A new method for post Genome-Wide Association Study (GWAS) analysis of colorectal cancer in Taiwan

Recently, single nucleotide polymorphisms (SNPs) located in specific loci or genes have been identified associated with susceptibility to colorectal cancer (CRC) in Genome-Wide Association Studies (GWAS). However, in different ethnicities and regions, the genetic variations and the environmental factors can widely vary. Therefore, here we propose a post-GWAS analysis method to investigate the CRC susceptibility SNPs in Taiwan by conducting a replication analysis and bioinformatics analysis. One hundred and forty-four significant SNPs from published GWAS results were collected by a literature survey, and two hundred and eighteen CRC samples and 385 normal samples were collected for post-GWAS analysis. Finally, twenty-six significant SNPs were identified and reported as associated with susceptibility to colorectal cancer, other cancers, obesity, and celiac disease in a previous GWAS study. Functional analysis results of 26 SNPs indicate that most biological processes identified are involved in regulating immune responses and apoptosis. In addition, an efficient prediction model was constructed by applying Jackknife feature selection and ANOVA testing. As compared to another risk prediction model of CRC for European Caucasians population, which performs 0.616 of AUC by using 54 SNPs, the proposed model shows good performance in predicting CRC risk within the Taiwanese population, i.e., 0.724 AUC by using 16 SNPs. We believe that the proposed risk prediction model is highly promising for predicting CRC risk within the Taiwanese population. In addition, the functional analysis results could be helpful to explore the potential associated regulatory mechanisms that may be involved in CRC development.     

Host genetic risk factors for community-acquired pneumonia

This study was conducted to establish the contribution of genetic host factors in the susceptibility to community acquired pneumonia (CAP) in the Russian population. Patients with CAP (n = 334), volunteers without a previous history of CAP, constantly exposed to infectious agents, control A group (n = 141) and a second control group B consisted of healthy persons (n = 314) were included in the study. All subjects were genotyped for 13 polymorphic variants in the genes of xenobiotics detoxification CYP1A1 (rs2606345, rs4646903, and rs1048943), GSTM1 (Ins/del), GSTT1 (Ins/del), ABCB1 rs1045642); immune and inflammation response IL-6 (rs1800795), TNF-a (rs1800629), MBL2 (rs7096206), CCR5 (rs333), NOS3 (rs1799983), angiotensin-converting enzyme ACE (rs4340), and occlusive vascular disease/hyperhomocysteinemia MTHFR (rs1801133). Seven polymorphic variants in genes CYP1A1, GSTM1, ABCB1, NOS3, IL6, CCR5 and ACE were associated with CAP. For two genes CYP1A1 and GSTM1 associations remained significant after correction for multiple comparisons. Multiple analysis by the number of all risk genotypes showed a highly significant association with CAP (P = 2.4 × 10^− 7, OR = 3.03, 95% CI 1.98–4.64) with the threshold for three risk genotypes. Using the ROC-analysis, the AUC value for multi-locus model was estimated as 68.38.     

Compensatory nature of Chargaff’s second parity rule

The second parity rule of Chargaff (A≈T and G≈C within one strand) holds all over the living world with minor exceptions. It is maintained with higher accuracy for long sequences. The question addressed in the article is how different sequence types, with different biases from the parity, contribute to the general effect. It appears that the sequence segments with biases of opposite sign are intermingled, so that with sufficient sequence lengths the parity is established. The parity rule seems to be a cumulative result of a number of independent processes in the genome evolution, with the parity as their intrinsic property. Symmetrical appearance of simple repeats and of Alu sequences in the human DNA strands, and other contributions to the Chargaff parity II rule are discussed.     

