Efficient methodology to produce a duloxetine precursor using whole cells of Rhodotorula rubra

Different types of yeasts were employed as biocatalysts in the reduction of \u3b2-ketonitriles. The red microorganism, Rhodotorula rubra, was selected as the best performing catalyst in the reduction of different substituted ketonitriles giving total stereoselectivity in most cases (90-99% ee). In particular, its use as fresh and lyophilised cells was expanded to a semi-preparative scale for the production of the duloxetine precursor 1a. R. rubra was screened in the reduction of alkylation products in comparison with Pichia henricii for assignment of configuration of products 2a and 11a after derivatisation with S-MPA

Complete genome sequence of the epidemic and highly virulent CTX-M-15-producing H30-Rx subclone of Escherichia coli ST131

We report the complete genome sequence, including five complete plasmid sequences, of Escherichia coli ST131 isolate JJ1886. The isolate was obtained in 2007 in the United States from a patient with fatal urosepsis and belongs to the virulent, CTX-M-15-producing H30-Rx sublineage

Preparation of Sterically Demanding 2,2-Disubstituted-2-Hydroxy Acids by Enzymatic Hydrolysis

Preparation of optically-pure derivatives of 2-hydroxy-2-(3-hydroxyphenyl)-2-phenylacetic acid of general structure 2 was accomplished by enzymatic hydrolysis of the correspondent esters. A screening with commercial hydrolases using the methyl ester of 2-hydroxy-2-(3-hydroxyphenyl)-2-phenylacetic acid (1a) showed that crude pig liver esterase (PLE) was the only preparation with catalytic activity. Low enantioselectivity was observed with substrates 1a\u2013d, whereas PLE-catalysed hydrolysis of 1e proceeded with good enantioselectivity (E = 28), after optimization. Enhancement of the enantioselectivity was obtained by chemical re-esterification of enantiomerically enriched 2e, followed by sequential enzymatic hydrolysis with PLE. The preparation of optically-pure (S)-2e was validated on multi-milligram scale

Male circumcision significantly reduces prevalence and load of genital anaerobic bacteria

Male circumcision reduces female-to-male HIV transmission. Hypothesized mechanisms for this protective effect include decreased HIV target cell recruitment and activation due to changes in the penis microbiome. We compared the coronal sulcus microbiota of men from a group of uncircumcised controls (n = 77) and from a circumcised intervention group (n = 79) at enrollment and year 1 follow-up in a randomized circumcision trial in Rakai, Uganda. We characterized microbiota using16S rRNA gene-based quantitative PCR (qPCR) and pyrosequencing, log response ratio (LRR), Bayesian classification, nonmetric multidimensional scaling (nMDS), and permutational multivariate analysis of variance (PerMANOVA). At baseline, men in both study arms had comparable coronal sulcus microbiota; however, by year 1, circumcision decreased the total bacterial load and reduced microbiota biodiversity. Specifically, the prevalence and absolute abundance of 12 anaerobic bacterial taxa decreased significantly in the circumcised men. While aerobic bacterial taxa also increased postcircumcision, these gains were minor. The reduction in anaerobes may partly account for the effects of circumcision on reduced HIV acquisition. IMPORTANCE The bacterial changes identified in this study may play an important role in the HIV risk reduction conferred by male circumcision. Decreasing the load of specific anaerobes could reduce HIV target cell recruitment to the foreskin. Understanding the mechanisms that underlie the benefits of male circumcision could help to identify new intervention strategies for decreasing HIV transmission, applicable to populations with high HIV prevalence where male circumcision is culturally less acceptable

