Analysis of biological and technical variability in gene expression assays from formalin-fixed paraffin-embedded classical Hodgkin lymphomas

Formalin-fixed paraffin-embedded (FFPE) tissues are invaluable sources of biological material for research and diagnostic purposes. In this study, we aimed to identify biological and technical variability in RT-qPCR TaqMan® assays performed with FFPE-RNA from lymph nodes of classical Hodgkin lymphoma samples. An ANOVA-nested 6-level design was employed to evaluate BCL2, CASP3, IRF4, LYZ and STAT1 gene expression. The most variable genes were CASP3 (low expression) and LYZ (high expression). Total variability decreased after normalization for all genes, except by LYZ. Genes with moderate and low expression were identified and suffered more the effects of the technical manipulation than high-expression genes. Pre-amplification was shown to introduce significant technical variability, which was partially alleviated by lowering to a half the amount of input RNA. Ct and Cy0 quantification methods, based on cycle-threshold and the kinetic of amplification curves, respectively, were compared. Cy0 method resulted in higher quantification values, leading to the decrease of total variability in CASP3 and LYZ genes. The mean individual noise was 0.45 (0.31 to 0.61 SD), indicating a variation of gene expression over ~1.5 folds from one case to another. We showed that total variability in RT-qPCR from FFPE-RNA is not higher than that reported for fresh complex tissues, and identified gene-, and expression level-sources of biological and technical variability, which can allow better strategies for designing RT-qPCR assays from highly degraded and inhibited samples

Differential Effects of Migration and Deportation on HIV Infection among Male and Female Injection Drug Users in Tijuana, Mexico

HIV prevalence is rising, especially among high risk females in Tijuana, Baja California, a Mexico-US border city situated on major migration and drug trafficking routes. We compared factors associated with HIV infection among male and female injection drug users (IDUs) in Tijuana in an effort to inform HIV prevention and treatment programs. IDUs aged ≥18 years were recruited using respondent-driven sampling and underwent testing for HIV, syphilis and structured interviews. Logistic regression identified correlates of HIV infection, stratified by gender. Among 1056 IDUs, most were Mexican-born but 67% were born outside Tijuana. Reasons for moving to Tijuana included deportation from the US (56% for males, 29% for females), and looking for work/better life (34% for females, 15% for males). HIV prevalence was higher in females versus males (10.2% vs. 3.5%, p = 0.001). Among females (N = 158), factors independently associated with higher HIV prevalence included younger age, lifetime syphilis infection and living in Tijuana for longer durations. Among males (N = 898), factors independently associated with higher HIV prevalence were syphilis titers consistent with active infection, being arrested for having ‘track-marks’, having larger numbers of recent injection partners and living in Tijuana for shorter durations. An interaction between gender and number of years lived in Tijuana regressed on HIV infection was significant (p = 0.03). Upon further analysis, deportation from the U.S. explained the association between shorter duration lived in Tijuana and HIV infection among males; odds of HIV infection were four-fold higher among male injectors deported from the US, compared to other males, adjusting for all other significant correlates (p = 0.002). Geographic mobility has a profound influence on Tijuana's evolving HIV epidemic, and its impact is significantly modified by gender. Future studies are needed to elucidate the context of mobility and HIV acquisition in this region, and whether US immigration policies adversely affect HIV risk

Track D Social Science, Human Rights and Political Science

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138414/1/jia218442.pd

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

Padrões alimentares de adolescentes obesos e diferentes repercussões metabólicas Dietary patterns of obese adolescents and different metabolic effects

