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121.
122.
Background
The chondrichthyan or cartilaginous fish (chimeras, sharks, skates and rays) occupy an important phylogenetic position as the sister group to all other jawed vertebrates and as an early lineage to diverge from the vertebrate lineage following two whole genome duplication events in vertebrate evolution. There have been few comparative genomic analyses incorporating data from chondrichthyan fish and none comparing genomic information from within the group. We have sequenced the complete Hoxa cluster of the Little Skate (Leucoraja erinacea) and compared to the published Hoxa cluster of the Horn Shark (Heterodontus francisci) and to available data from the Elephant Shark (Callorhinchus milii) genome project. 相似文献123.
Christina Backes Eckart Meese Hans-Peter Lenhof Andreas Keller 《Nucleic acids research》2010,38(13):4476-4486
While in the last decade mRNA expression profiling was among the most popular research areas, over the past years the study of non-coding RNAs, especially microRNAs (miRNAs), has gained increasing interest. For almost 900 known human miRNAs hundreds of pretended targets are known. However, there is only limited knowledge about putative systemic effects of changes in the expression of miRNAs and their regulatory influence. We determined for each known miRNA the biochemical pathways in the KEGG and TRANSPATH database and the Gene Ontology categories that are enriched with respect to its target genes. We refer to these pathways and categories as target pathways of the corresponding miRNA. Investigating target pathways of miRNAs we found a strong relation to disease-related regulatory pathways, including mitogen-activated protein kinase (MAPK) signaling cascade, Transforming growth factor (TGF)-beta signaling pathway or the p53 network. Performing a sophisticated analysis of differentially expressed genes of 13 cancer data sets extracted from gene expression omnibus (GEO) showed that targets of specific miRNAs were significantly deregulated in these sets. The respective miRNA target analysis is also a novel part of our gene set analysis pipeline GeneTrail. Our study represents a comprehensive theoretical analysis of the relationship between miRNAs and their predicted target pathways. Our target pathways analysis provides a ‘miRNA-target pathway’ dictionary, which enables researchers to identify target pathways of differentially regulated miRNAs. 相似文献
124.
The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias 总被引:45,自引:14,他引:31
Genes sequences from Escherichia coli, Salmonella typhimurium, and other
members of the Enterobacteriaceae show a negative correlation between the
degree of synonymous-codon usage bias and the rate of nucleotide
substitution at synonymous sites. In particular, very highly expressed
genes have very biased codon usage and accumulate synonymous substitutions
very slowly. In contrast, there is little correlation between the degree of
codon bias and the rate of protein evolution. It is concluded that both the
rate of synonymous substitution and the degree of codon usage bias largely
reflect the intensity of selection at the translational level. Because of
the high variability among genes in rates of synonymous substitution,
separate molecular clocks of synonymous substitution might be required for
different genes.
相似文献
125.
We present a simple Monte Carlo method for estimating the age of the most
recent common ancestor (MRCA) of a sample of DNA sequences. We show that
Templeton's (1993) estimator of the age of the MRCA based on the maximum
number of nucleotide differences between two sequences in a sample is
inaccurate, and we demonstrate the new method by reanalyzing a sample of
DNA sequences from human Y chromosomes and a sample of human Alu sequences.
相似文献
126.
The effect of substrate on LM2 reduction was examined using a reconstituted system containing dilauroylphosphatidylcholine, NADPH-cytochrome P-450 reductase, and cytochrome P-450 LM2 in a 160:1.5:1 molar ratio. In general, most substrates increased the rate constants of both the first and second phases of reduction as well as the fraction of LM2 reduced in the first phase. The correlation between the high spin content of the cytochrome and each of these kinetic parameters was weaker than expected if spin state controlled LM2 reduction. Further, substrate was shown to exert a rapid effect on both the high spin content and stimulation of reduction indicating that the low spin to high spin shift cannot be responsible for the slow phase of reduction for this particular isoform. Cytochrome P-450 reduction was also examined in both phospholipid-containing and soluble systems where the LM2 and reductase were not present as a preformed complex. In these systems the reactions were substantially slower than with the standard reconstituted system. Addition of substrate enhanced the rate of reduction, indicating that the rate of association between LM2 and the reductase was increased by substrate addition. The strong correlation between the rate of LM2 reduction in a preformed complex and the logarithm of the rate of LM2 and reductase association implicates the rate of functional complex formation as the factor controlling the slow phase of reduction. 相似文献
127.
Peter WH Holland 《Genome biology》2000,1(4):reports4017.1-reports40172
A report on the 'Nuclear architecture and control of gene expression' minisymposium at the first meeting of the European Life Scientists Organisation (ELSO), Geneva, Switzerland, September 2-6, 2000. 相似文献
128.
Human red and green visual pigment genes are X-linked duplicate genes. To
study their evolutionary history, introns 2 and 4 (1,987 and 1,552 bp,
respectively) of human red and green pigment genes were sequenced.
Surprisingly, we found that intron 4 sequences of these two genes are
identical and that the intron 2 sequences differ by only 0.3%. The low
divergences are unexpected because the duplication event producing the two
genes is believed to have occurred before the separation of the human and
Old World monkey (OWM) lineages. Indeed, the divergences in the two introns
are significantly lower than both the synonymous divergence (3.2% +/- 1.1%)
and the nonsynonymous divergence (2.0% +/- 0.5%) in the coding sequences
(exons 1-6). A comparison of partial sequences of exons 4 and 5 of human
and OWM red and green pigment genes supports the hypothesis that the gene
duplication occurred before the human-OWM split. In conclusion, the high
similarities in the two intron sequences might be due to very recent gene
conversion, probably during evolution of the human lineage.
相似文献
129.
130.
J L Harris A Niles K Burdick M Maffitt B J Backes J A Ellman I Kuntz M Haak-Frendscho C S Craik 《The Journal of biological chemistry》2001,276(37):34941-34947
Tryptases betaI and betaII were heterologously expressed and purified in yeast to functionally characterize the substrate specificity of each enzyme. Three positional scanning combinatorial tetrapeptide substrate libraries were used to determine the primary and extended substrate specificity of the proteases. Both enzymes have a strict primary preference for cleavage after the basic amino acids, lysine and arginine, with only a slight preference for lysine over arginine. betaI and betaII tryptase share similar extended substrate specificity, with preference for proline at P4, preference for arginine or lysine at P3, and P2 showing a slight preference for asparagine. Measurement of kinetic constants with multiple substrates designed for beta-tryptases reveal that selectivity is highly dependent on ground state substrate binding. Coupled with the functional determinants, structural determinants of tryptase substrate specificity were identified. Molecular docking of the preferred substrate sequence to the three-dimensional tetrameric tryptase structure reveals a novel extended substrate binding mode that involves interactions from two adjacent protomers, including P4 Thr-96', P3 Asp-60B' and Glu-217, and P1 Asp-189. Based on the determined substrate information, a mechanism-based tetrapeptide-chloromethylketone inhibitor was designed and shown to be a potent tryptase inhibitor. Finally, the cleavage sites of several physiologically relevant substrates of beta-tryptases show consistency with the specificity data presented here. 相似文献