Molecular phylogeny of African hinge‐back tortoises (Kinixys): implications for phylogeography and taxonomy (Testudines: Testudinidae)

We examine the phylogeography, phylogeny and taxonomy of hinge‐back tortoises using a comprehensive sampling of all currently recognized Kinixys species and subspecies and sequence data of three mitochondrial DNA fragments (2273 bp: 12S rRNA, ND4 + adjacent DNA coding for tRNAs, cytb) and three nuclear loci (2569 bp: C‐mos, ODC, R35). Combined and individual analyses of the two data sets using Bayesian and Maximum Likelihood methods suggest that the savannah species of Kinixys are paraphyletic with respect to the rainforest species K. homeana and K. erosa, and that the rainforest species may be derived from a savannah‐living ancestor. The previously recognized savannah species K. belliana was a conglomerate of three deeply divergent clades that we treat here as distinct species. We restrict the name K. belliana (Gray, 1830) to hinge‐back tortoises ranging from Angola to Burundi, while five‐clawed hinge‐back tortoises from the northernmost part of the formerly recognized range of K. belliana, together with four‐clawed tortoises from West Africa, are assigned to the species K. nogueyi (Lataste, 1886). These two species are allied to K. spekii, whereas Southeast African and Malagasy hinge‐back tortoises formerly lumped together with K. belliana represent the distinct species K. zombensis Hewitt, 1931, which is sister to K. lobatsiana. The latter two species together constitute the sister group of the rainforest species K. homeana and K. erosa. Mitochondrial data suggest that K. natalensis has a basal phylogenetic position in a clade embracing K. belliana sensu stricto, K. nogueyi and K. spekii, while nuclear data and the two data sets combined favour a sister group relationship of K. natalensis to all other hinge‐back tortoises. Phylogeographic structure is present in all wide‐ranging species and correlates in K. homeana and K. erosa with the Dahomey Gap and former rainforest refugia. The Malagasy population of K. zombensis is weakly differentiated from its South African conspecifics and further sampling is needed to determine whether there is support for the subspecific distinctness of Malagasy tortoises.     

Dietary Fiber and Saturated Fat Intake Associations with Cardiovascular Disease Differ by Sex in the Malm? Diet and Cancer Cohort: A Prospective Study

Background

The aim of the study was to examine associations between intake of macronutrients and dietary fiber and incident ischemic cardiovascular disease (iCVD) in men and women.

Methods

We used data from 8,139 male and 12,535 female participants (aged 44–73 y) of the Swedish population-based Malmö Diet and Cancer cohort. The participants were without history of CVD and diabetes mellitus, and had reported stable dietary habits in the study questionnaire. Diet was assessed by a validated modified diet history method, combining a 7-d registration of cooked meals and cold beverages, a 168-item food questionnaire (covering other foods and meal patterns), and a 1-hour diet interview. Sociodemographic and lifestyle data were collected by questionnaire. iCVD cases, which included coronary events (myocardial infarctions or deaths from chronic ischemic heart disease) and ischemic strokes, were ascertained via national and local registries. Nutrient-disease associations were examined by multivariate Cox regressions.

Results

During a mean follow-up of 13.5 years, we identified 1,089 male and 687 female iCVD cases. High fiber intakes were associated with lower incidence rates of iCVD in women and of ischemic stroke in men. In post-hoc analysis, we discovered statistically significant interactions between intake of fiber and saturated fat; these interactions also differed between men and women (p<0.001).

Conclusions

In this well-defined population, a high fiber intake was associated with lower risk of iCVD, but there were no robust associations between other macronutrients and iCVD risk. Judging from this study, gender-specific nutrient analysis may be preferable in epidemiology.     

Uracil-DNA glycosylases SMUG1 and UNG2 coordinate the initial steps of base excision repair by distinct mechanisms

DNA glycosylases UNG and SMUG1 excise uracil from DNA and belong to the same protein superfamily. Vertebrates contain both SMUG1 and UNG, but their distinct roles in base excision repair (BER) of deaminated cytosine (U:G) are still not fully defined. Here we have examined the ability of human SMUG1 and UNG2 (nuclear UNG) to initiate and coordinate repair of U:G mismatches. When expressed in Escherichia coli cells, human UNG2 initiates complete repair of deaminated cytosine, while SMUG1 inhibits cell proliferation. In vitro, we show that SMUG1 binds tightly to AP-sites and inhibits AP-site cleavage by AP-endonucleases. Furthermore, a specific motif important for the AP-site product binding has been identified. Mutations in this motif increase catalytic turnover due to reduced product binding. In contrast, the highly efficient UNG2 lacks product-binding capacity and stimulates AP-site cleavage by APE1, facilitating the two first steps in BER. In summary, this work reveals that SMUG1 and UNG2 coordinate the initial steps of BER by distinct mechanisms. UNG2 is apparently adapted to rapid and highly coordinated repair of uracil (U:G and U:A) in replicating DNA, while the less efficient SMUG1 may be more important in repair of deaminated cytosine (U:G) in non-replicating chromatin.     

