Fidelity of SNP array genotyping using Epstein Barr virus-transformed B-lymphocyte cell lines: Implications for genome-wide association studies

Background: As availability of primary cells can be limited for genetic studies of human disease, lymphoblastoid cell lines (LCL) are common sources of genomic DNA. LCL are created in a transformation process that entails in vitro infection of human B-lymphocytes with the Epstein-Barr Virus (EBV). Methodology/Principal Findings: To test for genotypic errors potentially induced by the Epstein-Barr Virus transformation process, we compared single nucleotide polymorphism (SNP) genotype calls in peripheral blood mononuclear cells (PBMC) and LCL from the same individuals. The average mismatch rate across 19 comparisons was 0.12% for SNPs with a population call rate of at least 95%, and 0.03% at SNPs with a call rate of at least 99%. Mismatch rates were not correlated across genotype subarrays run on all sample pairs. Conclusions/Significance: Genotypic discrepancies found in PBMC and LCL pairs were not significantly different than control pairs, and were not correlated across subarrays. These results suggest that mismatch rates are minimal with stringent quality control, and that most genotypic discrepancies are due to technical artifacts rather than the EBV transformation process. Thus, LCL likely constitute a reliable DNA source for host genotype analysis. © 2009 Herbeck et al

Steady-state pharmacokinetics of Nevirapine in HIV-1 infected adults in India

Background and Objectives: A variety of demographic factors, sex, and degree of immunosuppression can influence antiretroviral drug concentratians. The authors studied the influence of immune status, sex, and body mass index (BMI) on the steady-state pharmacokinetics of nevirapine delivered as a fixed-dose combination in HIV-1-infected patients in India. Methods: Twenty-six HIV-l-infected adult patients undergoing treatment with nevirapine-based highly active antiretroviral therapy regimens participated in the study. Pharmacokinetic variables were compared between patients divided based an CD4 cell counts, sex, and BMI. Results: Patients with higher BMI had lower peak and trough concentration and exposure of nevirapine than those with lower BMI; none of the differences in the pharmacokinetic variables of nevirapine between the various patient groups was statistically significant. Conclusions: Patients' immune status, sex, or BMI had no impact on the pharmacokinetics of nevirapine. Plasma nevirapine concentrations were maintained within the therapeutic range of the drug in the majority of the patients

Liquid-gas phase transition in nuclear multifragmentation

The equation of state of nuclear matter suggests that at suitable beam energies the disassembling hot system formed in heavy ion collisions will pass through a liquid-gas coexistence region. Searching for the signatures of the phase transition has been a very important focal point of experimental endeavours in heavy ion collisions, in the last fifteen years. Simultaneously theoretical models have been developed to provide information about the equation of state and reaction mechanisms consistent with the experimental observables. This article is a review of this endeavour.Comment: 63 pages, 27 figures, submitted to Adv. Nucl. Phys. Some typos corrected, minor text change

Contribution of Cell Elongation to the Biofilm Formation of Pseudomonas aeruginosa during Anaerobic Respiration

Pseudomonas aeruginosa, a gram-negative bacterium of clinical importance, forms more robust biofilm during anaerobic respiration, a mode of growth presumed to occur in abnormally thickened mucus layer lining the cystic fibrosis (CF) patient airway. However, molecular basis behind this anaerobiosis-triggered robust biofilm formation is not clearly defined yet. Here, we identified a morphological change naturally accompanied by anaerobic respiration in P. aeruginosa and investigated its effect on the biofilm formation in vitro. A standard laboratory strain, PAO1 was highly elongated during anaerobic respiration compared with bacteria grown aerobically. Microscopic analysis demonstrated that cell elongation likely occurred as a consequence of defective cell division. Cell elongation was dependent on the presence of nitrite reductase (NIR) that reduces nitrite (NO2−) to nitric oxide (NO) and was repressed in PAO1 in the presence of carboxy-PTIO, a NO antagonist, demonstrating that cell elongation involves a process to respond to NO, a spontaneous byproduct of the anaerobic respiration. Importantly, the non-elongated NIR-deficient mutant failed to form biofilm, while a mutant of nitrate reductase (NAR) and wild type PAO1, both of which were highly elongated, formed robust biofilm. Taken together, our data reveal a role of previously undescribed cell biological event in P. aeruginosa biofilm formation and suggest NIR as a key player involved in such process

Maior sobrevida em pacientes com marcadores imunogenéticos de rápida progressão para a AIDS: subsídios para a assistência de enfermagem

