Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

Background  

The pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pan-genome sequence analysis program, Panseq.     

民勤绿洲生态需水与生态恢复对策

生态需水是当前水问题的一个研究热点,对于生态环境急剧恶化的内陆干旱区,这一研究尤为紧迫。以民勤绿洲作为研究区,采用阿维里扬诺夫估算方法,对其生态需水量进行了计算。结果表明,民勤绿洲现有植被最低生态需水量为1.4927×108m3,而目前的生态用水量只有0.3525×108m3,远没有达到维持极限抗性面积下的生态需水量。民勤绿洲生态用水的严重不足,主要是受到农田灌溉用水的严重挤占,从而加快了生态环境的日益恶化。通过分析,提出了生态恢复的对策与建议。     

巨桉根系分解对菊苣生长及光合特性的影响

巨桉是我国退耕还林过程中采用的重要速生树种之一,被广泛用于人工造林。采用盆栽试验,研究了巨桉根系分解初期对菊苣幼苗生长和光合生理特性的影响。试验设置A1(50 g/盆)、A2(100 g/盆)和对照(CK)3个根系水平,将各处理的根系分别与10 kg土壤混合后装盆,播种菊苣。待A2处理植株的第3片真叶完全展开后测定菊苣光合生理指标及相关生长指标。结果表明:在巨桉根系分解初期,明显抑制了菊苣高生长、根生长、生物量积累、叶面积扩展及光合色素的合成,且随着根系添加量的增加抑制作用加大;菊苣叶片胞间CO2浓度(Ci)增加,而净光合速率(Pn)、气孔导度(Gs)和蒸腾速率(Tr)均显著低于对照;随土壤中根系含量的增加,除CO2补偿点(CCP)呈增加趋势外,其他光响应和CO2响应的特征参数均呈明显的下降趋势,并与对照差异显著;各生长指标除与胞间CO2浓度呈现出负相关外,与其它光合特征参数、光合色素以及相应的响应曲线参数之间均呈现出显著或极显著的正相关关系;通过GC-MS检测表明,巨桉根系中含有2,6-二叔丁基对甲酚、N-甲基苯乙胺等多种具有化感潜力化学物质,在其分解过程中,这些化感物质逐步释放并作用于受体植物,抑制其光合色素合成和光合作用,降低其环境适应能力,从而抑制菊苣的生长。     

Flock House Virus RNA Polymerase Initiates RNA Synthesis De Novo and Possesses a Terminal Nucleotidyl Transferase Activity

Flock House virus (FHV) is a positive-stranded RNA virus with a bipartite genome of RNAs, RNA1 and RNA2, and belongs to the family Nodaviridae. As the most extensively studied nodavirus, FHV has become a well-recognized model for studying various aspects of RNA virology, particularly viral RNA replication and antiviral innate immunity. FHV RNA1 encodes protein A, which is an RNA-dependent RNA polymerase (RdRP) and functions as the sole viral replicase protein responsible for RNA replication. Although the RNA replication of FHV has been studied in considerable detail, the mechanism employed by FHV protein A to initiate RNA synthesis has not been determined. In this study, we characterized the RdRP activity of FHV protein A in detail and revealed that it can initiate RNA synthesis via a de novo (primer-independent) mechanism. Moreover, we found that FHV protein A also possesses a terminal nucleotidyl transferase (TNTase) activity, which was able to restore the nucleotide loss at the 3′-end initiation site of RNA template to rescue RNA synthesis initiation in vitro, and may function as a rescue and protection mechanism to protect the 3′ initiation site, and ensure the efficiency and accuracy of viral RNA synthesis. Altogether, our study establishes the de novo initiation mechanism of RdRP and the terminal rescue mechanism of TNTase for FHV protein A, and represents an important advance toward understanding FHV RNA replication.     

