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131.
132.
A bioinformatic strategy to rapidly characterize cDNA libraries 总被引:3,自引:0,他引:3
133.
Alignment algorithms can be used to infer a relationship between sequences when the true relationship is unknown. Simple alignment algorithms use a cost function that gives a fixed cost to each possible point mutation-mismatch, deletion, insertion. These algorithms tend to find optimal alignments that have many small gaps. It is more biologically plausible to have fewer longer gaps rather than many small gaps in an alignment. To address this issue, linear gap cost algorithms are in common use for aligning biological sequence data. More reliable inferences are obtained by aligning more than two sequences at a time. The obvious dynamic programming algorithm for optimally aligning k sequences of length n runs in O(n(k)) time. This is impractical if k>/=3 and n is of any reasonable length. Thus, for this problem there are many heuristics for aligning k sequences, however, they are not guaranteed to find an optimal alignment. In this paper, we present a new algorithm guaranteed to find the optimal alignment for three sequences using linear gap costs. This gives the same results as the dynamic programming algorithm for three sequences, but typically does so much more quickly. It is particularly fast when the (three-way) edit distance is small. Our algorithm uses a speed-up technique based on Ukkonen's greedy algorithm (Ukkonen, 1983) which he presented for two sequences and simple costs. 相似文献
134.
MARTINA VYSKOILOV MARKTA ONDRAKOV ANDREA IMKOV JEAN‐FRANOIS MARTIN 《Molecular ecology resources》2007,7(4):701-704
Fourteen polymorphic microsatellites were isolated from Neogobius kessleri, a benthic fish of Ponto‐Caspian origin which has been recently introduced into the Middle and Upper Danube River. Number of alleles and heterozygosity per locus in a sample of 32 fish individuals ranged from two to four and from 0.13 to 0.75, respectively. These primers will be useful in determining the population structure of N. kessleri. In addition, successful cross‐amplification was obtained for four related species, N. melanostomus, N. fluviatilis, N. gymnotrachelus and Proterorhinus marmoratus. These microsatellite loci may be useful for the evaluation of the origin of non‐native goby populations. 相似文献
135.
Bas Brinkhof Helena TA van Tol Marian JA Groot Koerkamp Frank M Riemers Sascha G IJzer Kaveh Mashayekhi Henk P Haagsman Bernard AJ Roelen 《BMC genomics》2015,16(1)
Background
Genes and signalling pathways involved in pluripotency have been studied extensively in mouse and human pre-implantation embryos and embryonic stem (ES) cells. The unsuccessful attempts to generate ES cell lines from other species including cattle suggests that other genes and pathways are involved in maintaining pluripotency in these species. To investigate which genes are involved in bovine pluripotency, expression profiles were generated from morula, blastocyst, trophectoderm and inner cell mass (ICM) samples using microarray analysis. As MAPK inhibition can increase the NANOG/GATA6 ratio in the inner cell mass, additionally blastocysts were cultured in the presence of a MAPK inhibitor and changes in gene expression in the inner cell mass were analysed.Results
Between morula and blastocyst 3,774 genes were differentially expressed and the largest differences were found in blastocyst up-regulated genes. Gene ontology (GO) analysis shows lipid metabolic process as the term most enriched with genes expressed at higher levels in blastocysts. Genes with higher expression levels in morulae were enriched in the RNA processing GO term. Of the 497 differentially expressed genes comparing ICM and TE, the expression of NANOG, SOX2 and POU5F1 was increased in the ICM confirming their evolutionary preserved role in pluripotency. Several genes implicated to be involved in differentiation or fate determination were also expressed at higher levels in the ICM. Genes expressed at higher levels in the ICM were enriched in the RNA splicing and regulation of gene expression GO term. Although NANOG expression was elevated upon MAPK inhibition, SOX2 and POU5F1 expression showed little increase. Expression of other genes in the MAPK pathway including DUSP4 and SPRY4, or influenced by MAPK inhibition such as IFNT, was down-regulated.Conclusion
The data obtained from the microarray studies provide further insight in gene expression during bovine embryonic development. They show an expression profile in pluripotent cells that indicates a pluripotent, epiblast-like state. The inability to culture ICM cells as stem cells in the presence of an inhibitor of MAPK activity together with the reported data indicates that MAPK inhibition alone is not sufficient to maintain a pluripotent character in bovine cells.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1448-x) contains supplementary material, which is available to authorized users. 相似文献136.
A method to detect and quantify curcumin and two curcuminoid metabolites in biological matrices, including mouse serum and mouse lung cell cultures, was developed. Standard curves between 0.04 and 10.00 nmol curcumin were prepared in serum, giving correlation coefficients of 0.94-0.99. Alcoholic extraction, concentration, and addition of dilute hydrochloric acid to stabilize the curcumin were essential to the reproducibility of the protocol. Untreated and curcumin-treated mouse lung fibrotic and nonfibrotic cell cultures were analyzed by matrix-assisted laser desorption ionization time of flight mass spectrometry utilizing this method. Curcumin uptake was calculated to be 7.0-11.6% for the saline-treated cells and 7.4-11.9% for the bleomycin-treated cultures. Curcumin was not detected in untreated cells. Two additional peaks (m/z=399 and 429) were observed in the curcumin-treated cells. These may be curcumin-derived products resulting from HCl treatment of the tissue samples. 相似文献
137.
