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1.
2.
Borrelia burgdorferi is a spirochete pathogen transmitted among warm-
blooded hosts by ixodid ticks. Frequency-dependent selection for variant
outer-surface proteins might be expected to arise in this species, since
rare variants are more likely to avoid immune surveillance in previously
infected hosts. We sequenced the OspA and OspB genes of nine North American
strains and compared them with nine strains previously described. For each
gene, the mean number of synonymous substitutions per synonymous site and
the mean number of nonsynonymous substitutions per nonsynonymous site show
only a twofold excess of silent mutations. Synonymous rates vary widely
along the OspB protein. Some regions show a significant excess of silent
substitutions, while divergence in other regions is constrained by biased
base composition or selection. The presence, in antigenically important
regions of the protein, of significant variation among strains, as well as
evidence for recombination among strains, should be considered in attempts
to develop vaccines against this disease.
相似文献
3.
Oliver JL Carpena P Román-Roldán R Mata-Balaguer T Mejías-Romero A Hackenberg M Bernaola-Galván P 《Gene》2002,300(1-2):117-127
The human genome is a mosaic of isochores, which are long DNA segments (300 kbp) relatively homogeneous in G+C. Human isochores were first identified by density-gradient ultracentrifugation of bulk DNA, and differ in important features, e.g. genes are found predominantly in the GC-richest isochores. Here, we use a reliable segmentation method to partition the longest contigs in the human genome draft sequence into long homogeneous genome regions (LHGRs), thereby revealing the isochore structure of the human genome. The advantages of the isochore maps presented here are: (1) sequence heterogeneities at different scales are shown in the same plot; (2) pair-wise compositional differences between adjacent regions are all statistically significant; (3) isochore boundaries are accurately defined to single base pair resolution; and (4) both gradual and abrupt isochore boundaries are simultaneously revealed. Taking advantage of the wide sample of genome sequence analyzed, we investigate the correspondence between LHGRs and true human isochores revealed through DNA centrifugation. LHGRs show many of the typical isochore features, mainly size distribution, G+C range, and proportions of the isochore classes. The relative density of genes, Alu and long interspersed nuclear element repeats and the different types of single nucleotide polymorphisms on LHGRs also coincide with expectations in true isochores. Potential applications of isochore maps range from the improvement of gene-finding algorithms to the prediction of linkage disequilibrium levels in association studies between marker genes and complex traits. The coordinates for the LHGRs identified in all the contigs longer than 2 Mb in the human genome sequence are available at the online resource on isochore mapping: http://bioinfo2.ugr.es/isochores. 相似文献
4.
Leonhardt A Glaser A Wegmann M Hackenberg R Nüsing RM 《Prostaglandins, leukotrienes, and essential fatty acids》2003,69(5):307-313
Prostanoids, especially prostaglandin (PG) E(2), are important mediators of uterine relaxation and contractions during gestation and parturition. Inhibitors of PG formation as well as PG analogues are used to modulate uterine tonus. So far, only limited data are available regarding the expression of prostanoid receptors in human pregnant myometrium. In the present study, the expression of the receptors for PGE(2) (EP1, EP2, EP3, EP4), PGF(2alpha) (FP), prostacyclin (IP), and thromboxane A(2) (TP) in human pregnant myometrium was studied by RT-PCR, in situ hybridization and immunohistochemistry. Myometrial tissue was obtained from five women at term and not in labour and from two women who delivered preterm. Tissue specimens were excised from the upper edge of the transverse lower uterine segment incision. In all tissues analysed, EP1, EP2, EP3, EP4, FP, TP and IP receptor mRNA and protein was detected. mRNA expression for PGD(2) (DP) receptor was not detected in the majority of tissue specimens. EP1, EP2, EP4, IP, TP and FP receptor protein was detected on myometrial smooth muscle cells, whereas EP3 receptor protein was only expressed by stromal and endothelial cells. In situ hybridization experiments yielded similar results. The expression of the EP2 receptor mRNA was inversely related to gestational age. We suggest that the contractile effect of PGE(2) at term is probably mediated directly by the EP1 receptor expressed in myometrial smooth muscle cells and indirectly by the EP3 receptor expressed in stromal cells and a decrease in EP2 receptor expression. 相似文献
5.
Michael Hackenberg Pedro Carpena Pedro Bernaola-Galván Guillermo Barturen ángel M Alganza José L Oliver 《Algorithms for molecular biology : AMB》2011,6(1):2
Background
Many k-mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statistically comprehensible way. The detection of clustering often relies on densities and sliding-window approaches or arbitrarily chosen distance thresholds. 相似文献6.
Michael Hackenberg Christopher Previti Pedro Luis Luque-Escamilla Pedro Carpena José Martínez-Aroza José L Oliver 《BMC bioinformatics》2006,7(1):446-13
Background
Despite their involvement in the regulation of gene expression and their importance as genomic markers for promoter prediction, no objective standard exists for defining CpG islands (CGIs), since all current approaches rely on a large parameter space formed by the thresholds of length, CpG fraction and G+C content. 相似文献7.
8.
Monitoring on the Lowveld reaches of the Olifants River, Limpopo River System, and its Steelpoort, Blyde, Klaserie and Selati tributaries was initiated in 2009. Analysis of the 2009–2015 data from four Olifants River sites showed deterioration in the river’s ecological condition between where it enters the Lowveld and where it enters the Kruger National Park, with a slight recovery within the Kruger National Park. Physico-chemical, aquatic macroinvertebrate and fish data collected in 2009–2015 at six sites on the Steelpoort, Blyde, Klaserie and Selati tributaries of the Olifants River corroborated the ecological condition of these tributaries. The Selati was the most polluted and was in a critically modified condition, whereas the Klaserie and Steelpoort were in fair condition and the Blyde was in good condition. The Selati appeared to have a significant negative impact on the water quality, macroinvertebrates and fish of the Olifants River within the Kruger National Park. 相似文献
9.
Martin Sturm Michael Hackenberg David Langenberger Dmitrij Frishman 《BMC bioinformatics》2010,11(1):292