Role of glutathione in detoxification of copper and cadmium by yeast cells having different abilities to express cup1 protein

ABSTRACT Although copper is an essential metal and cadmium is an environmental pollutant, both are toxic when present in excess. Metallothionein and glutathione are two of the key components that participate in detoxification of copper and cadmium. In the present study the role of glutathione in resistance to copper and cadmium was investigated with the yeast Saccharomyces cerevisiae. The yeast cells used in this study have different abilities to produce glutathione and Cup1 protein, the yeast metallothionein homolog encoded by CUP1 gene. It was demonstrated that Cup1 protein plays a dominant role in buffering excess copper, and yeast does not depend on glutathione to reduce copper toxicity whether it possesses single or multiple copies of CUP1. In fact, excess copper can cause glutathione oxidation and depletion and damage the glutathione system. On the other hand, it was indicated that Cup1 protein is an important cadmium-detoxifying component, and the glutathione system can positively respond to cadmium. In yeast containing single or multiple copies of CUP1, glutathione is an indispensable line of defense against cadmium. Yeast having glutathione and no Cup1 protein is not able to grow in medium containing excess copper, but can tolerate higher concentrations of cadmium. In addition, it was found that yeast, independent of glutathione, can efficiently remove excess copper, whereas it cannot promptly eliminate accumulated cadmium regardless of having glutathione or not.

A new partition testing strategy for multiple endpoints

To evaluate efficacy in multiple endpoints in confirmatory clinical trials is a challenging problem in multiple hypotheses testing. The difficulty comes from the different importance of each endpoint and their underlying correlation. Current approaches to this problem, which test the efficacy in certain dose-endpoint combinations and collate the results, are based on closed testing or partition testing. Despite their different formulations, all current approaches test their dose-endpoint combinations as intersection hypotheses and apply various union-intersection tests. Likelihood ratio test is seldom used owing to the extensive computation and lack of consistent inferences. In this article, we first generalize the formulation of multiple endpoints problem to include the cases of alternative primary endpoints and co-primary endpoints. Then we propose a new partition testing approach that is based on consonance-adjusted likelihood ratio test. The new procedure provides consistent inferences, and yet, it is still conservative and does not rely on the estimation of endpoint correlation or independence assumptions that might be challenged by regulatory agencies.

Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology

Improvements to oligonucleotide fingerprinting of rRNA genes (OFRG) were obtained by implementing polony microarray technology. OFRG is an array-based method for analyzing microbial community composition. Polonies are discrete clusters of DNA, produced by solid-phase PCR in hydrogels, and derived from individual, spatially isolated DNA molecules. The advantages of a polony-based OFRG method include higher throughput and reductions in the PCR-induced errors and compositional skew inherent in all other PCR-based community composition methods, including high-throughput sequencing of rRNA genes. Given the similarities between polony microarrays and certain aspects of sequencing methods such as the Illumina platform, we suggest that if concepts presented in this study were implemented in high-throughput sequencing protocols, a reduction of PCR-induced errors and compositional skew may be realized.

Directed flow of identified particles in Au+Au collisions at √[SNN]=200 GeV at RHIC

STAR's measurements of directed flow (v1) around midrapidity for π±, K±, KS0, p, and p[over ¯] in Au+Au collisions at √[sNN]=200  GeV are presented. A negative v1(y) slope is observed for most of produced particles (π±, K±, KS0, and p[over ¯]). In 5%-30% central collisions, a sizable difference is present between the v1(y) slope of protons and antiprotons, with the former being consistent with zero within errors. The v1 excitation function is presented. Comparisons to model calculations (RQMD, UrQMD, AMPT, QGSM with parton recombination, and a hydrodynamics model with a tilted source) are made. For those models which have calculations of v1 for both pions and protons, none of them can describe v1(y) for pions and protons simultaneously. The hydrodynamics model with a tilted source as currently implemented cannot explain the centrality dependence of the difference between the v1(y) slopes of protons and antiprotons.

Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)

BACKGROUND

High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa).

RESULTS

We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types.

CONCLUSION

By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously.

Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)

BACKGROUND

High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa).

RESULTS

We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types.

CONCLUSION

By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously.

Products of oxidized L-ascorbic acid damage acellular DNA

OBJECTIVE

L-ascorbic acid can be pro-oxidant and anti-oxidant in different reaction. This study aims to test the effects about products of oxidized L-Ascorbic Acid on acellular DNA.

MEASUREMENT

Acellular DNA, nuclear DNA fixed on slides, are used in our experiment. There are four groups and one negative. Negative control is sham-treated with buffer(pH 7.2 and AA/ H2O2/fenton free). Experimental groups are treated separately with 0.06 mM L-ascorbic acid (AA) alone(exposed in air), 0.06 mM L-ascorbic acid (AA) alone(no exposure in air), 1.2 mM hydrogen peroxide (H2O2) alone, and a mixture of final concentration of 0.03 mM L-ascorbic acid and 0. 6 mM hydrogen peroxide (AA+ H2O2). Each experimental group consists of 4 slides and each slide is treated for 4 hours at 4 °C in a dark place. The DNA damage is quantified by alkaline Comet Assay. The comet images are analysed by Comet A1.0 software. Differences among groups are compared with SPSS 11.0.

