Viral self-assembly as a thermodynamic process

The protein shells, or capsids, of nearly all spherelike viruses adopt icosahedral symmetry. In the present Letter, we propose a statistical thermodynamic model for viral self-assembly. We find that icosahedral symmetry is not expected for viral capsids constructed from structurally identical protein subunits and that this symmetry requires (at least) two internal switching configurations of the protein. Our results indicate that icosahedral symmetry is not a generic consequence of free energy minimization but requires optimization of internal structural parameters of the capsid proteins

Hepatitis B and C virus coinfection: a novel model system reveals the absence of direct viral interference.

Coinfection with hepatitis B virus (HBV) and hepatitis C virus (HCV) has been associated with severe liver disease and frequent progression to cirrhosis and hepatocellular carcinoma. Clinical evidence suggests reciprocal replicative suppression of the two viruses, or viral interference. However, interactions between HBV and HCV have been difficult to study due to the lack of appropriate model systems. We have established a novel model system to investigate interactions between HBV and HCV. Stable Huh-7 cell lines inducibly replicating HBV were transfected with selectable HCV replicons or infected with cell culture-derived HCV. In this system, both viruses were found to replicate in the same cell without overt interference. Specific inhibition of one virus did not affect the replication and gene expression of the other. Furthermore, cells harboring replicating HBV could be infected with cell culture-derived HCV, arguing against superinfection exclusion. Finally, cells harboring replicating HBV supported efficient production of infectious HCV. Conclusion: HBV and HCV can replicate in the same cell without evidence for direct interference in vitro. Therefore, the viral interference observed in coinfected patients is probably due to indirect mechanisms mediated by innate and/or adaptive host immune responses. These findings provide new insights into the pathogenesis of HBV-HCV coinfection and may contribute to its clinical management in the future.

Altura de Pastejo de Braquiária e Carga Animal Limitada pelos Atributos Físicos do Solo em Sistema Integração Lavoura-Pecuária com Soja

O manejo da altura de pastejo das forrageiras pelos bovinos pode comprometer os atributos físicos do solo. O objetivo deste trabalho foi avaliar a influência da altura de pastejo de braquiária (Urochloa ruziziensis) e a carga animal média, após três anos de sistema integração lavoura-pecuária com soja, nos atributos físicos de um Latossolo Vermelho distrófico típico. O delineamento experimental foi de blocos casualizados, com três repetições. Cinco tratamentos com 10, 20, 30 e 40 cm de altura de pastejo, após 84 dias de pastejo contínuo mantidos com carga variável de bovinos, e um tratamento testemunha sem pastejo foram avaliados em parcelas experimentais de 1 ha. Em novembro de 2012, após o terceiro período de pastejo, com carga animal média de 1.262, 919, 892 e 724 kg ha-1 de peso vivo, respectivamente, para as alturas de pastejo de 10, 20, 30 e 40 cm, coletaram-se amostras indeformadas de solo nas camadas de 0-10, 10-20 e 20-30 cm, as quais foram utilizadas para determinar as curvas de retenção de água e de resistência do solo à penetração e a densidade do solo (Ds), bem como para calcular o intervalo hídrico ótimo (IHO). A menor Ds ocorreu na camada de 0-10 cm para a altura de pastejo de 31 cm da braquiária que correspondeu a 72 % da carga animal máxima. O maior IHO ocorreu na camada de 10-20 cm para a altura de pastejo de 23 cm da braquiária que correspondeu a 83 % da carga animal máxima. O manejo da altura de pastejo da braquiária foi limitado em 23 cm pela maior carga animal e melhores atributos físicos na camada de 10-20 cm do Latossolo Vermelho distrófico típico.

Capacidade de Suporte de Carga do Solo em Sistemas de Produção de Laranja Conservacionistas

