排序方式: 共有35条查询结果,搜索用时 15 毫秒
11.
Rebecca S LaRue Stefán R Jónsson Kevin AT Silverstein Mathieu Lajoie Denis Bertrand Nadia El-Mabrouk Isidro Hötzel Valgerdur Andrésdóttir Timothy PL Smith Reuben S Harris 《BMC molecular biology》2008,9(1):104
Background
APOBEC3 (A3) proteins deaminate DNA cytosines and block the replication of retroviruses and retrotransposons. Each A3 gene encodes a protein with one or two conserved zinc-coordinating motifs (Z1, Z2 or Z3). The presence of one A3 gene in mice (Z2–Z3) and seven in humans, A3A-H (Z1a, Z2a-Z1b, Z2b, Z2c-Z2d, Z2e-Z2f, Z2g-Z1c, Z3), suggests extraordinary evolutionary flexibility. To gain insights into the mechanism and timing of A3 gene expansion and into the functional modularity of these genes, we analyzed the genomic sequences, expressed cDNAs and activities of the full A3 repertoire of three artiodactyl lineages: sheep, cattle and pigs. 相似文献12.
Intraspecific DNA sequence variation of the mitochondrial control region of white sturgeon (Acipenser transmontanus) 总被引:3,自引:0,他引:3
Intraspecific sequence variation in the D-loop region of mtDNA in white
sturgeon (Acipenser transmontanus), a relict North American fish species,
was examined in 27 individuals from populations of the Columbia and Fraser
rivers. Thirty-three varied nucleotide positions were present in a
462-nucleotide D-loop sequence, amplified using the polymerase chain
reaction. Bootstrapped neighbor-joining and maximum- parsimony trees of
sequences from 19 haplotypes suggest that the two populations have recently
diverged. This is consistent with the hypothesis that the Columbia River, a
Pleistocene refugium habitat, was the source of founders for the Fraser
River after the last glacial recession. On the basis of a divergence time
of 10-12 thousand years ago, the estimated substitution rate of the white
sturgeon D-loop region is 1.1-1.3 x 10(-7) nucleotides/site/year, which is
comparable to rates for hypervariable sequences in the human D-loop region.
Furthermore, the ratio of mean percent nucleotide differences in the D-
loop (2.27%) to that in whole mtDNA (0.54%, as estimated from
restriction-enzyme data) is 4.3, which is similar to the fourfold-to-
fivefold-higher substitution rate estimated for the human D-loop. The high
nucleotide substitution rate of the hypervariable region indicates that the
vertebrate D-loop has potential as a genetic marker in molecular population
studies.
相似文献
13.
Sean R Landman Tae Hyun Hwang Kevin AT Silverstein Yingming Li Scott M Dehm Michael Steinbach Vipin Kumar 《BMC genomics》2014,15(1)
Background
Personal genome assembly is a critical process when studying tumor genomes and other highly divergent sequences. The accuracy of downstream analyses, such as RNA-seq and ChIP-seq, can be greatly enhanced by using personal genomic sequences rather than standard references. Unfortunately, reads sequenced from these types of samples often have a heterogeneous mix of various subpopulations with different variants, making assembly extremely difficult using existing assembly tools. To address these challenges, we developed SHEAR (Sample Heterogeneity Estimation and Assembly by Reference; http://vk.cs.umn.edu/SHEAR), a tool that predicts SVs, accounts for heterogeneous variants by estimating their representative percentages, and generates personal genomic sequences to be used for downstream analysis.Results
By making use of structural variant detection algorithms, SHEAR offers improved performance in the form of a stronger ability to handle difficult structural variant types and better computational efficiency. We compare against the lead competing approach using a variety of simulated scenarios as well as real tumor cell line data with known heterogeneous variants. SHEAR is shown to successfully estimate heterogeneity percentages in both cases, and demonstrates an improved efficiency and better ability to handle tandem duplications.Conclusion
SHEAR allows for accurate and efficient SV detection and personal genomic sequence generation. It is also able to account for heterogeneous sequencing samples, such as from tumor tissue, by estimating the subpopulation percentage for each heterogeneous variant.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-84) contains supplementary material, which is available to authorized users. 相似文献14.
