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Obligate intracellular bacteria comprising the order Chlamydiales lack the ability to synthesize nucleotides de novo and must acquire these essential compounds from the cytosol of the host cell. The environmental protozoan endosymbiont Protochlamydia amoebophila UWE25 encodes five nucleotide transporters with specificities for different nucleotide substrates, including ATP, GTP, CTP, UTP, and NAD. In contrast, the human pathogen Chlamydia trachomatis encodes only two nucleotide transporters, the ATP/ADP translocase C. trachomatis Npt1 (Npt1Ct) and the nucleotide uniporter Npt2Ct, which transports GTP, UTP, CTP, and ATP. The notable absence of a NAD transporter, coupled with the lack of alternative nucleotide transporters on the basis of bioinformatic analysis of multiple C. trachomatis genomes, led us to re-evaluate the previously characterized transport properties of Npt1Ct. Using [adenylate-32P]NAD, we demonstrate that Npt1Ct expressed in Escherichia coli enables the transport of NAD with an apparent Km and Vmax of 1.7 μM and 5.8 nM mg-1 h-1, respectively. The Km for NAD transport is comparable to the Km for ATP transport of 2.2 μM, as evaluated in this study. Efflux and substrate competition assays demonstrate that NAD is a preferred substrate of Npt1Ct compared to ATP. These results suggest that during reductive evolution, the pathogenic chlamydiae lost individual nucleotide transporters, in contrast to their environmental endosymbiont relatives, without compromising their ability to obtain nucleotides from the host cytosol through relaxation of transport specificity. The novel properties of Npt1Ct and its conservation in chlamydiae make it a potential target for the development of antimicrobial compounds and a model for studying the evolution of transport specificity. [ABSTRACT FROM AUTHOR]

Abstract: Ion-pair, reverse-phase high-performance liquid chromatography (HPLC) is a standard analytical platform for separating, purifying, and analyzing RNAs. However, a single-nucleotide resolution by using HPLC is currently limited to RNAs shorter than 25 nucleotides (nt). Here we describe a method of separating three RNA aptamers with 57, 58, and 59nt on an XBridge ion-pair, reverse-phase HPLC column by a single-nucleotide resolution. Under a similar condition, we also show the capability of our method to resolve two structurally different, yet sequence or mass identical, 59-nt aptamers. We establish that the optimal condition to achieve a single-nucleotide resolution correlates to 50°C and zero magnesium concentration in mobile phases. The ion-pairing agent, the buffer, and the solvent we use are also compatible for post-HPLC analysis such as mass spectrometry. Therefore, our method provides a new way of detecting, analyzing, and separating RNAs by conformation or structure and extends the ability to separate RNAs that are longer than 25nt by single-nucleotide resolution. [Copyright &y& Elsevier]

The article presents a study that determines the distribution of fragile X mental retardation 1 (FMR1) alleles and the prevalence of permutation (PM) and full mutation (FM) of the gene in Korean women. It describes the method of the study that uses polymerase chain reaction and Southern blot on 5829 of reproductive age. It notes the result of the study which indicates the carrier frequency in Korean women of reproductive age, which is lower than the Caucasians.

Background and Objective: During periodontitis or orthodontic tooth movement, the periodontal vasculature is severely impaired by chronic inflammation or excessive mechanical force. This leads to a hypoxic microenvironment of the periodontal cells and enhances the expression of various cytokines and growth factors that may regulate angiogenesis and alveolar bone remodeling. However, the role of hypoxia in regulating the communication between endothelial cells (ECs) and osteoblast progenitors during the remodeling and repair of periodontal tissue is still poorly defined. The aim of this study was to investigate the effects of vascular ECs on osteogenic differentiation, mineralization and the paracrine function of noncontact co-cultured periodontal ligament stem cells (PDLSCs) under hypoxia, and further reveal the involvement of MEK/ERK and p38 MAPK pathways in the process. Material and Methods: First, PDLSCs were obtained and a noncontact co-culture system of PDLSCs and human umbilical vein endothelial cells was established. Second, the effects of different time-periods of hypoxia (2% O2) on the osteogenic potential, mineralization and paracrine function of co-cultured PDLSCs were investigated. Third, ERK1/2 and p38 MAPK activities of PDLSCs under hypoxia were measured by western blotting. Finally, we employed specific MAPK inhibitors (PD98059 and SB20350) to investigate the involvement of ERK1/2 and p38 MAPK in PDLSC osteogenesis under hypoxia. Results: We observed further increased osteogenic differentiation of co-cultured PDLSCs, manifested by markedly enhanced alkaline phosphatase (ALP) activity and prostaglandin E2 (PGE2) levels, vascular endothelial growth factor (VEGF) release, runt-related transcription factor 2 (Runx2) and Sp7 transcriptional and protein levels and mineralized nodule formation, compared with PDLSCs cultured alone. ERK1/2 was phosphorylated in a rapid but transient manner, whereas p38 MAPK was activated in a slow and sustained way under hypoxia. Furthermore, hypoxia-stimulated transcription and expression of osteogenic regulators (hypoxia-inducible factor-1α, ALP, Runx2, Sp7, PGE2 and VEGF) were also inhibited by PD98059 and SB203580 to different degrees. Conclusion: Further increased osteogenic differentiation and mineralization of co-cultured PDLSCs under hypoxia were regulated by MEK/ERK and p38 MAPK pathways. And the ECs-mediated paracrine of PGE2 and VEGF may facilitate the unidirectional PDLSC-EC communication and promote PDLSCs osteogenesis. [ABSTRACT FROM AUTHOR]

RAC1 is a small, Ras-related GTPase that was recently reported to harbor a recurrent UV-induced signature mutation in melanoma, resulting in substitution of P29 to serine (RAC1P29S), ranking this the third most frequently occurring gain-of-function mutation in melanoma. Although the Ras family GTPases are mutated in about 30% of all cancers, mutations in the Rho family GTPases have rarely been observed. In this study, we demonstrate that unlike oncogenic Ras proteins, which are primarily activated by mutations that eliminate GTPase activity, the activated melanoma RAC1P29S protein maintains intrinsic GTP hydrolysis and is spontaneously activated by substantially increased inherent GDP/GTP nucleotide exchange. Determination and comparison of crystal structures for activated RAC1 GTPases suggest that RAC1F28L—a known spontaneously activated RAC1 mutant—and RAC1P29S are self-activated in distinct fashions. Moreover, the mechanism of RAC1P29S and RAC1F28L activation differs from the common oncogenic mutations found in Ras-like GTPases that abrogate GTP hydrolysis. The melanoma RAC1P29S gain-of-function point mutation therefore represents a previously undescribed class of cancer-related GTPase activity. [ABSTRACT FROM AUTHOR]

