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Background
Cancer and other disorders are due to genomic lesions. SNP-microarrays are able to measure simultaneously both genotype and copy number (CN) at several Single Nucleotide Polymorphisms (SNPs) along the genome. CN is defined as the number of DNA copies, and the normal is two, since we have two copies of each chromosome. The genotype of a SNP is the status given by the nucleotides (alleles) which are present on the two copies of DNA. It is defined homozygous or heterozygous if the two alleles are the same or if they differ, respectively. Loss of heterozygosity (LOH) is the loss of the heterozygous status due to genomic events. 相似文献13.
Background
Paracoccidioides brasiliensis (Eukaryota, Fungi, Ascomycota) is a thermodimorphic fungus, the etiological agent of paracoccidioidomycosis, the most important systemic mycoses in Latin America. Three isolates corresponding to distinct phylogenetic lineages of the Paracoccidioides species complex had their genomes sequenced. In this study the identification and characterization of class II transposable elements in the genomes of these fungi was carried out.Results
A genomic survey for DNA transposons in the sequence assemblies of Paracoccidioides, a genus recently proposed to encompass species P. brasiliensis (harboring phylogenetic lineages S1, PS2, PS3) and P. lutzii (Pb01-like isolates), has been completed. Eight new Tc1/mariner families, referred to as Trem (Tr ansposable e lement m ariner), labeled A through H were identified. Elements from each family have 65-80% sequence similarity with other Tc1/mariner elements. They are flanked by 2-bp TA target site duplications and different termini. Encoded DDD-transposases, some of which have complete ORFs, indicated that they could be functionally active. The distribution of Trem elements varied between the genomic sequences characterized as belonging to P. brasiliensis (S1 and PS2) and P. lutzii. TremC and H elements would have been present in a hypothetical ancestor common to P. brasiliensis and P. lutzii, while TremA, B and F elements were either acquired by P. brasiliensis or lost by P. lutzii after speciation. Although TremD and TremE share about 70% similarity, they are specific to P. brasiliensis and P. lutzii, respectively. This suggests that these elements could either have been present in a hypothetical common ancestor and have evolved divergently after the split between P. brasiliensis and P. Lutzii, or have been independently acquired by horizontal transfer.Conclusions
New families of Tc1/mariner DNA transposons in the genomic assemblies of the Paracoccidioides species complex are described. Families were distinguished based on significant BLAST identities between transposases and/or TIRs. The expansion of Trem in a putative ancestor common to the species P. brasiliensis and P. lutzii would have given origin to TremC and TremH, while other elements could have been acquired or lost after speciation had occurred. The results may contribute to our understanding of the organization and architecture of genomes in the genus Paracoccidioides. 相似文献14.
Tarskaia L. A. Zinchenko R. A. Elchinova G. I. Egorova A. G. Korotov M. N. Basova E. V. Prokopeva A. M. Sivtseva E. N. Nikolaeva E. E. Banshikova E. S. Samarkina M. V. Sannikova A. N. Danilova G. I. Jhelobtsova A. F. Danilova A. P. Popova G. N. 《Russian Journal of Genetics》2004,40(11):1264-1272
The diversity of Mendelian hereditary pathology has been studied in Sakha Republic (Yakutia). The sample comprised 1 000 700 subjects, including 363 316 Yakuts, 14 428 Evenks, 8668 Evens, 550 263 Russians, and 64 025 subjects from other ethnic groups. Fifty-one autosomal dominant (AD) diseases, including five diseases with frequencies of 1 : 50 000 or higher; 40 autosomal recessive (AR) diseases, including eight diseases with frequencies of 1 : 50 000 or higher in the Yakut population; and five X-linked diseases have been detected. 相似文献
15.
Gibson S Kibiki Bert Mulder Wil MV Dolmans Jessica L de Beer Martin Boeree Noel Sam Dick van Soolingen Christophe Sola Adri GM van der Zanden 《BMC microbiology》2007,7(1):51
Background
Tuberculosis (TB) is a major health problem and HIV is the major cause of the increase in TB. Sub-Saharan Africa is endemic for both TB and HIV infection. Determination of the prevalence of M. tuberculosis strains and their drug susceptibility is important for TB control. 相似文献16.