Sistemas conservacionistas em pomares de laranja podem aumentar a capacidade de suporte de carga do solo minimizando os seus riscos de compactação. O objetivo deste trabalho foi avaliar a capacidade de suporte de carga por meio da pressão de preconsolidação e sua dependência a conteúdo de água, densidade e carbono orgânico de um Argissolo Vermelho distrófico latossólico, após 18 anos de implantação de plantas de cobertura permanentes nas entrelinhas de um pomar de laranja. O delineamento experimental foi de blocos ao acaso, com três repetições. Foram estudados três tratamentos de manejo por meio de roçadas nas entrelinhas do pomar, desde o plantio do pomar em 1993: gramínea Paspalum notatum, leguminosa Arachis pintoi e vegetação espontânea. Cento e oito amostras indeformadas de solo foram coletadas em 2011 sob o rodado e entrerrodado das máquinas nas estrelinhas do pomar com textura arenosa nas camadas de 0,00-0,10 m (87 g kg-1 de argila) e 0,10-0,20 m (122 g kg-1 de argila). Determinaram-se as pressões de preconsolidação das curvas de compressão do solo (25, 50, 100, 200, 400, 800 e 1.600 kPa) em conteúdos de água sob três potenciais (-80, -330 e -1.000 hPa), a densidade do solo e o teor de carbono orgânico do solo. A pressão de preconsolidação não foi dependente do conteúdo de água, da densidade do solo e do teor de carbono orgânico do solo. A pressão de preconsolidação sob o rodado na camada de 0,00-0,10 m foi menor nos tratamentos leguminosa e vegetação espontânea. A manutenção permanente da gramínea manejada com roçadas nas entrelinhas do pomar de laranja proporcionou maior capacidade de suporte de carga do solo sob o rodado na camada superficial arenosa.

La estimación de la carga de trabajo del estudiante. Análisis de una propuesta para los estudios universitarios de las artes

El artículo analiza la carga de trabajo autónomo del estudiante en algunas asignaturas de los estudios universitarios de las artes. Este aspecto constituye la faceta más dificultosa y controvertida del sistema europeo de transferencia y acumulación de créditos, y por consiguiente, la razón principal que recomienda la verificación regular de su ajuste en las nuevas titulaciones. Tras pasar sucinta revista a la naturaleza del crédito europeo y a la problemática que afecta al cálculo de las horas de dicho trabajo autónomo, se propone un procedimiento de estimación basado en las actividades realizadas por el alumno en el marco de dos modelos de carpeta de aprendizaje. La carga de trabajo total del estudiante en la asignatura sería así el producto de añadir, a la estimación anterior, las horas dedicadas a los otros bloques recogidos inicialmente en el programa: el trabajo en el aula y las actividades de aprendizaje guiadas.

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.

HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran >3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations to a total of 48 HIV-1 amino acid variants (p<2.4 × 10(-12)). All associated SNPs mapped to the HLA class I region. Clinical relevance of host and pathogen variation was assessed using VL results. We identified two critical advantages to the use of viral variation for identifying host factors: (1) association signals are much stronger for HIV-1 sequence variants than VL, reflecting the 'intermediate phenotype' nature of viral variation; (2) association testing can be run without any clinical data. The proposed genome-to-genome approach highlights sites of genomic conflict and is a strategy generally applicable to studies of host-pathogen interaction. DOI:http://dx.doi.org/10.7554/eLife.01123.001.

Raw sewage harbors diverse viral populations

At this time, about 3,000 different viruses are recognized, but metagenomic studies suggest that these viruses are a small fraction of the viruses that exist in nature. We have explored viral diversity by deep sequencing nucleic acids obtained from virion populations enriched from raw sewage. We identified 234 known viruses, including 17 that infect humans. Plant, insect, and algal viruses as well as bacteriophages were also present. These viruses represented 26 taxonomic families and included viruses with single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), positive-sense ssRNA [ssRNA(¿)], and dsRNA genomes. Novel viruses that could be placed in specific taxa represented 51 different families, making untreated wastewater the most diverse viral metagenome (genetic material recovered directly from environmental samples) examined thus far. However, the vast majority of sequence reads bore little or no sequence relation to known viruses and thus could not be placed into specific taxa. These results show that the vast majority of the viruses on Earth have not yet been characterized. Untreated wastewater provides a rich matrix for identifying novel viruses and for studying virus diversity.

Viral superantigen-induced negative selection of TCR transgenic CD4+ CD8+ thymocytes depends on activation, but not proliferation.

T-cell negative selection, a process by which intrathymic immunological tolerance is induced, involves the apoptosis-mediated clonal deletion of potentially autoreactive T cells. Although different experimental approaches suggest that this process is triggered as the result of activation-mediated cell death, the signal transduction pathways underlying this process is not fully understood. In the present report we have used an in vitro system to analyze the cell activation and proliferation requirements for the deletion of viral superantigen (SAg)-reactive Vbeta8.1 T-cell receptor (TCR) transgenic (TG) thymocytes. Our results indicate that in vitro negative selection of viral SAg-reactive CD4+ CD8+ thymocytes is dependent on thymocyte activation but does not require the proliferation of the negatively signaled thymocytes.

Clinical Disease Severity of Respiratory Viral Co-Infection versus Single Viral Infection: A Systematic Review and Meta-Analysis.

