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101.
Background
In many studies, researchers may recruit samples consisting of independent trios and unrelated individuals. However, most of the currently available haplotype inference methods do not cope well with these kinds of mixed data sets.Methods
We propose a general and simple methodology using a mixture of weighted multinomial (MIXMUL) approach that combines separate haplotype information from unrelated individuals and independent trios for haplotype inference to the individual level.Results
The new MIXMUL procedure improves over existing methods in that it can accurately estimate haplotype frequencies from mixed data sets and output probable haplotype pairs in optimized reconstruction outcomes for all subjects that have contributed to estimation. Simulation results showed that this new MIXMUL procedure competes well with the EM-based method, i.e. FAMHAP, under a few assumed scenarios.Conclusion
The results showed that MIXMUL can provide accurate estimates similar to those haplotype frequencies obtained from FAMHAP and output the probable haplotype pairs in the most optimal reconstruction outcome for all subjects that have contributed to estimation. If available data consist of combinations of unrelated individuals and independent trios, the MIXMUL procedure can be used to estimate the haplotype frequencies accurately and output the most likely reconstructed haplotype pairs of each subject in the estimation. 相似文献102.
103.
Molecular Ecology Resources Primer Development Consortium Anderson CM Aparicio GJ Atangana AR Beaulieu J Bruford MW Cain F Campos T Cariani A Carvalho MA Chen N Chen PP Clamens AL Clark AM Coeur D'Acier A Connolly P Cordero-Rivera A Coughlan JP Cross TS David B DE Bruyn C DE Meyer M DE Ridder C Delatte H Dettori MT Downer SJ Dubreuil C Evans KJ Fan B Ferrara G Gagné A Gaillard M Gigliarelli L Giovinazzi J Gomez DR Grünwald NJ Hansson B Huotari T Jank L Jousselin E Jungmann L Kaczmarek ME 《Molecular ecology resources》2010,10(3):576-579
This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross-tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mülleri, Spongilla lacustris, Geodia cydonium, Axinella sp., Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus. 相似文献
104.
Changes in Amines and Biosynthetic Enzyme Activities in p-Fluorophenylalanine Resistant and Wild Type Tobacco Cell Cultures 总被引:1,自引:1,他引:0
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The levels of free amines and the activities of their biosynthetic enzymes were measured in a p-fluorophenylalanine resistant Nicotiana tabacum L. cv Xanthi cell line (TX4) which accumulates high levels of cinnamoylamides, and a wild type cell line (TX1). Putrescine in TX1 and spermidine in TX1 and TX4 increased 4-fold by day 4 but declined by day 8 of the culture period. Spermine levels were consistently low, while tyramine was not found in TX1 until day 9 when a gradual rise was noted. Ornithine decarboxylase activity in TX1 and TX4 increased slightly through day 2 but declined gradually thereafter. S-Adenosylmethionine decarboxylase activity remained low throughout the culture period, and tyrosine and arginine decarboxylases in TX1 were very low in activity. In contrast, the activities of tyrosine and arginine decarboxylases were elevated in TX4, but a 3-fold increase in tyramine after a subculture was not accompanied by a rise in tyrosine decarboxylase. However, tyrosine decarboxylase activity did increase during a second rise in tyramine levels in aging cells, late in the culture period. Although significant differences exist in amine levels, between TX4 and TX1, it is unclear how altered amine metabolism relates to p-fluorophenylalanine resistance. 相似文献
105.
The reversible association of a low molecular weight hemolymph protein (mol wt 20,000 estimated by SDS-polyacrylamide gel electrophoresis) with lipophorin, following treatment with adipokinetic hormone (AKH), was demonstrated by density gradient ultracentrifugation and by specific precipitation of lipophorin from the hemolymph of resting and AKH-injected locusts. The injection of AKH also stimulated the loading of diacylglycerol from fat body by lipophorin and resulted in a lower density lipophorin ("activated lipophorin"). The activated lipophorin particles (diameter 21.7 +/- 3.0 nm, 15.8 to 33.6 nm) were larger and more heterogeneous in size than those of resting lipophorin (14.5 +/- 1.6 nm, 11.9 to 19.2 nm). A theoretical analysis based on the experimental data (e.g., density gradient profile, electron microscopic observation, and diacylglycerol content) suggests that very large lipophorin particles result from intermolecular fusion of the lipophorin molecules that are activated by AKH. Attempts to demonstrate the effect of AKH on the structure of lipophorin, in vitro, were unsuccessful. 相似文献
106.