The Algicidal Characteristics of One Algae-Lysing FDT5 Bacterium on Microcystis aeruginosa

One strain of algicidal bacterium which can inhibit Harmful algal blooms (HABs), FDT5, was isolated from activated sludge and found to have good algicidal effects on Microcystis aeruginosa. It was revealed that: The FDT5 was a Gram-negative bacterium and identified as Ochrobactrum sp.; The greater the initial bacterial cell density, the faster the degradation of chlorophyll a.; The algicidal efficiency was evaluated at the most favorable conditions which were a temperature of 30–35°C, a pH of 7.6 and complete darkness; The FDT5 strain lysed Microcystis aeruginosa not directly but by secreting metabolites which could withstand high temperatures and pressure.     

基于光谱特征变量的湿地典型植物生态类型识别方法——以北京野鸭湖湿地为例

光谱特征变量的选择对于湿地植被识别的精度和效率有着直接的影响作用.以华北地区典型的淡水湿地——野鸭湖湿地为研究区,采用Field Spec 3野外高光谱辐射仪,获取了野鸭湖典型湿地植物的冠层光谱.以野外高光谱数据为基础,首先利用一阶导数与包络线去除的方法,分析和对比不同植物生态类型的光谱特征,选定了用于识别植物生态类型的光谱特征变量,选定的8个光谱特征变量为红边位置WP_r、红边幅值Dr、绿峰位置WP_g、绿峰幅值Rg、510 nm附近的吸收深度DEP-510和吸收面积AREA-510、675 nm附近的吸收深度DEP-675和吸收面积AREA-675.其中,7种植物生态类型的一阶导数光谱特征差异较小,吸收特征差异性相对较大.除WP_r和WP _g外,沉水植物Rg和Dr平均值最低,湿生植物的Rg平均值最高,达到0.164,栽培植物的Dr平均值最高,达到0.012.7种植物生态类型在675 nm附近的DEP-675和AREA-675均高于510 nm附近的DEP-510与AREA-510,除去栽培植物,随着水分梯度的变化,其他6种植物生态类型的吸收深度和吸收面积都表现出先升高后降低的趋势.然后利用单因素方差分析(One-way ANOVA)验证了所选光谱特征变量的区分度,在P≤0.01的置信水平下,选取的8个光谱特征变量都能够较好的区分7种植物生态类型,区分度的最小值为13,最大值为18,并且吸收特征参数的区分度优于一阶导数参数.最后应用非线性的反向传播人工神经网络(BP-ANN)与线性判别分析(FLDA)的类型识别方法,利用选定的8个光谱特征变量进行湿地植物生态类型识别,取得了较好的识别精度,两种方法的总分类精度分别达到85.5％和87.98％.单因素方差分析(One-way ANOVA)和不同分类器的分类精度表明,所选的8个光谱特征变量具有一定的普适性和可靠性.     

牛源无乳链球菌长尾噬菌体的特性

【目的】分离鉴定噬菌体,对其生物学特性进行研究,并筛选候选毒株为防控牛源无乳链球菌的感染提供依据。【方法】分别采用从牛奶或环境中分离、溶原菌诱导两种方法分离鉴定无乳链球菌噬菌体,利用双层琼脂平板法纯化。将新分离鉴定毒株与前期已分离鉴定的源自乳腺炎牛奶的无乳链球菌噬菌体JX01进行分析和比较,包括噬菌体透射电镜形态观察、对55株无乳链球菌和其他细菌的宿主谱鉴定、噬菌体基因Eco R I、Sal I、Xba I或Pst I的酶切图谱、最适MOI、吸附曲线和一步生长曲线、不同保存条件下的稳定性等。【结果】分离鉴定的3株噬菌体LYGO9、HZ04和p A11(诱导自牛源菌株HAJL2011070601)与JX01比对分析,结果显示,4株噬菌体均为长尾噬菌体;Eco R I、Sal I、Xba I、Pst I的酶切图谱分获4、3、3或2种带型,显示4株噬菌体为不同毒株;均特异性裂解牛源无乳链球菌,对42株牛源无乳链球菌的裂解率如下:LYGO9为28.6%(12/42)、p A11为31%(13/42)、HZ04为47.6%(20/42)、JX01为54.8%(23/42);同时,LYGO9与p A11、HZ04和JX01分别有共同宿主11、12和11株;HZ04与JX01有共同宿主18株,提示它们具有同源性。LYGO9感染宿主的潜伏期短,仅5 min,平均裂解量为30。分离株在SM液中4°C至少可保存1个月。【结论】分离鉴定的3株牛源无乳链球菌噬菌体均为长尾噬菌体,其中LYGO9潜伏期短、裂解量较大。     

