580 research outputs found
Re-annotation of protein-coding genes in 10 complete genomes of Neisseriaceae family by combining similarity-based and composition-based methods.
published_or_final_versio
Identification and analysis of genomic islands in Burkholderia cenocepacia AU 1054 with emphasis on pathogenicity islands
published_or_final_versio
Resummations with renormalon effects for the hadronic vacuum polarization contribution to the muon (g-2)
The hadronic vacuum polarization contribution to the muon (g-2) value is
calculated by considering a known dispersion integral which involves the ratio. The theoretical part stemming from the region below 1.8 GeV is
the largest contribution in our approach, and is calculated by using a contour
integral involving the associated Adler function . In the resummations,
we explicitly take into account the exactly known renormalon singularity of the
leading infrared renormalon in the usual and in the modified Borel transform of
, and map further away from the origin the other renormalon
singularities by employing judiciously chosen conformal transformations. The
renormalon effect increases the predicted value of the hadronic vacuum
polarization contribution to the muon (g-2), and therefore diminishes the
difference between the recently measured and the SM/QCD-predicted value of
(g-2). It is also shown that the total QED correction to the hadronic vacuum
polarization is very small, about 0.06 percent.Comment: 16 pages, 2 eps-figures, revtex; changes in presentation; different
consideration of the (rho -> pi pi gamma) channel in the data part; as a
consequence, the results change slightl
Immunotherapy Targeting Adenosine Synthase A Decreases Severity of Staphylococcus aureus Infection in Mouse Model
published_or_final_versio
Micelles as Delivery Vehicles for Oligofluorene for Bioimaging
With the successful development of organic/polymeric light emitting diodes, many organic and polymeric fluorophores with high quantum efficiencies and optical stability were synthesized. However, most of these materials which have excellent optical properties are insoluble in water, limiting their applications in biological fields. Herein, we used micelles formed from an amino-group-containing poly(ε-caprolactone)-block-poly(ethylene glycol) (PCL-b-PEG-NH2) to incorporate a hydrophobic blue emitter oligofluorene (OF) to enable its application in biological conditions. Although OF is completely insoluble in water, it was successfully transferred into aqueous solutions with a good retention of its photophysical properties. OF exhibited a high quantum efficiency of 0.84 in a typical organic solvent of tetrahydrofuran (THF). In addition, OF also showed a good quantum efficiency of 0.46 after being encapsulated into micelles. Two cells lines, human glioblastoma (U87MG) and esophagus premalignant (CP-A), were used to study the cellular internalization of the OF incorporated micelles. Results showed that the hydrophobic OF was located in the cytoplasm, which was confirmed by co-staining the cells with nucleic acid specific SYTO 9, lysosome specific LysoTracker Red®, and mitochondria specific MitoTracker Red. MTT assay indicated non-toxicity of the OF-incorporated micelles. This study will broaden the application of hydrophobic functional organic compounds, oligomers, and polymers with good optical properties to enable their applications in biological research fields
Location and Level of Etk Expression in Neurons Are Associated with Varied Severity of Traumatic Brain Injury
Much recent research effort in traumatic brain injury (TBI) has been devoted to the discovery of a reliable biomarker correlating with severity of injury. Currently, no consensus has been reached regarding a representative marker for traumatic brain injury. In this study, we explored the potential of epithelial/endothelial tyrosine kinase (Etk) as a novel marker for TBI.TBI was induced in Sprague Dawley (SD) rats by controlled cortical impact. Brain tissue samples were analyzed by Western blot, Q-PCR, and immunofluorescence staining using various markers including glial fibrillary acidic protein, and epithelial/endothelial tyrosine kinase (Etk). Results show increased Etk expression with increased number and severity of impacts. Expression increased 2.36 to 7-fold relative to trauma severity. Significant upregulation of Etk appeared at 1 hour after injury. The expression level of Etk was inversely correlated with distance from injury site. Etk and trauma/inflammation related markers increased post-TBI, while other tyrosine kinases did not.The observed correlation between Etk level and the number of impacts, the severity of impact, and the time course after impact, as well as its inverse correlation with distance away from injury site, support the potential of Etk as a possible indicator of trauma severity
Genetic Variation of the Human α-2-Heremans-Schmid Glycoprotein (AHSG) Gene Associated with the Risk of SARS-CoV Infection
Genetic background may play an important role in the process of SARS-CoV
infection and SARS development. We found several proteins that could interact
with the nucleocapsid protein of the SARS coronavirus (SARS-CoV).
α-2-Heremans-Schmid Glycoprotein (AHSG), which is required for macrophage
deactivation by endogenous cations, is associated with inflammatory regulation.
Cytochrome P450 Family 3A (CYP4F3A) is an ω-oxidase that
inactivates Leukotriene B4 (LTB4) in human neutrophils and the liver. We
investigated the association between the polymorphisms of these two
inflammation-associated genes and SARS development. The linkage disequilibrium
(LD) maps of these two genes were built with Haploview using data on
CHB+JPT (version 2) from the HapMap. A total of ten tag SNPs were selected
and genotyped. In the Guangzhou cohort study, after adjusting for age and sex,
two AHSG SNPs and one CYP4F3 SNP were found to
be associated with SARS susceptibility: rs2248690 (adjusted odds ratio
[AOR] 2.42; 95% confidence interval [CI] 1.30-4.51);
rs4917 (AOR 1.84; 95% CI 1.02-3.34); and rs3794987 (AOR 2.01; 95%
CI 1.10–3.68). To further validate the association, the ten tag SNPs were
genotyped in the Beijing cohort. After adjusting for age and sex, only rs2248690
(AOR, 1.63; 95% CI, 1.30–2.04) was found to be associated with SARS
susceptibility. The combined analysis of the two studies confirmed tag SNP
rs2248690 in AHSG as a susceptibility variant (AOR 1.70;
95% CI 1.37–2.09). The statistical analysis of the rs2248690
genotype data among the patients and healthy controls in the HCW cohort, who
were all similarly exposed to the SARS virus, also supported the findings.
