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Rates of DNA sequence evolution are not sex-biased in Drosophila melanogaster and D. simulans 总被引:2,自引:0,他引:2
To determine whether male- or female-biased mutation rates have affected
the molecular evolution of Drosophila melanogaster and D. simulans, we
calculated the male-to-female ratio of germline cell divisions ([symbol:
see text]) from germline generation data and the male-to-female ratio of
mutation rate ([symbol: see text]) by comparing chromosomal levels of
nucleotide divergence. We found that the ratio of germline cell divisions
changes from indicating a weak female bias to indicating a weak male bias
as the age of reproduction increases. The range of [symbol: see text]
values that we observed, however, does not lead us to expect much, if any,
difference in mutation rate between the sexes. Silent and intron nucleotide
divergence were compared between nine loci on the X chromosome and nine
loci on the second and third chromosomes. The average levels of nucleotide
divergence were not significantly different across the chromosomes,
although both silent and intron sites show a trend toward slightly more
divergence on the X. These results indicate a lack of sex- or
chromosome-biased molecular evolution in D. melanogaster and D. simulans.
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Lara Vojnov Sergio Carmona Clement Zeh Jessica Markby Debrah Boeras Marta R. Prescott Anthony L. H. Mayne Souleymane Sawadogo Christiane Adje-Toure Guoqing Zhang Mercedes Perez Gonzalez Wendy S. Stevens Meg Doherty Chunfu Yang Heather Alexander Trevor F. Peter John Nkengasong the DBS for VL Diagnostics Investigation Consortium 《PLoS medicine》2022,19(8)
BackgroundAccurate routine HIV viral load testing is essential for assessing the efficacy of antiretroviral treatment (ART) regimens and the emergence of drug resistance. While the use of plasma specimens is the standard for viral load testing, its use is restricted by the limited ambient temperature stability of viral load biomarkers in whole blood and plasma during storage and transportation and the limited cold chain available between many health care facilities in resource-limited settings. Alternative specimen types and technologies, such as dried blood spots, may address these issues and increase access to viral load testing; however, their technical performance is unclear. To address this, we conducted a meta-analysis comparing viral load results from paired dried blood spot and plasma specimens analyzed with commonly used viral load testing technologies.Methods and findingsStandard databases, conferences, and gray literature were searched in 2013 and 2018. Nearly all studies identified (60) were conducted between 2007 and 2018. Data from 40 of the 60 studies were included in the meta-analysis, which accounted for a total of 10,871 paired dried blood spot:plasma data points. We used random effects models to determine the bias, accuracy, precision, and misclassification for each viral load technology and to account for between-study variation. Dried blood spot specimens produced consistently higher mean viral loads across all technologies when compared to plasma specimens. However, when used to identify treatment failure, each technology compared best to plasma at a threshold of 1,000 copies/ml, the present World Health Organization recommended treatment failure threshold. Some heterogeneity existed between technologies; however, 5 technologies had a sensitivity greater than 95%. Furthermore, 5 technologies had a specificity greater than 85% yet 2 technologies had a specificity less than 60% using a treatment failure threshold of 1,000 copies/ml. The study’s main limitation was the direct applicability of findings as nearly all studies to date used dried blood spot samples prepared in laboratories using precision pipetting that resulted in consistent input volumes.ConclusionsThis analysis provides evidence to support the implementation and scale-up of dried blood spot specimens for viral load testing using the same 1,000 copies/ml treatment failure threshold as used with plasma specimens. This may support improved access to viral load testing in resource-limited settings lacking the required infrastructure and cold chain storage for testing with plasma specimens.Lara Vojnov and co-workers report on the use of dried blood spots for HIV viral load testing. 相似文献
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Nicola VL Serão Kristin R Delfino Bruce R Southey Jonathan E Beever Sandra L Rodriguez-Zas 《BMC medical genomics》2011,4(1):1-21
Background
Glioblastoma is a complex multifactorial disorder that has swift and devastating consequences. Few genes have been consistently identified as prognostic biomarkers of glioblastoma survival. The goal of this study was to identify general and clinical-dependent biomarker genes and biological processes of three complementary events: lifetime, overall and progression-free glioblastoma survival.Methods
A novel analytical strategy was developed to identify general associations between the biomarkers and glioblastoma, and associations that depend on cohort groups, such as race, gender, and therapy. Gene network inference, cross-validation and functional analyses further supported the identified biomarkers.Results
A total of 61, 47 and 60 gene expression profiles were significantly associated with lifetime, overall, and progression-free survival, respectively. The vast majority of these genes have been previously reported to be associated with glioblastoma (35, 24, and 35 genes, respectively) or with other cancers (10, 19, and 15 genes, respectively) and the rest (16, 4, and 10 genes, respectively) are novel associations. Pik3r1, E2f3, Akr1c3, Csf1, Jag2, Plcg1, Rpl37a, Sod2, Topors, Hras, Mdm2, Camk2g, Fstl1, Il13ra1, Mtap and Tp53 were associated with multiple survival events. Most genes (from 90 to 96%) were associated with survival in a general or cohort-independent manner and thus the same trend is observed across all clinical levels studied. The most extreme associations between profiles and survival were observed for Syne1, Pdcd4, Ighg1, Tgfa, Pla2g7, and Paics. Several genes were found to have a cohort-dependent association with survival and these associations are the basis for individualized prognostic and gene-based therapies. C2, Egfr, Prkcb, Igf2bp3, and Gdf10 had gender-dependent associations; Sox10, Rps20, Rab31, and Vav3 had race-dependent associations; Chi3l1, Prkcb, Polr2d, and Apool had therapy-dependent associations. Biological processes associated glioblastoma survival included morphogenesis, cell cycle, aging, response to stimuli, and programmed cell death.Conclusions
Known biomarkers of glioblastoma survival were confirmed, and new general and clinical-dependent gene profiles were uncovered. The comparison of biomarkers across glioblastoma phases and functional analyses offered insights into the role of genes. These findings support the development of more accurate and personalized prognostic tools and gene-based therapies that improve the survival and quality of life of individuals afflicted by glioblastoma multiforme. 相似文献27.