Repression of Phenolic Acid-Synthesizing Enzymes and Its Relation to Iron Uptake in Bacillus subtilis 总被引:8,自引:8,他引:0
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Excretion of the metal-chelating phenolic acid, 2,3-dihydroxybenzoate, by a tryptophan-requiring strain (M-13) of Bacillus subtilis was inversely proportional to the iron added to the medium. Addition of iron as the ferric chelates of two secondary hydroxamates (ferri-schizokinen and Desferal) markedly reduced excretion. Synthesis of 2,3-dihydroxybenzoate from chorismate by extracts of B. subtilis M-13, grown in low-iron medium, was unaltered by additions of FeSO(4), FeCl(3), ferrischizokinen, 2,3-dihydroxybenzoate, the 2,3-dihydroxybenzoate-iron complex, or by extracts of cells grown in high-iron medium (which contained no demonstrable 2,3-dihydroxybenzoate-synthesizing activity) to the extracts of "low-iron cells." Iron control seemed to involve repression of synthesis of the enzymes in the 2,3-dihydroxybenzoate pathway. Both ferri-schizokinen and 2,3-dihydroxybenzoate plus iron enhanced considerably the otherwise minimal repressive effects of iron at low concentrations. Ferri-schizokinen delayed derepression of the pathway in B. subtilis M-13, and reduced its rate of synthesis after derepression. Addition of FeSO(4) to derepressed cells of B. subtilis M-13 halted synthesis of the enzymes after a lag period. The effect of the ferric hydroxamates was related to the capacity of B. subtilis M-13 to incorporate (59)Fe(3+) from Desferal-(59)Fe(3+). Cellular accumulation of (59)Fe(3+) from Desferal-(59)Fe(3+) after 20 min was nearly double that incorporated from (59)FeCl(3). 相似文献
107.
Gold salts and phenylbutazone selectively inhibit the synthesis of PGF2α and PGE2 respectively. Lowered production of one prostaglandin species is accompanied by an increased production of the other. Selective inhibition by these drugs was observed in the presence of adrenaline, reduced glutathione and copper sulphate under conditions when most anti-inflammatory compounds inhibited PGE2 and PGF2α syntheses equally. It is postulated that selective inhibitors may have a different mode of action in vivo and beneficial effects may be related to the endogenous ratio of PGE to PGF required for normal function. 相似文献
108.
Beef heart cytochrome c oxidase has been resolved into seven subunits by electrophoresis in highly cross-linked gels containing urea and sodium dodecyl sulfate. The molecular weights of the polypeptides are estimated to be I, 35 400; II, 24 100; III, 21 000; IV, 16 800; V, 12 400; VI, 8200; and VII, 4400. It has been shown that subunits II and III can coelectrophorese on standard sodium dodecyl sulfate-polyacrylamide gels and appear as a single component with an apparent molecular weight of 22 500. This accounts for previous reports that the beef heart enzyme contains only six subunits. Amino acid analysis of the isolated subunits I, II, and III revealed that they have polarities of 35.5, 44.7, and 39.9%, respectively. All three subunits have an extremely high leucine content and a low percentage of basic amino acids relative to subunits IV-VII. The size, number, and properties of subunits in the beef heart cytochrome c oxidase complex suggest that it has essentially the same subunit structure as the complexes isolated from Saccharomyces cerevisiae and Neurospora crassa. 相似文献
109.
Cilia and flagella are rare in nongerminal tissues of anthropods, and are generally thought to be restricted to sperm and sensory cells in insects (2). Whitten (5) has reported the presence of kinetosomes at the base of mitotrichia in the dipteran fly Sarcophaga bullata, but reports no evidence of the organization of fibrous elements characteristic of cilia and or flagella. During an ultrastructural analysis of morphogenesis of the colleterial gland of the silk moth Hyalophora cecropia, we found the first example of paired flagella associated with an insect secretory cell. These structures are also unusual in that they serve a temporary role in morphogenesis and subsequently disappear at the terminal stages of differentiation. 相似文献
110.
Lopez JV; Culver M; Stephens JC; Johnson WE; O'Brien SJ 《Molecular biology and evolution》1997,14(3):277-286
Differential rates of nucleotide substitution among different gene segments
and between distinct evolutionary lineages is well documented among
mitochondrial genes and is likely a consequence of locus-specific selective
constraints that delimit mutational divergence over evolutionary time. We
compared sequence variation of 18 homologous loci (15 coding genes and 3
parts of the control region) among 10 mammalian mitochondrial DNA genomes
which allowed us to describe different mitochondrial evolutionary patterns
and to produce an estimation of the relative order of gene divergence. The
relative rates of divergence of mitochondrial DNA genes in the family
Felidae were estimated by comparing their divergence from homologous
counterpart genes included in nuclear mitochondrial DNA (Numt, pronounced
"new might"), a genomic fossil that represents an ancient transfer of 7.9
kb of mitochondrial DNA to the nuclear genome of an ancestral species of
the domestic cat (Felis catus). Phylogenetic analyses of mitochondrial
(mtDNA) sequences with multiple outgroup species were conducted to date the
ancestral node common to the Numt and the cytoplasmic (Cymt) mtDNA genes
and to calibrate the rate of sequence divergence of mitochondrial genes
relative to nuclear homologous counterparts. By setting the fastest
substitution rate as strictly mutational, an empirical "selective
retardation index" is computed to quantify the sum of all constraints,
selective and otherwise, that limit sequence divergence of mitochondrial
gene sequences over time.
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