Predicting synthetic lethal genetic interactions in <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> using short polypeptide clusters

Background

Protein synthetic lethal genetic interactions are useful to define functional relationships between proteins and pathways. However, the molecular mechanism of synthetic lethal genetic interactions remains unclear.

Results

In this study we used the clusters of short polypeptide sequences, which are typically shorter than the classically defined protein domains, to characterize the functionalities of proteins. We developed a framework to identify significant short polypeptide clusters from yeast protein sequences, and then used these short polypeptide clusters as features to predict yeast synthetic lethal genetic interactions. The short polypeptide clusters based approach provides much higher coverage for predicting yeast synthetic lethal genetic interactions. Evaluation using experimental data sets showed that the short polypeptide clusters based approach is superior to the previous protein domain based one.

Conclusion

We were able to achieve higher performance in yeast synthetic lethal genetic interactions prediction using short polypeptide clusters as features. Our study suggests that the short polypeptide cluster may help better understand the functionalities of proteins.

     

Alteration of Components of Leaf Water Potential and Water Content in Velvetleaf under the Effects of Long-Term Humidity Difference

Velvetleaf (Abutilon theophrasti Medik.) was grown in growth chambers set at 45 or 85% relative humidity at 30°C, CO₂ 350 microliters per liter and 1000 micromoles per square meter per second of photosynthetically active radiation. Soil water potential was maintained at −0.05 megapascal by subirrigation with half strength Hoagland solution. The third, fourth, and fifth leaves from the base of 21- and 25-day-old plants were used for pressure-volume measurements. Components of leaf water status including water potential (osmotic and potential associated with the apoplast), leaf water content (apoplasmic and symplasmic water), and elastic modulus of leaf tissue were determined. Results indicate: (a) persistent dry air generated leaves with lower water potential at a given relative water content than did humid air; (b) the higher total leaf water content in plants grown in dry air was related to an increase in apoplasmic water, whereas symplasmic water remained similar in both humidity treatments; (c) difference in leaf water potential between low and high humidity treatments was related to decreased potential associated with the apoplast but not to a change in cell wall elasticity.     

Rain use efficiency as affected by climate warming and biofuel harvest: results from a 12‐year field experiment

The efficiency of a terrestrial ecosystem to use rainfall in production is critical in regulating the ecological functions of the earth system under global change. However, it remains unclear how rain use efficiency (RUE) will be altered by changes in climate and human activities such as biofuel harvest. In this study, we used RUE data from a long‐term experiment in a tallgrass prairie to analyze the effects of warming and biofuel harvest (clipping). From 2000 to 2011, experimental warming enhanced RUE in most years, with larger positive effects in normal and wet than dry hydrological years. Clipping decreased RUE in dry and normal hydrological years, but had no impact on RUE in wet years. The observed RUE responses resulted from treatment‐induced changes in both biologically ineffective (i.e., runoff and soil evaporation) and effective (i.e., transpiration) parts of precipitation. For example, litter cover was increased in warming plots, but reduced by clipping, leading to negative and positive effects on runoff and soil evaporation, respectively. The dominance of C₄ species, which usually have higher water use efficiency than C₃ species, was enhanced by warming, but reduced by clipping. Moreover, RUE was positively correlated with ratios of rainfall in the late growing season (June–August), when the growth of C₄ plants was most active, relative to that in the other seasons. Our results indicate that RUE is positively influenced by climate warming, but negatively affected by biofuel harvest in tallgrass prairie of the Great Plains. These findings highlight the important roles of plant community structure and temporal distribution of precipitation in regulating ecosystem RUE.     

Comparison of the Efficacy of Rosuvastatin versus Atorvastatin in Preventing Contrast Induced Nephropathy in Patient with Chronic Kidney Disease Undergoing Percutaneous Coronary Intervention

Objectives

We prospectively compared the preventive effects of rosuvastatin and atorvastatin on contrast-induced nephropathy (CIN) in patients with chronic kidney disease (CKD) undergoing percutaneous coronary intervention (PCI).

Methods

We enrolled 1078 consecutive patients with CKD undergoing elective PCI. Patients in Group 1 (n = 273) received rosuvastatin (10 mg), and those in group 2 (n = 805) received atorvastatin (20 mg). The primary end-point was the development of CIN, defined as an absolute increase in serum creatinine ≥0.5 mg/dL, or an increase ≥25% from baseline within 48–72 h after contrast medium exposure.