Taneli Tirkkonen Jaakko Pakarinen Elina Rintala Terhi Ali-Vehmas Harri Marttila Olli AT Peltoniemi Johanna M?kinen 《Acta veterinaria Scandinavica》2010,52(1):21
Background
Animal mycobacterioses are regarded as a potential zoonotic risk and cause economical losses world wide. M. avium subsp. hominissuis is a slow-growing subspecies found in mycobacterial infected humans and pigs and therefore rapid and discriminatory typing methods are needed for epidemiological studies. The genetic similarity of M. avium subsp. hominissuis from human and porcine origins using two different typing methods have not been studied earlier. The objective of this study was to compare the IS1245 RFLP pattern and MIRU-VNTR typing to study the genetic relatedness of M. avium strains isolated from slaughter pigs and humans in Finland with regard to public health aspects. 相似文献15.
Catechol 2, 3-dioxygenase is present in several types of bacteria and undergoes degradation of environmental pollutants through
an important key biochemical pathways. Specifically, this enzyme cleaves aromatic rings of several environmental pollutants such
as toluene, xylene, naphthalene and biphenyl derivatives. Hence, the importance of Catechol 2, 3-dioxygenase and its role in the
degradation of environmental pollutants made us to predict the three-dimensional structure of Catechol 2, 3-dioxygenase from
Burkholderia cepacia. The 10ns molecular dynamics simulation was carried out to check the stability of the modeled Catechol 2, 3-
dioxygenase. The results show that the model was energetically stable, and it attains their equilibrium within 2000 ps of production
MD run. The docking of various petroleum hydrocarbons into the Catechol 2,3-dioxygenase reveals that the benzene, O-xylene,
Toluene, Fluorene, Naphthalene, Carbazol, Pyrene, Dibenzothiophene, Anthracene, Phenanthrene, Biphenyl makes strong
hydrogen bond and Van der waals interaction with the active site residues of H150, L152, W198, H206, H220, H252, I254, T255,
Y261, E271, L276 and F309. Free energy of binding and estimated inhibition constant of these compounds demonstrates that they
are energetically stable in their binding cavity. Chrysene shows positive energy of binding in the active site atom of Fe. Except
Pyrene all the substrates made close contact with Fe atom by the distance ranges from 1.67 to 2.43 Å. In addition to that, the above
mentioned substrate except pyrene all other made π-π stacking interaction with H252 by the distance ranges from 3.40 to 3.90 Å.
All these docking results reveal that, except Chrysene all other substrate has good free energy of binding to hold enough in the
active site and makes strong VdW interaction with Catechol-2,3-dioxygenase. These results suggest that, the enzyme is capable of
catalyzing the above-mentioned substrate. 相似文献
16.
Cleide G da Silva César A J Ribeiro Guilhian Leipnitz Carlos S Dutra-Filho Angela T S Wyse AT Clóvis M D Wannmacher Jo?o J F Sarkis Cornelis Jakobs Moacir Wajner 《Biochimica et biophysica acta》2002,1586(1):81-91
L-2-Hydroxyglutaric (LGA) and D-2-hydroxyglutaric (DGA) acids are the characteristic metabolites accumulating in the neurometabolic disorders known as L-2-hydroxyglutaric aciduria and D-2-hydroxyglutaric aciduria, respectively. Although these disorders are predominantly characterized by severe neurological symptoms, the neurotoxic mechanisms of brain damage are virtually unknown. In this study we have evaluated the role of LGA and DGA at concentrations ranging from 0.01 to 5.0 mM on various parameters of energy metabolism in cerebral cortex slices and homogenates of 30-day-old Wistar rats, namely glucose uptake, CO(2) production and the respiratory chain enzyme activities of complexes I to IV. DGA significantly decreased glucose utilization (2.5 and 5.0 mM) by brain homogenates and CO(2) production (5 mM) by brain homogenates and slices, whereas LGA had no effect on either measurement. Furthermore, DGA significantly inhibited cytochrome c oxidase activity (complex IV) (EC 1.9.3.1) in a dose-dependent manner (35-95%) at doses as low as 0.5 mM, without compromising the other respiratory chain enzyme activities. In contrast, LGA did not interfere with these activities. Our results suggest that the strong inhibition of cytochrome c oxidase activity by increased levels of DGA could be related to the neurodegeneration of patients affected by D-2-hydroxyglutaric aciduria. 相似文献
17.
