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11.
Relationships in the Drosophila obscura species group, inferred from mitochondrial cytochrome oxidase II sequences 总被引:2,自引:0,他引:2
We compare the sequences for the mitochondrial cytochrome oxidase II gene
of 13 species of the Drosophila obscura group. The survey includes six
members of the D. affinis subgroup, four of the D. pseudoobscura subgroup,
and three of the D. obscura subgroup. In all species, the gene is 688
nucleotides in length, encoding a protein of 229 amino acids plus the first
position T of the stop codon. The sequences show the typical
high-transition bias for closely related species, but that bias is
essentially eliminated for species pairs of > 5% sequence divergence.
The phylogenetic relationships in the species group are inferred using both
neighbor-joining and maximum parsimony. The two procedures give comparable
results, showing that the D. affinis and D. pseudoobscura subgroups are
monophyletic groupings that appear to have closer affinities to one another
than either has to the D. obscura subgroup. We use transversion distances
to estimate times of divergence, on the basis of three different estimates
of the time of separation of the D. obscura species group from the D.
melanogaster group. If that event occurred 35 Mya, then we can estimate the
origin of the nearctic forms at approximately 22 Mya and the separation of
the D. affinis and D. pseudoobscura subgroups at approximately 17 Mya.
相似文献
12.
土典霉金色变种AT8951菊粉酶粗酶液经硫酸铵分段沉淀、DEAE Cellulose DE32离子交换、超滤、Sephadex G-150凝胶过滤和FPLC,获得两个菊粉酶组分EⅠ和EⅡ,经分析型FPLG和PAGE鉴定为单一纯和分析纯。EⅠ分子量为66KD,最适作用温度和pH分别55℃和5.8;EⅡ分子量为56KD,最适作用温度为57℃,最适pH为6.0。EⅠ和EⅡ皆为糖蛋白,多糖含量分别为24.7%和22%,都属于内切酶。本文还对EⅠ和EⅡ的Km值和I/s值,温度、pH、离子对酶活作用的影响等进行了研究。 相似文献
13.
Differences in growth and water relations among Phaseolus vulgaris cultivars in response to induced drought stress 总被引:3,自引:0,他引:3
Costa França MG Pham Thi AT Pimentel C Pereyra Rossiello RO Zuily-Fodil Y Laffray D 《Environmental and Experimental Botany》2000,43(3):227-237
Relatively little ecophysiological research has been conducted to determine the responses to drought of Phaseolus vulgaris. Four bean cultivars (cvs.) from Brazil, A320, Carioca, Ouro Negro and Xodó were submitted to an imposed water deficit in order to evaluate the importance of some adaptive mechanisms of drought resistance through the analysis of growth parameters, water status, gas exchange and indicators of tolerance mechanisms at the cellular level. During the drought treatment, relative growth rates were more reduced for A320 and Xodó than Carioca and Ouro Negro. A320 closed its stomata very rapidly and complete stomatal closure was obtained at Psi(w)=-0.6 MPa, in contrast to the other cvs. where stomata were fully closed only at Psi(w)=-0.9 MPa. Net assimilation rates were closely related to stomatal conductances. Mechanisms at the cellular level appeared to be mostly important for higher tolerance. Carioca and Ouro Negro, when compared to A320 and Xodó, were characterized by having better drought tolerance mechanisms and higher tissue water retention capacity leading to a better growth under water deficits. The leaf dehydration rates of those cvs. were slow whereas those of the drought sensitive cvs. were rapid. The results were confirmed by the electrolyte leakage test and leaf osmotic potential measurements, which indicated higher membrane resistance and osmotic adjustment in the two tolerant cvs. Carioca and Ouro Negro. It appears from this study that despite being cultivated in the same geographical region, the four cvs. of P. vulgaris displayed somewhat different drought adaptive capacities for prolonged drought during the vegetative phase. 相似文献
14.
Sivakumaran TA Igo RP Kidd JM Itsara A Kopplin LJ Chen W Hagstrom SA Peachey NS Francis PJ Klein ML Chew EY Ramprasad VL Tay WT Mitchell P Seielstad M Stambolian DE Edwards AO Lee KE Leontiev DV Jun G Wang Y Tian L Qiu F Henning AK LaFramboise T Sen P Aarthi M George R Raman R Das MK Vijaya L Kumaramanickavel G Wong TY Swaroop A Abecasis GR Klein R Klein BE Nickerson DA Eichler EE Iyengar SK 《PloS one》2011,6(10):e25598
Complement factor H shows very strong association with Age-related Macular Degeneration (AMD), and recent data suggest that multiple causal variants are associated with disease. To refine the location of the disease associated variants, we characterized in detail the structural variation at CFH and its paralogs, including two copy number polymorphisms (CNP), CNP147 and CNP148, and several rare deletions and duplications. Examination of 34 AMD-enriched extended families (N = 293) and AMD cases (White N = 4210 Indian = 134; Malay = 140) and controls (White N = 3229; Indian = 117; Malay = 2390) demonstrated that deletion CNP148 was protective against AMD, independent of SNPs at CFH. Regression analysis of seven common haplotypes showed three haplotypes, H1, H6 and H7, as conferring risk for AMD development. Being the most common haplotype H1 confers the greatest risk by increasing the odds of AMD by 2.75-fold (95% CI = [2.51, 3.01]; p = 8.31×10−109); Caucasian (H6) and Indian-specific (H7) recombinant haplotypes increase the odds of AMD by 1.85-fold (p = 3.52×10−9) and by 15.57-fold (P = 0.007), respectively. We identified a 32-kb region downstream of Y402H (rs1061170), shared by all three risk haplotypes, suggesting that this region may be critical for AMD development. Further analysis showed that two SNPs within the 32 kb block, rs1329428 and rs203687, optimally explain disease association. rs1329428 resides in 20 kb unique sequence block, but rs203687 resides in a 12 kb block that is 89% similar to a noncoding region contained in ΔCNP148. We conclude that causal variation in this region potentially encompasses both regulatory effects at single markers and copy number. 相似文献
15.
16.
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17.
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
18.
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19.
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20.
Beevi Syed Sultan Mangamoori Lakshmi Narasu Reddy Lingam Venkata 《World journal of microbiology & biotechnology》2010,26(8):1519-1525
Raphanus sativus, a common cruciferous vegetable has been attributed to possess a number of pharmacological and therapeutic properties. This
present study evaluated the protective effect of different parts of R. sativus such as root, stem and leaf obtained with a variety of extraction solvents against cell death and oxidative DNA damage induced
by hydrogen peroxide (H2O2) in normal human lymphocytes. R. sativus extracts as such showed no cytotoxicity and genotoxicity to the lymphocytes at the tested concentrations. Of the different
extracts, hexane extract of root and methanolic extract of stem and leaf showed significant protective effect against oxidative
damage induced by 200 μM H2O2 in a dose dependent manner, as compared to cells exposed only to H2O2. Our results suggest that the protective effect afforded by R. sativus extract could be related to the presence of isothiocyanates and polyphenolics, as they possess significant capacity to remove
reactive species by virtue of their ability to scavenge free radicals and induce antioxidant enzyme system in the cells. 相似文献