Gene-based Genomewide Association Analysis: A Comparison Study

The study of gene-based genetic associations has gained conceptual popularity recently. Biologic insight into the etiology of a complex disease can be gained by focusing on genes as testing units. Several gene-based methods (e.g., minimum p-value (or maximum test statistic) or entropy-based method) have been developed and have more power than a single nucleotide polymorphism (SNP)-based analysis. The objective of this study is to compare the performance of the entropy-based method with the minimum p-value and single SNP–based analysis and to explore their strengths and weaknesses. Simulation studies show that: 1) all three methods can reasonably control the false-positive rate; 2) the minimum p-value method outperforms the entropy-based and the single SNP–based method when only one disease-related SNP occurs within the gene; 3) the entropy-based method outperforms the other methods when there are more than two disease-related SNPs in the gene; and 4) the entropy-based method is computationally more efficient than the minimum p-value method. Application to a real data set shows that more significant genes were identified by the entropy-based method than by the other two methods.     

Assembly and annotation of full mitochondrial genomes for the corn rootworm species, Diabrotica virgifera virgifera and Diabroticabarberi (Insecta: Coleoptera: Chrysomelidae), using Next Generation Sequence data

Complete mitochondrial genomes for two corn rootworm species, Diabrotica virgifera virgifera (16,747 bp) and Diabrotica barberi (16,632; Insecta: Coleoptera: Chrysomelidae), were assembled from Illumina HiSeq2000 read data. Annotation indicated that the order and orientation of 13 protein coding genes (PCGs), and 22 tRNA and 2 rRNA sequences were in typical of insect mitochondrial genomes. Non-standard nad4 and cox3 stop codons were composed of single T nucleotides and likely completed by adenylation, and atypical TTT start codons was predicted for both D. v. virgifera and D. barberinad1 genes. The D. v. virgifera and D. barberi haplotypes showed 819 variable nucleotide positions within PCG regions (7.36% divergence), which suggest that speciation may have occurred ~ 3.68 million years ago assuming a linear rate of short-term substitution. Phylogenetic analyses of Coleopteran MtD genome show clustering based on family level, and may have the capacity to resolve the evolutionary history within this Order of insects.     

Addressing the critical challenge for rhamnolipid production: Discontinued synthesis in extended stationary phase

Rhamnolipids are commonly produced using N-limited Pseudomonas aeruginosa fermentations, with active production in the stationary phase. The production, however, stops after certain period. This causes lower productivity and yield because of downtime between batches and the substrate consumed for cell growth. This discontinued production is the significant problem addressed in this study. Rhamnolipid synthesis involves complex regulatory mechanisms, including quorum-sensing systems and alternative sigma factors. Current knowledge on these mechanisms, however, cannot adequately explain the discontinued rhamnolipid production at extended stationary phase. Four hypotheses to causes of this discontinued production were examined here with carefully planned fermentation designs using different initial N-source concentrations and different ways of adding oil and nutrients. Results rejected three of the hypothetical causes: accumulation of rhamnolipids or other inhibitory metabolites, presence of high amounts of oil phase, and exhaustion of non-N nutrients, and supported the hypothesis that the stopped production was caused solely by the extended N-starvation experienced by the cells. The discontinued production was found to be fully reactivated by partial broth replacements with fresh media containing N-source. The finding is important to production economics and promotes new designs to maximize rhamnolipid productivity and yield using extended stationary-phase production instead of short repeated batches.     

Self‐Awareness of Impairment and the Decision to Drive after an Extended Period of Wakefulness

