IMPROVING PROJECT MANAGEMENT FOR SUSTAINABLE DEVELOPMENT

Institutional and Behavioral Economics,

Effective Sample Size: Quick Estimation of the Effect of Related Samples in Genetic Case-Control Association Analyses

Correlated samples have been frequently avoided in case-control
genetic association
 studies in part because the methods for handling them are either not
easily implemented or not widely known. We
advocate one method for case-control association analysis of correlated
samples -- the effective sample size method -- as a simple and
accessible approach that does not require specialized computer programs.
The effective sample size method captures the variance inflation
of allele frequency estimation exactly, and can be used to modify the
chi-square test statistic, p-value, and 95% confidence interval of
odds-ratio simply by replacing the apparent number of allele counts with the
effective ones. For genotype frequency estimation, although a single
effective sample size is unable to completely characterize the variance inflation,
an averaged one can satisfactorily approximate the simulated result.
The effective sample size method is applied to the rheumatoid arthritis
siblings data collected from the North American Rheumatoid Arthritis Consortium (NARAC)
to establish a significant association with the interferon-induced
helicasel gene (IFIH1) previously being identified as a type 1 diabetes
susceptibility locus. Connections between the effective sample size
method and other methods, such as generalized estimation equation,
variance of eigenvalues for correlation matrices, and genomic controls,
are also discussed.
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Inflammatory and Oxidative Stress Responses to High-Carbohydrate and High-Fat Meals in Healthy Humans

The postprandial state is hypothesised to be proinflammatory and prooxidative, but the relative contributions of fat versus carbohydrate are unclear. Therefore, we examined inflammation and oxidative stress responses in serum and skeletal muscle before and after 1000 kcal meals, which were high in either fat or carbohydrate in 15 healthy individuals. Serum and muscle expression of IL6 was elevated 3 hours after each meal, independently of macronutrient composition (P < 0.01). Serum IL18 was decreased after high-fat meal only (P < 0.01). Plasma total antioxidative status and muscle Cu/Zn-superoxide dismutase were decreased after high-carbohydrate meal only (P < 0.05). We conclude that a high-carbohydrate meal may evoke a greater postprandial oxidative stress response, whereas both fat and carbohydrate increased IL6. We speculate that the observed increases in postprandial IL6, without increases in any other markers of inflammation, may indicate a normal IL6 response to enhance glucose uptake, similar to its role postexercise

NAC transcription factors in senescence:from molecular structure to function in crops

Within the last decade, NAC transcription factors have been shown to play essential roles in senescence, which is the focus of this review. Transcriptome analyses associate approximately one third of Arabidopsis NAC genes and many crop NAC genes with senescence, thereby implicating NAC genes as important regulators of the senescence process. The consensus DNA binding site of the NAC domain is used to predict NAC target genes, and protein interaction sites can be predicted for the intrinsically disordered transcription regulatory domains of NAC proteins. The molecular characteristics of these domains determine the interactions in gene regulatory networks. Emerging local NAC-centered gene regulatory networks reveal complex molecular mechanisms of stress- and hormone-regulated senescence and basic physiological steps of the senescence process. For example, through molecular interactions involving the hormone abscisic acid, Arabidopsis NAP promotes chlorophyll degradation, a hallmark of senescence. Furthermore, studies of the functional rice ortholog, OsNAP, suggest that NAC genes can be targeted to obtain specific changes in lifespan control and nutrient remobilization in crop plants. This is also exemplified by the wheat NAM1 genes which promote senescence and increase grain zinc, iron, and protein content. Thus, NAC genes are promising targets for fine-tuning senescence for increased yield and quality

Contemporary temperature-driven divergence in a Nordic freshwater fish under conditions commonly thought to hinder adaptation