Effective representation of DNA sequences is one of the important tasks in the study of genome sequences. In this paper, we propose a graphical representation of DNA sequences based on nucleotide ring structure. In the proposed representation, we convert DNA sequences into 16 dinucleotides on the surface of the hexagon so that it can preserve nucleotide's chemical property and positional information. Our approach can provide capability of efficient similarity comparison between DNA sequences and also high comparison accuracy. Furthermore, our approach satisfies uniqueness and no degeneracy of DNA sequences. In the experimental study, we use phylogeny analysis for evolutionary relationship among different species. Extensive performance study shows that the proposed method can give better performance than existing methods in comparison with the degree of similarity. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are small (20-22 nucleotides) regulatory non-coding RNAs that strongly influence gene expression. Most prior studies addressing the role of miRNAs in neurodegenerative diseases (NDs) have focused on individual diseases such as Alzheimer's disease (AD), making disease-to-disease comparisons impossible. Using RNA deep sequencing, we sought to analyze in detail the small RNAs (including miRNAs) in the temporal neocortex gray matter from non-demented controls (n = 2), AD (n = 5), dementia with Lewy bodies (n = 4), hippocampal sclerosis of aging (n = 4), and frontotemporal lobar dementia (FTLD) (n = 5) cases, together accounting for the most prevalent ND subtypes. All cases had short postmortem intervals, relatively high-quality RNA, and state-of-the-art neuropathological diagnoses. The resulting data (over 113 million reads in total, averaging 5.6 million reads per sample) and secondary expression analyses constitute an unprecedented look into the human cerebral cortical miRNome at a nucleotide resolution. While we find no apparent changes in isomiR or miRNA editing patterns in correlation with ND pathology, our results validate and extend previous miRNA profiling studies with regard to quantitative changes in NDs. In agreement with this idea, we provide independent cohort validation for changes in miR-132 expression levels in AD (n = 8) and FTLD (n = 14) cases when compared to controls (n = 8). The identification of common and ND-specific putative novel brain miRNAs and/or short-hairpin molecules is also presented. The challenge now is to better understand the impact of these and other alterations on neuronal gene expression networks and neuropathologies. [ABSTRACT FROM AUTHOR]

Objective. To evaluate the role of IL-32 in granulomatosis with polyangiitis (GPA) patients and the relationship between IL-32 and disease activity, as PR3 has the ability to bind and activate IL-32, which has been described as a novel cytokine that induces inflammatory cytokines.Methods. We investigated the level of IL-32, PR3, TNF-α and IL-6 in GPA patients by using ELISA. Northern blot was used to analyse the level of IL-32 mRNA in leucocytes of GPA patients. The intracellular colocalization of IL-32 and PR3 in leucocytes was examined by IF staining.Results. We observed that IL-32 and PR3 levels in GPA patients were increased significantly when compared with normal individuals and each was tightly associated (P < 0.001). Northern blot analysis revealed that the mRNA level of IL-32 was prominently elevated in leucocytes of GPA patients. The intracellular colocalization of IL-32 and PR3 in leucocytes from GPA patients vs normal individuals was verified by IF staining.Conclusion. IL-32 level was elevated in GPA patients but its level was changed by treatment response. IL-32 could be an index in GPA and play a role in the aetiology of GPA. [ABSTRACT FROM AUTHOR]

Factors affecting the reliability of Roche/454 pyrosequencing for analyzing sequence polymorphism in within-host viral populations were assessed by two experiments: 1) sequencing four clonal simian immunodeficiency virus (SIV) stocks and 2) sequencing mixtures in different proportions of two SIV strains with known fixed nucleotide differences. Observed nucleotide diversity and frequency of undetermined nucleotides were increased at sites in homopolymer runs of four or more identical nucleotides, particularly at AT sites. However, in the mixed-strain experiments, the effects on estimated nucleotide diversity of such errors were small in comparison to known strain differences. The results suggest that biologically meaningful variants present at a frequency of around 10% and possibly much lower are easily distinguished from artifacts of the sequencing process. Analysis of the clonal stocks revealed numerous rare variants that showed the signature of purifying selection and that elimination of variants at frequencies of less than 1% reduced estimates of nucleotide diversity by about an order of magnitude. Thus, using a 1% frequency cutoff for accepting a variant as real represents a conservative standard, which may be useful in studies that are focused on the discovery of specific mutations (such as those conferring immune escape or drug resistance). On the other hand, if the goal is to estimate nucleotide diversity, an optimal strategy might be to include all observed variants (even those at less than 1% frequency), while masking out homopolymer runs of four or more nucleotides. [ABSTRACT FROM AUTHOR]

Background: Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of perfect microsatellites in assembled contig sequences of the apple genome. Results: A total of 28,538 SSRs have been identified in the apple genome, with an overall density of 40.8 SSRs per Mb. Di-nucleotide repeats are the most frequent microsatellites in the apple genome, accounting for 71.9% of all microsatellites. AT/TA repeats are the most frequent in genomic regions, accounting for 38.3% of all the G-SSRs, while AG/GA dimers prevail in transcribed sequences, and account for 59.4% of all EST-SSRs. A total set of 310 SSRs is selected to amplify eight apple genotypes. Of these, 245 (79.0%) are found to be polymorphic among cultivars and wild species tested. AG/GA motifs in genomic regions have detected more alleles and higher PIC values than AT/TA or AC/CA motifs. Moreover, AG/GA repeats are more variable than any other dimers in apple, and should be preferentially selected for studies, such as genetic diversity and linkage map construction. A total of 54 newly developed apple SSRs have been genetically mapped. Interestingly, clustering of markers with distorted segregation is observed on linkage groups 1, 2, 10, 15, and 16. A QTL responsible for malic acid content of apple fruits is detected on linkage group 8, and accounts for ~13.5% of the observed phenotypic variation. Conclusions: This study demonstrates that di-nucleotide repeats are prevalent in the apple genome and that AT/ TA and AG/GA repeats are the most frequent in genomic and transcribed sequences of apple, respectively. All SSR motifs identified in this study as well as those newly mapped SSRs will serve as valuable resources for pursuing apple genetic studies, aiding the apple breeding community in marker-assisted breeding, and for performing comparative genomic studies in Rosaceae. [ABSTRACT FROM AUTHOR]

Background. Previous knowledge of cervical lymph node compromise may be crucial to choose the best treatment strategy in oral squamous cell carcinoma (OSCC). Here we propose a set four genes, whose mRNA expression in the primary tumor predicts nodal status in OSCC, excluding tongue. Material and methods. We identified differentially expressed genes in OSCC with and without compromised lymph nodes using Differential Display RT-PCR. Known genes were chosen to be validated by means of Northern blotting or real time RT-PCR (qRT-PCR). Thereafter we constructed a Nodal Index (NI) using discriminant analysis in a learning set of 35 patients, which was further validated in a second independent group of 20 patients. Results. Of die 63 differentially expressed known genes identified comparing three lymph node positive (pN +) and three negative (pNO) primary tumors, 23 were analyzed by Northern analysis or RT-PCR in 49 primary tumors. Six genes confirmed as differentially expressed were used to construct a NI, as the best set predictive of lymph nodal status, with the final result including four genes. The NI was able to correctly classify 32 of 35 patients comprising the learning group (88.6%; p = 0.009). Casein kinase lalphal and scavenger receptor class B, member 2 were found to be up regulated in pN + group in contrast to small proline-rich protein 2B and Ras-GTPase activating protein SH3 domain-binding protein 2 which were upregulated in the pNO group. We validated further our NI in an independent set of 20 primary tumors, 11 of them pNO and nine pN + with an accuracy of 80.0% (p = 0.012). Conclusions. The NI was an independent predictor of compromised lymph nodes, taking into the consideration tumor size and histological grade. The genes identified here that integrate our "Nodal Index" model are predictive of lymph node metastasis in OSCC. [ABSTRACT FROM AUTHOR]

In this article, the authors discuss the role of recombination in the species-tree analysis. They state that the analysis by the specie-tree method assumes recombination to be interlocus for the examination of nucleotide substitution within gene lineages and random sorting among the gene lineages. They opine that uncertainty due to intralocus recombination usually remains unrecognized and influences the accuracy of data estimated in the field of phylogenetics.