This study sought subsidies for improving nursing care programs for AIDS patients and aimed to verify the influence of changes in sexual behavior, including the adoption of safe sex practices, associated with the survival of AIDS patients with immunogenetic markers of rapid disease progression. 27 AIDS patients were interviewed, with genetic predisposition to rapid progression to AIDS. Genes were typified through the polymerase chain reaction. In spite of the presence of immunogenetic factors, associated with individual predisposition to a rapid evolution of the disease, changes in sexual behavior, including safe sex practices and antiretroviral therapy, may be related to greater survival. This suggests that counseling, detection of risk attitudes and health education, focusing on positive health behavior, are tools nursing must use with HIV-positive patients, with a view to better quality of life and greater survival among these individuals, even among those with genetic predisposition to rapid disease progression.Los autores buscan apoyo para el perfeccionamiento de programas de enfermería, orientados a pacientes con SIDA. La finalidad de este estudio fue la de verificar la influencia del comportamiento sexual en la supervivencia de pacientes con SIDA, portadores de genes asociados a la rápida progresión de la enfermedad. Fueron estudiados 27 pacientes con SIDA. Las tipificaciones de genes fueron realizadas por la reacción en cadena de la polimerasa. No obstante la presencia de factores inmunogenéticos, asociados a la predisposición individual a la rápida evolución de la enfermedad, cambios en el comportamiento sexual, con prácticas sexuales seguras y el uso de terapia antiretroviral, pueden estar relacionados con mayor supervivencia. La orientación, la detección de actitudes de riesgo y la educación de salud con enfoque en el comportamiento positivo de salud son herramientas que la enfermería debe utilizar con portadores del VIH, buscando la mejor calidad de vida y mayor supervivencia de esos individuos, incluso en aquellos que tienen predisposición genética a la rápida progresión de la enfermedad.Com enfoque em subsídios para o aperfeiçoamento de programas de enfermagem, direcionados a pacientes com aids, o presente estudo foi realizado com o objetivo de verificar a influência do comportamento sexual na sobrevida de pacientes com aids, portadores de genes associados à rápida progressão da doença. Foram entrevistados 27 pacientes com aids, geneticamente predispostos à rápida progressão da doença. As tipificações dos genes foram realizadas pela reação em cadeia da polimerase. Os resultados sugerem que, apesar da presença de fatores imunogenéticos, associados à predisposição individual para rápida evolução da doença, as mudanças do comportamento sexual, com adoção de práticas de sexo seguro, junto ao uso da terapia anti-retroviral, podem estar relacionadas com maior sobrevida. O aconselhamento, a detecção de atitudes de risco e a educação para saúde, enfocando o comportamento positivo de saúde, são ferramentas que a enfermagem deve utilizar a portadores do HIV, visando à melhor qualidade de vida e maior sobrevida desses indivíduos, mesmo naqueles geneticamente predispostos à rápida progressão da doença

Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering

<p>Abstract</p> <p>Background</p> <p>Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortunately the scarce availability of data still limits our understanding of the intrinsic characteristics of complex pathologies like cancer: acquiring information for a system understanding of complex reaction networks is time consuming and expensive. Stimulus response experiments (SRE) have been used to gain a deeper insight into the details of biochemical mechanisms underlying cell life and functioning. Optimisation of the input time-profile, however, still remains a major area of research due to the complexity of the problem and its relevance for the task of information retrieval in systems biology-related experiments.</p> <p>Results</p> <p>We have addressed the problem of quantifying the information associated to an experiment using the Fisher Information Matrix and we have proposed an optimal experimental design strategy based on evolutionary algorithm to cope with the problem of information gathering in Systems Biology. On the basis of the theoretical results obtained in the field of control systems theory, we have studied the dynamical properties of the signals to be used in cell stimulation. The results of this study have been used to develop a microfluidic device for the automation of the process of cell stimulation for system identification.</p> <p>Conclusion</p> <p>We have applied the proposed approach to the Epidermal Growth Factor Receptor pathway and we observed that it minimises the amount of parametric uncertainty associated to the identified model. A statistical framework based on Monte-Carlo estimations of the uncertainty ellipsoid confirmed the superiority of optimally designed experiments over canonical inputs. The proposed approach can be easily extended to multiobjective formulations that can also take advantage of identifiability analysis. Moreover, the availability of fully automated microfluidic platforms explicitly developed for the task of biochemical model identification will hopefully reduce the effects of the 'data rich-data poor' paradox in Systems Biology.</p

Differences in hepatitis C virus prevalence and clearance by mode of acquisition among men who have sex with men

We examined the characteristics associated with hepatitis C virus (HCV) antibody (anti-HCV) prevalence and HCV clearance between injection drug using (IDU) and non-IDU men who have sex with men (MSM). Stored serum and plasma samples were tested for anti-HCV and HCV RNA to determine the HCV status of 6925 MSM at enrolment into the Multicentre AIDS Cohort Study (MACS). Prevalence and clearance ratios were calculated to determine the characteristics associated with HCV prevalence and clearance. Multivariable analyses were performed using Poisson regression methods with robust variance estimation. Anti-HCV prevalence was significantly higher among IDU than among non-IDU MSM (42.9% vs 4.0%), while clearance was significantly lower among IDU MSM (11.5% vs 34.5% among non-IDU MSM). HIV infection, Black race, and older age were independently associated with higher prevalence in both groups, while smoking, transfusion history, and syphilis were significantly associated with prevalence only among non-IDU MSM. The rs12979860-C/C genotype was the only characteristic independently associated with HCV clearance in both groups, but the effects of both rs12979860-C/C genotype [clearance ratio (CR) = 4.16 IDUs vs 1.71 non-IDUs; P = 0.03] and HBsAg positivity (CR = 5.06 IDUs vs 1.62 non-IDUs; P = 0.03) were significantly larger among IDU MSM. HIV infection was independently associated with lower HCV clearance only among non-IDU MSM (CR = 0.59, 95% CI = 0.40-0.87). IDU MSM have higher anti-HCV prevalence and lower HCV clearance than non-IDU MSM. Differences in the factors associated with HCV clearance suggest that the mechanisms driving the response to HCV may differ according to the mode of acquisition