BACKGROUND: Results from cohort studies evaluating the severity of respiratory viral co-infections are conflicting. We conducted a systematic review and meta-analysis to assess the clinical severity of viral co-infections as compared to single viral respiratory infections. METHODS: We searched electronic databases and other sources for studies published up to January 28, 2013. We included observational studies on inpatients with respiratory illnesses comparing the clinical severity of viral co-infections to single viral infections as detected by molecular assays. The primary outcome reflecting clinical disease severity was length of hospital stay (LOS). A random-effects model was used to conduct the meta-analyses. RESULTS: Twenty-one studies involving 4,280 patients were included. The overall quality of evidence applying the GRADE approach ranged from moderate for oxygen requirements to low for all other outcomes. No significant differences in length of hospital stay (LOS) (mean difference (MD) -0.20 days, 95% CI -0.94, 0.53, p = 0.59), or mortality (RR 2.44, 95% CI 0.86, 6.91, p = 0.09) were documented in subjects with viral co-infections compared to those with a single viral infection. There was no evidence for differences in effects across age subgroups in post hoc analyses with the exception of the higher mortality in preschool children (RR 9.82, 95% CI 3.09, 31.20, p<0.001) with viral co-infection as compared to other age groups (I2 for subgroup analysis 64%, p = 0.04). CONCLUSIONS: No differences in clinical disease severity between viral co-infections and single respiratory infections were documented. The suggested increased risk of mortality observed amongst children with viral co-infections requires further investigation.

How reliable is an undetectable viral load?

OBJECTIVES: An article by the Swiss AIDS Commission states that patients with stably suppressed viraemia [i.e. several successive HIV-1 RNA plasma concentrations (viral loads, VL) below the limits of detection during 6 months or more of highly active antiretroviral therapy (HAART)] are unlikely to be infectious. Questions then arise: how reliable is the undetectability of the VL, given the history of measures? What factors determine reliability? METHODS: We assessed the probability (henceforth termed reliability) that the n+1 VL would exceed 50 or 1000 HIV-1 RNA copies/mL when the nth one had been <50 copies/mL in 6168 patients of the Swiss HIV Cohort Study who were continuing to take HAART between 2003 and 2007. General estimating equations were used to analyse potential factors of reliability. RESULTS: With a cut-off at 50 copies/mL, reliability was 84.5% (n=1), increasing to 94.5% (n=5). Compliance, the current type of HAART and the first antiretroviral therapy (ART) received (HAART or not) were predictive factors of reliability. With a cut-off at 1000 copies/mL, reliability was 97.5% (n=1), increasing to 99.1% (n=4). Chart review revealed that patients had stopped their treatment, admitted to major problems with compliance or were taking non-HAART ART in 72.2% of these cases. Viral escape caused by resistance was found in 5.6%. No explanation was found in the charts of 22.2% of cases. CONCLUSIONS: After several successive VLs at <50 copies/mL, reliability reaches approximately 94% with a cut-off of 50 copies/mL and approximately 99% with a cut-off at 1000 copies/mL. Compliance is the most important factor predicting reliability.

Polymorphisms in toll-like receptor 4 and toll-like receptor 9 influence viral load in a seroincident cohort of HIV-1-infected individuals.

OBJECTIVES: Toll-like receptors (TLRs) are innate immune sensors that are integral to resisting chronic and opportunistic infections. Mounting evidence implicates TLR polymorphisms in susceptibilities to various infectious diseases, including HIV-1. We investigated the impact of TLR single nucleotide polymorphisms (SNPs) on clinical outcome in a seroincident cohort of HIV-1-infected volunteers. DESIGN: We analyzed TLR SNPs in 201 antiretroviral treatment-naive HIV-1-infected volunteers from a longitudinal seroincident cohort with regular follow-up intervals (median follow-up 4.2 years, interquartile range 4.4). Participants were stratified into two groups according to either disease progression, defined as peripheral blood CD4(+) T-cell decline over time, or peak and setpoint viral load. METHODS: Haplotype tagging SNPs from TLR2, TLR3, TLR4, and TLR9 were detected by mass array genotyping, and CD4(+) T-cell counts and viral load measurements were determined prior to antiretroviral therapy initiation. The association of TLR haplotypes with viral load and rapid progression was assessed by multivariate regression models using age and sex as covariates. RESULTS: Two TLR4 SNPs in strong linkage disequilibrium [1063 A/G (D299G) and 1363 C/T (T399I)] were more frequent among individuals with high peak viral load compared with low/moderate peak viral load (odds ratio 6.65, 95% confidence interval 2.19-20.46, P < 0.001; adjusted P = 0.002 for 1063 A/G). In addition, a TLR9 SNP previously associated with slow progression was found less frequently among individuals with high viral setpoint compared with low/moderate setpoint (odds ratio 0.29, 95% confidence interval 0.13-0.65, P = 0.003, adjusted P = 0.04). CONCLUSION: This study suggests a potentially new role for TLR4 polymorphisms in HIV-1 peak viral load and confirms a role for TLR9 polymorphisms in disease progression.