In order to (i) establish the biological systematics necessary to interpret nitrogen (N) and oxygen (O) isotope ratios of nitrate (15N/14N and 18O/16O) in the environment and (ii) investigate the potential for isotopes to elucidate the mechanism of a key N cycle enzyme, we measured the nitrate N and O isotope effects (15ϵ and 18ϵ) for nitrate reduction by two assimilatory eukaryotic nitrate reductase (eukNR) enzymes. The 15ϵ for purified extracts of NADPH eukNR from the fungus Aspergillus niger and the 15ϵ for NADH eukNR from cell homogenates of the marine diatom Thalassiosira weissflogii were indistinguisha±ble, yielding a mean 15ϵ for the enzyme of 26.6 ± 0.2%. Both forms of eukNR imparted near equivalent fractionation on N and O isotopes. The increase in 18O/16O versus the increase in 15N/14N (relative to their natural abundances) was 0.96 ± 0.01 for NADPH eukNR and 1.09 ± 0.03 for NADH eukNR. These results are the first reliable measurements of the coupled N and O isotope effects for any form of eukNR. They support the prevailing view that intracellular reduction by eukNR is the dominant step in isotope fractionation during nitrate assimilation and that it drives the 18ϵ:15ϵ ≈ 1 observed in phytoplankton cultures, suggesting that this O-to-N isotope signature will apply broadly in the environment. Our measured 15ϵ and 18ϵ may represent the intrinsic isotope effects for eukNR-mediated N-O bond rupture, a potential constraint on the nature of the enzyme's transition state. [ABSTRACT FROM AUTHOR]

Abstract: Application of a voltage ramp can result in denaturation of dsDNA and strand separation. We show that the potential at which half of the surface immobilised duplexes denature (the melting potential, E m) directly correlates with the calculated nearest neighbour and experimental melting temperatures; T m, for a duplex is solution. The results demonstrate that the electrochemical melting potential measures the stability of the dsDNA, and therefore existing nearest neighbour melting models can be utilized to design DNA probes with predictable electrochemical melting potentials for future assay applications. [Copyright &y& Elsevier]

Introduction: Characterized by the development of hundreds to thousands of colonic adenomas, classic familial adenomatous polyposis (FAP) is one of the most common hereditary syndromes associated with an increased risk of colorectal cancer. Several studies have attempted to correlate specific APC mutations with clinical phenotype. However, there is considerable variability in the expression of specific phenotypes within families and among individuals with identical mutations. Case presentation: A 30 year-old Hispanic female presented to the emergency department with a 2-week history of persistent, worsening, left lower quadrant abdominal pain. She had no family history of malignancy. Sigmoidoscopy revealed innumerable polyps in the rectum and sigmoid colon and a large mass in the sigmoid colon. Biopsy of the mass revealed a moderately differentiated adenocarcinoma invading the subserosa. Endoscopy revealed innumerable polyps. Genetic testing of the patient via southern blot revealed a germline APC mutation 3927del5, resulting in a premature truncation of the APC protein at amino acid position 1312. Conclusion: Genetic information has only recently started being incorporated into clinical care. More research and randomized clinical trials need to be conducted to definitively characterize random mutations. Once these mutations are further understood, FAP patients may be able to be risk stratified and this may ultimately improve the screening, diagnosis, and treatment of this rare condition. [ABSTRACT FROM AUTHOR]

UV-sensitive syndrome (UVSS) is a genodermatosis characterized by cutaneous photosensitivity without skin carcinoma. Despite mild clinical features, cells from individuals with UVSS, like Cockayne syndrome cells, are very UV sensitive and are deficient in transcription-coupled nucleotide-excision repair (TC-NER), which removes DNA damage in actively transcribed genes. Three of the seven known UVSS cases carry mutations in the Cockayne syndrome genes ERCC8 or ERCC6 (also known as CSA and CSB, respectively). The remaining four individuals with UVSS, one of whom is described for the first time here, formed a separate UVSS-A complementation group; however, the responsible gene was unknown. Using exome sequencing, we determine that mutations in the UVSSA gene (formerly known as KIAA1530) cause UVSS-A. The UVSSA protein interacts with TC-NER machinery and stabilizes the ERCC6 complex; it also facilitates ubiquitination of RNA polymerase IIo stalled at DNA damage sites. Our findings provide mechanistic insights into the processing of stalled RNA polymerase and explain the different clinical features across these TC-NER-deficient disorders. [ABSTRACT FROM AUTHOR]

Transcription-coupled nucleotide-excision repair (TC-NER) is a subpathway of NER that efficiently removes the highly toxic RNA polymerase II blocking lesions in DNA. Defective TC-NER gives rise to the human disorders Cockayne syndrome and UV-sensitive syndrome (UVSS). NER initiating factors are known to be regulated by ubiquitination. Using a SILAC-based proteomic approach, we identified UVSSA (formerly known as KIAA1530) as part of a UV-induced ubiquitinated protein complex. Knockdown of UVSSA resulted in TC-NER deficiency. UVSSA was found to be the causative gene for UVSS, an unresolved NER deficiency disorder. The UVSSA protein interacts with elongating RNA polymerase II, localizes specifically to UV-induced lesions, resides in chromatin-associated TC-NER complexes and is implicated in stabilizing the TC-NER master organizing protein ERCC6 (also known as CSB) by delivering the deubiquitinating enzyme USP7 to TC-NER complexes. Together, these findings indicate that UVSSA-USP7-mediated stabilization of ERCC6 represents a critical regulatory mechanism of TC-NER in restoring gene expression. [ABSTRACT FROM AUTHOR]

Background:Upregulation of the matrix metalloproteinases MMP-2 and MMP-9 in various cancers has been associated with worse survival of the patients.Methods:We assessed MMP-2 and MMP-9 levels in normal colorectal mucosa from colorectal cancer patients in relation to the course of the disease.Results:A high protein expression of MMP-2 as well as MMP-9 in normal mucosa was found to be correlated with worse 5-year survival. The combination of both parameters was an even stronger prognostic factor. These protein levels were found not to be related to the corresponding single nucleotide polymorphisms of MMP-2 (−1306C>T) and MMP-9 (−1562C>T). Multivariate analyses indicated that the MMP-2 and MMP-9 levels in normal mucosa are prognostic for survival, independent of TNM classification.Conclusion:MMP-2 and MMP-9 levels in normal mucosa are indicative of the course of disease in colorectal cancer patients. [ABSTRACT FROM AUTHOR]