Growing and shrinking in the smallest tortoise, <Emphasis Type="Italic">Homopus signatus signatus</Emphasis>: the importance of rain

Climate change models predict that the range of the world’s smallest tortoise, Homopus signatus signatus, will aridify and contract in the next decades. To evaluate the effects of annual variation in rainfall on the growth of H. s. signatus, we recorded annual growth rates of wild individuals from spring 2000 to spring 2004. Juveniles grew faster than did adults, and females grew faster than did males. Growth correlated strongly with the amount of rain that fell during the time just before and within the growth periods. Growth rates were lowest in 2002–2003, when almost no rain fell between September 2002 and August 2003. In this period, more than 54% of the tortoises had negative growth rates for their straight carapace length (SCL), shell height (SH), and shell volume (SV); maximum shrinking for SCL, SH, and SV was 4, 11, and 12%, respectively. The shell of H. s. signatus has some flexibility dorso-ventrally, so a reduction in internal matter due to starvation or dehydration may have caused SH to shrink. Because the length and width of the shell seem more rigid, reversible bone resorption may have contributed to shrinkage, particularly of the shell width and plastron length. Based on growth rates for all years, female H. s. signatus need 11–12 years to mature, approximately twice as long as would be expected allometrically for such a small species. However, if aridification lowers average growth rates to the level of 2002–2003, females would require 30 years to mature. Additionally, aridification would lower average and maximum female size, resulting in smaller eggs and hatchlings. These projected life history responses to aridification heighten the threat posed by the predicted range contraction of this red-listed species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

HIF1α induced switch from bivalent to exclusively glycolytic metabolism during ESC-to-EpiSC/hESC transition

The function of metabolic state in stemness is poorly understood. Mouse embryonic stem cells (ESC) and epiblast stem cells (EpiSC) are at distinct pluripotent states representing the inner cell mass (ICM) and epiblast embryos. Human embryonic stem cells (hESC) are similar to EpiSC stage. We now show a dramatic metabolic difference between these two stages. EpiSC/hESC are highly glycolytic, while ESC are bivalent in their energy production, dynamically switching from glycolysis to mitochondrial respiration on demand. Despite having a more developed and expanding mitochondrial content, EpiSC/hESC have low mitochondrial respiratory capacity due to low cytochrome c oxidase (COX) expression. Similarly, in vivo epiblasts suppress COX levels. These data reveal EpiSC/hESC functional similarity to the glycolytic phenotype in cancer (Warburg effect). We further show that hypoxia-inducible factor 1α (HIF1α) is sufficient to drive ESC to a glycolytic Activin/Nodal-dependent EpiSC-like stage. This metabolic switch during early stem-cell development may be deterministic.     

A High Diet Quality Is Associated with Lower Incidence of Cardiovascular Events in the Malm? Diet and Cancer Cohort

Aims

To investigate if diet quality is related to incidence of cardiovascular (CV) events.

Subjects and Methods

A diet quality index based on the 2005 Swedish Nutrition Recommendations and the Swedish Dietary Guidelines was created and included six dietary components: saturated fatty acids, polyunsaturated fatty acids, fish and shellfish, dietary fiber, fruit and vegetables, and sucrose. The index ranked 17126 participants (59% women) of the population-based Malmö Diet and Cancer cohort (Sweden) on their dietary intakes. Total index score was categorized as low, medium or high. Cox proportional hazard regression was used to model associations between index score categories and index components with risk of incident CV events, with adjustment for potential confounders. The incidence of first CV events (non-fatal or fatal myocardial infarction or ischemic stroke or death from ischemic heart disease) was monitored from baseline (1991–1996) until December 31, 2008; 703 CV events occurred in women and 1093 in men.

Results

A high diet quality was associated with decreased risk of CV events when compared to a low diet quality. In multivariate analysis, the risk reduction was 32% (hazard ratio = 0.68, 95% confidence interval: 0.49–0.73) in men and 27% (hazard ratio = 0.73, 95% confidence interval: 0.59–0.91) in women. When examined separately and mutually adjusted for each other, the individual components were either not associated with CV risk or marginally decreased risks were seen.

Conclusion

High quality diets in line with current recommendations may reduce the risk of CV events. This study illustrates the importance of considering a combination of dietary factors when evaluating diet-disease associations.     