Fatigue is an increasingly noted factor in road accidents. The ability to predict and be aware of impairment in terms of driving capability is important for potential legal liability and road safety. However, to date, there have been few studies that have investigated the accuracy of individuals in predicting how safely they could drive during conditions of sleep loss. Research has demonstrated that individuals rate themselves as better than the population average in a number of domains, including driving‐related skills. Therefore, this study also aimed to investigate self‐ratings of predicted driving ability during extended wakefulness and compare them to ratings made of a hypothetical other person under the same conditions. Thirty‐two participants remained awake for a period of 40 h. Every 2 h, they completed the Psychomotor Vigilance Task (PVT) and rated on a seven‐point scale how well they thought they could drive safely, react quickly in an emergency, and stay in their own lane. They were also asked to assess how they thought someone else in their own position could drive. The participants rated their driving ability as becoming significantly poorer at the same time that their PVT performance became significantly slower. Self‐ratings indicating a qualitative assessment of poorer than neutral driving occurred at 03:00 h for both the “drive safely” and “react quickly” questions, after 19 h of continuous wakefulness (starting at 08:00 h). This occurred at 05:00 h for the “keep in my lane” question. Previous studies with a similar protocol demonstrated that under these conditions, individuals exhibit a performance decrements equivalent to someone with a blood alcohol concentration of 0.05% (the legal driving limit in Australia). Participants consistently rated the ability of others to drive as poorer than their own. The main implication from this study for road safety and legal liability is that it is reasonable to focus on a person's perception of the situation, as it does align with objective reality to a certain extent. A concern in terms of road safety is potential overconfidence, indicated by rating others consistently poorer than themselves.     

Post-Sleep Inertia Performance Benefits of Longer Naps in Simulated Nightwork and Extended Operations

Operational settings involving shiftwork or extended operations require periods of prolonged wakefulness, which in conjunction with sleep loss and circadian factors, can have a negative impact on performance, alertness, and workplace safety. Napping has been shown to improve performance and alertness after periods of prolonged wakefulness and sleep loss. Longer naps may not only result in longer-lasting benefits but also increase the risk of sleep inertia immediately upon waking. The time course of performance after naps of differing durations is thus an important consideration in weighing the benefits and risks of napping in workplace settings. The objective of this study was to evaluate the effectiveness of nap opportunities of 20, 40, or 60 min for maintaining alertness and performance 1.5–6 h post-nap in simulated nightwork (P1) or extended operations (P2). Each protocol included 12 participants in a within-subjects design in a controlled laboratory environment. After a baseline 8 h time-in-bed, healthy young males (P1 mean age 25.1 yr; P2 mean age 23.2 yr) underwent either ≈20 h (P1) or ≈30 h (P2) of sleep deprivation on four separate occasions, followed by nap opportunities of 0, 20, 40, and 60 min. Sleep on the baseline night and during the naps was recorded polysomnographically. During the nap opportunities, sleep onset latency was short and sleep efficiency was high. A greater proportion of slow-wave sleep (SWS) was obtained in nap opportunities of 40 and 60 min compared with 20 min. Rapid eye movement (REM) sleep occurred infrequently. A subjective sleepiness rating (Karolinska Sleepiness Scale, KSS), 2-Back Working Memory Task (WMT), and Psychomotor Vigilance Task (PVT) were completed 1.5, 2, 2.5, 3, 4, 5, and 6 h post-nap. The slowest 10% of PVT responses were significantly faster after 40 and 60 min naps compared with a 20 min (P1) or no (P2) nap. There were significantly fewer PVT lapses after 40 and 60 min naps compared with no nap (P2), and after 60 min naps compared with 20 min naps (P1). Participants felt significantly less sleepy and made more correct responses and fewer omissions on the WMT after 60 min naps compared with no nap (P2). Subjective sleepiness and WMT performance were not related to the amount of nap-time spent in SWS. However, PVT response speed was significantly slower when time in SWS was <10 min compared with 20–29.9 min. In conclusion, in operationally relevant scenarios, nap opportunities of 40 and 60 min show more prolonged benefits 1.5–6 h post-nap, than a 20 min or no nap opportunity. Benefits were more apparent when the homeostatic pressure for sleep was high and post-nap performance testing occurred across the afternoon (P2). For sustained improvement in cognitive performance, naps of 40–60 min are recommended. (Author correspondence: t.l.signal@massey.ac.nz)     

Association of MTHFR and PPARγ2 gene polymorphisms in relation to type 2 diabetes mellitus cases among north Indian population

Background

Type 2 diabetes mellitus is a multifactorial and polygenic disease, which is considered as a major life threatening problem all over the world. There has been a worldwide effort in the identification of susceptibility genes for type 2 diabetes mellitus and its complications. At present, adequate data is not available dealing with MTHFR (rs1801133) and PPARγ2 (rs1801282) gene polymorphisms and its association with type 2 diabetes mellitus cases among north Indian populations. Thus, we conceived the need for further studies to investigate MTHFR and PPARγ2 gene polymorphisms and their susceptibility to type 2 diabetes mellitus in north Indian population.