Abstract: Background: Telomeres are special chromatin sequences located at the end of eukaryotic chromosomes, protecting these regions from recombination and degradation. Previous studies have reported a decrease in telomere length on white blood cells from hemodialysis (HD) patients, which suggests premature senescence. Active vitamin D treatment has been reported to have an effect on telomere length and beneficial effects on HD patients, but the mechanisms are unknown. Objective: Our aim was to assess the potential protective role of active vitamin D treatment on telomere length in peripheral mononuclear cells (PBMC) from HD patients. Methods: A retrospective case–control study of 62 stable HD patients and 60 healthy sex-matched controls was undertaken. Telomere length was measured in PBMC by Southern blot. After telomere length measurement, 5 control samples that did not reach quality-control standards were excluded. Standard epidemiological and biochemical parameters were recorded. Blood biochemistries were performed at the Biochemistry Department of the University Hospital Arnau de Vilanova in Lleida, Spain, using standard routine techniques. Differences in telomere length were analyzed using Student''s t test. Multiple regression analysis examined the independent contribution of the factors that significantly affected telomere length in the bivariate analysis. Results: HD patients presented shorter telomere length in PBMC, independent of age and sex (mean [SD] 8.8 [1.5] kbp vs 10.5 [2.9] kbp; P = 0.0001). Multivariate regression analysis of the HD subgroup suggested that patients under active vitamin D treatment have greater telomere length in PBMC than untreated patients (9.5 [0.2] kbp vs 8.4 [0.2] kbp; P = 0.003). Conclusions: HD patients were observed to have decreased PBMC telomere length compared with healthy controls. HD patients treated with active vitamin D compounds had greater PBMC telomere length than untreated patients. Prospective studies are required to assess the potential role of active vitamin D treatment in PBMC telomere length. [Copyright &y& Elsevier]

BACKGROUND: Alloantibodies against human neutrophil antigen-3 (HNA-3) are responsible for the fatalities reported in transfusion-related acute lung injury. Consequently, reliable detection of these alloantibodies is mandatory to improve blood transfusion safety. In this study, we developed stable cell lines for the detection of HNA-3 antibodies. STUDY DESIGN AND METHODS: HEK293T were transfected with HNA-3a or HNA-3b constructs and sorted by flow cytometry according to high surface expression. Transfected cells were tested with sera containing HNA-3 antibodies in flow cytometry and antibody capture assay (ACA). The results were compared with granulocyte agglutination test and granulocyte immunofluorescence test. RESULTS: In flow cytometry, 12 of 14 HNA-3a sera reacted specifically with HNA-3aa cells. One serum sample showed positive reaction with HNA-3bb cells. All HNA-3b sera recognized HNA-3bb cells. No reaction was observed with broad reactive antibodies against HLA Class I. In ACA, all HNA-3a sera (12/12) showed positive reactivity with HNA-3aa cells with no cross-reactivity with HNA-3bb cells. Again, all HNA-3b sera reacted with HNA-3bb cells only. Furthermore, genotyping of 249 individuals detected a new HNA-3 allele caused by a nucleotide substitution C>T at Position 457 leading to L153F mutation in choline transporter-like protein-2. This mutation impairs polymerase chain reaction with sequence-specific primers based HNA-3a typing. However, analysis with cells expressing F153 isoform showed that this mutation did not alter the binding of HNA-3 antibodies. CONCLUSIONS: This study demonstrated that HEK293T cells expressing stable recombinant HNA-3 are suitable for the detection of HNA-3 alloantibodies allowing reliable screening of blood products. [ABSTRACT FROM AUTHOR]

Transcription-coupled DNA repair targets DNA lesions that block progression of elongating RNA polymerases. In bacteria, the transcription-repair coupling factor (TRCF; also known as Mfd) SF2 ATPase recognizes RNA polymerase stalled at a site of DNA damage, removes the enzyme from the DNA, and recruits the Uvr(A)BC nucleotide excision repair machinery via UvrA binding. Previous studies of TRCF revealed a molecular architecture incompatible with UvrA binding, leaving its recruitment mechanism unclear. Here, we examine the UvrA recognition determinants of TRCF using X-ray crystallography of a core TRCF-UvrA complex and probe the conformational flexibility of TRCF in the absence and presence of nucleotides using small-angle X-ray scattering. We demonstrate that the C-terminal domain of TRCF is inhibitory for UvrA binding, but not RNA polymerase release, and show that nucleotide binding induces concerted multidomain motions. Our studies suggest that autoinhibition of UvrA binding in TRCF may be relieved only upon engaging the DNA damage. [ABSTRACT FROM AUTHOR]

We investigate the extent by which the estimates of the rate of adaptive molecular evolution obtained by extending the McDonald-Kreitman test are biased if the species, subjected to analysis, diverged recently. We show that estimates can be biased if the nucleotide divergence between the species is low relative to within species variation, and that the magnitude of the bias depends on the rate of adaptive evolution and the distribution of fitness effects of new mutations. Bias appears to be because of three factors: (1) misattribution of polymorphism to divergence; (2) the contribution of ancestral polymorphism to divergence; and (3) different rates of fixation of neutral and advantageous mutations. If there is little adaptive molecular evolution, then slightly deleterious mutations inflate estimates of the rate of adaptive evolution, because these contribute proportionately more to polymorphism than to nucleotide divergence than neutral mutations. However, if there is substantial adaptive evolution, polymorphism contributing to apparent divergence may downwardly bias estimates. We propose a simple method for correcting the different contributions of slightly deleterious and neutral mutations to polymorphism and divergence, and apply it to datasets from several species. We find that estimates of the rate of adaptive molecular evolution from closely related species may be underestimates by ~10% or more. However, after the contribution of polymorphism to divergence is removed, the rate of adaptive evolution may still be overestimated as a consequence of ancestral polymorphism and time for fixation effects. This bias may be substantial if branch lengths are less than 10 N generations. [ABSTRACT FROM AUTHOR]

Oxidative damage, mitochondrial dysfunction, genomic instability, and telomere shortening represent all molecular processes proposed as causal factors in aging. Lifespan can be increased by metabolism through an influence on such processes. Glucose reduction extends chronological lifespan (CLS) of Saccharomyces cerevisiae through metabolic adaptation to respiration. To answer the question if the reduced CLS could be ascribed to glucose per se or to glucose repression of respiratory enzymes, we used the Kluyveromyces lactis yeast, where glucose repression does not affect the respiratory function.We identified the unique hexokinase, encoded by RAG5 gene, as an important player in influencing yeast lifespan by modulating mitochondrial functionality and the level of the mitochondrial chaperonin Hsp60. In this context, this hexokinase might have a regulatory role in the influence of CLS, shedding new light on the complex regulation played by hexokinases. [ABSTRACT FROM AUTHOR]

Dickkopf (DKK) family proteins are secreted modulators of the Wnt signaling pathway and are capable of regulating the development of many organs and tissues. We previously identified Dkk3 to be a molecule predominantly expressed in the mouse embryonic retina. However, which cell expresses Dkk3 in the developing and mature mouse retina remains to be elucidated. To examine the precise expression of the Dkk3 protein, we generated BAC-Dkk3-EGFP transgenic mice that express EGFP integrated into the Dkk3 gene in a BAC plasmid. Expression analysis using the BAC-Dkk3-EGFP transgenic mice revealed that Dkk3 is expressed in retinal progenitor cells (RPCs) at embryonic stages and in Müller glial cells in the adult retina. Since Müller glial cells may play a potential role in retinal regeneration, BAC-Dkk3-EGFP mice could be useful for retinal regeneration studies. [ABSTRACT FROM AUTHOR]

