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31.
Background
Binding of serum components by surface M-related proteins, encoded by the emm genes, in streptococci constitutes a major virulence factor in this important group of organisms. The present study demonstrates fibrinogen binding by S. iniae, a Lancefield non-typeable pathogen causing devastating fish losses in the aquaculture industry and an opportunistic pathogen of humans, and identifies the proteins involved and their encoding genes. 相似文献32.
Evolution at the tip and base of the X chromosome in an African population of Drosophila melanogaster 总被引:1,自引:0,他引:1
Hitchhiking effects of advantageous mutations have been invoked to explain
reduced polymorphism in regions of low crossing-over in Drosophila. Besides
reducing DNA heterozygosity, hitchhiking effects should produce strong
linkage disequilibrium and a frequency spectrum skewed toward an excess of
rare polymorphisms (compared to the neutral expectation). We measured DNA
polymorphism in a Zimbabwe population of D. melanogaster at three loci,
yellow, achaete, and suppressor of forked, located in regions of reduced
crossing-over. Similar to previously published surveys of these genomic
regions in other populations, we observed low levels of nucleotide
variability. However, the frequency spectrum was compatible with a neutral
model, and there was abundant evidence for recombination in the history of
the yellow and ac genes. Thus, some aspects of the data cannot be accounted
for by a simple hitchhiking model. An alternative hypothesis, background
selection, might be compatible with the observed patterns of linkage
disequilibrium and the frequency spectrum. However, this model cannot
account for the observed reduction in nucleotide heterozygosity. Thus,
there is currently no satisfactory theoretical model for the data from the
tip and base of the X chromosome in D. melanogaster.
相似文献
33.
Tempo and mode of concerted evolution in the L1 repeat family of mice 总被引:10,自引:0,他引:10
Martin SL; Voliva CF; Hardies SC; Edgell MH; Hutchison CA d 《Molecular biology and evolution》1985,2(2):127-140
A 300-bp DNA sequence has been determined for 30 (10 from each of three
species of mice) random isolates of a subset of the long interspersed
repeat family L1. From these data we conclude that members of the L1 family
are evolving in concert at the DNA sequence level in Mus domesticus, Mus
caroli, and Mus platythrix. The mechanism responsible for this phenomenon
may be either duplicative transposition, gene conversion, or a combination
of the two. The amount of intraspecies divergence averages 4.4%, although
between species base substitutions accumulate at the rate of approximately
0.85%/Myr to a maximum divergence of 9.1% between M. platythrix and both M.
domesticus and M. caroli. Parsimony analysis reveals that the M. platythrix
L1 family has evolved into a distinct clade in the 10-12 Myr since M.
platythrix last shared a common ancestor with M. domesticus and M. caroli.
The parsimony tree also provides a means to derive the average half-life of
L1 sequences in the genome. The rates of gain and loss of individual copies
of L1 were estimated to be approximately equal, such that approximately
one-half of them turn over every 3.3 Myr.
相似文献
34.
Polymorphism and divergence at the 5' flanking region of the sex- determining locus, Sry, in mice 总被引:3,自引:0,他引:3
We have investigated patterns of evolution in the nonrecombining portion of
the Y chromosome in mice by comparing levels of polymorphism within Mus
domesticus with levels of divergence between M. domesticus and M. spretus.
A 1,277-bp fragment of noncoding sequence flanking the sex determining
locus (Sry) was PCR amplified, and 1,063 bases were sequenced and compared
among 20 M. domesticus and 1 M. spretus. Two polymorphic base substitutions
and two polymorphic insertion/deletion sites were identified within M.
domesticus; nucleotide diversity was estimated to be 0.1%. Divergence
between M. domesticus and M. spretus for this region (1.9%) was slightly
lower than the average divergence of single-copy nuclear DNA for these
species. Comparison of levels of polymorphism and divergence at Sry with
levels of polymorphism and divergence in the mitochondrial DNA control
region provided no evidence of a departure from the expectations of neutral
molecular evolution. These findings are consistent with the presumed lack
of function for much of the Y chromosome.
相似文献
35.
We describe a new scaffold-free three-dimensional (3D) cell culture model using cholesteryl ester based lyotropic liquid crystal (LC) substrates. Keratinocytes were deposited randomly on the LC surface where they self-assembled into 3D microtissues or keratinospheroids. The cell density required to form spheroids was optimized. We investigated cell viability using dead/live cell assays. The adhesion characteristics of cells within the microtissues were determined using histological sectioning and immunofluorescence staining. Fourier transform infrared spectroscopy (FTIR) was used to characterize the biochemistry of the keratinospheroids. We found that both cells and microtissues could migrate on the LC surface. The viability study indicated approximately 80% viability of cells in the microtissues up to 20 days of culture. Strong intercellular adhesion was observed in the stratification of the multi-layered microspheroids using field emission-scanning electron microscopy (FE-SEM) and histochemical staining. The cytoskeleton and vinculins of the cells in the microtissues were expressed diffusely, but the microtissues were enriched with lipids and nucleic acids, which indicates close resemblance to the conditions in vivo. The basic 3D culture model based on LC may be used for cell and microtissue migration studies in response to cytochemical treatment. 相似文献
36.
