扁藻光合甘油脂的UPLC-Q-TOF-MS鉴定

运用超高效液相色谱-四级杆飞行时间质谱联用分析系统（UPLC-Q-TOF-MS）,直接分析总脂并建立了海洋扁藻（Tetr aselmis chuii）中光合甘油脂的精确结构鉴定方法.质谱采用电喷雾电离源（ESI）,TOF采用V飞行模式,分别在正负离子模式下对总脂进行检测.根据在ESI-MS/MS下各种甘油脂产生的特征离子碎片对甘油脂进行结构鉴定,并根据负离子模式下产生的羧酸阴离子,确定各个甘油脂分子的脂肪酰基组成.结果从扁藻中共检测到40多种甘油脂,包括11种单半乳糖甘油二酯（MGDG）,7种双半乳糖甘油二酯（DGDG）,16种硫代异鼠李糖甘油二酯（SQDG）和9种磷脂酰甘油（PG）,对这种微藻进行光合甘油脂的结构鉴定还不多见.此外,还鉴定出了一些传统GC-MS方法检测不到的羟基化脂肪酸,提供了扁藻光合脂质组的新信息.通过对sn-2位脂肪酸的比较研究表明,MGDG和SQDG主要通过原核途径合成,PG的形成是一种混合型生物合成途径;而DGDG在sn-2位特有C14：0和C16：0.这种方法提供了所有光合甘油脂的完整结构图谱,可以通过监测脂类的变化运用于海洋微藻的生理生态研究中.     

Effects of apricot trees on insect pests and their natural enemies in nearby cotton fields in southern Xinjiang

2008-2011年在新疆莎车县调查研究了杏树对棉田主要害虫及自然天敌种群发生的影响.研究表明杏棉间作田主要害虫及天敌种类与棉单作田一致.杏树间作种植模式对棉田牧草盲蝽Lygus pratensis、棉蓟马Thrips tabaci和棉长管蚜Acyrthosiphon gossyfii的种群发生有一定影响,不利于其在田间发生;对棉蚜Aphis gossyfii、棉叶螨Tetrangchus urtieae影响不大.棉田瓢虫和食虫蝽天敌受间作和棉蚜发生量的双重影响.间作有利于蜘蛛数量的增加.     

线粒体假基因用作分子化石推算两个榕小蜂姐妹种的分化时间（英文）

线粒体假基因(nuclear mitochondrial pseudogenes, NUMTs)是指由生物体的线粒体基因组转移至核基因组内的DNA片段。由于其独立进化的特点, NUMTs在用于系统发育分析时是一把双刃剑。我们用基于PCR扩增的方法研究了对叶榕Ficus hispida上两姐妹种榕小蜂Philotrypesis pilosa和Philotrypesis sp.中起源于线粒体Nad1 12S片段的NUMTs。该两姐妹种榕小蜂由同域物种形成过程产生, 它们生活在同一生态环境里（即同一榕果内）, 因此可以用作很好的模型来研究在相同生态环境里物种的行为学及遗传学细微差异的进化。这些深入研究都依赖于对两个物种分化时间的正确估算。通过对所获取的NUMTs进行进化分析, 我们发现： 1）这些NUMTs都是最近引入核基因组事件; 2）NUMTs引入事件发生在物种分化之前。由于这些NUMTs引入核内时间尚短, 其碱基替换速率与线粒体基因相似, 而节肢动物线粒体基因的平均碱基替换速率约为2.3×10^-8 替换/位点·年。根据这些进化历史特征可帮助我们将这两个姐妹种榕小蜂的分化时间追溯至0.40-0.48百万年以前。结果提示, 一些线粒体假基因可以很好的用作分子化石来推断一些重要进化事件如物种形成。     

构建CRISPR-Cas9介导的耻垢分枝杆菌基因组高效删除系统

【背景】耻垢分枝杆菌具有生长迅速和非致病性的特点,可作为结核分枝杆菌致病机理研究替代菌株和类固醇激素生产的工程菌,但目前耻垢分枝杆菌中缺乏高效率的基因组敲除方法。【目的】基于CRISPR-Cas9介导的定点、高效的DNA切割能力,构建耻垢分枝杆菌染色体DNA片段无痕敲除系统。【方法】构建了包含四环素诱导型启动子驱动的密码子优化的cas9基础载体pCas9101,在双侧同源臂长度约为1 kb条件下选用合适的gRNA表达模块,分别测试了对耻垢分枝杆菌mc2155染色体上的3β-羟基类固醇脱氢酶基因(MSMEG_5228,1 071 bp)和胆固醇降解基因簇(MSMEG_5990-MSMEG_6043,约48kb)敲除效率,使用相同大小的同源臂以经典p2NIL-pGOAL方法进行对照,并计算效率。【结果】使用CRISPR-Cas9方法对耻垢分枝杆菌mc2155的3β-羟基类固醇脱氢酶基因敲除效率为22%,胆固醇降解基因簇敲除效率也达到18%,两者连续敲除效率为4%。但对照p2NIL-pGOAL方法未能获得目标DNA片段敲除的菌株。【结论】本文建立的基于CRISPR-Cas9的耻垢分枝杆菌基因组无痕敲除系统显示出较高的敲除效率,该方法可为耻垢分枝杆菌后续研究提供快速高效的基因组操作方法。     

Fungal genome size and composition reflect ecological strategies along soil fertility gradients

Genomic traits reflect the evolutionary processes that have led to ecological variation among extant organisms, including variation in how they acquire and use resources. Soil fungi have diverse nutritional strategies and exhibit extensive variation in fitness along resource gradients. We tested for trade-offs in genomic traits with mycelial nutritional traits and hypothesize that such trade-offs differ among fungal guilds as they reflect contrasting resource exploitation and habitat preferences. We found species with large genomes exhibited nutrient-poor mycelium and low GC content. These patterns were observed across fungal guilds but with varying explanatory power. We then matched trait data to fungal species observed in 463 Australian grassland, woodland and forest soil samples. Fungi with large genomes and lower GC content dominated in nutrient-poor soils, associated with shifts in guild composition and with species turnover within guilds. These findings highlight fundamental mechanisms that underpin successful ecological strategies for soil fungi.     

