observed.\nThe HSP70 haplotype diversities were low across all populations. The nucleotide diversity values for both mtDNA and HSP70\nwere generally low. Most mtDNA genetic variations occurred among populations for the three hierarchical categories considered\nwhile most variations in the HSP70 gene occurred among individuals within population. The lack of population structure among\nthe domestic populations could suggest intensive genetic intermixing. The differentiation of the wild population may be due to\na clearly distinct demographic history that shaped its genetic profile. Analysis of the Kenyan Guinea fowl population structure\nand history based on mtDNA D-loop variations and HSP70 gene functional polymorphisms complimented by archaeological and\nlinguistic insight supports the hypothesis that most domesticated helmeted Guinea fowls in Kenya are related to theWest African\ndomesticated helmeted Guinea fowls.We recommend more molecular studies on this emerging poultry species with potential for\npoverty alleviation and food security against a backdrop of climate change in Africa....
Background: In our previous genome-wide association study (GWAS) on the piglet splay leg (PSL) syndrome, the\nhomer scaffolding protein 1 (HOMER1) was detected as a candidate gene. The aim of this work was to further verify\nthe candidate gene by sequencing the gene and find the significantly associated mutation. Then we preliminarily\nanalyzed the effect of the significant SNP on intronic promoter activity. This research provided a reference for\nfurther investigation of the pathogenesis of PSL.\nResult: We investigated the 19 SNPs on HOMER1 and found 12 SNPs significant associated with PSL, including 8\nSNPs resided in the potential intronic promoter region in intron 4. The â?? 663â?¦â?¦â?¦â?¦...
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