The local environment of neurosecretory cells contains the major components of the plasminogen activation system, including the plasminogen activators, tissue plasminogen activator (t-PA) and urokinase-type plasminogen activator (u-PA), as well as binding sites for t-PA, the receptor for u-PA (uPAR), and also the plasminogen activator inhibitor, PAI-1. Furthermore, these cells express specific binding sites for plasminogen, which is available in the circulation and in interstitial fluid. Colocalization of plasminogen and its activators on cell surfaces provides a mechanism for promoting local plasminogen activation. Plasmin is retained on the cell surface where it is protected from its inhibitor, α2-antiplasmin. In neurosecretory cells, localized plasmin activity provides amechanism for extracellular processing of secreted hormones. Neurotransmitter release fromcatecholaminergic cells is negatively regulated by cleavage products formed by plasmin-mediated proteolysis. Recently, we have identified a major plasminogen receptor, Plg-RKT. We have found that Plg-RKT is highly expressed in chromaffin cells of the adrenal medulla as well as in other catecholaminergic cells and tissues. Plg-RKT-dependent plasminogen activation plays a key role in regulating catecholaminergic neurosecretory cell function. [ABSTRACT FROM AUTHOR]

The article focuses on a study related to anticancer property of Bryophyllum pinnata. A chloroform extract derived from a bulk of botanically well-characterized pulverized B. pinnata leaves was separated using column chromatography with step- gradient of petroleum ether and ethyl acetate. Fractions were characterized for phyto-chemical compounds by TLC, HPTLC and NMR and Biological activity of the fractions were examined by MTT-based cell viability assay.

MicroRNA-125b-1 (miR-125b-1) is a target of a chromosomal translocation t(11;14)(q24;q32) recurrently found in human B-cell precursor acute lymphoblastic leukemia (BCP-ALL). This translocation results in overexpression of miR-125b controlled by immunoglobulin heavy chain gene (IGH) regulatory elements. In addition, we found that six out of twenty-one BCP-ALL patients without t(11;14)(q24;q32) showed overexpression of miR-125b. Interestingly, four out of nine patients with BCR/ABL-positive BCP-ALL and one patient with B-cell lymphoid crisis that had progressed from chronic myelogenous leukemia overexpressed miR-125b. To examine the role of the deregulated expression of miR-125b in the development of B-cell tumor in vivo, we generated transgenic mice mimicking the t(11;14)(q24;q32) (Eμ/miR-125b-TG mice). Eμ/miR-125b-TG mice overexpressed miR-125b driven by IGH enhancer and promoter and developed IgM-negative or IgM-positive lethal B-cell malignancies with clonal proliferation. B cells obtained from the Eμ/miR-125b-TG mice were resistant to apoptosis induced by serum starvation. We identified Trp53inp1, a pro-apoptotic gene induced by cell stress, as a novel target gene of miR-125b in hematopoietic cells in vitro and in vivo. Our results provide direct evidence that miR-125b has important roles in the tumorigenesis of precursor B cells. [ABSTRACT FROM AUTHOR]

Abstract: Hydrophilic interaction chromatography (HILIC) is a liquid chromatographic separation mechanism commonly used for polar biological molecules. The use of enhanced-fluidity liquid chromatography (EFLC) with mixtures of methanol/water/carbon dioxide is compared to acetonitrile/water mobile phases for the separation of nucleosides and nucleotides under HILIC conditions. Enhanced-fluidity liquid chromatography involves using common mobile phases with the addition of substantial proportions of a dissolved gas which provides greater mobile phase diffusivity and lower viscosity. The impact of varying several experimental parameters, including temperature, addition of base, salt, and CO2 was studied to provide optimized HILIC separations. Each of these parameters plays a key role in the retention of the analytes, which demonstrates the complexity of the retention mechanism in HILIC. The tailing of phosphorylated compounds was overcome with the use of phosphate salts and the addition of a strong base; efficiency and peak asymmetry were compared with the addition of either triethylamine (TEA), 1,4-diazabicyclo [2.2.2] octane (DABCO) or 1,5-diazabicyclo [4.3.0] non-5-ene (DBN). DBN and DABCO both led to increased efficiency and lower peak asymmetry; DBN provided the best results. Sodium chloride and carbon dioxide were added to enhance the selectivity between the analytes, giving a successful isocratic separation of nucleosides and nucleotides within 8min. The retention mechanism involved in EFL-HILIC was explored by varying the temperature and the mole fraction of CO2. These studies showed that partitioning was the dominant mechanism. The thermodynamics study confirmed that the solvent strength is maintained in EFLC and that a change in entropy was mainly responsible for the improved selectivity. The selectivity using methanol/water/carbon dioxide varied greatly compared to that obtained with acetonitrile/water. Finally while this study highlights the optimization of EFL-HILIC for the separation of nucleosides and nucleotides under isocratic conditions, this is also an example of the broad range of polarities of compounds that EFL-HILIC can separate. [Copyright &y& Elsevier]

AbstractThe consumption of soy protein lowers blood cholesterol in humans and animals. Breeding may alter the physiological effects of soybeans, such as its cholesterol-lowering property. Our hypothesis is that breeding affects the hypocholesterolemic effect of soy by modulating the expression of key hepatic enzymes related to cholesterol and bile acid biosynthesis, as well as altering fecal neutral and acidic steroid excretion. Therefore the aim of this study was to evaluate the effect of a new Brazilian soybean cultivar (UFV-116), lacking lipoxygenases 2 and 3, compared with a commercial cultivar (OCEPAR-19), on 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) and cholesterol 7α-hydroxylase (CYP7A) mRNA expression and fecal steroid output in rats. Thirty-six male rats were fed UFV-116, OCEPAR-19, or casein as the protein source, with or without addition of dietary cholesterol (0.25%). Blood and liver cholesterol, HMGR and CYP7A mRNA abundance, and fecal excretion of steroids were measured. Blood and liver cholesterol levels were lowered by both soybean cultivars, with and without cholesterol, but UFV-116 was more effective when included in the cholesterol-free diet. Both soy diets promoted lower levels of HMGR mRNA, higher levels of CYP7A mRNA, and higher excretion of fecal secondary bile acids. There was higher fecal neutral steroid output when cholesterol was added to all diets. These data show that both soybean cultivars acted similarly in lowering serum and hepatic cholesterol; therefore, breeding did not affect the hypocholesterolemic effect of the new cultivar. [ABSTRACT FROM AUTHOR]

The objectives of the present study were to characterize γ-ray, 1 GeV/n proton, and 1 GeV/n iron ion radiation-induced adverse biological effects in terms of toxicity and transformation of HTori-3 human thyroid epithelial cells; to evaluate the ability of L-selenomethionine (SeM) to protect against radiation-induced transformation when present at different times during the assay period; and to evaluate the tumorigenicity of HTori-3 cells derived from anchorage-independent colonies following iron ion radiation exposure. Cell survival was determined by a clonogenic assay, transformation was measured by a soft agar colony formation assay, and the tumorigenic potential of the cells was determined by injecting them subcutaneously into athymic nude mice and monitoring tumor formation. The results demonstrate that exposure of HTori-3 cells to γ-ray, proton, or iron ion radiation resulted in decreased clonogenic survival, which persisted for weeks after the radiation exposure. Treatment with SeM initiated up to 7 days after the radiation exposure conferred significant protection against radiation-induced anchorage-independent growth. HTori-3 cells derived from all evaluated anchorage-independent colonies formed tumors when injected into athymic nude mice, indicating that these cells are tumorigenic and that anchorage-independent colony growth is a reliable surrogate endpoint biomarker for the radiation-induced malignant transformation of HTori-3 cells. [ABSTRACT FROM PUBLISHER]

The article presents a research study investigating how context-dependent individualization of nucleotides and virtual genomic hybridization enables the exact location of human single nucleotide polymorphism (SNP). A strategy for identifying SNP, named COIN-VGH, is used in the study which was established using the X-chromosome-specific regions. The study indentified the signature regions in the human reference genome (HRG) and in the query genome (QG).

