OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

We present a new method, OMSV, for accurately and comprehensively identifying structural variations (SVs) from optical maps. OMSV detects both homozygous and heterozygous SVs, SVs of various types and sizes, and SVs with or without creating or destroying restriction sites. We show that OMSV has high sensitivity and specificity, with clear performance gains over the latest method. Applying OMSV to a human cell line, we identified hundreds of SVs >2 kbp, with 68 % of them missed by sequencing-based callers. Independent experimental validation confirmed the high accuracy of these SVs. The OMSV software is available at http://yiplab.cse.cuhk.edu.hk/omsv/.     

Crystallization and Gelation Behavior of Low- and High Melting Waxes in Rice Bran Oil: a Case-Study on Berry Wax and Sunflower Wax

Low-melting berry wax (BEW) has proven to be a good oil gelator with a positive contribution to the consistency and flexibility of the structured oil. Nevertheless, the properties of BEW and the corresponding oleogel have not yet been investigated in-depth. In this research, the difference in crystallization and gelling behavior between sunflower wax (SW), a high melting wax, and BEW, a low-melting wax, in rice bran oil (RBO) was investigated. The difference in melting and crystallization temperatures can be explained by the different chemical composition (long-chain wax esters in SW and short-chain fatty acids in BEW). The heterogeneity in crystal habits (unidirectional platelets versus microcrystalline particles) and polymorphism (orthorhombic versus hexagonal) are responsible for the varying gel strength and hardness of the respective SW- and BEW-oleogels. The microcrystalline BEW particles aligned and reorganized during 1-month storage at 5 °C, which leaded to an increase in the gel strength and hardness of BEW-oleogel. The gelling property of SW-oleogel however did not significantly differ after 4 weeks at 5 °C, despite of the appearance of spherulitic crystalline clusters. The changes in the physical properties of wax-based oleogels during storage time were further explored using differential scanning calorimetry, polarized light microscope, powder X-ray diffraction and rheology.     

Influence of Warming Tendency on <Emphasis Type="Italic">Culex pipiens</Emphasis> Population Abundance and on the Probability of West Nile Fever Outbreaks (Israeli Case Study: 2001–2005)

Climate change and West Nile fever (WNV) are both subjects of global importance. Many mosquitoes and the diseases they carry, including West Nile virus (WNV), are sensitive to temperature increase. The current study analyzes the lag correlations between weather conditions (especially air temperature) and 1) Culex pipiens mosquito population abundance, and 2) WNF frequency in humans, between 2001 and 2005 in Israel. These 5 years follow a long period with a documented tendency for temperature increase in the hot season in the country. Monthly anomalies of minimum and maximum temperatures, relative seasonal rainfall contribution, mosquito samplings (hazard level), and WNF cases (hospital admission dates and patients’ addresses) were analyzed. Logistic regression was calculated between the climatic data and the mosquito samples, as Spearman correlations and Pearson cross-correlations were calculated between daily temperature values (or daily precipitation amounts) and the hospital admission dates. It was found that the disease appearance reflects the population distribution, while the risk tends to escalate around the metropolis characterized by an urban heat island. Positive anomalies of the temperature during the study period appear to have facilitated the mosquito abundance and, consequently, the disease emergence in humans. An important finding is the potential influence of extreme heat in the early spring on the vector population increase and on the disease’s appearance weeks later. Awareness of such situations at the beginning of the spring may help authorities to reduce the disease risk before it becomes a real danger.     

Association of the MC4R V103I polymorphism with the metabolic syndrome: the KORA Study