BACKGROUND: Evaluating the limits of adaptation to temperature is important given the IPCC-predicted rise in global temperatures. The rate and scope of evolutionary adaptation can be limited by low genetic diversity, gene flow, and costs associated with adaptive change. Freshwater organisms are physically confined to lakes and rivers, and must therefore deal directly with climate variation and change. In this study, we take advantage of a system characterised by low genetic variation, small population size, gene flow and between-trait trade-offs to study how such conditions affect the ability of a freshwater fish to adapt to climate change. We test for genetically-based differences in developmental traits indicating local adaptation, by conducting a common-garden experiment using embryos and larvae from replicate pairs of sympatric grayling demes that spawn and develop in natural cold and warm water, respectively. These demes have common ancestors from a colonization event 22 generations ago. Consequently, we explore if diversification may occur under severely constraining conditions. RESULTS: We found evidence for divergence in ontogenetic rates. The divergence pattern followed adaptation predictions as cold-deme individuals displayed higher growth rates and yolk conversion efficiency than warm-deme individuals at the same temperature. The cold-deme embryos had a higher rate of muscle mass development. Most of the growth- and development differences occurred prior to hatch. The divergence was probably not caused by genetic drift as there was a strong degree of parallelism in the divergence pattern and because phenotypic differentiation (Q(ST)) was larger than estimated genetic drift levels (microsatellite F(ST)) between demes from different temperature groups. We also document that these particular grayling populations cannot develop successfully at temperatures above 12°C, whereas other European populations can, and that increasing the muscle mass development rate comes at the cost of some skeletal trait development rates. CONCLUSIONS: This study shows that genetically based phenotypic divergence can prevail even under conditions of low genetic variation and ongoing gene flow. Furthermore, population-specific maximum development temperatures along with musculoskeletal developmental trade-offs may constrain adaptation

Clinical Outcomes and Counselling Issues regarding Partial Trisomy of Terminal Xp in a Child with Developmental Delay

Female carriers of balanced translocations involving an X chromosome and an autosome offer genetic counselling challenges. This is in view of the number of possible meiotic outcomes, but also due to the impact of X chromosome-localised genes that are no longer subject to gene silencing through the X chromosome inactivation centre. We present a case where delineation of the extent of X chromosome-localised genes on the derivative autosome using molecular karyotyping offers critical information in the context of genetic counselling.

First results from a VLBA proper motion survey of H2O masers in low-mass YSOs: the Serpens core and RNO15-FIR

This article reports first results of a long-term observational program aimed to study the earliest evolution of jet/disk systems in low-mass YSOs by means of VLBI observations of the 22.2 GHz water masers. We report here data for the cluster of low-mass YSOs in the Serpens molecular core and for the single object RNO~15-FIR. Towards Serpens SMM1, the most luminous sub-mm source of the Serpens cluster, the water maser emission comes from two small (< 5 AU in size) clusters of features separated by ~25 AU, having line of sight velocities strongly red-shifted (by more than 10 km/s) with respect to the LSR velocity of the molecular cloud. The two maser clusters are oriented on the sky along a direction that is approximately perpendicular to the axis of the radio continuum jet observed with the VLA towards SMM1. The spatial and velocity distribution of the maser features lead us to favor the interpretation that the maser emission is excited by interaction of the receding lobe of the jet with dense gas in the accretion disk surrounding the YSO in SMM1. Towards RNO~15-FIR, the few detected maser features have both positions and (absolute) velocities aligned along a direction that is parallel to the axis of the molecular outflow observed on much larger angular scales. In this case the maser emission likely emerges from dense, shocked molecular clumps displaced along the axis of the jet emerging from the YSO. The protostar in Serpens SMM1 is more massive than the one in RNO~15-FIR. We discuss the case where a high mass ejection rate can generate jets sufficiently powerful to sweep away from their course the densest portions of circumstellar gas. In this case, the excitation conditions for water masers might preferably occur at the interface between the jet and the accretion disk, rather than along the jet axis.Comment: 18 pages (postscript format); 9 figures; to be published into Astronomy & Astrophysics, Main Journa