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Downstream Analysis (downstream + analysis)

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Life Sciences100%

Selected Abstracts

Do marker-based paternity assignments favour heterozygous and unrelated males?

MOLECULAR ECOLOGY, Issue 9 2010
JINLIANG WANG
Abstract Genetic marker-based parentage analyses are widely applied to studies of natural populations in the fields of evolutionary biology, conservation biology and ecology. When the same markers used in a parentage analysis are used together with the inferred parentage in a downstream analysis, such as the analysis of mate choice in terms of heterozygosity or relatedness, a bias may be incurred because a subset of the genotypes are favoured in parentage assignments or non-exclusions. A previous simulation study shows that exclusion-based paternity analyses are biased in favour of heterozygous males, and males less related to the mothers than expected under random mating. In this study, I investigated the biases of genetic paternity analyses achieved by both exclusion- and likelihood-based methods, using both analytical and simulation approaches. It is concluded that while both exclusion- and likelihood-based methods can lead to biased paternity assignments or non-exclusions in favour of a subset of genotypes, the bias is not consistently towards heterozygous males or males apparently less related to mothers. Both the direction and extent of the bias depend heavily on the allele frequency distribution and the number of markers, the methods used for paternity assignments, and the estimators of relatedness. There exist important differences in the patterns of the biases between exclusion- and likelihood-based paternity analysis methods. It is concluded that the markers, except when they are highly informative to yield accurate paternity assignments or exclusions, should be split into two subsets which are used separately in the paternity and downstream analyses. [source]

Hypoxia-like effect of Cobalt Chromium alloy micro particles on fibroblasts in vitro

JOURNAL OF ORTHOPAEDIC RESEARCH, Issue 10 2010
Bernadette K. Madathil
Abstract Periprosthetic osteolysis leading to asceptic loosening remains the primary cause of failure of joint replacement. Although many inflammatory cell types have been implicated, the exact pathomechanisms of asceptic loosening have not been delineated. In the present study we have adopted a proteomic approach to elucidate the initial signals that are expressed to particulate material, using an in vitro cell culture system. Human lung fibroblasts MRC-5 were cultured with Cobalt Chromium (CoCr ASTM F-75, 1,7,µm) particles. Cells were harvested after 72,h incubation and total cellular proteins extracted for downstream analysis via 2D Gel Electrophoresis and tandem mass spectrometry using MALDI-TOF-TOF-MS. Thirteen protein spots showed greater than twofold increase, following 72,h incubation of fibroblast with CoCr particles. Four of these proteins were identified by tandem mass spectrometry. These were Annexin II, Pyruvate kinase, Triose phosphate isomerase, and N-myc downstream regulated gene 1 protein. Cobalt is a hypoxia mimicking agent and N-myc downstream regulated gene 1 protein, Triose phosphate isomerase, Pyruvate kinase, and Annexin II are important hypoxia regulated gene products that are found to be over expressed in cellular oxidative stress response. Our data indicates that exposure of fibroblast to CoCr alloy induces the transition of these cells into a hypoxia like state and oxidative stress even in normoxic culture conditions. The study reflects the possibility of the presence of a hypoxic environment in the periprosthetic tissue surrounding metallic implants. Published by Wiley Periodicals, Inc. J Orthop Res 28:1360,1367, 2010 [source]

Do marker-based paternity assignments favour heterozygous and unrelated males?

MOLECULAR ECOLOGY, Issue 9 2010
JINLIANG WANG
Abstract Genetic marker-based parentage analyses are widely applied to studies of natural populations in the fields of evolutionary biology, conservation biology and ecology. When the same markers used in a parentage analysis are used together with the inferred parentage in a downstream analysis, such as the analysis of mate choice in terms of heterozygosity or relatedness, a bias may be incurred because a subset of the genotypes are favoured in parentage assignments or non-exclusions. A previous simulation study shows that exclusion-based paternity analyses are biased in favour of heterozygous males, and males less related to the mothers than expected under random mating. In this study, I investigated the biases of genetic paternity analyses achieved by both exclusion- and likelihood-based methods, using both analytical and simulation approaches. It is concluded that while both exclusion- and likelihood-based methods can lead to biased paternity assignments or non-exclusions in favour of a subset of genotypes, the bias is not consistently towards heterozygous males or males apparently less related to mothers. Both the direction and extent of the bias depend heavily on the allele frequency distribution and the number of markers, the methods used for paternity assignments, and the estimators of relatedness. There exist important differences in the patterns of the biases between exclusion- and likelihood-based paternity analysis methods. It is concluded that the markers, except when they are highly informative to yield accurate paternity assignments or exclusions, should be split into two subsets which are used separately in the paternity and downstream analyses. [source]

Investigating lipoprotein biogenesis and function in the model Gram-positive bacterium Streptomyces coelicolor

MOLECULAR MICROBIOLOGY, Issue 4 2010
Benjamin J. Thompson
Summary Lipoproteins are a distinct class of bacterial membrane proteins that are translocated across the cytoplasmic membrane primarily by the Sec general secretory pathway and then lipidated on a conserved cysteine by the enzyme lipoprotein diacylglycerol transferase (Lgt). The signal peptide is cleaved by lipoprotein signal peptidase (Lsp) to leave the lipid-modified cysteine at the N-terminus of the mature lipoprotein. In all Gram-positive bacteria tested to date this pathway is non-essential and the lipid attaches the protein to the outer leaflet of the cytoplasmic membrane. Here we identify lipoproteins in the model Gram-positive bacterium Streptomyces coelicolor using bioinformatics coupled with proteomic and downstream analysis. We report that Streptomyces species translocate large numbers of lipoproteins out via the Tat (twin arginine translocase) pathway and we present evidence that lipoprotein biogenesis might be an essential pathway in S. coelicolor. This is the first analysis of lipoproteins and lipoprotein biogenesis in Streptomyces and provides the first evidence that lipoprotein biogenesis could be essential in a Gram-positive bacterium. This report also provides the first experimental evidence that Tat plays a major role in the translocation of lipoproteins in a specific bacterium. [source]