The article presents a research study examining the impact of alternative splicing of a single transcription factor on the reproductive behavior of honeybee workers. The study demonstrates how worker sterility is influenced by alternative splicing of a gene homologous to the gemini transcription factor of Drosophila. Moreover, it discusses the sufficiency of removing nucleotides from altruistic worker genome in turning an altruistic honeybee worker into a parasite.

Human follicular B-cell lymphoma is associated with the t(14;18) chromosomal translocation that juxtaposes the Bcl2 proto-oncogene with the immunoglobulin heavy chain (Igh) locus, resulting in the deregulated expression of Bcl2. Our previous studies have shown that the Igh 3' enhancers deregulate the Bcl2 expression in vitro. However, the effects of the Igh 3' enhancer elements on Bcl2 expression in vivo are not known. To investigate the role of the Igh 3' enhancers in Bcl2 deregulation, we used gene targeting to generate knock-in mice in which four DNase I-hypersensitive regions from the murine Igh 3' region were integrated 3' of the Bcl2 locus. Increased levels of Bcl2 mRNA and protein were observed in the B cells of Igh-3'E-bcl2 mice. B cells from Igh-3'E-bcl2 mice showed an extended survival in vitro compared with B cells from wild-type (Wt) mice. The Bcl2 promoter shift from P1 (the 5' promoter) to P2 (the 3' promoter) was observed in B cells from Igh-3'E-bcl2 mice, similar to human t(14;18) lymphomas. The IgH-3'E-bcl2 mice developed monoclonal B-cell follicular lymphomas, which were slowly progressive. These studies show that the Igh 3' enhancers have an important role in the deregulation of Bcl2 and B-cell lymphomagenesis in vivo. [ABSTRACT FROM AUTHOR]

Translocation of RNA polymerase on DNA is thought to involve oscillations between pretranslocated and posttranslocated states that are rectified by nucleotide addition or pyrophosphorolysis. The pretranslocated register is also a precursor to transcriptional pause states that mediate regulation of transcript elongation. However, the determinants of bias between the pretranslocated and posttranslocated states are incompletely understood. To investigate translocation bias in multisubunit RNA polymerases, we measured rates of pyrophosphorolysis, which occurs in the pretranslocated register, in minimal elongation complexes containing T. thermophilus or E. coli RNA polymerase. Our results suggest that the identity of RNA:DNA nucleotides in the active site are strong determinants of susceptibility to pyrophosphorolysis, and thus translocation bias, with the 3' RNA nucleotide favoring the pretranslocated state in the order U > C > A > G. The preference of 3' U vs G for the pretranslocated register appeared to be universal among both bacterial and eukaryotic RNA polymerases and was confirmed by exonuclease III footprinting of defined elongation complexes. However, the relationship of pyrophosphate concentration to the rate of pyrophosphorolysis of 3' U-containing versus 3' G-containing elongation complexes did not match predictions of a simple mechanism in which 3'-RNA seqeunce affects only translocation bias and pyrophosphate (PPi) binds only to the pretranslocated state. [ABSTRACT FROM AUTHOR]

The determination of single nucleotide polymorphisms (SNPs) has become faster and more cost effective since the advent of short read data from next generation sequencing platforms such as Roche's 454 Sequencer, Illumina's Solexa platform, and Applied Biosystems SOLiD sequencer. The SOLiD sequencing platform, which is capable of producing more than 6 GB of sequence data in a single run, uses a unique encoding scheme where color reads represent transitions between adjacent nucleotides. The determination of SNPs from color reads usually involves the translation of color alignments to likely nucleotide strings to facilitate the use of tools designed for nucleotide reads. This technique results in the loss of significant information in the color read, producing many incorrect SNP calls, especially if regions exist with dense or adjacent polymorphism. Additionally, color reads align ambiguously and incorrectly more often than nucleotide reads making integrated SNP calling a difficult challenge. We have developed ComB, a SNP calling tool which operates directly in color space, using a Bayesian model to incorporate unique and ambiguous reads to iteratively determine SNP identity. ComB is capable of accurately calling short consecutive nucleotide polymorphisms and densely clustered SNPs; both of which other SNP calling tools fail to identify. ComB, which is capable of using billions of short reads to accurately and efficiently perform whole human genome SNP calling in parallel, is also capable of using sequence data or even integrating sequence and color space data sets. We use real and simulated data to demonstrate that ComB's iterative strategy and recalibration of quality scores allow it to discover more true SNPs while calling fewer false positives than tools which use only color alignments as well as tools which translate color reads to nucleotide strings. [ABSTRACT FROM AUTHOR]

The paper is focused on the powerful prediction ability of the quantitative DNA sieving model in DNA separations by capillary electrophoresis, which was proposed by us previously. First, the DNA resolution can be predicted by the theory. The model predicts that the most difficult and easiest separation will be 184bp/192bp and 234bp/267bp respectively, which is consist with experimental results. Furthermore, the average relative differences of predicted and experimental resolution values (RS) for ssDNA 184b/192b or dsDNA 184bp/192bp were all smaller than 2.8% if the diffuse parameter Dconsidered was 8 × 10–5cm2/s. Secondly, the optimum polymer concentrations for DNA separation were also calculated by the model, and the results show that polymer concentration should be as high as possible in DNA separation. Thirdly, the sieving ability of polymer will be predicted by the model. Polymer with smaller k, a polymer parameter calculated by the model, is prior to use as DNA sieving media. [ABSTRACT FROM AUTHOR]

A novel separation method of urinary 8-hydroxy-2'-deoxyguanosine (8-OHdG) was developed. The C18and the strong cation-exchange (SCX) columns were employed to separate urinary 8-OHdG. The major interfering substances were removed by the consecutive processes of the C18and the SCX columns. This newly developed procedure allows researchers to quantitatively measure urinary 8-OHdG by high performance liquid chromatography-electrochemical detector (HPLC–ECD) successfully. The newly developed separation method produces the optimized procedure of 8-OHdG measurement, and followed by the evaluation of its basic performance. The optimized measurement was highly reproducible (CV = 2.0–2.9%, n= 10). A correlation was observed between the proposed HPLC–ECD method and the column switching method (r= 0.96). [ABSTRACT FROM AUTHOR]

