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71.
72.
Mateus F Santana José CF Silva Eduardo SG Mizubuti Elza F Araújo Bradford J Condon B Gillian Turgeon Marisa V Queiroz 《BMC genomics》2014,15(1)
Background
Cochliobolus heterostrophus is a dothideomycete that causes Southern Corn Leaf Blight disease. There are two races, race O and race T that differ by the absence (race O) and presence (race T) of ~ 1.2-Mb of DNA encoding genes responsible for the production of T-toxin, which makes race T much more virulent than race O. The presence of repetitive elements in fungal genomes is considered to be an important source of genetic variability between different species.Results
A detailed analysis of class I and II TEs identified in the near complete genome sequence of race O was performed. In total in race O, 12 new families of transposons were identified. In silico evidence of recent activity was found for many of the transposons and analyses of expressed sequence tags (ESTs) demonstrated that these elements were actively transcribed. Various potentially active TEs were found near coding regions and may modify the expression and structure of these genes by acting as ectopic recombination sites. Transposons were found on scaffolds carrying polyketide synthase encoding genes, responsible for production of T-toxin in race T. Strong evidence of ectopic recombination was found, demonstrating that TEs can play an important role in the modulation of genome architecture of this species. The Repeat Induced Point mutation (RIP) silencing mechanism was shown to have high specificity in C. heterostrophus, acting only on transposons near coding regions.Conclusions
New families of transposons were identified. In C. heterostrophus, the RIP silencing mechanism is efficient and selective. The co-localization of effector genes and TEs, therefore, exposes those genes to high rates of point mutations. This may accelerate the rate of evolution of these genes, providing a potential advantage for the host. Additionally, it was shown that ectopic recombination promoted by TEs appears to be the major event in the genome reorganization of this species and that a large number of elements are still potentially active. So, this study provides information about the potential impact of TEs on the evolution of C. heterostrophus.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-536) contains supplementary material, which is available to authorized users. 相似文献73.
Mattia CF Prosperi Susana Marinho Angela Simpson Adnan Custovic Iain E Buchan 《BMC medical genomics》2014,7(Z1):S7
Background
There is increasing recognition that asthma and eczema are heterogeneous diseases. We investigated the predictive ability of a spectrum of machine learning methods to disambiguate clinical sub-groups of asthma, wheeze and eczema, using a large heterogeneous set of attributes in an unselected population. The aim was to identify to what extent such heterogeneous information can be combined to reveal specific clinical manifestations.Methods
The study population comprised a cross-sectional sample of adults, and included representatives of the general population enriched by subjects with asthma. Linear and non-linear machine learning methods, from logistic regression to random forests, were fit on a large attribute set including demographic, clinical and laboratory features, genetic profiles and environmental exposures. Outcome of interest were asthma, wheeze and eczema encoded by different operational definitions. Model validation was performed via bootstrapping.Results
The study population included 554 adults, 42% male, 38% previous or current smokers. Proportion of asthma, wheeze, and eczema diagnoses was 16.7%, 12.3%, and 21.7%, respectively. Models were fit on 223 non-genetic variables plus 215 single nucleotide polymorphisms. In general, non-linear models achieved higher sensitivity and specificity than other methods, especially for asthma and wheeze, less for eczema, with areas under receiver operating characteristic curve of 84%, 76% and 64%, respectively. Our findings confirm that allergen sensitisation and lung function characterise asthma better in combination than separately. The predictive ability of genetic markers alone is limited. For eczema, new predictors such as bio-impedance were discovered.Conclusions
More usefully-complex modelling is the key to a better understanding of disease mechanisms and personalised healthcare: further advances are likely with the incorporation of more factors/attributes and longitudinal measures.74.