RESULTS

DNA singlestrand breakage is found to be treatment-dependent in the following sequence: AA+ H2O2> AA(oxidized) > H2O2, AA(without oxidization) and Control.

CONCLUSION

Acellular DNA can tolerate the low concentration H2O2, but is sensitive to free radical. The results indicate that AA expose in air and mixture of AA and H2O2 can produce •OH and L-dehydroascorbate (DHA), •OH can damage DNA.

Host-microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosal-luminal interface

BACKGROUND

Host-microbe interactions at the intestinal mucosal-luminal interface (MLI) are critical factors in the biology of inflammatory bowel disease (IBD).

METHODS

To address this issue, we performed a series of investigations integrating analysis of the bacteria and metaproteome at the MLI of Crohn's disease, ulcerative colitis, and healthy human subjects. After quantifying these variables in mucosal specimens from a first sample set, we searched for bacteria exhibiting strong correlations with host proteins. This assessment identified a small subset of bacterial phylotypes possessing this host interaction property. Using a second and independent sample set, we tested the association of disease state with levels of these 14 "host interaction" bacterial phylotypes.

RESULTS

A high frequency of these bacteria (35%) significantly differentiated human subjects by disease type. Analysis of the MLI metaproteomes also yielded disease classification with exceptional confidence levels. Examination of the relationships between the bacteria and proteins, using regularized canonical correlation analysis (RCCA), sorted most subjects by disease type, supporting the concept that host-microbe interactions are involved in the biology underlying IBD. Moreover, this correlation analysis identified bacteria and proteins that were undetected by standard means-based methods such as analysis of variance, and identified associations of specific bacterial phylotypes with particular protein features of the innate immune response, some of which have been documented in model systems.

CONCLUSIONS

These findings suggest that computational mining of mucosa-associated bacteria for host interaction provides an unsupervised strategy to uncover networks of bacterial taxa and host processes relevant to normal and disease states. (Inflamm Bowel Dis 2012;).

Identified hadron compositions in p+p and Au+Au collisions at high transverse momenta at √S(NN)=200 GeV

We report transverse momentum (p(T)≤15  GeV/c) spectra of π(±), K(±), p, p[over ¯], K(S)(0), and ρ(0) at midrapidity in p+p and Au+Au collisions at √S(NN)=200  GeV. Perturbative QCD calculations are consistent with π(±) spectra in p+p collisions but do not reproduce K and p(p[over ¯]) spectra. The observed decreasing antiparticle-to-particle ratios with increasing p(T) provide experimental evidence for varying quark and gluon jet contributions to high-p(T) hadron yields. The relative hadron abundances in Au+Au at p(T)≳8  GeV/c are measured to be similar to the p+p results, despite the expected Casimir effect for parton energy loss.

Strangeness enhancement in Cu-Cu and Au-Au collisions at √S(NN)=200 GeV

We report new STAR measurements of midrapidity yields for the Λ, Λ[over ¯], K(S)(0), Ξ(-), Ξ[over ¯](+), Ω(-), Ω[over ¯](+) particles in Cu+Cu collisions at √S(NN)==200  GeV, and midrapidity yields for the Λ, Λ[over ¯], K(S)(0) particles in Au+Au at √S(NN)==200  GeV. We show that, at a given number of participating nucleons, the production of strange hadrons is higher in Cu+Cu collisions than in Au+Au collisions at the same center-of-mass energy. We find that aspects of the enhancement factors for all particles can be described by a parametrization based on the fraction of participants that undergo multiple collisions.

Diffusion Tensor Imaging for Predicting Hand Motor Outcome in Chronic Stroke Patients

OBJECTIVE: Previous studies have indicated that diffusion tensor imaging (DTI) values are related to clinical outcome in stroke patients. This prospective study explored whether DTI values were predictive for hand function outcome in chronic stroke patients. METHODS: The DTI parameters (rλ1, rλ23, fractional anisotropy [rFA] and mean diffusivity [rMD]) were investigated in patients with completely paralysed hands (CPH; n = 10) or partially paralysed hands (PPH; n = 10), by two methods of analysis: segment of the corticospinal tract [sCST] analysis; pure region of interest [ROI] analysis. Spearman's correlation coefficient was used to assess the correlation between the DTI parameters and the following clinical measures: Fugl—Meyer Assessment [FMA]; National Institutes of Health Stroke Scale [NIHSS]. RESULTS: Significant differences were found between CPH and PPH for rFA and rλ23 (sCST analysis) and for rMD and rλ23 (ROI analysis). The rλ23 (sCST analysis) correlated with the NIHSS; the rMD (sCST analysis) correlated with the FMA (hand). CONCLUSION: The three parameters, rFA, rλ23 and rMD may have predictive value for evaluating hand function outcome in chronic stroke patients.

