Disruption of phospholipase B gene, PLB1, increases the survival of baker's yeast Torulaspora delbrueckii

Abstract An uracil auxotrophic mutant of baker's yeast Torulaspora delbrueckii , which is resitant to 5-fluoro-orotic acid, was complemented by transformation with YEp24 which harbors 2 μm origin and URA3 derived from Saccharomyces cerevisiae . The phospholipase B in T. delbrueckii cells is active in both acidic and alkaline conditions. However, activity of phospholipase B gene ( PLB1 ) in cells of disruption mutant ( plbI : : URA3 ) was lost in both conditions, which indicates that all phospholipase B activity is encoded by a single gene (or a single polypeptide) in these yeast cells. Over-expression of PLB1 with YEp plasmid vector in T. delbrueckii cells showed ∼ 2.5-fold increase in phospholipase B activity, comparing with that in wild-type cells. Cells of plb1 Δ mutant showed increased survival when cells of plb1 Δ mutant and wild-type strain were incubated in water at 30 °C. Cells of PLB1 -over-expressed strain died rapidly even during the cultivation period, indicating that phospholipase B activity may be a determinant for the survival of this yeast.     

Improve survival prediction using principal components of gene expression data

The purpose of many microarray studies is to find the association between gene expression and sample characteristics such as treatment type or sample phenotype. There has been a surge of efforts developing different methods for delineating the association. Aside from the high dimensionality of microarray data, one well recognized challenge is the fact that genes could be complicatedly inter-related, thus making many statistical methods inappropriate to use directly on the expression data. Multivariate methods such as principal component analysis （PCA） and clustering are often used as a part of the effort to capture the gene correlation, and the derived components or clusters are used to describe the association between gene expression and sample phenotype. We propose a method for patient population dichotomization using maximally selected test statistics in combination with the PCA method, which shows favorable results. The proposed method is compared with a currently well-recognized method.     

The genetic effects of competition in seaweed flies

In spite of abundant evidence that intra- and inter-specific competition occurs in natural communities, there is surprisingly little to suggest it is a major force promoting genetic change. This report assesses the genetic effects of competition in two species of seaweed fly, Coelopa frigida and C. pilipes. In laboratory cultures of C. frigida the relative survival of heterozygotes at the Adh locus, which was being used as a marker for the large αβ chromosomal inversion, was greater than that of homozygotes. In monocultures of C. frigida this competitive superiority was dependent on larval density. At low densities facilitation was seen, whereas at high larval densities there was competition. In mixed cultures of the two species, interspecific competition contributed to the differential mortality of C. frigida , and observations of natural populations suggested that competition may have similar effects to those described in laboratory culture. A possible mechanism involving the supply of nutritive microorganisms is proposed to underly both intra- and inter-specific competition. In seaweed flies, competition and the consequent differential mortality appear to be forces maintaining rather than reducing genetic variation.     

The histological type of endometrial cancer is not associated with menopause status at diagnosis

The latest evidence suggests that type 2 endometrial cancer may not be completely oestrogen-independent, indicating that the status of hormonal change may not be associated with the traditional classification of endometrial cancer, including the histological subtypes. However, this has not been investigated. Menopause is commonly considered a state of hormonal change in women. In the present study, we investigated the association of menopause with the histological types of endometrial cancer. Data on the histological type, menopause status at diagnosis, age at diagnosis, parity, body mass index (BMI), and overall survival rate from 2122 cases were collected. The difference in risk in developing type 1 or type 2 endometrial cancer between premenopausal and postmenopausal patients was 5.457%. A statistical difference in the association of menopause with the histological types between the two groups was seen in endometrioid and serous carcinoma, with a risk difference of 5.6 or 3.8%. A statistical difference in the association of menopause with parity between the groups was only seen in endometrioid and adenosquamous carcinoma, with a risk difference of 7.1 or 3.7%. However, BMI was not associated with histological type and the overall survival rate was not associated with menopause (P=0.764). We reported a relatively small difference in the association of menopause with type 1 or type 2, or the histological types of endometrial cancer. The survival rate was not associated with menopause. Our study suggests that menopause status at diagnosis was not strongly associated with the histological subtypes of endometrial cancer.     

基于肿瘤免疫微环境鉴定IDH突变型弥漫性胶质瘤的预后标志物

异柠檬酸脱氢酶(IDH)突变存在于大多数低级别胶质细胞瘤中,免疫逃逸是肿瘤标志性特征之一,免疫治疗在胶质瘤的治疗中的作用越来越重要。利用生信手段分析TCGA、CGGA、GEO数据集中IDH突变胶质瘤的770个免疫相关基因及其临床相关数据,从而获得每个患者的免疫风险评分(IMRS);结合IMRS和临床信息,筛选出6个差异表达基因(TRAF3、ATG10、BID、TAB1、MAP3K1、RPS6)组成IMRS模型并生成诺莫图对患者预后进行评估,发现低风险组患者的总生存期(OS)较高风险组均明显延长。此外,签名相关免疫细胞浸润分析发现肿瘤相关巨噬细胞浸润评分(TAM)与肿瘤相关T细胞浸润评分(TIS)呈明显的负相关,表明高IMRS富集了促肿瘤免疫浸润,而低IMRS则富集了相对较多的抗肿瘤免疫浸润。     

