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排序方式: 共有177条查询结果,搜索用时 15 毫秒
1.
Somatic hypermutagenesis in immunoglobulin genes. II. Influence of neighbouring base sequences on mutagenesis. 总被引:16,自引:0,他引:16
A new approach for the analysis of hotspots of mutations is described. It is based on the classification of hotspot site sequences. Using this approach, the consensuses RGYW and TAA of hotspot sites were revealed in the V gene. Correlation between somatic mutations and these consensuses is investigated by the statistical weight method in 323 somatic substitutions in 14 V genes. Assuming the absence of any correlation, the probability of observing such data in the sample would be very low (0.0003). These results support the idea that emergence of somatic mutation is significantly influenced by neighbouring base sequences. This idea was also supported by the analysis of 296 somatic mutations in flanking sequences of V genes. It is supposed that this influence is an important feature of somatic hypermutagenesis. 相似文献
2.
Several LINE-1s have been isolated and characterized from genomic DNA of the vole, Microtus kirgisorum. Blot hybridization revealed specific restriction patterns of L1 elements in vole genomes. Rehybridization of the genomic
blot with a cloned 5′-end fragment revealed two major bands indicating the presence of two different L1 subfamilies. The copy
numbers are estimated for different parts of M. kirgisorum L1 elements. Data also demonstrate that most vole L1 elements are truncated at the 5′-end; however, in contrast to mouse,
the ORF1 copy number is higher in vole. A difference between the substitution rates of the ORF1 5′-region (approximately 330
nucleotides) and the rest of the L1 coding regions is revealed.
Received: 12 January, 1999 / Accepted: 18 March, 1999 相似文献
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Barkhatov Yuri V. Khromechek Elena B. Zykov Vladimir V. Rogozin Denis Y. 《Hydrobiologia》2022,849(15):3373-3387
Hydrobiologia - We conducted a monitoring study on the dynamics of the abundance, biomass, and vertical distribution of the cryptophyte population in meromictic saline Lake Shira (90.11 E,... 相似文献
7.
D. Y. Rogozin V. V. Zykov M. Y. Chernetsky A. G. Degermendzhy R. D. Gulati 《Aquatic Ecology》2009,43(3):661-672
The year-to-year variations of vertical distribution and biomass of anoxic phototrophic bacteria were studied during ice periods
2003–2005 and 2007–2008 in meromictic lakes Shira and Shunet (Southern Siberia, Russian Federation). The bacterial layers
in chemocline of both lakes were sampled with a thin-layer hydraulic multi-syringe sampler. In winter, biomass of purple sulphur
bacteria varied considerably depending on the amount of light penetrating into the chemocline through the ice and snow cover.
In relatively weakly stratified, brackish Shira Lake, the depth of chemocline varied between winters, so that light intensity
for purple sulphur bacteria inhabiting this zone differed. In Shira Lake, increased transparency of mixolimnion in winter,
high chemocline position and absence of snow resulted in light intensity and biomass of purple sulphur bacteria exceeding
the summer values in the chemocline of the lake. We could monitor snow cover at the lake surface using remote sensing and
therefore estimate dynamics and amount of light under ice and its availability for phototrophic organisms. In Shunet Lake,
the light intensities in the chemocline and biomasses of purple sulphur bacteria were always lower in winter than in summer,
but the biomasses of green sulphur bacteria were similar. 相似文献
8.
Background
Predicting and proper ranking of canonical splice sites (SSs) is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detection tool MHMMotif to intronic ends and exons. We combine elements found with sensor information using Naive Bayesian Network, as implemented in our new tool SpliceScan. 相似文献9.
Bayanmunkh Baatar Pei-Wen Chiang Denis Yu Rogozin Yu-Ting Wu Ching-Hung Tseng Cheng-Yu Yang Hsiu-Hui Chiu Bolormaa Oyuntsetseg Andrey G. Degermendzhy Sen-Lin Tang 《PloS one》2016,11(3)
Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches. 相似文献
10.
Resch AM Carmel L Mariño-Ramírez L Ogurtsov AY Shabalina SA Rogozin IB Koonin EV 《Molecular biology and evolution》2007,24(8):1821-1831
Evolution of protein sequences is largely governed by purifying selection, with a small fraction of proteins evolving under positive selection. The evolution at synonymous positions in protein-coding genes is not nearly as well understood, with the extent and types of selection remaining, largely, unclear. A statistical test to identify purifying and positive selection at synonymous sites in protein-coding genes was developed. The method compares the rate of evolution at synonymous sites (Ks) to that in intron sequences of the same gene after sampling the aligned intron sequences to mimic the statistical properties of coding sequences. We detected purifying selection at synonymous sites in approximately 28% of the 1,562 analyzed orthologous genes from mouse and rat, and positive selection in approximately 12% of the genes. Thus, the fraction of genes with readily detectable positive selection at synonymous sites is much greater than the fraction of genes with comparable positive selection at nonsynonymous sites, i.e., at the level of the protein sequence. Unlike other genes, the genes with positive selection at synonymous sites showed no correlation between Ks and the rate of evolution in nonsynonymous sites (Ka), indicating that evolution of synonymous sites under positive selection is decoupled from protein evolution. The genes with purifying selection at synonymous sites showed significant anticorrelation between Ks and expression level and breadth, indicating that highly expressed genes evolve slowly. The genes with positive selection at synonymous sites showed the opposite trend, i.e., highly expressed genes had, on average, higher Ks. For the genes with positive selection at synonymous sites, a significantly lower mRNA stability is predicted compared to the genes with negative selection. Thus, mRNA destabilization could be an important factor driving positive selection in nonsynonymous sites, probably, through regulation of expression at the level of mRNA degradation and, possibly, also translation rate. So, unexpectedly, we found that positive selection at synonymous sites of mammalian genes is substantially more common than positive selection at the level of protein sequences. Positive selection at synonymous sites might act through mRNA destabilization affecting mRNA levels and translation. 相似文献