First Report of Black Leaf Spot Caused by Alternaria alternata on Ramie in China

In 2012 and 2013, black leaf spot disease was observed on ramie plants in Hunan and Hubei Provinces, China. In the field, the symptoms of this disease included dark green to black big spots on leaves, often resulting in upwardly curled leaf margins. The pathogen isolates were identified as Alternaria alternata (Fr.) Keissler on the basis of morphology and sequence similarity of 99–100% to the published data for internal transcribed spacer (ITS), and glyceraldehyde‐3‐phosphate dehydrogenase (gdp). To our knowledge, this is the first report of Alternaria leaf spot of ramie in China.     

木本植物木质部的冻融栓塞应对研究进展

冻融栓塞在中高纬度地区木本植物中普遍存在。抗冻融栓塞能力对在寒冷环境中木本植物的生长和安全越冬十分关键, 这直接决定植物分布范围。冻融栓塞是由于冰中气体溶解度低, 木质部水分在低温下冷冻, 使之前水中溶解的气体逸出到导管中, 随后木质部中的冰融化又使气泡扩张而引发的栓塞现象。木质部解剖结构的差异会影响植物的抗冻融栓塞能力, 植物还可以通过调节木质部正压、代谢耗能等方式主动修复冻融栓塞, 也可通过增加树液溶质含量等逃避冷冻, 以减少低温损伤。然而, 与干旱栓塞相比, 目前对木质部冻融栓塞的形成以及植物响应和调节机制的理解不足。为此, 该文首先综述了木质部冻融栓塞的形成机制和植物的逃避、忍耐、修复等3种冻融栓塞的应对策略, 然后总结了木质部抗低温胁迫能力的生理表现、影响因子和评价指标, 并在此基础上讨论了低温抗性、干旱抗性和水力效率之间的多元权衡关系, 最后提出今后该领域中的5个优先研究问题: (1)不同植物冰冻的最低温度阈值; (2)是否存在应对低温胁迫的水力脆弱性分割机制; (3)冻融栓塞修复与代谢消耗的关系; (4)低温抗性、干旱抗性和水力效率之间的权衡关系; (5)抗冻融栓塞性状是否能够纳入经济性状谱系。     

基于SPEI指数的淮河流域干旱时空演变特征及影响研究

运用淮河流域149个气象站1962—2016年逐日气温、降水资料以及历史旱情资料,基于SPEI、EOF和M-K等方法分析淮河流域的干旱时空特征,研究干旱的时空演变规律并揭示其对农业生产的影响。结果表明:(1)基于SPEI得到的干旱频次与受灾、成灾面积的相关性通过了0.1的显著性水平检验,表明SPEI在淮河流域具有较好的适用性;(2)淮河流域干旱发生时间差异明显,干旱次数呈现波动变化,发生重旱和特旱次数占总干旱的比重是20.0%,其中重旱和特旱在1960s比重最大(24.8%),其次是2010s(15.8%),在1980s比重最低(10.0%);(3)干旱的空间分布差异大,淮河流域干旱频率在27.76%—36.04%之间,西北部和东南部发生干旱强度较西南部、东北部及中部低;(4)淮河流域总体呈干旱化的趋势,从中部到四周呈现由高到低递减的趋势变化,且空间模态表现为全区一致型、南北相反型和东西相反型。