Myostatin is a potent negative regulator of skeletal muscle mass, but its role in human skeletal muscle hypertrophy and atrophy is sparsely described. Muscle biopsies were obtained from young male subjects before and after 30 and 90 days of resistance training as well as after 3, 10, 30, 60 and 90 days of subsequent detraining. Myostatin mRNA increased significantly with detraining. We observed a 28 kDa myostatin immunoreactive protein, which, however, was also present in myostatin knock out mice skeletal muscle. As a novel finding we consistently detected a 10 kDa band, which may represent a mature myostatin monomer under reducing conditions or a novel, unknown myostatin form. Further, we observed a significant increase in this 10 kDa band after 3 days of detraining preceding the rapid type II fiber atrophy, in which almost half of the acquired fiber area was lost after only 10 days of detraining. Accordingly, an increase in the level of the 10 kDa protein is associated with rapid type II fiber atrophy, suggesting myostatin-mediated specific type II fiber atrophy, which in combination with our mRNA data support a role for myostatin in the negative regulation of adult human skeletal muscle mass. [ABSTRACT FROM AUTHOR]

Yang S-Y, Ko H-M, Kang J-H, Moon Y-H, Yoo H-I, Jung N-R, Kim M-S, Cho J-H, Oh W-M, Kim S-H. Relaxin is up-regulated in the rat ovary by orthodontic tooth movement. Eur J Oral Sci 2011; 119: 115-120. © 2011 Eur J Oral Sci Relaxin (Rln) is an ovarian hormone that stimulates osteoclastic and osteoblastic activities and connective tissue turnover. To investigate the expression of Rln during orthodontic tooth movement, rats were implanted with orthodontic appliances that connected a spring from the upper incisors to the first molar with a 70 cN force. Rats in each group were killed 6, 48, and 144 h after activating the appliance, and the levels of Rln1 and Rln3 expression in the ovary were determined by real-time RT-PCR, northern blots, western blots, and immunofluorescence analyses. The amount of tooth movement induced by the orthodontic force increased in a time-dependent manner. The levels of Rln1 mRNA increased by 12-, 41-, and 263-fold at 6, 48, and 144 h, respectively, after orthodontic tooth movement. The time-dependent increase in the concentration of Rln 1 protein in the ovary was also confirmed by western blotting. Rln 1 was localized in the granulosa cells of the ovarian follicles, and the immunoreactivity against Rln 1 was increased by the movement. In contrast, the concentration of Rln 3 was below the level of detection. The results of this study suggest that local changes in periodontal tissues induced by orthodontic tooth movement may affect Rln1 expression in the ovary. However, further studies are needed to decipher the mechanisms involved and the possible contribution of the increased level of expression of Rln 1 to the tooth movement. [ABSTRACT FROM AUTHOR]

The aim of the study was to elucidate the effect of unloading and reloading on the collagen expression and synthesis rate of myofibrillar proteins in fast-twitch (FT) muscle in relation to changes in muscle strength and motor activity. Northern blot analysis was used for testing the specificity of cDNA probes and protein synthesis rate was measured according to incorporation of radioactive leucine into different protein fractions. Unloading depresses collagen type I and III (p < 0.001), type IV (p < 0.05) and reloading enhances collagen expression in fast-twitch skeletal muscle in comparison with unloading. Enhanced expression of matrix metalloproteinase- 2 continued during the first week of reloading (p < 0.01) and tissue inhibitor of metalloproteinase-2 during reloading (p < 0.05). Changes in collagen expression in FT muscle are in good agreement with changes in myofibrillar protein synthesis during unloading and reloading. In conclusion alterations in extracellular matrix and myofibrillar apparatus in FT skeletal muscle are related to changes in muscle strength and motor activity, are significant in exercise training and determination of recovery periods in the training process as well as in athletes' rehabilitation. [ABSTRACT FROM AUTHOR]

Background: Many studies have shown that short telomere length (TL) is associated with high oxidative stress and various age-related diseases. Parkinson's disease (PD) is an age-related disease, and although its pathogenic mechanism is uncertain, oxidative stress is believed to be implicated in this pathology. The aim of this case-control study was to assess both TL and the different markers of oxidative stress in elderly patients with PD compared to age control subjects. Methods: 20 PD patients and 15 age-matched controls, >65 years were studied. TL was measured by Southern blotting from DNA samples extracted from white blood cells. Superoxide dismutase (SOD) activity and plasma levels of total glutathione and protein carbonyls were determined. Results: There was a trend for lower TL in PD patients: 6.06 ± 0.81 kb in PD versus 6.45± 0.73 kb in controls (p = 0.08). No significant difference was found between the two groups in terms of oxidative stress markers. In controls, age was the main determinant of telomere shortening (r = −0.547; p = 0.03) whereas, in PD patients, telomere shortening was mainly dependent on plasmatic concentrations of carbonyl proteins (r= −0.544; p=0.044). In PD patients, a negative association was observed between plasma carbonyl protein levels and SOD activity (r= − 0.622, p=0.004). Conclusions: In PD, TL is shorter in presence of high oxidative stress as measured by carbonyl protein levels. The absence of telomere attrition with age among patients with PD could reflect a telomere regulation by mechanisms other than age. [ABSTRACT FROM AUTHOR]

Objective: This study investigated the correlation between the chronological age, telomere length in peripheral blood leukocytes and blood laboratory data of female patients with mild hypertension to identify laboratory data that reflect the biological aging of individuals. Design: Cross-sectional population-based study. Setting: Outpatient clinic of the Department of Cardiovascular, Respiratory, and Geriatric Medicine Kyushu University Hospital at Beppu in Japan. Participants: Outpatients with mild hypertension treated with a low dose of amlodipine. Measurements: The laboratory data of female patients were collected and the telomere length parameters in their peripheral blood leukocytes were determined by Southern blotting. Any correlations between the laboratory data and the telomere length parameters were assessed. Results: The patients showed a positive correlation between the telomere length and the high density lipoprotein, albumin, creatinine, hemoglobin levels, red blood cell counts, and a negative correlation with the globulin level. The extent of subtelomeric methylation of long telomeres tended to correlate negatively with the telomeric attrition. Only the creatinine level correlated with subtelomeric methylation, but not with telomeric length. Conclusion: HDL and the albumin/globulin ratio were potential indicators for individual somatic genomic aging. Creatinine may therefore be a useful indicator for a predisposition for telomeric attrition. [ABSTRACT FROM AUTHOR]