Effects of double bands on Magellanic Penguins

ABSTRACT Banding penguins is controversial because bands can alter the survival, reproduction, and behavior of marked individuals. The effects of bands are not consistent among band types and, although stainless steel is thought to be better than other materials, tests of the long‐term impact of bands on tag‐loss rates and the reproduction and survival of individuals are needed. We tested three types of external tags on Magellanic Penguins (Spheniscus magellanicus) to measure band effects and tag‐loss rates. In 1993, we double‐tagged 300 penguins with aluminum flipper bands, stainless‐steel flipper bands, or small (2 mm × 10 mm) metal tags attached to foot webbing. We searched for double‐tagged birds for 13 of 15 yrs (1994–2008). Aluminum bands deformed, caused feather wear, injured and killed some penguins, and were lost more often than stainless‐steel bands or web tags. During the first 2 yrs of our study, at least nine penguins lost one aluminum band (N= 71 penguins resighted), but no penguins lost a stainless‐steel band (N= 84) or a web tag (N= 88). During the next 13 yrs, five penguins lost one of their two web tags (N= 89), but none lost a stainless‐steel band (N= 84). Females laid eggs of similar size before they carried a band and in the year following tagging (P= 0.09). The type of tags a female carried did not significantly change egg size (P > 0.22). During the first breeding season after tagging, penguins with aluminum bands had lower reproductive success than penguins with stainless‐steel bands or web‐tags (P= 0.04). The annual survival of females with two stainless‐steel bands was lower (0.79) than that of males with two stainless‐steel bands or males and females with two web‐tags (0.87). Aluminum bands injured Magellanic Penguins, were lost at high rates, and should not be used. Double stainless‐steel bands had no apparent effects on adult male Magellanic Penguins, but reduced survival rates of adult females. A single stainless‐steel band would likely have less impact than two bands, and our results suggest that the impact of a single band would be difficult to measure.     

Artificial sowing of endangered dry grassland species into disused basalt quarries

Steppe-like dry (semi) natural grasslands are valuable and endangered habitats in central Europe. In the study area (the ?eské st?edoho?í Hills, Czech Republic), they occur in fragments on southern slopes of volcanic hills, often in the vicinity of quarries, which are numerous there. We performed sowing experiments and observed seedling recruitment of six species, typical for the dry grasslands, in 9 basalt quarries located in 3 different climatic regions over 3 yr. The sowing experiments were established in young successional stages, 5–12 yr after quarrying was stopped. The objectives of the experiments were to evaluate: (i) if seedling recruitment and survival of the target species are possible regarding different climatic regions and (ii) what is the influence of weather fluctuations among years on seedling survival. Seedlings of all studied species were able to recruit and survive in the early successional stages at least in some quarries. The species, except one, showed significant differences in recruitment among the climatic regions, with the best recruitment and survival in the driest and warmest region. Seedlings of two species did not recruit in the wettest and coldest region. All species survived in the driest and warmest region, while only one did so in the coldest and wettest region. Different weather conditions in the studied years significantly influenced recruitment of two species. The number of localities (floristic records) of particular species in the regions was the best predictor of species germination and survival. Thus a traditional floristic survey may help to predict success of species in restoration projects. It emerged that artificial sowing can be considered in restoration programs as a way of contributing to restoration of dry grasslands in disused quarries.     

Tarsal asymmetry, nutritional condition, and survival in water boatmen (Callicorixa Vulnerata)

Fluctuating asymmetry (FA) has been used as a measure of developmental stability and may indicate individual phenotypic or genotypic quality. Using water boatmen (Callicorixa vulnerata) from a natural population, we examined the relationship between tarsal FA (tarsal spine number, tarsal length) and indices of body condition in two habitats. We used body weight and residual body weight (controlling for body length) as indices of condition because experimental food deprivation in water boatmen led to a reduction in each. We detected a negative relationship between FA and both indices of condition in two ecologically distinct pond habitats. We predicted this association was due to a negative relationship between FA and competitive feeding ability. Consequently, we examined associations between survival time and tarsal FA in C. vulnerata under resource-limited laboratory conditions. Univariate analyses revealed a negative correlation between survival and tarsal FA in each trait. Inclusion of survival time, body length, gender, tarsal spine number, tarsal length, and measures of FA into multivariate analyses revealed a negative correlation between survival and FA. Individuals with the greatest survival had higher nutritional condition than individuals that succumbed early in the experiment. Asymmetric individuals may suffer a foraging handicap as a result of the use of tarsi in feeding or they may be of poor genetic quality. Our results suggest elevated FA may limit resource acquisition and are consistent with the use of FA as a measure of fitness.