Results

CIN was observed in 58 (5.4%) patients. The incidence of CIN was similar in patients pretreated with either rosuvastatin or atorvastatin (5.9% vs. 5.2%, p = 0.684). The same results were also observed when using other definitions of CIN. Clinical and procedural characteristics did not show significant differences between the two groups (p>0.05). Additionally, there were no significant inter-group differences with respect to in-hospital mortality rates (0.4% vs. 1.5%, p = 0.141), or other in-hospital complications. Multivariate logistic regression analysis revealed that rosuvastatin and atorvastatin demonstrated similar efficacies for preventing CIN, after adjusting for potential confounding risk factors (odds ratio = 1.17, 95% confidence interval, 0.62–2.20, p = 0.623). A Kaplan–Meier survival analysis showed that patients taking either rosuvastatin or atorvastatin had similar incidences of all-cause mortality (9.4% vs. 7.1%, respectively; p = 0.290) and major adverse cardiovascular events (29.32% vs. 23.14%, respectively; p = 0.135) during follow-up.

Conclusions

Rosuvastatin and atorvastatin have similar efficacies for preventing CIN in patients with CKD undergoing PCI.     

热性癫痫发作大鼠海马齿状回外侧支的可塑性和再可塑性

热性癫痫发作是儿童常见病,能损害认知功能,而突触可塑性和再可塑性(metaplasticity)是维系大脑认知功能的重要神经基础.本文通过脑片灌流和细胞外场电位记录术研究了热性癫痫发作大鼠海马齿状回外侧支的突触可塑性和再可塑性.制作对照组和热性癫痫发作组大鼠的脑切片后,记录电极置于齿状回外侧支的外分子层获取兴奋性突触后...     

Inhibition of the oxidative stress-induced miR-23a protects the human retinal pigment epithelium (RPE) cells from apoptosis through the upregulation of glutaminase and glutamine uptake

The degeneration of retinal pigment epithelium (RPE) cells in the sub retinal pigment epithelial space and choroid is an initial pathological characteristic for the age-related macular degeneration which is the leading cause of severe vision loss in old people. Moreover, oxidative stress is implicated as a major inducer of RPE cell death. Here, we assessed the correlation between the H₂O₂-induced RPE cell death and glutamine metabolism. We found under low glutamine supply (20 %), the ARPE-19 cells were more susceptive to H₂O₂-induced apoptosis. Moreover, the glutamine uptake and the glutaminase (GLS) were suppressed by H₂O₂ treatments. Moreover, we observed miR-23a was upregulated by H₂O₂ treatments and overexpression of miR-23a significantly sensitized ARPE-19 cells to H₂O₂. Importantly, Western blotting and luciferase assay demonstrated GLS1 is a direct target of miR-23a in RPE cells. Inhibition of the H₂O₂-induced miR-23a by antagomiR protected the RPE cells from the oxidative stress-induced cell death. In addition, recovery of GLS1 expression in miR-23a overexpressed RPE cells rescued the H₂O₂-induced cell death. This study illustrated a mechanism for the protection of the oxidative-induced RPE cell death through the recovery of glutamine metabolism by inhibition of miR-23a, contributing to the discovery of novel targets and the developments of therapeutic strategies for the prevention of RPE cells from oxidative stress.     

The Ku70 ?1310C/G promoter polymorphism is associated with breast cancer susceptibility in Chinese Han population

