Pig α₁-Acid Glycoprotein: Characterization and First Description in Any Species as a Negative Acute Phase Protein.

The serum protein α1-acid glycoprotein (AGP), also known as orosomucoid, is generally described as an archetypical positive acute phase protein. Here, porcine AGP was identified, purified and characterized from pooled pig serum. It was found to circulate as a single chain glycoprotein having an apparent molecular weight of 43 kDa by SDS-PAGE under reducing conditions, of which approximately 17 kDa were accounted for by N-bound oligosaccharides. Those data correspond well with the properties of the protein predicted from the single porcine AGP gene (ORM1, Q29014 (UniProt)), containing 5 putative glycosylation sites. A monoclonal antibody (MAb) was produced and shown to quantitatively and specifically react with all microheterogenous forms of pig AGP as analyzed by 2-D electrophoresis. This MAb was used to develop an immunoassay (ELISA) for quantification of AGP in pig serum samples. The adult serum concentrations of pig AGP were in the range of 1-3 mg/ml in a number of conventional pig breeds while it was lower in Göttingen and Ossabaw minipigs (in the 0.3 to 0.6 mg/ml range) and higher in young (2-5 days old) conventional pigs (mean: 6.6 mg/ml). Surprisingly, pig AGP was found to behave as a negative acute phase protein during a range of experimental infections and aseptic inflammation with significant decreases in serum concentration and in hepatic ORM1 expression during the acute phase response. To our knowledge this is the first description in any species of AGP being a negative acute phase protein

Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes

BACKGROUND: Lineage-specific, or taxonomically restricted genes (TRGs), especially those that are species and strain-specific, are of special interest because they are expected to play a role in defining exclusive ecological adaptations to particular niches. Despite this, they are relatively poorly studied and little understood, in large part because many are still orphans or only have homologues in very closely related isolates. This lack of homology confounds attempts to establish the likelihood that a hypothetical gene is expressed and, if so, to determine the putative function of the protein. METHODOLOGY/PRINCIPAL FINDINGS: We have developed "QIPP" ("Quality Index for Predicted Proteins"), an index that scores the "quality" of a protein based on non-homology-based criteria. QIPP can be used to assign a value between zero and one to any protein based on comparing its features to other proteins in a given genome. We have used QIPP to rank the predicted proteins in the proteomes of Bacteria and Archaea. This ranking reveals that there is a large amount of variation in QIPP scores, and identifies many high-scoring orphans as potentially "authentic" (expressed) orphans. There are significant differences in the distributions of QIPP scores between orphan and non-orphan genes for many genomes and a trend for less well-conserved genes to have lower QIPP scores. CONCLUSIONS: The implication of this work is that QIPP scores can be used to further annotate predicted proteins with information that is independent of homology. Such information can be used to prioritize candidates for further analysis. Data generated for this study can be found in the OrphanMine at http://www.genomics.ceh.ac.uk/orphan_mine

Structural basis for the changed substrate specificity of Drosophila melanogaster deoxyribonucleoside kinase mutant N64D

The Drosophila melanogaster deoxyribonucleoside kinase (Dm-dNK) double mutant N45D/N64D was identified during a previous directed evolution study. This mutant enzyme had a decreased activity towards the natural substrates and decreased feedback inhibition with dTTP, whereas the activity with 3'-modified nucleoside analogs like 3'-azidothymidine (AZT) was nearly unchanged. Here, we identify the mutation N64D as being responsible for these changes. Furthermore, we crystallized the mutant enzyme in the presence of one of its substrates, thymidine, and the feedback inhibitor, dTTP. The introduction of the charged Asp residue appears to destabilize the LID region (residues 167–176) of the enzyme by electrostatic repulsion and no hydrogen bond to the 3'-OH is made in the substrate complex by Glu172 of the LID region. This provides a binding space for more bulky 3'-substituents like the azido group in AZT but influences negatively the interactions between Dm-dNK, substrates and feedback inhibitors based on deoxyribose. The detailed picture of the structure–function relationship provides an improved background for future development of novel mutant suicide genes for Dm-dNK-mediated gene therapy

Problematic parent-infant relationships in two-parent families: prevalence and risk factors in a Brazilian neighborhood Relações problemáticas entre pais e criança em famílias com pai e mãe: prevalência e fatores de risco em um bairro brasileiro

Introduction: Although the quality of parent-child relationships is known to be associated with the offspring's mental health, little is known about the prevalence of problematic relationships in this scenario. This cross-sectional study aims to investigate the prevalence and risk factors of different types of early parent-infant relationships in a Brazilian population group. Methods: During 1 year, all families (n = 230) from an urban community of Porto Alegre, southern Brazil, with 4-month-old infants born in public hospitals were identified, and 148 were fully investigated by two family therapists. This study describes data on the 116 infants with two-parent families. Demographic, obstetric, and relational variables were collected through questionnaires and scales (Parent-Infant Relationship Global Assessment Scale, Global Assessment of Relational Functioning, and Self-Report Questionnaire). Prevalence ratios were calculated, and Poisson regression with robust variance was performed to adjust for covariates. Results: Almost 10% of mothers and 12% of fathers showed at least a significantly perturbed relationship with their 4-month-old infants. Inadequate mother-infant bonding coincided with evidence of paternal mental disorder, poor maternal social network, and discontinuation of breastfeeding at 4 months. A problematic father-infant relationship was associated with a dysfunctional couple relationship and with low infant birth weight. Conclusions: There is a high prevalence of early parent-child relationship problems, suggesting a need for health system interventions. Parent-infant relational problems are prevalent very early in life and more associated with other relational problems than with socioeconomic burden.<br>Introdução: Embora seja consenso que a qualidade das relações pais-filho influencie a saúde mental da prole, pouco se sabe sobre a prevalência de relações problemáticas nessa esfera. Este estudo transversal teve como objetivo investigar a prevalência e os fatores de risco de diferentes tipos de relações entre pais e lactentes em um bairro brasileiro. Métodos: Durante 1 ano, todas as famílias (n = 230) residentes em uma comunidade urbana de Porto Alegre, sul do Brasil, com filhos de 4 meses de idade nascidos em hospitais públicos foram identificadas, e 148 foram investigadas em detalhe por dois terapeutas familiares. Este estudo descreve os dados dos 116 lactentes com famílias formadas por pai e mãe. Variáveis demográficas, obstétricas e relacionais foram coletadas através de questionários e escalas (Parent-Infant Relationship Global Assessment Scale, Global Assessment of Relational Functioning e Self-Report Questionnaire). Razões de prevalência foram calculadas, e a regressão de Poisson com variância robusta foi utilizada para ajuste de covariáveis. Resultados: Quase 10% das mães e 12% dos pais mostraram pelo menos uma relação significativamente perturbada com seus lactentes de 4 meses de idade. Vínculo inadequado entre mãe e lactente coincidiu com evidências de transtorno mental paterno, uma rede social de apoio insatisfatória por parte da mãe e interrupção do aleitamento materno aos 4 meses. Relação problemática entre o pai e o lactente associou-se com relação disfuncional do casal e com baixo peso do lactente ao nascimento. Conclusões: Há uma alta prevalência de problemas nas relações precoces entre pais e filho, sugerindo a necessidade de intervenções do sistema de saúde. Problemas relacionais pais-filho são altamente prevalentes logo no início na vida do lactente e são mais associados a outros problemas relacionais do que a sobrecarga socioeconômica