Further, the SNP rs2248690 affected the transcriptional activity of the
AHSG promoter and thus regulated the AHSG serum level.
Therefore, our study has demonstrated that the AA genotype of rs2268690, which
leads to a higher AHSG serum concentration, was significantly associated with
protection against SARS development
Gene selection for classification of microarray data based on the Bayes error
<p>Abstract</p> <p>Background</p> <p>With DNA microarray data, selecting a compact subset of discriminative genes from thousands of genes is a critical step for accurate classification of phenotypes for, e.g., disease diagnosis. Several widely used gene selection methods often select top-ranked genes according to their individual discriminative power in classifying samples into distinct categories, without considering correlations among genes. A limitation of these gene selection methods is that they may result in gene sets with some redundancy and yield an unnecessary large number of candidate genes for classification analyses. Some latest studies show that incorporating gene to gene correlations into gene selection can remove redundant genes and improve classification accuracy.</p> <p>Results</p> <p>In this study, we propose a new method, Based Bayes error Filter (BBF), to select relevant genes and remove redundant genes in classification analyses of microarray data. The effectiveness and accuracy of this method is demonstrated through analyses of five publicly available microarray datasets. The results show that our gene selection method is capable of achieving better accuracies than previous studies, while being able to effectively select relevant genes, remove redundant genes and obtain efficient and small gene sets for sample classification purposes.</p> <p>Conclusion</p> <p>The proposed method can effectively identify a compact set of genes with high classification accuracy. This study also indicates that application of the Bayes error is a feasible and effective wayfor removing redundant genes in gene selection.</p
Rapid Chromosome Evolution in Recently Formed Polyploids in Tragopogon (Asteraceae)
Polyploidy, frequently termed "whole genome duplication", is a major force in the evolution of many eukaryotes. Indeed, most angiosperm species have undergone at least one round of polyploidy in their evolutionary history. Despite enormous progress in our understanding of many aspects of polyploidy, we essentially have no information about the role of chromosome divergence in the establishment of young polyploid populations. Here we investigate synthetic lines and natural populations of two recently and recurrently formed allotetraploids Tragopogon mirus and T. miscellus (formed within the past 80 years) to assess the role of aberrant meiosis in generating chromosomal/genomic diversity. That diversity is likely important in the formation, establishment and survival of polyploid populations and species.Applications of fluorescence in situ hybridisation (FISH) to natural populations of T. mirus and T. miscellus suggest that chromosomal rearrangements and other chromosomal changes are common in both allotetraploids. We detected extensive chromosomal polymorphism between individuals and populations, including (i) plants monosomic and trisomic for particular chromosomes (perhaps indicating compensatory trisomy), (ii) intergenomic translocations and (iii) variable sizes and expression patterns of individual ribosomal DNA (rDNA) loci. We even observed karyotypic variation among sibling plants. Significantly, translocations, chromosome loss, and meiotic irregularities, including quadrivalent formation, were observed in synthetic (S(0) and S(1) generations) polyploid lines. Our results not only provide a mechanism for chromosomal variation in natural populations, but also indicate that chromosomal changes occur rapidly following polyploidisation.These data shed new light on previous analyses of genome and transcriptome structures in de novo and establishing polyploid species. Crucially our results highlight the necessity of studying karyotypes in young (<150 years old) polyploid species and synthetic polyploids that resemble natural species. The data also provide insight into the mechanisms that perturb inheritance patterns of genetic markers in synthetic polyploids and populations of young natural polyploid species
Interaction of Temperature and Light in the Development of Freezing Tolerance in Plants
Abstract Freezing tolerance is the result of a wide range
of physical and biochemical processes, such as the induction
of antifreeze proteins, changes in membrane composition,
the accumulation of osmoprotectants, and changes
in the redox status, which allow plants to function at low
temperatures. Even in frost-tolerant species, a certain period
of growth at low but nonfreezing temperatures, known
as frost or cold hardening, is required for the development
of a high level of frost hardiness. It has long been known
that frost hardening at low temperature under low light
intensity is much less effective than under normal light
conditions; it has also been shown that elevated light
intensity at normal temperatures may partly replace the
cold-hardening period. Earlier results indicated that cold
acclimation reflects a response to a chloroplastic redox
signal while the effects of excitation pressure extend
beyond photosynthetic acclimation, influencing plant
morphology and the expression of certain nuclear genes
involved in cold acclimation. Recent results have shown
that not only are parameters closely linked to the photosynthetic
electron transport processes affected by light
during hardening at low temperature, but light may also
have an influence on the expression level of several other
cold-related genes; several cold-acclimation processes can
function efficiently only in the presence of light. The
present review provides an overview of mechanisms that
may explain how light improves the freezing tolerance of
plants during the cold-hardening period
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