Proteomic Analysis of Salt-Responsive Proteins in the Leaves of Mangrove Kandelia candel during Short-Term Stress

Salt stress is a major abiotic stress that limits crop productivity in many regions of the world. A comparative proteomic approach to identify salt stress-responsive proteins and to understand the molecular mechanisms was carried out in the woody halophyte Kandelia candel. Four-leaf-old K. candel seedlings were exposed to 150 (control), 300, 450, and 600 mM NaCl for 3 days. Proteins extracted from the leaves of K. candel seedlings were separated by two-dimensional gel electrophoresis (2-DE). More than 900 protein spots were detected on each gel, and 53 differentially expressed protein spots were located with at least two-fold differences in abundance on 2-DE maps, of which 48 were identified by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF-TOF/MS). The results showed that K. candel could withstand up to 450 mM NaCl stress by up-regulating proteins that are mainly involved in photosynthesis, respiration and energy metabolism, Na⁺ compartmentalization, protein folding and assembly, and signal transduction. Physiological data, including superoxide dismutase (SOD) and dehydroascorbate reductase (DHAR) activities, hydrogen peroxide (H₂O₂) and superoxide anion radicals (O₂ ⁻) contents, as well as Na⁺ content and K⁺/Na⁺ ratios all correlated well with our proteomic results. This study provides new global insights into woody halophyte salt stress responses. Identification of differentially expressed proteins promotes better understanding of the molecular basis for salt stress reduction in K. candel.     

Robotic total gastrectomy with <Emphasis Type="Italic">π</Emphasis>-shaped esophagojejunostomy using a linear stapler as a novel technique

Objective

To evaluate the intraoperative and short-term postoperative outcomes of a novel robotic intracorporeal π-shaped esophagojejunostomy (EJS) after D2 total gastrectomy (TG) using the Da Vinci robotic surgical system for intracorporeal anastomosis after TG.

Background

Intracorporeal π-shaped EJS, using a linear stapler, was recently reported for laparoscopic total gastrectomy in patients with gastric cancer. However, robotic intracorporeal π-shaped EJS using a linear stapler has not been reported. This report aimed to describe the use of a novel technique for π-shaped EJS using the Da Vinci robotic system.

Methods

Robotic intracorporeal π-shaped esophagojejunostomy after total gastrectomy was performed in 11 consecutive patients diagnosed with early gastric cancer, and their perioperative outcomes were analyzed.

Results

All the operations were successful without conversion to open or laparoscopic surgery and postoperative complications. The total number of patients was 11 (7 males and 4 females). The mean age of the patients was 63.36?±?10.56?years old. Seven patients were diagnosed with cardia cancer, 3 patients were diagnosed with gastric body cancer, and 1 patient was diagnosed with gastric antrum cancer. The patients’ mean proximal resection margin was 3.18?±?1.17?cm, the distal resection margin was 6.18?±?1.40?cm, the mean length of the incision was 4.55?±?0.69?cm, the mean operative time was 287.27?±?30.69?min, the mean day of first flatus was 3.27?±?0.79?days, the mean day of the start of diet was 2.91?±?0.94?days, the mean postoperative hospital stay was 11.45?±?5.13?days, and the mean operative blood loss was 47.27?±?31.33?ml. No complications were observed during anastomosis, and the median anastomosis time was 19.5?min. The mean number of lymph node dissections was 17.91?±?4.59, the mean number of positive lymph nodes was 0.45?±?0.69, all patients were diagnosed with stage I–II gastric cancer, and the mean maximum diameter of the tumor was 2.67?±?1.30?cm. All the patients had a smooth hospital discharge.

Conclusion

A novel robotic gastrectomy with intracorporeal π-shaped EJS for esophagojejunal anastomosis described and shows acceptable resulted. This technique has the potential to offer better short-term surgical outcomes and overcomes the drawbacks of laparoscopy with a decreased risk of complications during and after surgery.