Ku70 plays an important role in the DSBR (DNA double-strand breaks repair) and maintenance of genomic integrity. Genetic variations within human Ku70 have been demonstrated to be associated with increased risk of several types of cancers. In this hospital-based case–control study, we aimed to investigate whether a single nucleotide polymorphism (SNP) in the promoter region (rs2267437) of Ku70 gene is associated with susceptibility to breast cancer in Chinese Han population. A total of 293 patients with breast cancer and 301 age-matched healthy controls were enrolled in this study. The Ku70 −1310C/G polymorphism was determined by polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) analysis. A significant difference in genotype distribution and allele frequency was observed between patients and controls. The CG or GG carries were at higher risk of breast cancer compared with the CC homozygotes (OR = 1.43, 95% CI = 1.02–2.00, P = 0.038 and OR = 3.53, 95% CI = 1.60–7.80, P = 0.002, respectively). Further stratification analysis revealed that G allele was associated with an increased risk of breast cancer among premenopausal women (OR = 1.68, 95% CI = 1.21–2.33, P = 0.002), but not in postmenopausal women (OR = 1.33, 5% CI = 0.85–2.10, P = 0.216). Our study suggests that the Ku70 −1310C/G promoter polymorphism may be a susceptibility factor for breast cancer in Chinese Han population.     

Modeling human mitochondrial diseases in flies

Human mitochondrial diseases are associated with a wide range of clinical symptoms, and those that result from mutations in mitochondrial DNA affect at least 1 in 8500 individuals. The development of animal models that reproduce the variety of symptoms associated with this group of complex human disorders is a major focus of current research. Drosophila represents an attractive model, in large part because of its short life cycle, the availability of a number of powerful techniques to alter gene structure and regulation, and the presence of orthologs of many human disease genes. We describe here Drosophila models of mitochondrial DNA depletion, deafness, encephalopathy, Freidreich's ataxia, and diseases due to mitochondrial DNA mutations. We also describe several genetic approaches for gene manipulation in flies, including the recently developed method of targeted mutagenesis by recombinational knock-in.     

人胎视网膜含NOS神经元的发育

本文用一氧化氮合酶（ＮＯＳ）的组织化学方法对胎龄１５周至３６周的人胎视网膜含ＮＯＳ神经元的发育进行了研究。胚胎１５周视网膜颞侧半少部分神经元即有ＮＯＳ的表达,２０周视网膜含ＮＯＳ神经元数密度达峰值。大部分含ＮＯＳ神经元胞体位于内核层内带,只少部分位于节细胞层,其突起均分布于内同层,形成内同层的１、３、５亚层。含ＮＯＳ神经元的形态各异,依据其突起的多少分Ⅰ、Ⅱ、Ⅲ等三种类型,其中Ⅱ、Ⅲ型含ＮＯＳ神经元在２８周以后才开始出现,且愈近晚期胎龄,它们所占含ＮＯＳ神经元的数量比呈上升趋势。随视网膜发育成熟,含ＮＯＳ神经元胞体均面积呈不断增大的变化。本文结果显示：人胎视网膜内核层含ＮＯＳ神经元为无长突细胞,节细胞层的Ⅰ型含ＮＯＳ神经元为移位无长突细胞,推测它们在视网膜的发育过程中对内网层突触的形成与修饰可能起有重要作用。     

Microbial community responses reduce soil carbon loss in Tibetan alpine grasslands under short‐term warming

Changes in labile carbon (LC) pools and microbial communities are the primary factors controlling soil heterotrophic respiration (R_h) in warming experiments. Warming is expected to initially increase R_h but studies show this increase may not be continuous or sustained. Specifically, LC and soil microbiome have been shown to contribute to the effect of extended warming on R_h. However, their relative contribution is unclear and this gap in knowledge causes considerable uncertainty in the prediction of carbon cycle feedbacks to climate change. In this study, we used a two‐step incubation approach to reveal the relative contribution of LC limitation and soil microbial community responses in attenuating the effect that extended warming has on R_h. Soil samples from three Tibetan ecosystems—an alpine meadow (AM), alpine steppe (AS), and desert steppe (DS)—were exposed to a temperature gradient of 5–25°C. After an initial incubation period, soils were processed in one of two methods: (a) soils were sterilized then inoculated with parent soil microbes to assess the LC limitation effects, while controlling for microbial community responses; or (b) soil microbes from the incubations were used to inoculate sterilized parent soils to assess the microbial community effects, while controlling for LC limitation. We found both LC limitation and microbial community responses led to significant declines in R_h by 37% and 30%, respectively, but their relative contributions were ecosystem specific. LC limitation alone caused a greater R_h decrease for DS soils than AMs or ASs. Our study demonstrates that soil carbon loss due to R_h in Tibetan alpine soils—especially in copiotrophic soils—will be weakened by microbial community responses under short‐term warming.