Comparative genome analysis of a Saccharomyces cerevisiae wine strain

Many industrial strains of Saccharomyces cerevisiae have been selected primarily for their ability to convert sugars into ethanol efficiently despite exposure to a variety of stresses. To begin investigation of the genetic basis of phenotypic variation in industrial strains of S. cerevisiae, we have sequenced the genome of a wine yeast, AWRI1631, and have compared this sequence with both the laboratory strain S288c and the human pathogenic isolate YJM789. AWRI1631 was found to be substantially different from S288c and YJM789, especially at the level of single-nucleotide polymorphisms, which were present, on average, every 150 bp between all three strains. In addition, there were major differences in the arrangement and number of Ty elements between the strains, as well as several regions of DNA that were specific to AWRI1631 and that were predicted to encode proteins that are unique to this industrial strain.     

Activity of resveratrol triesters against primary acute lymphoblastic leukemia cells

Resveratrol is a common polyphenol of plant origin known for its cancer prevention and other properties. Its wider application is limited due to poor water solubility, low stability, and weak bioavailability. To overcome these limitations, a series of 13 novel resveratrol triesters were synthesized previously. In this paper, we describe the synthesis of 3 additional derivatives and the activity of all 16 against primary acute lymphoblastic leukemia cells. Of these, 3 compounds were more potent than resveratrol (IC₅₀ = 10.5 µM) namely: resveratryl triacetate (IC₅₀ = 3.4 µM), resveratryl triisobutyrate (IC₅₀ = 5.1 µM), and resveratryl triisovalerate (IC₅₀ = 4.9 µM); all other derivatives had IC₅₀ values of >10 µM. Further studies indicated that the active compounds caused G1 phase arrest, increased expression of p53, and induced characteristics of apoptotic cell death. Moreover, the compounds were only effective in cycling cells, with cells arrested in G1 phase being refractory.     

Forest responses to simulated elevated CO2 under alternate hypotheses of size‐ and age‐dependent mortality

Elevated atmospheric carbon dioxide (eCO₂) is predicted to increase growth rates of forest trees. The extent to which increased growth translates to changes in biomass is dependent on the turnover time of the carbon, and thus tree mortality rates. Size‐ or age‐dependent mortality combined with increased growth rates could result in either decreased carbon turnover from a speeding up of tree life cycles, or increased biomass from trees reaching larger sizes, respectively. However, most vegetation models currently lack any representation of size‐ or age‐dependent mortality and the effect of eCO₂ on changes in biomass and carbon turnover times is thus a major source of uncertainty in predictions of future vegetation dynamics. Using a reduced‐complexity form of the vegetation demographic model the Functionally Assembled Terrestrial Ecosystem Simulator to simulate an idealised tropical forest, we find increases in biomass despite reductions in carbon turnover time in both size‐ and age‐dependent mortality scenarios in response to a hypothetical eCO₂‐driven 25% increase in woody net primary productivity (wNPP). Carbon turnover times decreased by 9.6% in size‐dependent mortality scenarios due to a speeding up of tree life cycles, but also by 2.0% when mortality was age‐dependent, as larger crowns led to increased light competition. Increases in aboveground biomass (AGB) were much larger when mortality was age‐dependent (24.3%) compared with size‐dependent (13.4%) as trees reached larger sizes before death. In simulations with a constant background mortality rate, carbon turnover time decreased by 2.1% and AGB increased by 24.0%, however, absolute values of AGB and carbon turnover were higher than in either size‐ or age‐dependent mortality scenario. The extent to which AGB increases and carbon turnover decreases will thus depend on the mechanisms of large tree mortality: if increased size itself results in elevated mortality rates, then this could reduce by about half the increase in AGB relative to the increase in wNPP.     

