Long non‐coding RNA expressed in macrophage co‐varies with the inflammatory phenotype during macrophage development and polarization

Advances in microarray, RNA‐seq and omics techniques, thousands of long non‐coding RNAs (lncRNAs) with unknown functions have been discovered. LncRNAs have presented a diverse perspective on gene regulation in diverse biological processes, especially in human immune response. Macrophages participate in the whole phase of immune inflammatory response. They are able to shape their phenotype and arouse extensive functional activation after receiving physiological and pathological stimuli. Emerging studies indicated that lncRNAs participated in the gene regulatory network during complex biological processes of macrophage, including macrophage‐induced inflammatory responses. Here, we reviewed the existing knowledges of lncRNAs in the processes of macrophage development and polarization, and their roles in several different inflammatory diseases. Specifically, we focused on how lncRNAs function in macrophage, which might help to discover some potential therapeutic targets and diagnostic biomarkers.     

Disease-driven detection of differential inherited SNP modules from SNP network

Detection of the synergetic effects between variants, such as single-nucleotide polymorphisms (SNPs), is crucial for understanding the genetic characters of complex diseases. Here, we proposed a two-step approach to detect differentially inherited SNP modules (synergetic SNP units) from a SNP network. First, SNP-SNP interactions are identified based on prior biological knowledge, such as their adjacency on the chromosome or degree of relatedness between the functional relationships of their genes. These interactions form SNP networks. Second, disease-risk SNP modules (or sub-networks) are prioritised by their differentially inherited properties in IBD (Identity by Descent) profiles of affected and unaffected sibpairs. The search process is driven by the disease information and follows the structure of a SNP network. Simulation studies have indicated that this approach achieves high accuracy and a low false-positive rate in the identification of known disease-susceptible SNPs. Applying this method to an alcoholism dataset, we found that flexible patterns of susceptible SNP combinations do play a role in complex diseases, and some known genes were detected through these risk SNP modules. One example is GRM7, a known alcoholism gene successfully detected by a SNP module comprised of two SNPs, but neither of the two SNPs was significantly associated with the disease in single-locus analysis. These identified genes are also enriched in some pathways associated with alcoholism, including the calcium signalling pathway, axon guidance and neuroactive ligand-receptor interaction. The integration of network biology and genetic analysis provides putative functional bridges between genetic variants and candidate genes or pathways, thereby providing new insight into the aetiology of complex diseases.     

Repetitive Transcranial Magnetic Stimulation Ameliorates Anxiety-Like Behavior and Impaired Sensorimotor Gating in a Rat Model of Post-Traumatic Stress Disorder

BackgroundRepetitive transcranial magnetic stimulation (rTMS) has been employed for decades as a non-pharmacologic treatment for post-traumatic stress disorder (PTSD). Although a link has been suggested between PTSD and impaired sensorimotor gating (SG), studies assessing the effects of rTMS against PTSD or PTSD with impaired SG are scarce.AimTo assess the benefit of rTMS in a rat model of PTSD.MethodsUsing a modified single prolonged stress (SPS&S) rat model of PTSD, behavioral parameters were acquired using open field test (OFT), elevated plus maze test (EPMT), and prepulse inhibition trial (PPI), with or without 7 days of high frequency (10Hz) rTMS treatment of SPS&S rats.ResultsAnxiety-like behavior, impaired SG and increased plasma level of cortisol were observed in SPS&S animals after stress for a prolonged time. Interestingly, rTMS administered immediately after stress prevented those impairment.ConclusionStress-induced anxiety-like behavior, increased plasma level of cortisol and impaired PPI occur after stress and high-frequency rTMS has the potential to ameliorate this behavior, suggesting that high frequency rTMS should be further evaluated for its use as a method for preventing PTSD.     