The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes

<p>Abstract</p> <p>Background</p> <p>A computational method (called p53HMM) is presented that utilizes Profile Hidden Markov Models (PHMMs) to estimate the relative binding affinities of putative p53 response elements (REs), both p53 single-sites and cluster-sites. These models incorporate a novel "Corresponded Baum-Welch" training algorithm that provides increased predictive power by exploiting the redundancy of information found in the repeated, palindromic p53-binding motif. The predictive accuracy of these new models are compared against other predictive models, including position specific score matrices (PSSMs, or weight matrices). We also present a new dynamic acceptance threshold, dependent upon a putative binding site's distance from the Transcription Start Site (TSS) and its estimated binding affinity. This new criteria for classifying putative p53-binding sites increases predictive accuracy by reducing the false positive rate.</p> <p>Results</p> <p>Training a Profile Hidden Markov Model with corresponding positions matching a combined-palindromic p53-binding motif creates the best p53-RE predictive model. The p53HMM algorithm is available on-line: <url>http://tools.csb.ias.edu</url></p> <p>Conclusion</p> <p>Using Profile Hidden Markov Models with training methods that exploit the redundant information of the homotetramer p53 binding site provides better predictive models than weight matrices (PSSMs). These methods may also boost performance when applied to other transcription factor binding sites.</p

Health-related quality of life and utilities in gastric premalignant conditions and malignant lesions: a multicentre study in a high prevalence country

BACKGROUND AND AIMS: A recent review of economic studies relating to gastric cancer revealed that authors use different tests to estimate utilities in patients with and without gastric cancer. Our aim was to determine the utilities of gastric premalignant conditions and adenocarcinoma with a single standardized health measure instrument. METHODS: Cross-sectional nationwide study of patients undergoing upper endoscopy (n=1,434) using the EQ-5D-5L quality of life (QoL) questionnaire. RESULTS: According to EQ-5D-5L, utilities in individuals without gastric lesions were 0.78 (95% confidence interval: 0.76-0.80), with gastric premalignant conditions 0.79 (0.77-0.81), previously treated for gastric cancer 0.77 (0.73-0.81) and with present cancer 0.68 (0.55-0.81). Self-reported QoL according to the visual analogue scale (VAS) for the same groups were 0.67 (0.66-0.69), 0.67 (0.66-0.69), 0.62 (0.59-0.65) and 0.62 (0.54-0.70) respectively. Utilities were consistently lower in women versus men (no lesions 0.71 vs. 0.78; premalignant conditions 0.70 vs. 0.82; treated for cancer 0.72 vs. 0.78 and present cancer 0.66 vs. 0.70). CONCLUSION: The health-related QoL utilities of patients with premalignant conditions are similar to those without gastric diseases whereas patients with present cancer show decreased utilities. Moreover, women had consistently lower utilities than men. These results confirm that the use of a single standardized instrument such as the EQ-5D-5L for all stages of the gastric carcinogenesis cascade is feasible and that it captures differences between conditions and gender dissimilarities, being relevant information for authors pretending to conduct further cost-utility analysis

The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer.

The detailed molecular characterization of lethal cancers is a prerequisite to understanding resistance to therapy and escape from cancer immunoediting. We performed extensive multi-platform profiling of multi-regional metastases in autopsies from 10 patients with therapy-resistant breast cancer. The integrated genomic and immune landscapes show that metastases propagate and evolve as communities of clones, reveal their predicted neo-antigen landscapes, and show that they can accumulate HLA loss of heterozygosity (LOH). The data further identify variable tumor microenvironments and reveal, through analyses of T cell receptor repertoires, that adaptive immune responses appear to co-evolve with the metastatic genomes. These findings reveal in fine detail the landscapes of lethal metastatic breast cancer.CRUK

Fuzzy Tandem Repeats Containing p53 Response Elements May Define Species-Specific p53 Target Genes

Evolutionary forces that shape regulatory networks remain poorly understood. In mammals, the Rb pathway is a classic example of species-specific gene regulation, as a germline mutation in one Rb allele promotes retinoblastoma in humans, but not in mice. Here we show that p53 transactivates the Retinoblastoma-like 2 (Rbl2) gene to produce p130 in murine, but not human, cells. We found intronic fuzzy tandem repeats containing perfect p53 response elements to be important for this regulation. We next identified two other murine genes regulated by p53 via fuzzy tandem repeats: Ncoa1 and Klhl26. The repeats are poorly conserved in evolution, and the p53-dependent regulation of the murine genes is lost in humans. Our results indicate a role for the rapid evolution of tandem repeats in shaping differences in p53 regulatory networks between mammalian species