Trophic Structure of One Deep-sea Benthic Fish Community in the Eastern Canadian Arctic: Application of Food, Parasites and Multivariate Analysis

Synopsis As new arctic marine fisheries develop there is need for a comprehensive ecosystem approach to long-term management. This approach recognizes the importance of community interactions such as food web structure and trophic patterns. We determined whether hierarchical clustering (guild formation) is an effective method of trophic evaluation in deep-sea Artic fish communities using stomach content and parasite data with size class, and evaluated the application of endohelminth communities (parasite species transmitted in the food) as indicators of trophic status. Cluster analysis using food group abundance with size class of fish revealed the presence of 11 guilds within the community, however the same analysis using parasite data showed little correlation between food and parasites. Redundancy analysis (RDA) within the 11 guilds also revealed no significant correlations between food group and parasite abundance suggesting that this type of ordination is not suited for environments containing mainly generalist feeders. RDA of individual taxa without a priori guild designation found that taxa in benthic deep-sea communities are defined by their ability to exploit prey species in more than one habitat zone. Benthic fish species were significantly correlated with benthic food groups and parasites that utilize benthic intermediate hosts whereas benthopelagic–pelagic species fed on a higher diversity of prey species and were infected by a larger number of non-host specific parasites. Eigenanalysis and Monte Carlo results showed that parasites and food groups are highly correlated, indicating that parasite community analysis is an effective tool for predicting feeding strategies in Arctic marine environments. It also suggests that in most cases endoparasite infections alone could be used for trophic evaluation in the absence of stomach content data.     

The multifunctional protein glyceraldehyde-3-phosphate dehydrogenase is both regulated and controls colony-stimulating factor-1 messenger RNA stability in ovarian cancer

Although glyceraldehyde-3-phosphate dehydrogenase's (GAPDH) predilection for AU-rich elements has long been known, the expected connection between GAPDH and control of mRNA stability has never been made. Recently, we described GAPDH binding the AU-rich terminal 144 nt of the colony-stimulating factor-1 (CSF-1) 3' untranslated region (UTR), which we showed to be an mRNA decay element in ovarian cancer cells. CSF-1 is strongly correlated with the poor prognosis of patients with ovarian cancer. We investigated the functional significance of GAPDH's association with CSF-1 mRNA and found that GAPDH small interfering RNA reduces both CSF-1 mRNA and protein levels by destabilizing CSF-1 mRNA. CSF-1 mRNA half-lives were decreased by 50% in the presence of GAPDH small interfering RNA. RNA footprinting analysis of the 144 nt CSF-1 sequence revealed that GAPDH associates with a large AU-rich-containing region. The effects of binding of GAPDH protein or ovarian extracts to mutations of the AU-rich regions within the footprint were consistent with this finding. In a tissue array containing 256 ovarian and fallopian tube cancer specimens, we found that GAPDH was regulated in these cancers, with almost 50% of specimens having no GAPDH staining. Furthermore, we found that low GAPDH staining was associated with a low CSF-1 score (P = 0.008). In summary, GAPDH, a multifunctional protein, now adds regulation of mRNA stability to its repertoire. We are the first to evaluate the clinical role of GAPDH protein in cancer. In ovarian cancers, we show that GAPDH expression is regulated, and we now recognize that one of the many functions of GAPDH is to promote mRNA stability of CSF-1, an important cytokine in tumor progression.     

PROP taster status interacts with the built environment to influence children's food acceptance and body weight status

Objectives:

Eating behaviors and obesity are complex phenotypes influenced by genes and the environment, but few studies have investigated the interaction of these two variables. The purpose of this study was to use a gene‐environment interaction model to test for differences in children's food acceptance and body weights.

Design and Methods:

Inherited ability to taste 6‐n‐propylthiouracil (PROP) was assessed as a marker of oral taste responsiveness. Food environment was classified as “healthy” or “unhealthy” based on proximity to outlets that sell fruits/vegetables and fast foods using Geographic Information Systems (GIS). The cohort consisted of 120 children, ages 4‐6 years, recruited from New York City over 2005‐2010. Home address and other demographic variables were reported by parents and PROP status, food acceptance, and anthropometrics were assessed in the laboratory. Based on a screening test, children were classified as PROP tasters or non‐tasters. Hierarchical linear models analysis of variance was performed to examine differences in food acceptance and body mass index (BMI) z‐scores as a function of PROP status, the food environment (“healthy” vs. “unhealthy”), and their interaction.

Results and Conclusion:

Results showed an interaction between taster status and the food environment on BMI z‐score and food acceptance. Non‐taster children living in healthy food environments had greater acceptance of vegetables than taster children living in healthy food environments (P ≤ 0.005). Moreover, non‐tasters from unhealthy food environments had higher BMI z‐scores than all other groups (P ≤ 0.005). Incorporating genetic markers of taste into studies that assess the built environment may improve the ability of these measures to predict risk for obesity and eating behaviors. Obesity (2012)