37.
Raffael AC Oliveira Ricardo VM Almeida Márcia DA Dantas Felipe N Castro Jo?o Paulo MS Lima Daniel CF Lanza 《BMC bioinformatics》2014,15(1)
Background
The PCR technique and its variations have been increasingly used in the clinical laboratory and recent advances in this field generated new higher resolution techniques based on nucleic acid denaturation dynamics. The principle of these new molecular tools is based on the comparison of melting profiles, after denaturation of a DNA double strand. Until now, the secondary structure of single-stranded nucleic acids has not been exploited to develop identification systems based on PCR. To test the potential of single-strand RNA denaturation as a new alternative to detect specific nucleic acid variations, sequences from viruses of the Totiviridae family were compared using a new in silico melting curve approach. This family comprises double-stranded RNA virus, with a genome constituted by two ORFs, ORF1 and ORF2, which encodes the capsid/RNA binding proteins and an RNA-dependent RNA polymerase (RdRp), respectively.Results
A phylogenetic tree based on RdRp amino acid sequences was constructed, and eight monophyletic groups were defined. Alignments of RdRp RNA sequences from each group were screened to identify RNA regions with conserved secondary structure. One region in the second half of ORF2 was identified and individually modeled using the RNAfold tool. Afterwards, each DNA or RNA sequence was denatured in silico using the softwares MELTSIM and RNAheat that generate melting curves considering the denaturation of a double stranded DNA and single stranded RNA, respectively. The same groups identified in the RdRp phylogenetic tree were retrieved by a clustering analysis of the melting curves data obtained from RNAheat. Moreover, the same approach was used to successfully discriminate different variants of Trichomonas vaginalis virus, which was not possible by the visual comparison of the double stranded melting curves generated by MELTSIM.Conclusion
In silico analysis indicate that ssRNA melting curves are more informative than dsDNA melting curves. Furthermore, conserved RNA structures may be determined from analysis of individuals that are phylogenetically related, and these regions may be used to support the reconstitution of their phylogenetic groups. These findings are a robust basis for the development of in vitro systems to ssRNA melting curves detection.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-243) contains supplementary material, which is available to authorized users. 相似文献38.
Ying J Nie Mo Y Mok Godfrey CF Chan Albert W Chan Ou Jin Sushma Kavikondala Albert KW Lie Chak S Lau 《Arthritis research & therapy》2010,12(3):R91
Introduction
Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by autoreactive T and B cells, which are believed to be secondary to deficient dendritic cells (DCs). However, whether DC abnormalities occur during their development in the bone marrow (BM) or in the periphery is not known. 相似文献39.
Managing agricultural phosphorus for water quality protection: principles for progress 总被引:1,自引:0,他引:1
Peter J. A. Kleinman Andrew N. Sharpley Richard W. McDowell Don N. Flaten Anthony R. Buda Liang Tao Lars Bergstrom Qing Zhu 《Plant and Soil》2011,349(1-2):169-182
Background
The eutrophication of aquatic systems due to diffuse pollution of agricultural phosphorus (P) is a local, even regional, water quality problem that can be found world-wide.Scope
Sustainable management of P requires prudent tempering of agronomic practices, recognizing that additional steps are often required to reduce the downstream impacts of most production systems.Conclusions
Strategies to mitigate diffuse losses of P must consider chronic (edaphic) and acute, temporary (fertilizer, manure, vegetation) sources. Even then, hydrology can readily convert modest sources into significant loads, including via subsurface pathways. Systemic drivers, particularly P surpluses that result in long-term over-application of P to soils, are the most recalcitrant causes of diffuse P loss. Even in systems where P application is in balance with withdrawal, diffuse pollution can be exacerbated by management systems that promote accumulation of P within the effective layer of effective interaction between soils and runoff water. Indeed, conventional conservation practices aimed at controlling soil erosion must be evaluated in light of their ability to exacerbate dissolved P pollution. Understanding the opportunities and limitations of P management strategies is essential to ensure that water quality expectations are realistic and that our beneficial management practices are both efficient and effective. 相似文献40.
Mattia CF Prosperi Luciano Prosperi Alessandro Bruselles Isabella Abbate Gabriella Rozera Donatella Vincenti Maria Carmela Solmone Maria Rosaria Capobianchi Giovanni Ulivi 《BMC bioinformatics》2011,12(1):5