Alexander T. Ciota Yongqing Jia Anne F. Payne Greta Jerzak Lauren J. Davis David S.Young Dylan Ehrbar Laura D. Kramer 《PloS one》2009,4(11)
St. Louis encephalitis virus (SLEV; Flaviviridae, flavivirus) was the major cause of epidemic flaviviral encephalitis in the U.S. prior to the introduction of West Nile virus (WNV) in 1999. However, outbreaks of SLEV have been significantly more limited then WNV in terms of levels of activity and geographic dispersal. One possible explanation for these variable levels of activity is that differences in the potential for each virus to adapt to its host cycle exist. The need for arboviruses to replicate in disparate hosts is thought to result in constraints on both evolution and host-specific adaptation. If cycling is the cause of genetic stability observed in nature and arboviruses lack host specialization, then sequential passage should result in both the accumulation of mutations and specialized viruses better suited for replication in that host. Previous studies suggest that WNV and SLEV differ in capacity for both genetic change and host specialization, and in the costs each accrues from specializing. In an attempt to clarify how selective pressures contribute to epidemiological patterns of WNV and SLEV, we evaluated mutant spectra size, consensus genetic change, and phenotypic changes for SLEV in vivo following 20 sequential passages via inoculation in either Culex pipiens mosquitoes or chickens. Results demonstrate that the capacity for genetic change is large for SLEV and that the size of the mutant spectrum is host-dependent using our passage methodology. Despite this, a general lack of consensus change resulted from passage in either host, a result that contrasts with the idea that constraints on evolution in nature result from host cycling alone. Results also suggest that a high level of adaptation to both hosts already exists, despite host cycling. A strain significantly more infectious in chickens did emerge from one lineage of chicken passage, yet other lineages and all mosquito passage strains did not display measurable host-specific fitness gains. In addition, increased infectivity in chickens did not decrease infectivity in mosquitoes, which further contrasts the concept of fitness trade-offs for arboviruses. 相似文献
18.
19.
Background
Plasmodium falciparum antigenic diversity and polymorphism confuses the issue of antimalarial vaccine development. Merozoite surface protein (MSP)-1 and -2 are two highly polymorphic vaccine candidates. Characterisation of their precise polymorphism in endemic regions may facilitate the design of an effective vaccine.Methods
Isolates obtained in 52 Gabonese children presenting with uncomplicated malaria were genotyped by nested-PCR of msp -1 block 2, and msp -2 block 3, to analyze both parasite population polymorphism and clone fluctuations.Results
Twenty-five and 19 different alleles were respectively obtained for msp-1 and msp-2 loci, the RO33 family of msp-1 being poorly polymorphic. Four cases of non-random distribution of alleles were reported of the FC27, and/or 3D7 families of msp-2. All but two isolates were composed of more than one genotype, and the multiplicity of infection (MOI) was 4.0. Neither parasite density nor age was related to MOI. Clone fluctuations were studied for ten subjects who were sampled again at reappearance of parasites in blood. Disappearance and reappearance of alleles were observed following treatment, suggesting difficulties in assessing polymorphism and in distinguishing reinfection from recrudescence.Conclusion
P. falciparum polymorphism is extensive in Southeast Gabon, and most of infections are composed of multiple clones. The fluctuation of clones contributes to parasite diversity. 相似文献20.
Kim AT Verheijden Linette EM Willemsen Saskia Braber Thea Leusink-Muis Dianne JM Delsing Johan Garssen Aletta D Kraneveld Gert Folkerts 《Respiratory research》2015,16(1)