Gene Ontology-based function prediction of long non-coding RNAs using bi-random walk

Background

With the development of sequencing technology, more and more long non-coding RNAs (lncRNAs) have been identified. Some lncRNAs have been confirmed that they play an important role in the process of development through the dosage compensation effect, epigenetic regulation, cell differentiation regulation and other aspects. However, the majority of the lncRNAs have not been functionally characterized. Explore the function of lncRNAs and the regulatory network has become a hot research topic currently.

Methods

In the work, a network-based model named BiRWLGO is developed. The ultimate goal is to predict the probable functions for lncRNAs at large scale. The new model starts with building a global network composed of three networks: lncRNA similarity network, lncRNA-protein association network and protein-protein interaction (PPI) network. After that, it utilizes bi-random walk algorithm to explore the similarities between lncRNAs and proteins. Finally, we can annotate an lncRNA with the Gene Ontology (GO) terms according to its neighboring proteins.

Results

We compare the performance of BiRWLGO with the state-of-the-art models on a manually annotated lncRNA benchmark with known GO terms. The experimental results assert that BiRWLGO outperforms other methods in terms of both maximum F-measure (F_max) and coverage.

Conclusions

BiRWLGO is a relatively efficient method to predict the functions of lncRNA. When protein interaction data is integrated, the predictive performance of BiRWLGO gains a great improvement.

     

美味猕猴桃和软枣猕猴桃种间杂交花粉管行为和早期胚胎发生的观察

美味猕猴桃（Ａｃｔｉｎｉｄｉａ ｄｅｌｉｃｉｏｓａ Ｎｏ．２６）和软枣猕猴桃（Ａ． ａｒｇｕｔａ）杂交,观察了花粉管在花柱内的行为和早期胚胎发生,结果如下： 花粉粒在柱头的乳突细胞表面萌发,在开放型的Ｖ 形花柱道内生长,生长速度比对照的缓慢, 到达胚珠珠孔处的时间延迟５０ 到６０ ｈ。当花粉管生长到花柱基部时出现波纹状弯曲;顶端膨大或尖细;部分花粉管的直径发生变化;少数花粉管生长极不规则。花粉管中胼胝质沿管壁不规则沉积, 有的不形成胼胝质塞,或整个管壁被胼胝质所覆盖。约有２６．７４％ 的胚珠受精, 并发育成种子,其中正常种子占６８．５０％ ;败育种子占３１．５０％ ,其中约有１１．４１％ 为空瘪种子;未受精胚珠占６１．４５％ 。正常种子及其胚均较对照的小。胚发育为茄型,胚乳为细胞型,合子保持休眠十几天后开始分裂形成胚,传粉后５０ｄ 见到子叶胚     

哀牢山中山湿性常绿阔叶林凋落物和粗死木质物的初步研究

中山湿性常绿阔叶林是我国山地常绿阔叶林中一个重要而特殊的类型。云南哀牢山原生中生湿性常绿阔叶林的小凋落物量（叶、直径＜ ２．５ ｃｍ 枝、花果和杂物）为（６．７７±１．４３）ｔ／（ｈｍ ２·ａ）,大枯枝（直径≥２．５ ｃｍ ）凋落量为（０．４５±０．１８） ｔ／（ｈｍ ２·ａ）,凋落高峰发生在干季末期４～５ 月和初冬时１０～１１ 月。由倒木、枯立木和大枯枝等组成的粗死木质物在该类森林中的现存量达９８．４６ ｔ／ｈｍ ２,其中倒木占其总量的８５．８％ ,且它们在林内分布不均匀,增加了森林生态系统结构和生境的多样性。粗死木质物是森林中重要的养分库,其中的Ｃ、Ｎ、Ｐ、Ｋ、Ｃａ、Ｍｇ、Ｍｎ、Ａｌ和Ｆｅ元素的总贮量达到４８６９９ ｔ／ｈｍ ２,每年通过凋落物方式积累于林地表的养分元素只占其总量的７．７７％     

L'orgasme de l'homme adulte

We provide data on several aspects of sexual behaviour: masturbation, age at first intercourse, sexual practices during first intercourse, homosexuality and heterosexuality, sexual practices over a lifetime, sexual activity in the past twelve months, frequency of sexual intercourse, last sexual intercourse, achieving orgasm (through vaginal penetration, masturbation by partners, fellatio and cunnilingus), sexual dysfunctions. Data come from recent national sex surveys in: Great Britain (1990–91; n=18.876), Finland (1991–92; n=2250), the United States (1992; n="3432) and especially from the ACSF survey (n=20.055), the French national telephone survey on sexual behaviour conducted between September 1991 and February 1992. Some results about the prevalence of sexual dysfunctions in sexually active men 18 to 69 years old, in France (in %):

- “You do not have an erection (impotence)”

- “often”: 7%, “sometimes”: 12%

-“You ejaculate too early, even before entering you partner” “often”: 5%; “sometimes”: 16%

- “You ejaculate too soon, upon or shortly after entering your partner” “often”: 10%; “sometimes”: 27%

- “It takes you too long to ejaculate once you have entered your partner” “often”: 4%; “sometimes”: 16%

- “You fail to ejaculate at all” “often”: 2%; “sometimes”: 5%

- “You don't have an orgasm” “often”: 7%; “sometimes”: 7%

- “You feel no or insufficient sexual desire” “often”: 3%; “sometimes”: 16%.