Our current understanding of clathrin-mediated endocytosis proposes that the process is initiated at a specialized anatomical structure called a coated pit. Electron microscopy has been required for elucidation of the morphology of coated pits and the vesicles produced therein, and the presence of a bristle coat has been taken as suggestive of clathrin surrounding these vesicles. More recently, immunocytochemical methods have confirmed that endocytic vesicles are surrounded by clathrin and its adaptor proteins, but there is a need to identify precisely and to follow the fate of the cellular organelles seen by fluorescence microscopy. We used quantum immune-electron microscopy to localize clathrin in a human adrenal cortical cell line (SW-13). Clathrin was shown to associate with a variety of vesicle types including the classic clathrin-coated vesicles and pits used in receptor internalization, pentilaminar annular gap junction vesicles, and multivesicular bodies. The images obtained with quantum dot technology allow accurate and specific localization of clathrin and the clathrin adaptor protein, AP-2, with cellular organelles and suggest that some of the structures classified as typical coated vesicles by immunocytochemical light microscopic techniques actually may be membrane bound pits. 相似文献
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Larvae of Axarus andLipiniella share several apparantly apomorphic features of the mouth-part structure, however adults ofLipiniella show possible relationships toDemeijerea andChironomus. In order to assist in refining the relationships ofAxarus toLipiniella the karyotype ofAxarus festivus was determined and compared to the karyotypes ofLipiniella arenicola andL. moderata. Larvae ofA. festivus from a population in Kansas were monomorphous, with 2n=8, the Ist, IInd and IIIrd chromosomes metacentric, and IVth acrocentric.Axarus festivus therefore differs fromL. arenicola in chromosome number (2n=6), however homologous sections of all chromosomes were identified. Inversions were detected in the Ist, IInd and IIIrd chromosomes ofA. festivus relative toL. arenicola. It was determined that both species have high functional activity, as indicated by the presence of three Balbiani rings, and more than one nucleolus per genome. Differing degrees of polyteny, a feature previously described forL. arenicola, were observed in the salivary glands, with highest degrees of polyteny in cells near the salivary duct. These similarities of chromosome structure indicate close genetic relationships betweenA. festivus andL. arenicola. However, we did not find evidence for similarity ofA. festivus toL. moderata, which supports the previous conclusions byKiknadze
et al. (1989) regardingL. arenicola andL. moderata. 相似文献
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VL. Chaloupecký 《Folia microbiologica》1964,9(6):387-388
Так как от остатков гомогенизированных клеток легко отделить растительные вирусы (Steere и Qckers, 1962; ?ech, 1962) и митохондрии (Hjertén, 1962), мы сделали попытку использовать этот простой метод и для отделения рибосом. Надосадок гомогената растущих клеток Bacillus megaterium 110 наносили на столбец 3% гранулированного агара (Polson, 1961) и промывали 66 мл буферного раствора Tris (pH 7,72, 0,005 M с 0,01 M?MgCl2) в течение часа при комнатной температуре. В элюате определяли абсорбцию при 260 мμ и белки (рис. 1). При ультрацентрифугировании образца были обнаружены рибосомы с S 20 0 107, 71, 5, 45 и 30S (рис. 2). Ультрацентрифугированием фракции № 10 были с помощью адсорбции в УФ лучах найдены рибосомы с s 20 0 107 и 44,6S (рис. 3). Группа 100S перекрывалась абсорбцией рибосом 70S, группа 30 не была обнаружена. Отделение рибосом как самостоятельной вершины не было получено. Однако, судя по соотношению нуклеиновых кислот и белков во главе вымываемой плазмы (где присутствует только РНК), здесь имела место концентрация практически чистых рибосом, как подтверждает и седиментация. ДНК удавалось определить только во фракциях второй половины элюата плазмы (рис. 4). 相似文献
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Sequence variation in the guillemot (Alcidae: Cepphus) mitochondrial control region and its nuclear homolog 总被引:4,自引:0,他引:4
We describe sequence variation in the mitochondrial control region and its
nuclear homolog in three species and seven subspecies of guillemots
(Cepphus spp.). Nuclear homologs of the 5' end of the control region were
found in all individuals. Nuclear sequences were approximately 50%
divergent from their mitochondrial counterparts and formed a distinct
phylogenetic clade; the mitochondrial-nuclear introgression event must have
predated the radiation of Cepphus. As in other vertebrates, the guillemot
control region has a relatively conserved central block flanked by
hypervariable 5' and 3' ends. Mean pairwise interspecific divergence values
among control regions were lower than those in other birds. All individuals
were heteroplasmic for the number of simple tandem nucleotide repeats
(A(n)C) at the 3' end of the control region. Phylogenetic analyses suggest
that black guillemots are basal to pigeon and spectacled guillemots, but
evolutionary relationships among subspecies remain unresolved, possibly due
to incomplete lineage sorting. Describing molecular variation in nuclear
homologs of mitochondrial genes is of general interest in phylogenetics
because, if undetected, the homologs may confound interpretations of
mitochondrial phylogenies.
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