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21.
Evolutionary rates for tuf genes in endosymbionts of aphids 总被引:5,自引:1,他引:4
The gene encoding elongation factor Tu (tuf) in aphid endosymbionts (genus
Buchnera) evolves at rates of 1.3 x 10(-10) to 2.5 x 10(-10) nonsynonymous
substitutions and 3.9 x 10(-9) to 8.0 x 10(-9) synonymous substitutions per
position per year. These rates, which are at present among the most
reliable substitution rates for protein-coding genes of bacteria, have been
obtained by calibrating the nodes in the phylogenetic tree produced from
the Buchnera EF-Tu sequences using divergence times for the corresponding
ancestral aphid hosts. We also present data suggesting that the rates of
nonsynonymous substitutions are significantly higher in the endosymbiont
lineages than in the closely related free-living bacteria Escherichia coli
and Salmonella typhimurium. Synonymous substitution rates for Buchnera
approximate estimated mutation rates for E. coli and S. typhimurium, as
expected if synonymous changes act as neutral mutations in Buchnera. We
relate the observed differences in substitution frequencies to the absence
of selective codon preferences in Buchnera and to the influence of Muller's
ratchet on small asexual populations.
相似文献
22.
Chuka Okoli Selvaraj Sengottaiyan N. Arul Murugan Asalapuram R. Pavankumar Hans Ågren Gunaratna Kuttuva Rajarao 《Journal of biomolecular structure & dynamics》2013,31(10):1182-1190
The design of novel protein–nanoparticle hybrid systems has applications in many fields of science ranging from biomedicine, catalysis, water treatment, etc. The main barrier in devising such tool is lack of adequate information or poor understanding of protein–ligand chemistry. Here, we establish a new strategy based on computational modeling for protein and precursor linkers that can decorate the nanoparticles. Moringa oleifera (MO2.1) seed protein that has coagulation and antimicrobial properties was used. Superparamagnetic nanoparticles (SPION) with precursor ligands were used for the protein–ligand interaction studies. The molecular docking studies reveal that there are two binding sites, one is located at the core binding site; tetraethoxysilane (TEOS) or 3-aminopropyl trimethoxysilane (APTES) binds to this site while the other one is located at the side chain residues where trisodium citrate (TSC) or Si60 binds to this site. The protein–ligand distance profile analysis explains the differences in functional activity of the decorated SPION. Experimentally, TSC-coated nanoparticles showed higher coagulation activity as compared to TEOS- and APTES-coated SPION. To our knowledge, this is the first report on in vitro experimental data, which endorses the computational modeling studies as a powerful tool to design novel precursors for functionalization of nanomaterials; and develop interface hybrid systems for various applications. 相似文献
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Paulo C Carvalho Juliana SG Fischer Emily I Chen John R YatesIII Valmir C Barbosa 《BMC bioinformatics》2008,9(1):316
Background
A goal of proteomics is to distinguish between states of a biological system by identifying protein expression differences. Liu et al. demonstrated a method to perform semi-relative protein quantitation in shotgun proteomics data by correlating the number of tandem mass spectra obtained for each protein, or "spectral count", with its abundance in a mixture; however, two issues have remained open: how to normalize spectral counting data and how to efficiently pinpoint differences between profiles. Moreover, Chen et al. recently showed how to increase the number of identified proteins in shotgun proteomics by analyzing samples with different MS-compatible detergents while performing proteolytic digestion. The latter introduced new challenges as seen from the data analysis perspective, since replicate readings are not acquired. 相似文献25.
Stringent microbial cell barriers limit the application of many substances in research and therapeutics. Carrier peptides that penetrate or translocate across cell membranes may help overcome this problem. To assess peptide-mediated delivery into two yeast and three bacterial species, a range of cell penetrating and signal peptide sequences were fused to green fluorescent protein (GFP), expressed in Escherichia coli, partially purified and incubated with growing cells. Fluorescence microscopy indicated several peptides that mediated delivery. In particular, VLTNENPFSDP efficiently delivered GFP into Candida albicans and Staphylococcus aureus, while YKKSNNPFSD was most efficient for Bacillus subtilis and CFFKDEL for Escherichia coli. Carrier peptides may improve delivery of certain large molecular mass molecules into microorganisms for research and therapeutic applications. 相似文献
26.
John E Moore Adrienne Shaw Jennifer L Howard James SG Dooley J Stuart Elborn 《Annals of clinical microbiology and antimicrobials》2004,3(1):1-5
Background
Although various hematologic abnormalities are seen in tuberculosis, immune thrombocytopenic purpura is a rare event.Case Presentation
We report a case of a 29 year-old male who was presented with immune thrombocytopenia-induced hemoptysis, macroscopic hematuria and generalized petechiae. The patient was found to have clinical, microbiological and radiological evidence of active pulmonary tuberculosis. The immune thrombocytopenic purpura was successfully treated with anti-tuberculous drugs combined with corticosteroids and high dose immune globulin therapy.Conclusion
Immune thrombocytopenic purpura can be one of the hematological manifestations of tuberculosis which has a global prevalence with increasing incidence secondary to HIV infection. 相似文献27.
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28.
Gabriela G Loots Patrick SG Chain Shalini Mabery Amy Rasley Emilio Garcia Ivan Ovcharenko 《BMC bioinformatics》2006,7(1):307-8
Background
There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility. 相似文献29.
SG Bradley F Marciano-Cabral 《Journal of industrial microbiology & biotechnology》1996,17(3-4):314-321
Amoeboid organisms are phylogenetically diverse, some being more closely related to plants or metazoans than to each other. Amoeboid organisms are ecologically successful, having been isolated on all continents, including Antarctica, as well as being the main predators controlling bacterial populations in soil. The classification of these organisms has historically relied upon morphological characteristics. The application of electron microscopy, comparison of enzymic profiles after electrophoretic separation, and analysis of nucleic acid fractions have provided reliable bases for classifying amoeboid organisms. The extent of diversity of these organisms has been recognized, as methods to detect, culture, characterize and identify them has increased. It is reasonable to anticipate that the current 40 000 species of protists will increase substantially as amoeboid organisms are cultivated from poorly accessible niches and from extreme environs. 相似文献
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