Bridging basic science and clinical research - The EASL Monothematic Conference on Translational Research in Viral Hepatitis.

The EASL Monothematic Conference on Translational Research in Viral Hepatitis brought together a group of leading scientists and clinicians working on both, basic and clinical aspects of viral hepatitis, thereby building bridges from bench to bedside. This report recapitulates the presentations and discussions at the conference held in Lyon, France on November 29-30, 2013. In recent years, great advances have been made in the field of viral hepatitis, particularly in hepatitis C virus (HCV) infection. The identification of IL28B genetic polymorphisms as a major determinant for spontaneous and treatment-induced HCV clearance was a seminal discovery. Currently, hepatologists are at the doorstep of even greater advances, with the advent of a wealth of directly acting antivirals (DAAs) against HCV. Indeed, promising results have accumulated over the last months and few years, showing sustained virological response (SVR) rates of up to 100% with interferon-free DAA combination therapies. Thus, less than 25years after its identification, HCV infection may soon be curable in the vast majority of patients, highlighting the great success of HCV research over the last decades. However, viral hepatitis and its clinical complications such as liver cirrhosis and hepatocellular carcinoma (HCC) remain major global challenges. New therapeutic strategies to tackle hepatitis B virus (HBV) and hepatitis D virus (HDV) infection are needed, as current therapies have undeniable limitations. Nucleoside/nucleotide analogues (NUC) can efficiently control HBV replication and reduce or even reverse liver damage. However, these drugs have to be given for indefinite periods in most patients to maintain virological and biochemical responses. Although sustained responses off treatment can be achieved by treatment with (pegylated) interferon-α, only about 10-30% of patients effectively resolve chronic hepatitis B. It was the goal of this conference to review the progress made over the last years in chronic viral hepatitis research and to identify key questions that need to be addressed in order to close the gap between basic and clinical research and to develop novel preventive and treatment approaches for this most common cause of liver cirrhosis and HCC.

Retenção de nitrato num solo de carga variável, influenciada por adubação fosfatada e calagem

O presente trabalho teve como objetivo avaliar o efeito da aplicação de fósforo e de calcário sobre a capacidade de retenção de nitrato (CRN) de um solo de carga variável. Entre 1982 e 1989, um Latossolo Vermelho-Escuro argiloso de cerrado foi cultivado com milho, trigo, arroz e feijão (2, 4, 5 e 6 cultivos, respectivamente), recebendo adubação fosfatada (total de 1530 kg/ha de P2O5: 90 kg/ha por cultivo) ou adubação fosfatada+calagem (5,5 t/ha de calcário dolomítico: 2,5 e 3,0 t/ha em 1982 e 1985, respectivamente). Testes realizados em amostras coletadas em 1991 mostraram que o solo apresentava CRN negativa (exclusão do nitrato) na camada arável (0-20 cm), e positiva e crescente com a profundidade, nas camadas subjacentes. Os tratamentos diminuíram a CRN original do solo na camada de 20-60 cm, sendo esse efeito mais intenso no tratamento com calagem. A adubação fosfatada e, especialmente, a calagem, exerceram considerável efeito residual sobre a capacidade de retenção de nitrato do latossolo estudado.

Dynamic models of viral replication and latency.

PURPOSE OF REVIEW: HIV targets primary CD4(+) T cells. The virus depends on the physiological state of its target cells for efficient replication, and, in turn, viral infection perturbs the cellular state significantly. Identifying the virus-host interactions that drive these dynamic changes is important for a better understanding of viral pathogenesis and persistence. The present review focuses on experimental and computational approaches to study the dynamics of viral replication and latency. RECENT FINDINGS: It was recently shown that only a fraction of the inducible latently infected reservoirs are successfully induced upon stimulation in ex-vivo models while additional rounds of stimulation make allowance for reactivation of more latently infected cells. This highlights the potential role of treatment duration and timing as important factors for successful reactivation of latently infected cells. The dynamics of HIV productive infection and latency have been investigated using transcriptome and proteome data. The cellular activation state has shown to be a major determinant of viral reactivation success. Mathematical models of latency have been used to explore the dynamics of the latent viral reservoir decay. SUMMARY: Timing is an important component of biological interactions. Temporal analyses covering aspects of viral life cycle are essential for gathering a comprehensive picture of HIV interaction with the host cell and untangling the complexity of latency. Understanding the dynamic changes tipping the balance between success and failure of HIV particle production might be key to eradicate the viral reservoir.