Objective: Epidemiological studies showing an association between the melanocortin‐4‐receptor (MC4R) 103I variant (rs2229616) and decreased BMI are complemented by functional studies; these suggest a mechanism for appetite regulation and a linkage signal for physical activity and dietary intake for the region encompassing the MC4R. This study aims to provide epidemiological evidence for showing the association of this polymorphism with features of the metabolic syndrome and with parameters related to energy expenditure and dietary habits as potential mediators. Methods and Procedures: We analyzed this polymorphism in 7,888 adults of a population‐based cross‐sectional study applying regression‐based statistical models. Results: Carriers of the MC4R 103I (3.7%) exhibited a significantly decreased waist circumference (–1.46 cm, P = 0.020), decreased glycosylated hemoglobin (HbA_1c) (–0.09%, P = 0.040), and increased HDL‐cholesterol (HDL‐C) (+1.76 mg/dl, P = 0.056), but no change in blood pressure. The odds of having three or more components of the metabolic syndrome were substantially reduced among carriers of MC4R 103I (odds ratio (OR) = 0.46, P = 0.003). Controlling for BMI reduced the HbA_1c and HDL‐C association. Mediator analyses revealed a borderline association of MC4R 103I with carbohydrate intake (OR = 1.26, P = 0.059) possibly mediating association with leanness. Discussion: Our representative study of well‐phenotyped Europeans is the first to describe the association of the MC4R V103I with the metabolic syndrome and with a nutrient‐related phenotype. Our data support the idea that this polymorphism plays a role in appetite regulation that not only affects BMI, but also other features of the metabolic syndrome. It further establishes that the association of the MC4R V103I with obesity and related phenotypes is genuine.     

Abundance of early functional HIV-specific CD8+ T cells does not predict AIDS-free survival time

Background

T-cell immunity is thought to play an important role in controlling HIV infection, and is a main target for HIV vaccine development. HIV-specific central memory CD8⁺ and CD4⁺ T cells producing IFNγ and IL-2 have been associated with control of viremia and are therefore hypothesized to be truly protective and determine subsequent clinical outcome. However, the cause-effect relationship between HIV-specific cellular immunity and disease progression is unknown. We investigated in a large prospective cohort study involving 96 individuals of the Amsterdam Cohort Studies with a known date of seroconversion whether the presence of cytokine-producing HIV-specific CD8⁺ T cells early in infection was associated with AIDS-free survival time.

Methods and Findings

The number and percentage of IFNγ and IL-2 producing CD8⁺ T cells was measured after in vitro stimulation with an overlapping Gag-peptide pool in T cells sampled approximately one year after seroconversion. Kaplan-Meier survival analysis and Cox proportional hazard models showed that frequencies of cytokine-producing Gag-specific CD8⁺ T cells (IFNγ, IL-2 or both) shortly after seroconversion were neither associated with time to AIDS nor with the rate of CD4⁺ T-cell decline.

Conclusions

These data show that high numbers of functional HIV-specific CD8⁺ T cells can be found early in HIV infection, irrespective of subsequent clinical outcome. The fact that both progressors and long-term non-progressors have abundant T cell immunity of the specificity associated with low viral load shortly after seroconversion suggests that the more rapid loss of T cell immunity observed in progressors may be a consequence rather than a cause of disease progression.     

Lifelong reduction of LDL-cholesterol related to a common variant in the LDL-receptor gene decreases the risk of coronary artery disease--a Mendelian Randomisation study

Background

Rare mutations of the low-density lipoprotein receptor gene (LDLR) cause familial hypercholesterolemia, which increases the risk for coronary artery disease (CAD). Less is known about the implications of common genetic variation in the LDLR gene regarding the variability of cholesterol levels and risk of CAD.

Methods

Imputed genotype data at the LDLR locus on 1 644 individuals of a population-based sample were explored for association with LDL-C level. Replication of association with LDL-C level was sought for the most significant single nucleotide polymorphism (SNP) within the LDLR gene in three European samples comprising 6 642 adults and 533 children. Association of this SNP with CAD was examined in six case-control studies involving more than 15 000 individuals.

Findings

Each copy of the minor T allele of SNP rs2228671 within LDLR (frequency 11%) was related to a decrease of LDL-C levels by 0.19 mmol/L (95% confidence interval (CI) [0.13–0.24] mmol/L, p = 1.5×10⁻¹⁰). This association with LDL-C was uniformly found in children, men, and women of all samples studied. In parallel, the T allele of rs2228671 was associated with a significantly lower risk of CAD (Odds Ratio per copy of the T allele: 0.82, 95% CI [0.76–0.89], p = 2.1×10⁻⁷). Adjustment for LDL-C levels by logistic regression or Mendelian Randomisation models abolished the significant association between rs2228671 with CAD completely, indicating a functional link between the genetic variant at the LDLR gene locus, change in LDL-C and risk of CAD.

Conclusion

A common variant at the LDLR gene locus affects LDL-C levels and, thereby, the risk for CAD.     