The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster 总被引:3,自引:1,他引:3
Schug MD; Hutter CM; Wetterstrand KA; Gaudette MS; Mackay TF; Aquadro CF 《Molecular biology and evolution》1998,15(12):1751-1760
In a recent study, we reported that the combined average mutation rate of
10 di-, 6 tri-, and 8 tetranucleotide repeats in Drosophila melanogaster
was 6.3 x 10(-6) mutations per locus per generation, a rate substantially
below that of microsatellite repeat units in mammals studied to date (range
= 10(-2)-10(-5) per locus per generation). To obtain a more precise
estimate of mutation rate for dinucleotide repeat motifs alone, we assayed
39 new dinucleotide repeat microsatellite loci in the mutation accumulation
lines from our earlier study. Our estimate of mutation rate for a total of
49 dinucleotide repeats is 9.3 x 10(-6) per locus per generation, only
slightly higher than the estimate from our earlier study. We also estimated
the relative difference in microsatellite mutation rate among di-, tri-,
and tetranucleotide repeats in the genome of D. melanogaster using a method
based on population variation, and we found that tri- and tetranucleotide
repeats mutate at rates 6.4 and 8.4 times slower than that of dinucleotide
repeats, respectively. The slower mutation rates of tri- and
tetranucleotide repeats appear to be associated with a relatively short
repeat unit length of these repeat motifs in the genome of D. melanogaster.
A positive correlation between repeat unit length and allelic variation
suggests that mutation rate increases as the repeat unit lengths of
microsatellites increase.
相似文献
75.
76.
Molecular evolution of the period gene in Drosophila athabasca 总被引:1,自引:0,他引:1
We measured nucleotide variability within and between the three semispecies
of the Drosophila athabasca complex, at the period (per) gene by using a
polymerase chain reaction-based four-cutter restriction- enzyme analysis.
The levels of polymorphism varied considerably between the three
semispecies. Our results for per, combined with previous data for X-linked
allozymes, suggest that the X chromosome in the western- northern
semispecies is less variable than expected under an equilibrium-neutral
model. Both the pattern of divergence between the semispecies and a
cladistic clustering of per haplotypes support the previously hypothesized
grouping of eastern A and eastern B as the two most recently diverged
semispecies. A 21-bp in-frame segment in the region of per which shares
sequence similarity with the neuronal development gene single minded is
deleted in all eastern A and eastern B flies examined but is present in all
of the western-northern flies and all other published per sequences.
Despite these hints that there may be significant differences at the per
gene between the semispecies, especially the western-northern group versus
the two eastern groups, there is no compelling evidence that per is
involved in the mating song differences between the semispecies.
相似文献
77.
Avise JC; Shapira JF; Daniel SW; Aquadro CF; Lansman RA 《Molecular biology and evolution》1983,1(1):38-56
We address the problem of the possible significance of biological
speciation to the magnitude and pattern of divergence of asexually
transmitted characters in bisexual species. The empirical data for this
report consist of restriction endonuclease site variability in maternally
transmitted mitochondrial DNA (mtDNA) isolated from 82 samples of
Peromyscus polionotus and P. leucopus collected from major portions of the
respective species' ranges. Data are analyzed together with previously
published information on P. maniculatus, a sibling species to polionotus.
Maps of restriction sites indicate that all of the variation observed can
be reasonably attributed to base substitutions leading to loss or gain of
particular recognition sites. Magnitude of mtDNA sequence divergence within
polionotus (maximum approximately equal to 2%) is roughly comparable to
that observed within any of five previously identified mtDNA assemblages in
maniculatus. Sequence divergence within leucopus (maximum approximately
equal to 4%) is somewhat greater than that within polionotus. Consideration
of probable evolutionary links among mtDNA restriction site maps allowed
estimation of matriarchal phylogenies within polionotus and leucopus.
Clustering algorithms and qualitative Wagner procedures were used to
generate phenograms and parsimony networks, respectively, for the
between-species comparisons. Three simple graphical models are presented to
illustrate some conceivable relationships of mtDNA differentiation to
speciation. In theoretical case I, each of two reproductively defined
species (A and B) is monophyletic in matriarchal genealogy; the common
female ancestor of either species can either predate or postdate the
speciation. In case II, neither species is monophyletic in matriarchal
genotype. In case III, species B is monophyletic but forms a subclade
within A which is thus paraphyletic with respect to B. The empirical
results for mtDNA in maniculatus and polionotus appear to conform closely
to case III. These theoretical and empirical considerations raise a number
of questions about the general relationship of the speciation process to
the evolution of uniparentally transmitted traits. Some of these
considerations are presented, and it is suggested that the distribution
patterns of mtDNA sequence variation within and among extant species should
be of considerable relevance to the particular demographies of speciation.