OBJETIVO: Avaliar a associação de padrões alimentares com alterações metabólicas em adolescentes obesos. MÉTODOS: Estudo transversal envolvendo 76 estudantes (ambos os sexos, 14-19 anos, IMC³P95 e Tanner ³4) de escolas públicas da cidade de São Paulo, Brasil. Foram coletados dados antropométricos e bioquímicos, e aplicados questionários com informações sociodemográficas e registro alimentar de 4 dias, entre 2006 e 2007. Escores fatoriais foram obtidos na análise fatorial e, após ajustes, três padrões alimentares identificados foram associados a fatores de risco biológico por regressão linear múltipla. RESULTADOS: O padrão Tradicional (arroz e massas, feijões, carnes vermelhas, embutidos, óleos e doces) foi positivamente associado com insulina, glicemia e triglicérides e negativamente associado com lipoproteína de alta densidade. O padrão Em Transição (peixe, aves, ovos, pães, manteiga, leite e derivados, hortaliças, frutas, sucos de frutas e açúcar refinado) apresentou as mesmas associações, além de associação similar com a pressão arterial diastólica. O padrão Fast Food (cafeteria, hambúrguer, maionese, bolacha, bolos e tortas, chocolate e refrigerantes) apresentou associação positiva com o colesterol, lipoproteína de baixa densidade e pressão arterial sistólica e diastólica, e associação negativa com insulina e lipoproteína de alta densidade. CONCLUSÃO: Os padrões Tradicional e Em transição apresentaram associações diferentes com o metabolismo lipídico e glicídico quando comparados com o padrão Fast Food. Os três padrões podem ser considerados obesogênicos, porém o padrão Fast Food pareceu ser o mais aterogênico e promotor de hipertensão arterial.<br>OBJECTIVE: This study assessed the association between dietary patterns and metabolic changes in obese adolescents. METHODS: This was a cross-sectional study of 76 students (both genders, 14-19 years old, BMI³P95 and Tanner stage ³4) enrolled in public schools from 2006 to 2007 in São Paulo city, Brazil. A sociodemographic questionnaire and 4-day food record were administered and anthropometric and biochemical data were collected. Scores for dietary patterns were assessed by factor analysis and after potential confounders were controlled, multilinear regression was used to associate the three identified patterns with biological risk factors. RESULTS: The Traditional Pattern (rice and cereals, beans, red meat, sausage, oils and sweets) was positively associated with insulin, blood glucose and triglycerides and negatively associated with high-density lipoprotein. The In-Transition pattern (fish, poultry, eggs, bread, butter, milk and dairy products, vegetables, fruits, fruit juice and white sugar), presented the same positive associations in addition to an association with diastolic blood pressure. The Fast Food pattern (high fat bakery products, hamburger, mayonnaise, cookies and crackers, chocolate and sodas) presented a positive association with cholesterol, low-density lipoprotein, systolic and diastolic blood pressure and a negative association with insulin and high-density lipoprotein. CONCLUSION: The Traditional and In-Transition patterns were differently related to glucose and lipid metabolism when compared with the fast food pattern. The three patterns could be considered obesogenic, however the Fast Food pattern seems to be the most atherogenic and promoter of hypertension

Improving cardiovascular and renal outcomes in gout: what should we target?

Epidemiological and experimental studies have shown that hyperuricaemia and gout are intricately linked with hypertension, metabolic syndrome, chronic kidney disease and cardiovascular disease. A number of studies suggest that hyperuricaemia and gout are independent risk factors for the development of these conditions and that these conditions account, in part, for the increased mortality rate of patients with gout. In this Review, we first discuss the links between hyperuricaemia, gout and these comorbidities, and present the mechanisms by which uric acid production and gout might favour the development of cardiovascular and renal diseases. We then emphasize the potential benefit of urate-lowering therapies on cardiovascular and renal outcomes in patients with hyperuricaemia. The mechanisms that link elevated serum uric acid levels and gout with these comorbidities seem to be multifactorial, implicating low-grade systemic inflammation and xanthine oxidase (XO) activity, as well as the deleterious effects of hyperuricaemia itself. Patients with asymptomatic hyperuricaemia should be treated by nonpharmacological means to lower their SUA levels. In patients with gout, long-term pharmacological inhibition of XO is a treatment strategy that might also reduce cardiovascular and renal comorbidities, because of its dual effect of lowering SUA levels as well as reducing free-radical production during uric acid formation