S Avidon SM Marr TA Bellingan KJ Esler OLF Weyl 《African Journal of Aquatic Science》2018,43(3):313-318
We evaluated the impact of non-native rainbow trout Oncorhynchus mykiss on a population of endemic Cedarberg ghost frog Heleophryne depressa in the upper Krom River (Olifants-Doring River Catchment, Cape Fold Ecoregion). We compared H. depressa abundance (using kick-sampling and underwater video analysis) and environmental conditions between sites above and below a waterfall that marks the upper distribution limit of O. mykiss. Heleophryne depressa abundance was significantly greater above the waterfall than that below it, and, because there was no significant difference in measured environmental variables, O. mykiss presence is identified as the most likely explanation for the observed decrease in H. depressa abundance. 相似文献
138.
Distribution and conservation of mobile elements in the genus Drosophila 总被引:13,自引:1,他引:12
Essentially nothing is known of the origin, mode of transmission, and
evolution of mobile elements within the genus Drosophila. To better
understand the evolutionary history of these mobile elements, we examined
the distribution and conservation of homologues to the P, I, gypsy, copia,
and F elements in 34 Drosophila species from three subgenera. Probes
specific for each element were prepared from D. melanogaster and hybridized
to genomic DNA. Filters were washed under conditions of increasing
stringency to estimate the similarity between D. melanogaster sequences and
their homologues in other species. The I element homologues show the most
limited distribution of all elements tested, being restricted to the
melanogaster species group. The P elements are found in many members of the
subgenus Sophophora but, with the notable exception of D. nasuta, are not
found in the other two subgenera. Copia-, gypsy-, and F-element homologues
are widespread in the genus, but their similarity to the D. melanogaster
probe differs markedly between species. The distribution of copia and P
elements and the conservation of the gypsy and P elements is inconsistent
with a model that postulates a single ancient origin for each type of
element followed by mating-dependent transmission. The data can be
explained by horizontal transmission of mobile elements between
reproductively isolated species.
相似文献
139.
Intrinsic tryptophan fluorescence in red cell ghost membranes labeled with N-ethylmaleimide (N-EM) is quenched in a dose-dependent manner by the organic mercurial p-chloromercuribenzene sulfonate (p-CMBS). Fluorescence lifetime analysis shows that quenching occurs by a static mechanism. Binding of p-CMBS occurs by a rapid (less than 5 s) biomolecular association (dissociation constant K1 = 1.8 mM) followed by a slower unimolecular transition with forward rate constant k2 = 0.015 s-1 and reverse rate constant k-2 = 0.0054 s-1. Analysis of the temperature dependence of k2 gives delta H = 6.5 kcal/mol and delta S = -21 eu. The mercurial compounds p-chloromercuribenzoic acid, p-aminophenylmercuric acetate, and mercuric chloride quench red cell tryptophan fluorescence by the same mechanism as p-CMBS does; the measured k2 value was the same for each compound, whereas K1 varied. p-CMBS also quenches the tryptophan fluorescence in vesicles reconstituted with purified band 3, the red cell anion exchange protein, in a manner similar to that in ghost membranes. These experiments define a mercurial binding site on band 3 in ghosts treated with N-EM and establish the binding mechanism to this site. The characteristics of this p-CMBS binding site on band 3 differ significantly from those of the p-CMBS binding site involved in red cell water and urea transport inhibition. 相似文献
140.
The Opa Reservoir, established for water supply to the Obafemi Awolowo University community, over the years has received direct linkage to township drains as a result of the widening and dredging of its river channels. The current study aimed at documenting monthly heavy metal loads at its riverine, transition and lacustrine zones in 2012–2013. Most of the heavy metals, analysed using an atomic absorption spectrophotometer, occurred within wide ranges, with coefficients of variation ranging from 60% to 300%, although the differences in heavy metal loads between the different zones were statistically insignificant at both the surface and bottom levels. The overall order of dominance of the metals was Ni > Cu > Fe > Zn > Cd = Cr > Pb, with nickel concentration being very high throughout. Heavy metal total mean concentration was higher during the rainy season (1.889 mg l?1) than the dry season (1.503 mg l?1) irrespective of sampling sites, having highly significant seasonal differences (p < 0.001) in Ni, Cd, Fe and Cu concentrations. The mean concentrations of Zn (0.074 mg l?1), Fe (0.176 mg l?1), Cu (0.507 mg l?1) and Pb (0.004 mg l?1) were within the WHO acceptable limit. However, the recorded levels of toxic elements Cd (0.031 mg l?1) and Ni (0.905 mg l?1) pose potential health risk to water consumers. 相似文献