Human single-nucleotide polymorphisms alter p53 sequence-specific binding at gene regulatory elements

p53 coordinates the expression of an intricate network of genes in response to stress signals. Sequence-specific DNA binding is essential for p53-mediated tumor suppression. We evaluated the impact of single-nucleotide polymorphisms (SNPs) in p53 response elements (p53RE) on DNA binding and gene expression in response to DNA damage. Using a bioinformatics approach based on incorporating p53 binding strength into a position weight matrix, we selected 32 SNPs in putative and validated p53REs. The microsphere assay for protein–DNA binding (MAPD) and allele-specific expression analysis was employed to assess the impact of SNPs on p53-DNA binding and gene expression, respectively. Comparing activated p53 binding in nuclear extracts from doxorubicin- or ionizing radiation (IR)-treated human cells, we observed little difference in binding profiles. Significant p53 binding was observed for most polymorphic REs and several displayed binding comparable to the p21 RE. SNP alleles predicted to lower p53 binding indeed reduced binding in 25 of the 32 sequences. Chromatin immunoprecipitation-sequencing in lymphoblastoid cells confirmed p53 binding to seven polymorphic p53 REs in response to doxorubicin. In addition, five polymorphisms were associated with altered gene expression following doxorubicin treatment. Our findings demonstrate an effective strategy to identify and evaluate SNPs that may alter p53-mediated stress responses

Trophic strategy of Atlantirivulus riograndensis (Cyprinodontiformes: Rivulidae), a non-annual rivulid threatened by extinction, in a perennial environment, Brazil)

Rivulidae includes non-annual fish of perennial habitats and annual fish of temporary wetlands. The objective of this research was to investigate the trophic strategy of Atlantirivulus riograndensis in a perennial environment. Sampling occurred in an environmental conservation unit in the Pampa biome, Brazil. Quantification of the diet followed the volumetric method. Consumption of autochthonous material as the main food source of the species followed the pattern of Rivulidae. Species is zooplanktonic when young. Food spectrum is broadened and insectivorousness increases with ontogeny, revealing a specialist trend in the feeding strategy of A. riograndensis. The most diverse feeding occurs in the spring and summer seasons in which the presence of larger fish was more frequent than in other seasons. The increased consumption of microcrustaceans in the fall was related to smaller individuals, captured in greater quantities in this post-reproductive period. The lowest diversity of dietary items occurs during the winter and may reflect the lower diversity of food resources available in this season or the transition from juvenile to adult diet, with consumption of autochthonous Diptera by medium sized fish.Rivulidae inclui peixes não anuais de habitats perenes e peixes anuais de alagados temporários. O objetivo desta pesquisa foi investigar a estratégia trófica de Atlantirivulus riograndensis em um ambiente perene. A amostragem ocorreu em uma unidade de conservação ambiental no bioma Pampa, Brasil. A quantificação da dieta seguiu o método volumétrico. O consumo de material autóctone como principal recurso alimentar da espécie seguiu o padrão da família Rivulidae. A espécie é zooplanctívora quando juvenil. O espectro alimentar é ampliado e a tendência à insetivoria aumenta com a ontogenia, revelando traços especialistas na estratégia alimentar de A. riograndensis. A alimentação mais diversificada ocorreu na primavera e no verão, estações em que a presença dos peixes maiores foi frequente que em outras estações. O aumento no consumo de microcrustáceos no inverno foi relacionado aos indivíduos menores, capturados em maior quantidade neste período pós-reprodutivo. A menor diversidade de itens alimentares ocorreu durante o inverno e pode refletir uma menor diversidade de recursos alimentares disponíveis nesta época do ano ou a transição da dieta de juvenil para adulto, com consumo de Diptera autóctone por peixes de tamanho médio