Abstract: Background: The effect of opioids on inflammation and immune responses is an important subject of investigation because immunoregulatory cytokines are produced in the central nervous system and opioid receptors are widespread in these cells. Objectives: The aim of this study was to evaluate the immunomodulatory effect of morphine on the C3 expression (both constitutive and proinflammatory cytokine-induced C3 expression) in primary rat astrocytes. Methods: Primary rat astrocytes were untreated or treated with morphine in different concentrations (10–6 to 10–2 M) before incubation without or with 5 U/mL tumor necrosis factor-α (TNF-α), and C3 protein and mRNA expressions were measured. Similarly, astrocytes were treated with 10–3 M morphine and stimulated with other proinflammatory cytokines, including 10 ng/mL interleukin-8 (IL-8) and 5 U/mL IL-1β. Astrocytes were exposed to 10–5 M naloxone for 2 hours before adding morphine, and TNF-α and C3 protein was measured. Tumor growth factor-β (TGF-β) was measured from the supernatants of each proinflammatory cytokine. Results: All results are expressed as mean percentages of C3 production by normalizing C3 without morphine or any cytokine treatment as 100%. Constitutive C3 protein production was decreased at morphine 10–3 M (57.2%) and 10–2 M (30.1%). Pretreatment with morphine suppressed induction of C3 expression at both the protein and mRNA levels in astrocytes stimulated with TNF-α, IL-8, and IL-1β (P < 0.05) in a dose-dependent manner. The inhibition of C3 protein production by morphine (10–3 M; 33%) was partially attenuated by naloxone (52.0%) (P < 0.05). The pretreatment of astrocytes with morphine (10–3 M) before stimulation with TNF-α, IL-8, and IL-1β increased by 33% (P < 0.05), decreased by 15.2% (P < 0.05), and did not change the production of TGF-β protein, respectively. Conclusions: Morphine downregulated both constitutive and proinflammatory cytokine-induced C3 expression of astrocytes at the transcriptional level, but not in a cytokine-specific manner. [Copyright &y& Elsevier]

In Corynebacterium glutamicum, the ArgR protein, a transcriptional repressor, affects the expression level of the argB gene through binding to its promoter region. The argB promoter region (positions -77 to -25) has been found by in vitro electrophoretic mobility shift assay (EMSA) results and in silico analysis to be important for the DNA binding of ArgR. Proline supplementation prevented the DNA binding of ArgR to the argB promoter region and triggered an increase of the argB mRNA level. Additional mutational analyses of the argB promoter region found nucleotides critical for ArgR binding (G located at position -58, C at position -55, and A at position -41 of the argB promoter) in that region. Another transcriptional repressor, FarR, was also demonstrated to bind to the argB promoter region. This binding was delimited to positions -57 to -77 on the argB promoter. FarR has only one putative binding domain located at positions -57 to -77, but this region exactly overlapped with the binding region located from positions -55 to -77 for the binding of ArgR within the argB promoter; thus, if ArgR bound with the argB promoter first, the binding of FarR was not observed in this region. However, if FarR bound to the binding domain located at positions -57 to -77 first, ArgR could bind other binding sites located at positions -49 to -25 within the argB promoter. Finally, this study suggests that ArgR can affect FarR binding to the argB promoter region, as protein binding is dominated by the protein most able to do so. [ABSTRACT FROM AUTHOR]

Abstract: Purpose of the study: Very few is known on genotype II hepatitis A virus (HAV) since it is rarely isolated. From 2002 to 2007, the French observatory of HAV identified six sub-genotype IIA strains of which one from a patient having travelled to West Africa. To investigate the possible African origin of sub-genotype IIA, we determined its prevalence among French travellers in 2008 and characterised its genetic variability. Patients and methods: The 2008 mandatory notification records were screened for travel to Africa. Viral genotype was determined on the nucleotide sequencing of the VP1/2A junction region. The P1 region coding for capsid proteins was used to compare the genetic diversity of IIA isolates to those of other genotypes. Results: In 2008, five out of 54 patients returning from West Africa were infected by IIA strains and an additional “autochthonous” case was identified. Two more African cases were identified in 2009. A total of 14 IIA isolates (eight African and six “autochthonous”) were analysed. Nucleotide and amino-acid variability of IIA sequences was lower than that of the other genotypes. Phylogenetic analysis revealed the clustering of two “autochthonous” cases with African isolates whereas the other ones belonged to a different lineage. Conclusion: Most IIA strains isolated in France are imported by travellers returning from West Africa. However, the unexplained contamination mode of some “autochthonous” cases suggests another geographical origin to discover or a French reservoir to explore. [Copyright &y& Elsevier]

Objective [ABSTRACT FROM AUTHOR]

DNA repair gene alterations may cause a reduction in DNA repair capacity and influence an individual's susceptibility to carcinogenesis. We hypothesized that single nucleotide polymorphisms of DNA repair genes may be a risk factor for prostate cancer (PCa) susceptibility, influencing expression of homologous recombination ( XRCC3) and nonhomologous end-joining ( XRCC7) genes and conferring predisposition to PCa. In a case-control study, genotyping was done in 192 patients with PCa and 224 age matched unrelated healthy controls of similar ethnicity to determine variants in XRCC3 Exon 7 (C18067T, rs861539), IVS5-14 (A17893G, rs1799796), and XRCC7 Intron 8 (G6721T, rs7003908) by polymerase chain reaction-restriction fragment-length polymorphism methods. Variant genotype GG (odds ratio [OR], 2.23; p = 0.003) and combined genotype TG + GG (OR, 1.541; p = 0.049), G allele of XRCC7 Intron 8 (G > T), demonstrated significant risk for PCa (OR, 1.529; p = 0.002). Stratification on bases of Gleason grade and bone metastasis, significant risk with high Gleason grade for CT genotype of XRCC3 Exon 7, and variant genotype GG of XRCC7 Intron 8 were observed. Our results strongly support that common sequence variants (GG) genotype of XRCC7 may increase risk of PCa. G allele being a risk allele in our study also suggests that this polymorphism be used as a marker for the PCa susceptibility. [ABSTRACT FROM AUTHOR]

Objective: To develop and validate a whole genome amplification and single nucleotide polymorphism (SNP) microarray protocol for accurate single cell 24 chromosome aneuploidy screening. Design: Prospective, randomized, and blinded study. Setting: Academic reproductive medicine center. Patient(s): Multiple euploid and aneuploid cell lines were obtained from a public repository and blastomeres were obtained after biopsy of cleavage stage embryos from 78 patients undergoing IVF. Main Outcome Measure(s): Accuracy of copy number assignment and consistency of individual SNPs, whole chromosomes, and single cell aneuploidy status were determined. Intervention(s): None. Result(s): Single cells extracted from karyotypically defined cell lines provided 99.2% accuracy for individual SNPs, 99.8% accuracy for whole chromosomes, and 98.6% accuracy when applying a quality control threshold for the overall assignment of aneuploidy status. The concurrence for more than 80 million SNPs in 335 single blastomeres was 96.5%. Conclusion(s): We have established and validated a SNP microarray-based single cell aneuploidy screening technology. Clinical validation studies are underway to determine the predictive value of this methodology. [ABSTRACT FROM AUTHOR]

Atomic force microscopy, which is normally used for DNA imaging to gain qualitative results, can also be used for quantitative DNA research, at a single-molecular level. Here, we evaluate the performance of AFM imaging specifically for quantifying supercoiled and relaxed plasmid DNA fractions within a mixture, and compare the results with the bulk material analysis method, gel electrophoresis. The advantages and shortcomings of both methods are discussed in detail. Gel electrophoresis is a quick and well-established quantification method. However, it requires a large amount of DNA, and needs to be carefully calibrated for even slightly different experimental conditions for accurate quantification. AFM imaging is accurate, in that single DNA molecules in different conformations can be seen and counted. When used carefully with necessary correction, both methods provide consistent results. Thus, AFM imaging can be used for DNA quantification, as an alternative to gel electrophoresis. [ABSTRACT FROM AUTHOR]