Testing nitrogen and water co-limitation of primary productivity in a temperate steppe

Background and aims

Studies have found significant differences in methane (CH₄) emissions among rice cultivars; however, it is unclear whether this difference is related to radial oxygen loss (ROL) from the roots.

Methods

Based on a 2-year in situ field study and solution culture experiments on 16 rice cultivars, we investigated CH₄ emission levels and their dependence on ROL.

Results

We detected significant differences in CH₄ emission and ROL among rice cultivars. The lowest and highest CH₄ emission levels were 4.10 and 7.35 g m^?2 for early rice, and 14.36 and 23.33 g m^?2 for late rice, respectively. The maximum and minimum ROL values were 3.77 and 1.73 mmol plant^?1 h^?1 for early rice, and 4.18 and 2.08 mmol plant^?1 h^?1 for late rice, respectively. Seasonal total CH₄ emission was negatively correlated with ROL in the early rice season (p?<?0.01), and (p?<?0.01) in the late rice season. ROL was positively correlated with the number of roots per plant (RN), root tips per plant (RT), and root volume per plant (RV).

Conclusions

We suggest that ROL can be used as a predictive index for CH₄ emissions. RN, RT, and RV were the most important factors influencing ROL in rice cultivars.

     

Gracillosides A-F, six new 8,14-seco-pregnane glycosides from Adelostemma gracillimum

Six new 8,14-seco-pregnane glycosides, gracillosides A-F (1-6), were isolated from the roots of Adelostemma gracillimum (Asclepiadaceae). All of them had the same aglycone as gracigenin with a rare 8,14-seco-pregnane type skeleton in nature and possessed an oligosaccharide chain consisting of four to six sugar units at C-3 of the aglycone. Their structures were determined on the basis of detailed spectroscopic analysis and chemical evidence.     

Sinorhizobium meliloti ExoR is the target of periplasmic proteolysis

Sinorhizobium meliloti ExoR regulates the production of succinoglycan and flagella through the ExoS/ChvI two-component regulatory system. ExoR has been proposed to inhibit the ExoS sensor through direct interaction in the periplasm. To understand how ExoR suppression of ExoS is relieved, which is required for the expression of ExoS/ChvI-regulated symbiosis genes, we characterized wild-type ExoR and ExoR95 mutant proteins. In addition to the previously identified precursor and mature forms of ExoR (designated ExoR(p) and ExoR(m), respectively), we detected a 20-kDa form of ExoR (designated ExoR(c20)) derived from the wild-type ExoR protein, but not from the ExoR95 mutant protein. ExoR(c20) was isolated directly from S. meliloti periplasm to identify its N-terminal amino acids and the site of the proteolysis, which is highly conserved among ExoR homologs. ExoR(c20) retains the C terminus of the wild-type ExoR. When expressed directly, ExoR(c20) did not complement the exoR95 mutation, suggesting that ExoR(c20) does not function directly in the ExoR-ExoS/ChvI regulatory pathway and that ExoR(m) is the functional form of ExoR. A single-amino-acid change (ExoRL81A) at the site of ExoR periplasmic proteolysis resulted in the reduction of the amount of ExoR(m) and the loss of the regulatory function of the ExoR protein. These findings suggest that ExoR(m) is a target of periplasmic proteolysis and that the amount of ExoR(m) could be reduced through effective proteolysis to relieve its suppression of ExoS.     

Identification of histone deacetylase 3 as a biomarker for tumor recurrence following liver transplantation in HBV-associated hepatocellular carcinoma

Background

Recent studies have shown that high expression levels of class I histone deacetylases (HDACs) correlate with malignant phenotype and poor prognosis in some human tumors. However, the expression patterns and prognostic role of class I HDAC isoforms in hepatocellular carcinoma (HCC) remain unclear.

Methodology/Principal Findings

The expression patterns and clinical significance of class I HDAC isoforms were assessed by immunohistochemistry in a cohort of 43 hepatitis B virus-associated HCC patients treated with liver transplantation. In addition, the effects of HDAC inhibition on HCC cell behavior were investigated by knockdown of the HDAC isoform with short interfering RNA. Class I HDACs were highly expressed in a subset of HCCs with positivity for HDAC1 in 51.2%, HDAC2 in 48.8%, and HDAC3 in 32.6% of cases. The expression levels of HDAC isoforms were significantly associated with the proliferation index of HCC. Kaplan-Meier curves showed that a high expression level of HDAC2 or HDAC3 implicated significantly reduced recurrence-free survival. Cox proportional hazards model analysis revealed HDAC3 overexpression was an unfavorable independent prognostic factor (P = 0.002; HR 3.907). In vitro, inhibition of HDAC2 and HDAC3, but not HDAC1, suppressed proliferation and the invasiveness of liver cancer cells.

Conclusions/Significance

Our findings demonstrate that HDAC3 plays a significant role in regulating tumor cell proliferation and invasion, and it could be served as a candidate biomarker for predicting the recurrence of hepatitis B virus-associated HCC following liver transplantation and a potential therapeutic target.