相似文献
78.
Debora Napoli Leonardo Lupori Raffaele Mazziotti Giulia Sagona Sara Bagnoli Muntaha Samad Erika K Sacramento Joanna Kirkpartick Elena Putignano Siwei Chen Eva Terzibasi Tozzini Paola Tognini Pierre Baldi Jessica CF Kwok Alessandro Cellerino Tommaso Pizzorusso 《EMBO reports》2021,22(1)
The authors regret having omitted grant attributions in the original publication. The funding section is herewith updated to reflect the change. “Funding attributed to Tommaso Pizzorusso was provided by EPIGEN Flagship project and PRIN2017HM8FA, funding attributed to Alessandro Cellerino was provided by Fondazione Pisa ETHERNA project, funding attributed to Pierre Baldi was provided by NIH (grant NIH ), funding attributed to Jessica Kwok was provided by the Leverhulme Trust project grant (RPG‐2018‐100).” GM123558相似文献
79.
Emily J. Yao Richard K. Babbs Julia C. Kelliher Kimberly P. Luttik Kristyn N. Borrelli M. Imad Damaj Megan K. Mulligan Camron D. Bryant 《Genes, Brain & Behavior》2021,20(6):e12751
Binge eating is a heritable trait associated with eating disorders and refers to the rapid consumption of a large quantity of energy-dense food that is, associated with loss of control and negative affect. Binge eating disorder is the most common eating disorder in the United States; however, the genetic basis is unknown. We previously identified robust mouse inbred strain differences between C57BL/6J and DBA/2J in binge-like eating of sweetened palatable food in an intermittent access, conditioned place preference paradigm. To map the genetic basis of changes in body weight and binge-like eating (BLE) and to identify candidate genes, we conducted quantitative trait locus (QTL) analysis in 128 C57BL/6J x DBA/2J-F2 mice combined with PheQTL and trait covariance analysis in GeneNetwork2 using legacy BXD-RI trait datasets. We identified a QTL on Chromosome 18 influencing changes in body weight across days in females (log of the odds [LOD] = 6.3; 1.5-LOD: 3–12 cM) that contains the candidate gene Zeb1. We also identified a sex-combined QTL influencing initial palatable food intake on Chromosome 5 (LOD = 5.8; 1.5-LOD: 21–28 cM) that contains the candidate gene Lcorl and a second QTL influencing escalated palatable food intake on Chromosome 6 in males (LOD = 5.4; 1.5-LOD: 50–59 cM) that contains the candidate genes Adipor2 and Plxnd1. Finally, we identified a suggestive QTL in females for slope of BLE on distal Chromosome 18 (LOD = 4.1; p = 0.055; 1.5-LOD: 23–35 cM). Future studies will use BXD-RI strains to fine map loci and support candidate gene nomination for gene editing. 相似文献
80.
A major impediment to the confirmation of free radical mechanisms in pathogenesis is a lack of direct, chemical evidence that oxygen centered free radicals actually arise in living tissues in quantities sufficient to cause serious damage. This investigation was conducted to validate the use of dimethyl sulfoxide (DMSO) as a quantitative molecular probe for the generation of hydroxyl radicals (HO.) under physiologic conditions. Reaction of HO. with DMSO produces methane sulfinic acid (MSA) as a primary product, which can be detected by a simple colorimetric assay. To develop a method for estimating total HO. production, we studied two model systems: the superoxide driven Fenton reaction in vitro, using xanthine oxidase as the source of superoxide, and a computer model of Fenton chemistry. Measured MSA production both in vitro and in the computer model was a predictable function of the concentrations of DMSO and competing scavengers of HO., according to the principle of competition kinetics. Both experimental results and model calculations showed that Scatchard analysis may be used to infer total HO. generation, despite the presence of scavengers other than DMSO, such as mannitol. Thus, methane sulfinic acid production from DMSO holds promise as an easily measured marker for HO. formation in biologic systems pretreated with DMSO, and Scatchard analysis of repeated experiments with varying DMSO concentrations can yield an estimate of total HO. generation. 相似文献