SE?Aleshin AV?Timofeev MV?Khoretonenko LG?Zakharova GV?Pashvykina JR?Stephenson AM?Shneider AD?AltsteinEmail author 《BMC microbiology》2005,5(1):45
Background
Heterologous prime-boost immunization protocols using different gene expression systems have proven to be successful tools in protecting against various diseases in experimental animal models. The main reason for using this approach is to exploit the ability of expression cassettes to prime or boost the immune system in different ways during vaccination procedures. The purpose of the project was to study the ability of recombinant vaccinia virus (VV) and bacterial plasmid, both carrying the NS1 gene from tick-borne encephalitis (TBE) virus under the control of different promoters, to protect mice against lethal challenge using a heterologous prime-boost vaccination protocol. 相似文献17.
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L. A. Tarskaya R. A. Zinchenko G. I. Elchinova A. G. Egorova M. N. Korotov E. V. Basova A. M. Prokopeva E. N. Sivtseva E. E. Nikolaeva E. S. Banshchikova M. V. Samarkina A. N. Sannikova G. I. Danilova A. F. Jhelobtsova A. P. Danilova G. N. Popova 《Russian Journal of Genetics》2003,39(12):1461-1464
Summarized data of medical genetic survey of the population of Republic of Sakha (Yakutia) are presented. The number of the population examined constituted 1 000 700 individuals (including 424 500 of urban and 576 200 of rural population, respectively). Regarding the ethnicity, 33 regions of the Republic examined were at most inhabited by Yakuts (36%) and Russians (55%). A total of 400 families (606 patients) with autosomal dominant, 274 families (369 patients) with autosomal recessive, and 42 families (53 patients) with X-linked pathologies were detected. The segregation analysis performed showed good correlation with the expected type of inheritance for both dominant and recessive diseases. The prevalence rate of monogenic hereditary diseases for rural and urban populations, as well as for solely Yakuts, was calculated. It was shown that weighted average prevalence of dominant (0.68; 1.44) and recessive (0.43; 0.86) disorders in Yakuts was two times higher than in total population examined. 相似文献
19.
Tobias Wauer Kirby N Swatek Jane L Wagstaff Christina Gladkova Jonathan N Pruneda Martin A Michel Malte Gersch Christopher M Johnson Stefan MV Freund David Komander 《The EMBO journal》2015,34(3):307-325
The protein kinase PINK1 was recently shown to phosphorylate ubiquitin (Ub) on Ser65, and phosphoUb activates the E3 ligase Parkin allosterically. Here, we show that PINK1 can phosphorylate every Ub in Ub chains. Moreover, Ser65 phosphorylation alters Ub structure, generating two conformations in solution. A crystal structure of the major conformation resembles Ub but has altered surface properties. NMR reveals a second phosphoUb conformation in which β5-strand slippage retracts the C-terminal tail by two residues into the Ub core. We further show that phosphoUb has no effect on E1-mediated E2 charging but can affect discharging of E2 enzymes to form polyUb chains. Notably, UBE2R1- (CDC34), UBE2N/UBE2V1- (UBC13/UEV1A), TRAF6- and HOIP-mediated chain assembly is inhibited by phosphoUb. While Lys63-linked poly-phosphoUb is recognized by the TAB2 NZF Ub binding domain (UBD), 10 out of 12 deubiquitinases (DUBs), including USP8, USP15 and USP30, are impaired in hydrolyzing phosphoUb chains. Hence, Ub phosphorylation has repercussions for ubiquitination and deubiquitination cascades beyond Parkin activation and may provide an independent layer of regulation in the Ub system. 相似文献
20.
Sheila C Rahal Reinaldo S Volpi Carlos R Teixeira Vania MV Machado Guilherme DP Soares Carlos Ramires Neto Kathleen Linn 《BMC veterinary research》2012,8(1):1-5