Challenges of phylogenetic analyses of aDNA sequences

One of the crucial steps of authentication of aDNA sequences is phylogenetic consistency. Amplified sequences should fit into the phylogenetic framework of their supposed origin. An inherent property of aDNA sequences however, is their short sequence length. Additionally, genes for aDNA studies are often chosen by their preservation potential rather than by phylogenetically informative content. This poses potential challenges regarding their analyses, and might result in an inaccurate reflection of the supposed phylogenetic history of the sequence or organism under study. In this paper some fundamental problems of phylogenetic analysis and interpretation of aDNA datasets are discussed. Suggestions for character sampling and treatment of missing data are made. The publication is the result of a talk from the 1st PAMINSA Meeting in Rio de Janeiro, July 2005.

Social Determinants of Child Health in Colombia: Can Community Education Moderate the Effect of Family Characteristics?

Contextual effects on child health have been investigated extensively in previous research. However, few studies have considered the interplay between community characteristics and individual-level variables. This study examines the influence of community education and family socioeconomic characteristics on child health (as measured by height and weight-for-age Z-scores), as well as their interactions. We adapted the Commission on Social Determinants of Health (CSDH) framework to the context of child health. Using data from the 2010 Colombian Demographic and Health Survey (DHS), weighted multilevel models are fitted since the data are not self-weighting. The results show a positive impact of the level of education of other women in the community on child health, even after controlling for individual and family socioeconomic characteristics. Different pathways through which community education can substitute for the effect of family characteristics on child nutrition are found. The interaction terms highlight the importance of community education as a moderator of the impact of the mother’s own education and autonomy, on child health. In addition, the results reveal differences between height and weight-for-age indicators in their responsiveness to individual and contextual factors. Our findings suggest that community intervention programmes may have differential effects on child health. Therefore, their identification can contribute to a better targeting of child care policies.

Psychophysiological activation during preparation, performance, and recovery in high- and low-anxious music students

The present study provides a comprehensive view of (a) the time dynamics of the psychophysiological responding in performing music students (n = 66) before, during, and after a private and a public performance and (b) the moderating effect of music performance anxiety (MPA). Heart rate (HR), minute ventilation (VE), and all affective and somatic self-report variables increased in the public session compared to the private session. Furthermore, the activation of all variables was stronger during the performances than before or after. Differences between phases were larger in the public than in the private session for HR, VE, total breath duration, anxiety, and trembling. Furthermore, while higher MPA scores were associated with higher scores and with larger changes between sessions and phases for self-reports, this association was less coherent for physiological variables. Finally, self-reported intra-individual performance improvements or deteriorations were not associated with MPA. This study makes a novel contribution by showing how the presence of an audience influences low- and high-anxious musicians' psychophysiological responding before, during and after performing. Overall, the findings are more consistent with models of anxiety that emphasize the importance of cognitive rather than physiological factors in MPA.

Crohn's disease-associated polymorphism within the PTPN2 gene affects muramyl-dipeptide-induced cytokine secretion and autophagy.

BACKGROUND: The single nucleotide polymorphism (SNP) rs2542151 within the gene locus region encoding protein tyrosine phosphatase non-receptor type 2 (PTPN2) has been associated with Crohn's disease (CD), ulcerative colitis (UC), type-I diabetes, and rheumatoid arthritis. We have previously shown that PTPN2 regulates mitogen-activated protein kinase (MAPK) signaling and cytokine secretion in human THP-1 monocytes and intestinal epithelial cells (IEC). Here, we studied whether intronic PTPN2 SNP rs1893217 regulates immune responses to the nucleotide-oligomerization domain 2 (NOD2) ligand, muramyl-dipeptide (MDP). MATERIALS AND METHODS: Genomic DNA samples from 343 CD and 663 non-IBD control patients (male and female) from a combined German, Swiss, and Polish cohort were genotyped for the presence of the PTPN2 SNPs, rs2542151, and rs1893217. PTPN2-variant rs1893217 was introduced into T(84) IEC or THP-1 cells using a lentiviral vector. RESULTS: We identified a novel association between the genetic variant, rs1893217, located in intron 7 of the PTPN2 gene and CD. Human THP-1 monocytes carrying this variant revealed increased MAPK activation as well as elevated mRNA expression of T-bet transcription factor and secretion of interferon-γ in response to the bacterial wall component, MDP. In contrast, secretion of interleukin-8 and tumor necrosis factor were reduced. In both, T(84) IEC and THP-1 monocytes, autophagosome formation was impaired. CONCLUSIONS: We identified a novel CD-associated PTPN2 variant that modulates innate immune responses to bacterial antigens. These findings not only provide key insights into the effects of a functional mutation on a clinically relevant gene, but also reveal how such a mutation could contribute to the onset of disease.

A new method to simulate the hydrological state of soil under natural conditions

Micro, macro and mesofauna in the soil often respond to fluctuating environmental conditions, resulting in changes of abundance and community structure. Effects of changing soil parameters are normally determined with samples taken in the field and brought to the laboratory, i.e. where natural environmental conditions may not apply. We devised a method (STAFD - soil tubes for artificial flood and drought), which simulates the hydrological state of soil in situ using implanted cores. Control tubes were compared with treatment tubes in which floods of 15, 30, 60 and 90 days, and droughts of 60, 90 and 120 days were simulated in the field. Flooding and drought were found to reduce number of individuals in all soil faunal groups, but the response to drought was slower and not in proportion to the expected decrease of the water content. The results of the simulated floods in particular show the value of the STAFD method for the investigation of such extreme events in natural habitats.