Spontaneous Mutations Occur near Dam Recognition Sites in a dam-Escherichia coli Host

The mismatch repair system of Escherichia coli K12 removes mispaired bases from DNA. Mismatch repair can occur on either strand of DNA if it lacks N6-methyladenines within 5'-GATC-3' sequences. In hemimethylated heteroduplexes, repair occurs preferentially on the unmethylated strand. If both strands are fully methylated, repair is inhibited. Mutant (dam-) strains of E. coli defective in the adenine methylase that recognizes 5'-GATC-3' sequences (Dam), and therefore defective in mismatch repair, show increased spontaneous mutation rates compared to otherwise isogenic dam+ hosts. We have isolated and characterized 91 independent mutations that arise as a consequence of the Dam- defect in a plasmid-borne phage P22 repressor gene, mnt. The majority of these mutations are A:T----G:C transitions that occur within six base pairs of the two 5'-GATC-3' sequences in the mnt gene. In contrast, the spectrum of mnt- mutations in a dam+ host is comprised of a majority of insertions of IS elements and deletions that do not cluster near Dam recognition sites. These results show that Dam-directed post-replicative mismatch repair plays a significant role in the rectification of potential transition mutations in vivo, and suggest that sequences associated with Dam recognition sites are particularly prone to replication or repair errors.     

Arsenic Exposure Affects Plasma Insulin-Like Growth Factor 1 (IGF-1) in Children in Rural Bangladesh

Background

Exposure to inorganic arsenic (As) through drinking water during pregnancy is associated with lower birth size and child growth. The aim of the study was to assess the effects of As exposure on child growth parameters to evaluate causal associations.

Methodology/Findings

Children born in a longitudinal mother-child cohort in rural Bangladesh were studied at 4.5 years (n=640) as well as at birth (n=134). Exposure to arsenic was assessed by concurrent and prenatal (maternal) urinary concentrations of arsenic metabolites (U-As). Associations with plasma concentrations of insulin-like growth factor 1 (IGF-1), calcium (Ca), vitamin D (Vit-D), bone-specific alkaline phosphatase (B-ALP), intact parathyroid hormone (iPTH), and phosphate (PO₄) were evaluated by linear regression analysis, adjusted for socioeconomic factor, parity and child sex. Child U-As (per 10 µg/L) was significantly inversely associated with concurrent plasma IGF-1 (β=-0.27; 95% confidence interval: -0.50, -0.0042) at 4.5 years. The effect was more obvious in girls (β=-0.29; -0.59, 0.021) than in boys, and particularly in girls with adequate height (β=-0.491; -0.97, -0.02) or weight (β=-0.47; 0.97, 0.01). Maternal U-As was inversely associated with child IGF-1 at birth (r=-0.254, P=0.003), but not at 4.5 years. There was a tendency of positive association between U-As and plasma PO₄ in stunted boys (β=0.27; 0.089, 0.46). When stratified by % monomethylarsonic acid (MMA, arsenic metabolite) (median split at 9.7%), a much stronger inverse association between U-As and IGF-1 in the girls (β=-0.41; -0.77, -0.03) was obtained above the median split.

Conclusion

The results suggest that As-related growth impairment in children is mediated, at least partly, through suppressed IGF-1 levels.     

Influence of Drought,Rain and Artificial Irrigation on Photosynthesis,Gas Exchange and Water Relations of the Fynbos Plant Protea acaulos (L.) Reich at the End of the Dry Season

Protea acaulos, a prostrate fynbos shrub, often experiences very low air humidity at leaf temperatures over 10°C higher than mean air temperature. We determined to what degree this particular microclimate influenced photosynthetic performance, leaf conductance and water relations of non-irrigated and trickle-irrigated plants. Measurements were made at the end of the dry summer season in the sand plain lowland fynbos on the west coast of South Africa. Independent of water supply, plants showed a pronounced midday depression of gas exchange. While in non-irrigated plants leaf water potential dropped to ? 2.0 MPa around noon, it never fell below ?1.0 MPa in irrigated plants. On the other hand minimum pressure potential was similar in irrigated and non-irrigated plants. The latter showed higher turgor after rain, due to osmotic acclimation, which resulted from a reduction in maximum water volume. The main osmoticum was 1,5-anhydro-D-glucitol. Leaf temperature, directly or via the vapour pressure deficit between leaf and air (Δw), rather than plant water status, was the determinant of the midday depression of gas exchange. High Δw caused stomatal closure during times of saturating light, thus limiting photosynthetic CO₂ uptake and availability and enhancing the susceptibility for photoinhibition. This, as well as high leaf temperature per se, decreased the efficiency of photochemistry of photosystem II. Initial fluorescence remained constant until temperatures exceeded 35 °C, above which changes in fluorescence indicated both photoinhibition and heat stress. Unlike other fynbos plants, Protea acaulos could not use the improved soil water supply to increase carbon gain under hot summer condition.