地下结实植物白番红花地下果实的生产与种子扩散特性

地下芽地下结实是指由植株地下芽分化形成的具长管状花被的花伸出地表开放、而子房在地下发育成果实的一种特殊结实现象。白番红花(Crocus alatavicus)是生长于天山西部亚高山带、具地下芽地下结实特性的多年生早春短命植物。本文采用野外观测和控制实验方法,对该物种地下子房和幼果的发育特点与种子扩散特性及其适应意义进行了研究。结果表明:白番红花从开花到地下果实露出地表的发育时间约需35 d,地下果实在花梗的伸长生长作用下露出地面开裂并扩散种子,且种子具有油质体等典型蚁传植物种子的特征。蚁类是白番红花种子的主要传播者。在搬运种子的Formica pressilabris、栗色林蚁和黑褐蚁中,F.pressilabris出现的频率最高,但栗色林蚁搬运的速度最快、距离最远。3种蚂蚁搬运白番红花种子的平均距离为62.4±1.7 cm。Formica pressilabris将白番红花种子搬运至蚁穴中后取食油质体,且有超过50%的种子被储藏在蚁穴中。啮齿类和鸟类不传播白番红花种子,但水媒和风媒对种子的短距离散布具有一定作用。这些结果说明:白番红花的地下结实及蚁传特性不仅可保护发育中的子房及果实躲避地表草食动物的取食,避免自然火灾对地上果实的伤害,以及延长果实和种子的发育时间以保障其安全成熟,还可避免真菌和其他病原体的侵扰、减少同胞之间以及母株与子代间的竞争,使种子在适宜环境中萌发并建立新的种群。     

Mining gene expression data for positive and negative co-regulated gene clusters

MOTIVATION: Analysis of gene expression data can provide insights into the positive and negative co-regulation of genes. However, existing methods such as association rule mining are computationally expensive and the quality and quantities of the rules are sensitive to the support and confidence values. In this paper, we introduce the concept of positive and negative co-regulated gene cluster (PNCGC) that more accurately reflects the co-regulation of genes, and propose an efficient algorithm to extract PNCGCs. RESULTS: We experimented with the Yeast dataset and compared our resulting PNCGCs with the association rules generated by the Apriori mining algorithm. Our results show that our PNCGCs identify some missing co-regulations of association rules, and our algorithm greatly reduces the large number of rules involving uncorrelated genes generated by the Apriori scheme. AVAILABILITY: The software is available upon request.     

The Caenorhabditis elegans sex determination protein FEM-1 is a CED-3 substrate that associates with CED-4 and mediates apoptosis in mammalian cells

Sex-specific elimination of cells by apoptosis plays a role in sex determination in Caenorhabditis elegans. Recently, a mammalian pro-apoptotic protein named F1Aalpha has been identified. F1Aalpha shares extensive homology throughout the entire protein with the C. elegans protein, FEM-1, which is essential for achieving all aspects of the male phenotype in the nematode. In this report, the role of FEM-1 in apoptosis was investigated. Overexpression of FEM-1 induces caspase-dependent apoptosis in mammalian cells. FEM-1 is cleaved in vitro by the C. elegans caspase, CED-3, generating an N-terminal cleavage product that corresponds to the minimal effector domain for apoptosis. Furthermore, CED-4 associates with FEM-1 in vitro and in vivo in mammalian cells and potentiates FEM-1-mediated apoptosis. Similarly, Apaf-1, the mammalian homologue of CED-4 was found to associate with F1Aalpha. These data suggest that FEM-1 and F1Aalpha may mediate apoptosis by communicating directly with the core machinery of apoptosis.     

油菜菌核病危害损失的初步研究

本文就油菜菌核病病情、发病期及发病部位与油菜产量损失的相互关系进行了模似研究。结果表明：病斑绕茎度是影响产量的主要因素,其大小与产量损失成正相关,而病斑纵向长度与产量损失无明显相关性;发病期不同产量差异显著,以初花期发病产量损失最重,发病期与产量损失线性相关,可利用线性回归方程对产量损失进行预测;主茎发病部位愈近基部,枝条发病部位愈趋于主茎,单株产量损失率愈高。     

Seasonal and spatial variations in microbial community structure and diversity in the acid stream draining across an ongoing surface mining site

This study examined the microbial community in an acidic stream draining across the Yun-Fu pyrite mine (Guangdong, China), where extremely acidic mine water is a persistent feature due to the intensive surface mining activities. Analysis of terminal restriction fragment length polymorphism (TRFLP) of 16S rRNA gene sequences showed that microbial populations varied spatially and seasonally and correlated with geochemical and physical conditions. After the stream moves from underground to the surface, the microbial community in the acidic water rapidly evolves into a distinct community close to that in the downstream storage pond. Comparisons of TRFLP peaks with sequenced clone libraries indicated that bacteria related to the recently isolated iron-oxidizer Ferrovum myxofaciens dominated the acidophilic community throughout the year except for the samples collected in spring from the storage pond, where Ferroplasma acidiphilum -like archaea represented the most abundant group. Acidithiobacillus ferrooxidans -affiliated organisms increased along the acid stream and remained common over the year, whereas Leptospirillum ferrooxidans -like bacteria were negligible or even not detected in the analyzed samples. The data indicate that changes in environmental conditions are accompanied by significant shifts in community structure of the prokaryotic assemblages at this opencast mining site.