On Two-Stage Hypothesis Testing Procedures Via Asymptotically Independent Statistics

Kooperberg and LeBlanc (2008) proposed a two-stage testing procedure to screen for significant interactions in genome-wide association (GWA) studies by a soft threshold on marginal associations (MA), though its theoretical properties and generalization have not been elaborated. In this article, we discuss conditions that are required to achieve strong control of the Family-Wise Error Rate (FWER) by such procedures for low or high-dimensional hypothesis testing. We provide proof of asymptotic independence of marginal association statistics and interaction statistics in linear regression, logistic regression, and Cox proportional hazard models in a randomized clinical trial (RCT) with a rare event. In case-control studies nested within a RCT, a complementary criterion, namely deviation from baseline independence (DBI) in the case-control sample, is advocated as a screening tool for discovering significant interactions or main effects. Simulations and an application to a GWA study in Women’s Health Initiative (WHI) are presented to show utilities of the proposed two-stage testing procedures in pharmacogenetic studies

Major features and forcing of high‐latitude northern hemisphere atmospheric circulation using a 110,000‐year‐long glaciochemical series

The Greenland Ice Sheet Project 2 glaciochemical series (sodium, potassium, ammonium, calcium, magnesium, sulfate, nitrate, and chloride) provides a unique view of the chemistry of the atmosphere and the history of atmospheric circulation over both the high latitudes and mid‐low latitudes of the northern hemisphere. Interpretation of this record reveals a diverse array of environmental signatures that include the documentation of anthropogenically derived pollutants, volcanic and biomass burning events, storminess over marine surfaces, continental aridity and biogenic source strength plus information related to the controls on both high‐ and low‐frequency climate events of the last 110,000 years. Climate forcings investigated include changes in insolation of the order of the major orbital cycles that control the long‐term behavior of atmospheric circulation patterns through changes in ice volume (sea level), events such as the Heinrich events (massive discharges of icebergs first identified in the marine record) that are found to operate on a 6100‐year cycle due largely to the lagged response of ice sheets to changes in insolation and consequent glacier dynamics, and rapid climate change events (massive reorganizations of atmospheric circulation) that are demonstrated to operate on 1450‐year cycles. Changes in insolation and associated positive feedbacks related to ice sheets may assist in explaining favorable time periods and controls on the amplitude of massive rapid climate change events. Explanation for the exact timing and global synchroneity of these events is, however, more complicated. Preliminary evidence points to possible solar variability‐climate associations for these events and perhaps others that are embedded in our ice‐core‐derived atmospheric circulation records

Solution structure of a bacterial microcompartment targeting peptide and its application in the construction of an ethanol bioreactor

Targeting of proteins to bacterial microcompartments (BMCs) is mediated by an 18-amino-acid peptide sequence. Herein, we report the solution structure of the N-terminal targeting peptide (P18) of PduP, the aldehyde dehydrogenase associated with the 1,2-propanediol utilization metabolosome from Citrobacter freundii. The solution structure reveals the peptide to have a well-defined helical conformation along its whole length. Saturation transfer difference and transferred NOE NMR has highlighted the observed interaction surface on the peptide with its main interacting shell protein, PduK. By tagging both a pyruvate decarboxylase and an alcohol dehydrogenase with targeting peptides, it has been possible to direct these enzymes to empty BMCs in vivo and to generate an ethanol bioreactor. Not only are the purified, redesigned BMCs able to transform pyruvate into ethanol efficiently, but the strains containing the modified BMCs produce elevated levels of alcohol

The development and validation of a fast and robust dried blood spot based lipid profiling method to study infant metabolism.

Early life exposures and metabolic programming are associated with later disease risk. In particular lipid metabolism is thought to play a key role in the development of the metabolic syndrome and insulin resistance in later life. Investigative studies of metabolic programming are limited by the ethics and practicalities of sample collection in small infants. Dried blood spots on filter paper, derived from heel pricks are considered as the most suitable option for this age group. We validated a novel lipid profiling method, based on high resolution mass spectrometry to successfully determine the lipid composition of infants using dried blood spots. The spotting and air drying of blood on paper has noticeable effects on many of the lipids, leading to lipid oxidation and hydrolysis, which demand careful interpretation of the obtained data. We compared the lipid profiles from plasma or whole blood samples and the results from dried blood spots to determine if these revealed the same inter-subject differences. The results from dried blood spots were no less reproducible than other lipid profiling methods which required comparatively larger sample volumes. Therefore, lipid profiles obtained from dried blood spots can be successfully used to monitor infancy lipid metabolism and we show significant differences in the lipid metabolism of infants at age 3 versus 12 months

Antarctic Glacial History Since the Last Glacial Maximum: An Overview of the Record on Land

This overview examines available circum-Antarctic glacial history archives on land, related to developments after the Last Glacial Maximum (LGM). It considers the glacial-stratigraphic and morphologic records and also biostratigraphical information from moss banks, lake sediments and penguin rookeries, with some reference to relevant glacial marine records. It is concluded that Holocene environmental development in Antarctica differed from that in the Northern Hemisphere. The initial deglaciation of the shelf areas surrounding Antarctica took place before 10000 C-14 yrs before present(sp), and was controlled by rising global sea level. This was followed by the deglaciation of some presently ice-free inner shelf and land areas between 10000 and 8000 yr sp. Continued deglaciation occurred gradually between 8000 yr sp and 5000 yr sp. Mid-Holocene glacial readvances are recorded from various sites around Antarctica. There are strong indications of a circum-Antarctic climate warmer than today 4700-2000 yr sp. The best dated records from the Antarctic Peninsula and coastal Victoria Land suggest climatic optimums there from 4000-3000 yr sp and 3600-2600 yr sp, respectively. Thereafter Neoglacial readvances are recorded. Relatively limited glacial expansions in Antarctica during the past few hundred years correlate with the Little Ice Age in the Northern Hemisphere