FOXC1 regulates the functions of human basal-like breast cancer cells by activating NF-κB signaling

Human basal-like breast cancer (BLBC) is an enigmatic and aggressive malignancy with a poor prognosis. There is an urgent need to identify therapeutic targets for BLBC, because current treatment modalities are limited and not effective. The forkhead box transcription factor FOXC1 has recently been identified as a critical functional biomarker for BLBC. However, how it orchestrates BLBC cells was not clear. Here we show that FOXC1 activates the transcription factor nuclear factor-κB (NF-κB) in BLBC cells by increasing p65/RelA protein stability. High NF-κB activity has been associated with estrogen receptor-negative breast cancer, particularly BLBC. The effect of FOXC1 on p65/RelA protein stability is mediated by increased expression of Pin1, a peptidyl-prolyl isomerase. FOXC1 requires NF-κB for its regulation of cell proliferation, migration and invasion. Notably, FOXC1 overexpression renders breast cancer cells more susceptible to pharmacological inhibition of NF-κB. These results suggest that BLBC cells may rely on FOXC1-driven NF-κB signaling. Interventions of this pathway may provide modalities for the treatment of BLBC.

SNP calling using genotype model selection on high-throughput sequencing data

MOTIVATION

A review of the available single nucleotide polymorphism (SNP) calling procedures for Illumina high-throughput sequencing (HTS) platform data reveals that most rely mainly on base-calling and mapping qualities as sources of error when calling SNPs. Thus, errors not involved in base-calling or alignment, such as those in genomic sample preparation, are not accounted for.

RESULTS

A novel method of consensus and SNP calling, Genotype Model Selection (GeMS), is given which accounts for the errors that occur during the preparation of the genomic sample. Simulations and real data analyses indicate that GeMS has the best performance balance of sensitivity and positive predictive value among the tested SNP callers.

AVAILABILITY

The GeMS package can be downloaded from https://sites.google.com/a/bioinformatics.ucr.edu/xinping-cui/home/software or http://computationalbioenergy.org/software.html.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Microarray analysis of normal and abnormal chick ventricular myocardial development

The left and right ventricle originate from distinct parts of the cardiac tube, and several genes are known to be differentially expressed in these compartments. The aims of this study were to determine developmental differences in gene expression between the left and right ventricle, and to assess the effect of altered hemodynamic loading. RNA was extracted from isolated left and right normal chick embryonic ventricles at embryonic day 6, 8, and 10, and from day 8 left atrial ligated hearts with hypoplastic left and dilated right ventricles. cRNA was hybridized to Affymetrix Chicken Genome array according to manufacturer protocols. Microarray analysis identified 302 transcripts that were differentially expressed between the left and right ventricle. Comparative analysis detected 91 genes that were different in left ventricles of ligated hearts compared to age-matched ventricles, while 66 were different in the right ones. A large number of the changes could be interpreted as a delay of normal maturation. The approach described in this study could be used as one of the measures to gauge success of surgical procedures for congenital heart disease and help in determining the optimal time frame for intervention to prevent onset of irreversible changes.

Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Cajanus spp.)

Single feature polymorphisms (SFPs) are microarray-based molecular markers that are detected by hybridization of DNA or cRNA to oligonucleotide probes. With an objective to identify the potential polymorphic markers for drought tolerance in pigeonpea [Cajanus cajan (L.) Millspaugh], an important legume crop for the semi-arid tropics but deficient in genomic resources, Affymetrix Genome Arrays of soybean (Glycine max), a closely related species of pigeonpea were used on cRNA of six parental genotypes of three mapping populations of pigeonpea segregating for agronomic traits like drought tolerance and pod borer (Helicoverpa armigiera) resistance. By using robustified projection pursuit method on 15 pair-wise comparisons for the six parental genotypes, 5,692 SFPs were identified. Number of SFPs varied from 780 (ICPL 8755 × ICPL 227) to 854 (ICPL 151 × ICPL 87) per parental combination of the mapping populations. Randomly selected 179 SFPs were used for validation by Sanger sequencing and good quality sequence data were obtained for 99 genes of which 75 genes showed sequence polymorphisms. While associating the sequence polymorphisms with SFPs detected, true positives were observed for 52.6% SFPs detected. In terms of parental combinations of the mapping populations, occurrence of true positives was 34.48% for ICPL 151 × ICPL 87, 41.86% for ICPL 8755 × ICPL 227, and 81.58% for ICP 28 × ICPW 94. In addition, a set of 139 candidate genes that may be associated with drought tolerance has been identified based on gene ontology analysis of the homologous pigeonpea genes to the soybean genes that detected SFPs between the parents of the mapping populations segregating for drought tolerance.