     

古国槐叶片溶磷内生真菌的筛选及其促生潜力初探

该试验从周公庙古国槐叶片内分离、筛选具有溶磷能力的内生真菌,采用溶磷圈法和钼锑抗比色法测定其溶解无机磷的能力,同时测定其回接后对国槐无菌苗叶绿素、可溶性蛋白质、超氧化物歧化酶(SOD)和过氧化物酶(POD)活性的影响,探究内生真菌的溶磷能力及其促生效应。结果表明:(1)从古国槐叶片中分离出的55株内生真菌中,28株具有溶磷能力,其中溶磷能力较强的活性菌株有12株:ZG-7为拟盘多毛孢(Pestalotiopsis sp.),ZG-9、ZG-23、ZG-32、ZG-36和ZG-53为镰刀菌(Fusariumsp.),ZG-15和ZG-34为曲霉(Aspergillus sp.),ZG-39和ZG-51为链格孢(Alternariasp.),ZG-42为木霉(Trichoderma sp.),ZG-48为附球菌(Epicoccumsp.)。(2)曲霉属真菌ZG-15和ZG-34的溶磷圈直径(d)及其与菌落直径(D)的比值d/D均高于其他菌株,对Ca_3(PO_4)_2的溶解能力最强(1 238.28和941.22mg·L-1),并极显著高于其他菌株(P0.01)。(3)4株内生真菌ZG-7、ZG-9、ZG-15和ZG-48回接至国槐无菌苗10d后,可从苗根组织的皮层细胞中观察到内生菌丝,其中黑曲霉(Aspergillus niger)ZG-15可显著提高国槐无菌苗的叶绿素含量、可溶性蛋白质含量、SOD、POD活性(P0.05),从而维持幼苗的正常生长和提高其抗逆能力,为该试验得到的促生潜力优势内生真菌,可为古国槐的有效保护及林木溶磷生物菌肥的生产提供依据。     

模拟氮沉降对华西雨屏区天然常绿阔叶林凋落叶分解过程中基质质量的影响

为理解氮沉降对华西雨屏区天然常绿阔叶林凋落物分解过程的影响,采用立地控制实验和凋落物分解袋法,研究了低氮沉降(L,50 kg N hm~(-2)a~(-1))、中氮沉降(M,150 kg N hm~(-2)a~(-1))和高氮沉降(H,300 kg N hm~(-2)a~(-1))对华西雨屏区天然常绿阔叶林凋落叶分解过程中基质质量的影响。结果表明:N沉降抑制了凋落叶的分解,并随着N沉降量的增加,抑制作用增强。N沉降遏制了凋落叶的C、N释放和纤维素降解,促进了P释放。N沉降提高了凋落叶的C/P比,中氮和高氮处理提高了凋落叶C/N比。N沉降显著增加了凋落叶N、木质素和纤维素的含量,分解1年后,各N沉降处理的木质素/N和纤维素/N均显著高于对照。N沉降提高了质量残留率与C/N、木质素/N和纤维素/N的相关性,降低了与C/P的相关性。可见,模拟N沉降显著影响了华西雨屏区天然常绿阔叶林凋落叶分解过程中的基质质量,进而影响了凋落叶的分解过程。     

CO2浓度升高与硝化抑制剂对冬小麦田间N2O排放量的影响

以冬小麦中麦175为供试品种,利用农田开放式CO_2浓度增高(FACE)系统,研究未来大气高CO_2浓度对冬小麦田间N_2O排放的影响,以及施用硝化抑制剂(2-氯-6-三氯甲基吡啶)是否可以起到抑制冬小麦田间N_2O的排放量升高的潜能。试验结果表明:CO_2浓度升高显著提高冬小麦田间N2O的排放增幅达到67.6%,追肥灌溉后小麦田N_2O排放量较大,随着冬小麦生育进程的推进N_2O的排放量逐渐减少,硝化抑制剂对中麦175田间N_2O排放量的影响并不明显。因此,在未来高CO_2浓度环境条件下,可以通过采取相应的耕作制度和栽培技术措施等来降低冬小麦田N_2O的排放量。试验结果对冬小麦田间是否选择施用2-氯-6-三氯甲基吡啶来控制N_2O的排放起到一定的参考作用。     

Link Prediction in Complex Networks: A Mutual Information Perspective

Topological properties of networks are widely applied to study the link-prediction problem recently. Common Neighbors, for example, is a natural yet efficient framework. Many variants of Common Neighbors have been thus proposed to further boost the discriminative resolution of candidate links. In this paper, we reexamine the role of network topology in predicting missing links from the perspective of information theory, and present a practical approach based on the mutual information of network structures. It not only can improve the prediction accuracy substantially, but also experiences reasonable computing complexity.