Late Miocene insular mice from the Tusco-Sardinian palaeobioprovince provide new insights on the palaeoecology of the Oreopithecus faunas

Oreopithecus bambolii is one of the few hominoids that evolved under insular conditions, resulting in the development of unique adaptations that have fueled an intensive debate. The palaeoenvironment associated with this great ape has been the subject of great controversy as well. On the one hand, palaeobotanical data indicate that Oreopithecus likely inhabited mixed mesophytic forests interrupted by swamps; on the other hand, an abundance of hypsodont bovids points towards the existence of dry and open environments. Here, we provide a new approach based on the ecomorphology of the extinct endemic Muridae (rats and mice) of the so-called Oreopithecus faunas. Our results show that the successive species of endemic insular murids (Huerzelerimys and Anthracomys) evolved a number of adaptations observed only in extant family members that include significant proportions of grass in their diet. While this fits the pattern exhibited by large mammals, it contrasts with the available palaeobotanical information, which indicates that grasses were minor components of the vegetation. This contradiction may be explained because these endemic murids may have been adapted to the consumption of particular food items such as hard parts of aquatic plants (as shown by some extant murid species). However, because it is unlikely that the remaining herbivore mammals were adapted to this diet as well, we favour an alternative hypothesis that takes into account the peculiar ecological conditions of insular ecosystems leading to a density-dependent selective regime with strong competition. Such a regime would promote the selection of dental adaptations to increase feeding efficiency and durability of the dentition (such as hypsodonty) as seen in some fossil insular ruminants. This hypothesis requires further testing, but may partly account for parallel evolution of dental traits in phylogenetically unrelated insular mammals.     

Generic phytosanitary radiation treatment for tephritid fruit flies provides quarantine security for Bactrocera latifrons (Diptera: Tephritidae)

Bactrocera latifrons (Hendel) (Diptera: Tephritidae) is a quarantine pest of several solanaceous crops and tropical fruits that are treated using irradiation before export from Hawaii to the U.S. mainland. A dose of 150 Gy is approved as a generic irradiation treatment for tephritid fruit flies, but no confirmation of efficacy has been reported for B. latifrons. Dose response of B. latifrons was used to determine the most tolerant life stage and identify a dose that prevents adult emergence. Data indicated doses (plus 95% confidence limits) required to prevent adult emergence of 13.4 (10.0-29.6), 17.5 (14.4-24.8), and 88.1 (68.0-133.8) Gy for eggs, first instars and third instars, respectively. In large-scale confirmatory tests of the most radiotolerant life stage, a radiation dose of 150 Gy applied to B. latifrons late third instars in bell peppers (Capsicum annuum L.) resulted in no survival to the adult stage of 157,112 individuals, a treatment efficacy consistent with Probit 9-level mortality. The relative radiotolerance of melon fly Bactrocera cucurbitae Coquillet, and B. latifrons also was tested using a diagnostic radiation dose of 30 Gy. In diet, a mean of 6.9% of irradiated B. cucurbitae third instars developed to the adult stage, whereas no B. latifrons third instars developed to adults. In papaya, Carica papaya L., fruit, a mean of 3.3% of irradiated B. cucurbitae third instars developed to the adult stage, whereas 0.5% B. latifrons third instars developed to adults. This report supports the use of a generic radiation dose of 150 Gy in quarantine scenarios to control tephritid fruit flies on fresh commodities.     

Diverse trends in shell weight of three Southern Ocean pteropod taxa collected with Polar Frontal Zone sediment traps from 1997 to 2007

The impact of ocean acidification on key ocean calcifiers is predicted to be imminent, particularly in high-latitude ecosystems. Long-term field observations are essential to ground truth predictions of change in regional ecosystems. Here, we report on aragonitic pteropods collected to sediment traps at 800 m depth at 54°S, 140°E in the Polar Frontal Zone (PFZ) of the Southern Ocean from 1997 to 2007. Statistically significant trends were not identified in either mass or number flux from 1997 to 2007; however, differences emerged in decadal trends seen in shell weight for each of the three common taxa collected: Limacina helicina antarctica forma antarctica shells became significantly lighter (P < 0.05), L. retroversa australis shells became significantly heavier (P < 0.05) and L. helicina antarctica forma rangi shells did not change significantly. These results suggest that factors other than ocean acidification affect pteropod population variations on decadal timescales, with the potential to either amplify or counter the impact of decreasing aragonite saturation state, at least in the short term. Comparison to sea surface temperature and chlorophyll biomass did not identify these as significant drivers of the observed changes, and attribution across these multiple variables requires better understanding of pteropod physiology and ecology. Our PFZ pelagic pteropod observations provide a reference for evaluation of southern polar pteropod responses to changing ocean conditions in coming decades. Importantly, these data also raise the issue of taxonomic care when monitoring the region for impacts of ocean acidification on calcifiers.     