The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081

The human enteropathogen, Yersinia enterocolitica, is a significant link in the range of Yersinia pathologies extending from mild gastroenteritis to bubonic plague. Comparison at the genomic level is a key step in our understanding of the genetic basis for this pathogenicity spectrum. Here we report the genome of Y. enterocolitica strain 8081 (serotype 0:8; biotype 1B) and extensive microarray data relating to the genetic diversity of the Y. enterocolitica species. Our analysis reveals that the genome of Y. enterocolitica strain 8081 is a patchwork of horizontally acquired genetic loci, including a plasticity zone of 199 kb containing an extraordinarily high density of virulence genes. Microarray analysis has provided insights into species-specific Y. enterocolitica gene functions and the intraspecies differences between the high, low, and nonpathogenic Y. enterocolitica biotypes. Through comparative genome sequence analysis we provide new information on the evolution of the Yersinia. We identify numerous loci that represent ancestral clusters of genes potentially important in enteric survival and pathogenesis, which have been lost or are in the process of being lost, in the other sequenced Yersinia lineages. Our analysis also highlights large metabolic operons in Y. enterocolitica that are absent in the related enteropathogen, Yersinia pseudotuberculosis, indicating major differences in niche and nutrients used within the mammalian gut. These include clusters directing, the production of hydrogenases, tetrathionate respiration, cobalamin synthesis, and propanediol utilisation. Along with ancestral gene clusters, the genome of Y. enterocolitica has revealed species-specific and enteropathogen-specific loci. This has provided important insights into the pathology of this bacterium and, more broadly, into the evolution of the genus. Moreover, wider investigations looking at the patterns of gene loss and gain in the Yersinia have highlighted common themes in the genome evolution of other human enteropathogens

UCP2 Regulates the Glucagon Response to Fasting and Starvation

Glucagon is important for maintaining euglycemia during fasting/starvation, and abnormal glucagon secretion is associated with type 1 and type 2 diabetes; however, the mechanisms of hypoglycemia-induced glucagon secretion are poorly understood. We previously demonstrated that global deletion of mitochondrial uncoupling protein 2 (UCP2−/−) in mice impaired glucagon secretion from isolated islets. Therefore, UCP2 may contribute to the regulation of hypoglycemia-induced glucagon secretion, which is supported by our current finding that UCP2 expression is increased in nutrient-deprived murine and human islets. Further to this, we created α-cell–specific UCP2 knockout (UCP2AKO) mice, which we used to demonstrate that blood glucose recovery in response to hypoglycemia is impaired owing to attenuated glucagon secretion. UCP2-deleted α-cells have higher levels of intracellular reactive oxygen species (ROS) due to enhanced mitochondrial coupling, which translated into defective stimulus/secretion coupling. The effects of UCP2 deletion were mimicked by the UCP2 inhibitor genipin on both murine and human islets and also by application of exogenous ROS, confirming that changes in oxidative status and electrical activity directly reduce glucagon secretion. Therefore, α-cell UCP2 deletion perturbs the fasting/hypoglycemic glucagon response and shows that UCP2 is necessary for normal α-cell glucose sensing and the maintenance of euglycemia

Dynamical origins of heat capacity changes in enzyme-catalysed reactions

Heat capacity changes affect the temperature dependence of enzyme catalysis, with implications for thermoadaptation, however their physical basis is unknown. Here the authors show that heat capacity changes are calculable by simulation, revealing distinct dynamical contributions from regions remote from the active site

Evaluating the utility of B/Ca ratios in planktic foraminifera as a proxy for the carbonate system: A case study of Globigerinoides ruber

B/Ca ratios in foraminifera have attracted considerable scientific attention as a proxy for past ocean carbonate system. However, the carbonate system controls on B/Ca ratios are not straightforward, with ?[ inline image] ([ inline image]in situ – [ inline image]at saturation) correlating best with B/Ca ratios in benthic foraminifera, rather than pH, inline image, or inline image (as a simple model of boron speciation in seawater and incorporation into CaCO3 would predict). Furthermore, culture experiments have shown that in planktic foraminifera properties such as salinity and [B]sw can have profound effects on B/Ca ratios beyond those predicted by simple partition coefficients. Here, we investigate the controls on B/Ca ratios in G. ruber via a combination of culture experiments and core-top measurements, and add to a growing body of evidence that suggests B/Ca ratios in symbiont-bearing foraminiferal carbonate are not a straightforward proxy for past seawater carbonate system conditions. We find that while B/Ca ratios in culture experiments covary with pH, in open ocean sediments this relationship is not seen. In fact, our B/Ca data correlate best with [ inline image] (a previously undocumented association) and in most regions, salinity. These findings might suggest a precipitation rate or crystallographic control on boron incorporation into foraminiferal calcite. Regardless, our results underscore the need for caution when attempting to interpret B/Ca records in terms of the ocean carbonate system, at the very least in the case of mixed-layer planktic foraminifera

Effects on mortality of a nutritional intervention for malnourished HIV-infected adults referred for antiretroviral therapy: a randomised controlled trial.

Malnourished HIV-infected African adults are at high risk of early mortality after starting antiretroviral therapy (ART). We hypothesized that short-course, high-dose vitamin and mineral supplementation in lipid nutritional supplements would decrease mortality