Regulation of leptin mRNA and protein expression in pituitary somatotropes.

Leptin, the ob protein, regulates food intake and satiety and can be found in the anterior pituitary. Leptin antigens and mRNA were studied in the anterior pituitary (AP) cells of male and female rats to learn more about its regulation. Leptin antigens were found in over 40% of cells in diestrous or proestrous female rats and in male rats. Lower percentages of AP cells were seen in the estrous population (21 +/- 7%). During peak expression of antigens, co-expression of leptin and growth hormone (GH) was found in 27 +/- 4% of AP cells. Affinity cytochemistry studies detected 24 +/- 3% of AP cells with leptin proteins and growth hormone releasing hormone (GHRH) receptors. These data suggested that somatotropes were a significant source of leptin. To test regulatory factors, estrous and diestrous AP populations were treated with estrogen (100 pM) and/or GHRH (2 nM) to learn if either would increase leptin expression in GH cells. To rule out the possibility that the immunoreactive leptin was bound to receptors in somatotropes, leptin mRNA was also detected by non-radioactive in situ hybridization in this group of cells. In estrous female rats, 39 +/- 0.9% of AP cells expressed leptin mRNA, indicating that the potential for leptin production was greater than predicted from the immunolabeling. Estrogen and GHRH together (but not alone) increased percentages of cells with leptin protein (41 +/- 9%) or mRNA (57 +/- 5%). Estrogen and GHRH also increased the percentages of AP cells that co-express leptin mRNA and GH antigens from 20 +/- 2% of AP cells to 37 +/- 5%. Although the significance of leptin in GH cells is not understood, it is clearly increased after stimulation with GHRH and estrogen. Because GH cells also have leptin receptors, this AP leptin may be an autocrine or paracrine regulator of pituitary cell function.     

Prediction of anaerobic power values from an abbreviated WAnT protocol

The traditional 30-second Wingate anaerobic test (WAnT) is a widely used anaerobic power assessment protocol. An abbreviated protocol has been shown to decrease the mild to severe physical discomfort often associated with the WAnT. Therefore, the purpose of this study was to determine whether a 20-second WAnT protocol could be used to accurately predict power values of a standard 30-second WAnT. In 96 college females, anaerobic power variables were assessed using a standard 30-second WAnT protocol. Maximum power values as well as instantaneous power at 10, 15, and 20 seconds were recorded. Based on these results, stepwise regression analysis was performed to determine the accuracy with which mean power, minimum power, 30-second power, and percentage of fatigue for a standard 30-second WAnT could be predicted from values obtained during the first 20 seconds of testing. Mean power values showed the highest level of predictability (R2 = 0.99) from the 20-second values. Minimum power, 30-second power, and percentage of fatigue also showed high levels of predictability (R2 = 0.91, 0.84, and 0.84, respectively) using only values obtained during the first 20 seconds of the protocol. An abbreviated (20-second) WAnT protocol appears to effectively predict results of a standard 30-second WAnT in college-age females, allowing for comparison of data to published norms. A shortened test may allow for a decrease in unwanted side effects associated with the traditional WAnT protocol.     

Effects of combination oral contraceptives on strength development in women athletes

This study was designed to investigate the effects of combination oral contraceptive agents (OCAs) on strength and torque production in collegiate women softball and water polo athletes who participated in a 12-week strength development program. A double-blind research design was used to mask subjects to the main outcome of interest. Thirty-one women collegiate softball and water polo players were divided into experimental (OCA users, n = 13), and control (non-OCA users, n = 18) groups. All subjects participated in the same supervised 12-week preseason strength development program. One-repetition maximum bench press (1RMBP), 10-repetition maximum leg extension (10RMLE), isokinetic peak torque bench press (IKBP), and isokinetic peak torque leg extension (IKLE) data were collected at weeks 0 (pre-test), 4, 8, and 12 (post-test). Significant increases in strength and torque production over time were identified regardless of group for 1RMBP, 10RMLE, and IKLE. No significant differences in IKBP torque production occurred during the 12-week strength training program. No significant differences in 1RMBP, 10RMLE, IKBP, or IKLE occurred between the OCA users and the non-OCA users groups. It was concluded that, within the limitations of the study, the use of combination OCAs did not provide sufficient androgenic effect to increase strength gains beyond the stimulus of the training protocol.