Determining the quality and complexity of next-generation sequencing data without a reference genome

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users.     

Effect of Vitamin D Supplementation on Cardiometabolic Risks and Health-Related Quality of Life among Urban Premenopausal Women in a Tropical Country – A Randomized Controlled Trial

Background

Many observational studies linked vitamin D to cardiometabolic risks besides its pivotal role in musculoskeletal diseases, but evidence from trials is lacking and inconsistent.

Aim

To determine whether Vitamin D supplementation in urban premenopausal women with vitamin D deficiency can improve cardiometabolic risks and health-related quality of life (HRQOL).

Design

A double-blind randomized controlled trial was conducted in Kuala Lumpur, Malaysia. A total of 192 vitamin D deficient (<50 nmol/l) premenopausal women were randomized to receive either vitamin D 50,000 IU or placebo once a week for 2 months and then monthly for 10 months. Primary outcomes were serum 25(OH)D, serum lipid profiles, blood pressure and HOMA-IR measured at baseline, 6 months and 12 months. HRQOL was assessed with SF-36 at baseline and 12 months.

Results

Ninety three and ninety-nine women were randomised into intervention and placebo groups respectively. After 12 months, there were significant differences in the serum 25(OH)D concentration (mean difference: 49.54; 95% CI: 43.94 to 55.14) nmol/l) and PTH levels (mean difference: −1.02; 95% CI: −1.67 to −0.38 pmol/l) in the intervention group compared to placebo group. There was significant difference between treatment group in both serum 25(OH)D and PTH. There was no effect of supplementation on HOMA-IR, serum lipid profiles and blood pressure (all p>0.05) between two groups. There was a small but significant improvement in HRQOL in the components of vitality (mean difference: 5.041; 95% CI: 0.709 to 9.374) and mental component score (mean difference: 2.951; 95% CI: 0.573 to 5.329) in the intervention group compared to placebo group.

Conclusion

Large and less frequent dosage vitamin D supplementation was safe and effective in the achievement of vitamin D sufficiency. However, there was no improvement in measured cardiometabolic risk factors in premenopausal women. Conversely vitamin D supplementation improves some components of HRQOL.

Trial Registration

Australian New Zealand Clinical Trial Registry ACTRN12612000452897     

Identification of DNA sequence variation in Campylobacter jejuni strains associated with the Guillain-Barré syndrome by high-throughput AFLP analysis

Background  

Campylobacter jejuni is the predominant cause of antecedent infection in post-infectious neuropathies such as the Guillain-Barré (GBS) and Miller Fisher syndromes (MFS). GBS and MFS are probably induced by molecular mimicry between human gangliosides and bacterial lipo-oligosaccharides (LOS). This study describes a new C. jejuni-specific high-throughput AFLP (htAFLP) approach for detection and identification of DNA polymorphism, in general, and of putative GBS/MFS-markers, in particular.     

KLOTHO allele status and the risk of early-onset occult coronary artery disease

We previously identified a functional variant of KLOTHO (termed "KL-VS"), which harbors two amino acid substitutions in complete linkage disequilibrium and is associated with reduced human longevity when in homozygosity. Klotho-deficient mice display extensive arteriosclerosis when fed a normal diet, suggesting a potent genetic predisposition. To determine whether klotho influences atherosclerotic risk in humans, we performed cross-sectional studies to assess the association between the KL-VS allele and occult coronary artery disease (CAD) in two independent samples of apparently healthy siblings of individuals with early-onset (age <60 years) CAD (SIBS-I [N=520] and SIBS-II [N=436]). Occult CAD was defined as the occurrence of a reversible perfusion defect during exercise thallium scintigraphy and/or as an abnormal result of an exercise electrocardiogram (SIBS-I, n=97; SIBS-II, n=56). In SIBS-I, the KL-VS allele conferred a relative odds of 1.90 (95% confidence interval 1.21-2.98) for occult CAD, after adjusting for familial intraclass correlations (P<.005). Logistic regression modeling, incorporating known CAD risk factors, demonstrated that the KL-VS allele is an independent risk factor (P<.019) and that the imposed risk of KL-VS allele status is influenced by modifiable risk factors. Hypertension (P<.022) and increasing high-density lipoprotein cholesterol (HDL-C) levels (P<.022) mask or reduce the risk conferred by the KL-VS allele, respectively, whereas current smoking (P<.004) increases the risk. Remarkably concordant effects of the KL-VS allele and modifying factors on the risk of occult CAD were seen in SIBS-II. These results demonstrate that the KL-VS allele is an independent risk factor for occult CAD in two independent high-risk samples. Modifiable risk factors, including hypertension, smoking status, and HDL-C level, appear to influence the risk imposed by this allele.