Materials and methods

In this study, a total 175 subjects including 87 type 2 diabetes mellitus cases and 88 controls were enrolled. MTHFR and PPARγ2 gene polymorphisms in the cases and controls were evaluated by polymerase chain reaction and restriction fragment length polymorphism (PCR–RFLP).

Results

The MTHFR gene CC, CT, TT genotype frequencies obtained were 40%, 43%, and 17% in type 2 diabetes mellitus cases and 56%, 29%, and 15% in healthy controls respectively. The OR for CC was 0.54 (95%CI 0.29–0.98, P = 0.041, χ2 = 4.18, power = 0.98), for CT 1.76 (95%CI 0.94–3.30, P = 0.07, χ2 = 3.2, power = 0.96), and for TT 1.2 (95%CI 0.53–2.70, P = 0.66, χ2 = 0.198, power = 0.76). The PPARγ2 gene GG CG, CC genotype frequencies obtained were 28%, 41%, and 31% in cases and 40%, 39%, and 21% in healthy controls respectively. OR for GG was 0.58 (95%CI 0.30–1.09, P = 0.08, χ2 = 2.9, power = 0.96), for CG 1.12 (95%CI 0.61–2.05, P = 0.71, χ2 = 0.137, power = 0.778), and for CC 1.63 (95%CI 0.82–3.23, P = 0.156, χ2 = 2.01, power = 0.92).

Conclusion

It might be recommended that MTHFR CC genotype seems to be a good marker for the early identification of population at risk of type 2 diabetes mellitus. While we have detected significant difference in allelic frequencies of PPARγ2 C (Proline) and G (Alanine), but at genotypic level significant difference was not detected in this case–control study. Further study with larger groups may be required to validate the study.     

2004～2010年武汉同济医院临床分离多重耐药菌株监测分析

目的了解武汉同济医院2004年至2010年临床分离多重耐药菌株的检出情况。方法对临床分离菌株,采用纸片扩散法按统一的方案进行药敏试验。按照CLSI 2009年标准进行判断。结果 2004年至2010年该院耐甲氧西林金葡菌（MRSA）和耐甲氧西林凝固酶阴性葡萄球菌（MRSCN）的检出率分别在35.6%～63.8%和21.5%～61.4%。2004年至2010年共检出36株耐万古霉素肠球菌（VRE）。大肠埃希菌产ESBLs株检出率在29.6%～81.7%,肺炎克雷伯菌产ESBLs株检出率在36.0%～56.6%,产酸克雷伯产ESBLs株检出率在35.3%～67.4%,奇异变形杆菌产ESBLs株检出率在0～26.2%。自2005年起每年均有泛耐药的铜绿假单胞菌和鲍曼不动杆菌的检出。结论该院2004年至2010年多重耐药菌株呈增多趋势,尤其是VRE和泛耐药的铜绿假单胞菌和鲍曼不动杆菌的出现,给临床治疗带来了严峻挑战。     

Masting of rowan <Emphasis Type="Italic">Sorbus aucuparia</Emphasis> L. and consequences for the apple fruit moth <Emphasis Type="Italic">Argyresthia conjugella</Emphasis> Zeller

 Masting of rowan Sorbus aucuparia L. has been studied in 45 sites in southern Norway for 22 years. We present data on the year-to-year variation in fruit setting of rowan, and show that masting is spatially synchronous in Norway and probably all over Fennoscandia. The apple fruit moth Argyresthia conjugella Zeller is an important seed predator on rowan. We present data on the abundance of apple fruit moth in rowanberries during these years and discuss the consequences of masting and intermasting of rowan for apple fruit moth as a pest of apple. We conclude that growth and climate have little impact on flowering intensity and suggest that masting of rowan is an adaptive defense against seed predation and a new example of predator satiation: intermast years inhibit predators and prepare the rowan for the subsequent mast. Received: September 3, 2001 / Accepted: February 24, 2003