     

Associations of polymorphisms in TXNIP and gene–environment interactions with the risk of coronary artery disease in a Chinese Han population

Single nucleotide polymorphisms (SNPs) in thioredoxin‐interacting protein (TXNIP) gene may modulate TXNIP expression, then increase the risk of coronary artery disease (CAD). In a two‐stage case–control study with a total of 1818 CAD patients and 1963 controls, we genotyped three SNPs in TXNIP and found that the variant genotypes of SNPs rs7212 [odds ratio (OR) = 1.26, P = 0.001] and rs7211 (OR = 1.23, P = 0.005) were significantly associated with increased CAD risk under a dominant model. In haplotype analyses, compared with the reference haplotype, haplotype ‘G‐T’ had a 1.22‐fold increased risk of CAD (P = 0.003). We also observed the cumulative effects of SNPs rs7212 and rs7211 on CAD risk and the severity of coronary atherosclerosis. Moreover, the gene–environment interactions among the variant genotypes of SNP rs7212, smoking habit, alcohol drinking habit and history of type 2 diabetes were associated with a 3.70‐fold increased risk of CAD (P < 0.001). Subsequent genotype‐phenotype correlation analyses further observed the significant effects of SNP rs7212 on TXNIP mRNA expression, plasma TXNIP and malondialdehyde levels. Taken together, our data suggest that TXNIP SNPs may individually and cumulatively affect CAD risk through a possible mechanism for regulating TXNIP expression and gene–environment interactions.     

Effect of acaricidal compound extracted from Arachis hypogaea Linn against Tetranychus cinnabarinus

Six plant crude extracts were chosen to evaluate their acaricidal activity against Tetranychus cinnabarinus adults. The crude extract from the stems and leaves of Arachis hypogaea L. presented the highest activity in leaf‐dip bioassays, with an LC₅₀ value of 3,545.98 mg/L. Further extraction using four different solvents (petroleum ether, ethyl acetate, n‐butyl alcohol and distilled water) demonstrated that the active components mainly existed in the petroleum ether phase. Then, the active compound, palmitic acid, was isolated from the petroleum ether phase via two‐step column chromatography using columns filled with silica gel and C‐18 and identified via mass spectrometry and nuclear magnetic resonance analyses. The LC₅₀ value of active palmitic acid against T. cinnabarinus was 534.58 mg/L. The present study demonstrated that the active compound extracted from A. hypogaea is a potential novel botanical acaricide for controlling T. cinnabarinus.     

Capillary electrophoresis coupled with electrochemiluminescence for determination of atomoxetine hydrochloride and the study on its interactions with three proteins

A simple, rapid and sensitive method for the determination of atomoxetine hydrochloride (AH) by capillary electrophoresis with electrochemiluminescence detection (CE‐ECL) using tris(2,2′‐bipyridyl) ruthenium (II) was developed. Under optimized conditions, the determinations of AH in capsules and rat plasmas and the study on its interactions with three plasma proteins, including bovine serum albumin, cytochrome c and myoglobin were performed successfully. Relative to some previous studies, in this paper the methodologies for the determination of AH in aqueous solution and spiked plasma systems were established, respectively. By comparing the difference between the two work curves of two systems, the matrix effect in plasma samples on the determination of AH by the CE‐ECL method was discussed in detail. The results indicated that the effect of the matrix in plasma samples should not be ignored even if no obvious interference was found in the electropherograms and the establishment of method validation in complex samples by the CE‐ECL method was necessary. Copyright © 2014 John Wiley & Sons, Ltd.     

Retracted: CYP2E1 Rsa Ι/Pst Ι polymorphism and lung cancer susceptibility: a meta‐analysis involving 10,947 subjects

Many studies have examined the association between the CYP2E1 Rsa Ι/Pst Ι (rs3813867) polymorphism gene polymorphisms and lung cancer risk in various populations, but their results have been inconsistent. The PubMed and CNKI database was searched for case–control studies published up to October 2013. Data were extracted and pooled odds ratios (OR) with 95% confidence intervals (CI) were calculated. In this meta‐analysis, we assessed 23 published studies involving comprising 4727 lung cancer cases and 6220 controls of the association between CYP2E1 Rsa Ι/Pst Ι polymorphism and lung cancer risk. For the homozygote c2/c2 and c2 allele carriers (c1/c2 + c2/c2), the pooled ORs for all studies were 0.73(95% CI = 0.62–0.84; P = 0.005 for heterogeneity) and 0.84 (95% CI = 0.77–0.92; P = 0.001 for heterogeneity) when compared with the homozygous wild‐type genotype (c1/c1). In the stratified analysis by ethnicity, the same significantly risks were found among Asians and mixed population for both the c2 allele carriers and homozygote c2/c2. However, no significant associations were found in Caucasian population all genetic models. This updated meta‐analysis suggests that CYP2E1 Rsa Ι/Pst Ι c2 allele is a decreased risk factor for the developing lung cancer among Asians and mixed population.     

A-NK细胞联合IL-2，IL-12在肿瘤免疫治疗中的作用

本文对A-NK细胞联合IL-2和IL-12在抗肿瘤免疫治疗中的作用进行了论述。强调联合应用可高效激活A-NK细胞,提高对肿瘤细胞的杀伤活性。减少IL-2和IL-12的用量及副作用,提高疗效。