Proteomic analysis of purified Newcastle disease virus particles

Background

Recent advances in liquid chromatography-mass spectrometry (LC-MS) technology have led to more effective approaches for measuring changes in peptide/protein abundances in biological samples. Label-free LC-MS methods have been used for extraction of quantitative information and for detection of differentially abundant peptides/proteins. However, difference detection by analysis of data derived from label-free LC-MS methods requires various preprocessing steps including filtering, baseline correction, peak detection, alignment, and normalization. Although several specialized tools have been developed to analyze LC-MS data, determining the most appropriate computational pipeline remains challenging partly due to lack of established gold standards.

Results

The work in this paper is an initial study to develop a simple model with "presence" or "absence" condition using spike-in experiments and to be able to identify these "true differences" using available software tools. In addition to the preprocessing pipelines, choosing appropriate statistical tests and determining critical values are important. We observe that individual statistical tests could lead to different results due to different assumptions and employed metrics. It is therefore preferable to incorporate several statistical tests for either exploration or confirmation purpose.

Conclusions

The LC-MS data from our spike-in experiment can be used for developing and optimizing LC-MS data preprocessing algorithms and to evaluate workflows implemented in existing software tools. Our current work is a stepping stone towards optimizing LC-MS data acquisition and testing the accuracy and validity of computational tools for difference detection in future studies that will be focused on spiking peptides of diverse physicochemical properties in different concentrations to better represent biomarker discovery of differentially abundant peptides/proteins.     

Inheritance and relationship between key agronomic and quality traits in an interspecific cross between Coffea pseudozanguebariae Bridson and C. canephora Pierre

The inheritance and relationships between four traits of agronomic and quality interest??fructification time, caffeine, and heteroside contents and 100-bean weight??were analyzed in the first backcross hybrids derived from an interspecific cross between Coffea pseudozanguebariae and Coffea canephora. We showed that short vs. long fructification time was governed by one major gene with two co-dominant alleles ft1 and ft2. Absence vs. presence of both caffeine and heteroside was also controlled by one major gene. The allele responsible for the presence of caffeine (caf2) dominated over the absence one (caf1) whereas both alleles controlling heteroside, het1 and het2, were co-dominant. The fructification time and the heteroside content were additive while the caffeine content seemed multiplicative. The 100-bean weight was additive and under a polygenic control. The two genes ft and caf were linked, separated by 30.8?cM, and were independent from the het gene. The relationships between the four traits were not strong enough, except between 100-bean weight and fructification time (r?=?0.43) or caffeine content (r?=?0.41). Recombination occurred between the genes controlling the four traits suggesting that new introgressed Robusta varieties, characterized by short, medium, or long fructification time depending on demand, bigger seeds with low or no caffeine content, and being heteroside-free, could be produced.     

二十二碳六烯酸对心房颤动大鼠心房肌生理改变及双孔钾通道TASK-1蛋白表达的影响

目的：探讨二十二碳六烯酸（DHA）对大鼠心房颤动（AF）模型心房肌生理特性的影响及相关机制研究。方法：80只乙酰胆碱-氯化钙混合液敏感的SD大鼠分为对照组（CTL组）、DHA处理组（DHA组）、房颤组（AF组）和房颤+DHA处理组（DHA+AF组）,观察房颤持续时间;采用全细胞膜片钳技术记录大鼠心房肌细胞动作电位时程（APD）和双孔钾通道TASK-1电流,Western blot测定大鼠心房组织TASK-1蛋白表达。结果：大鼠尾静脉注射乙酰胆碱-氯化钙混合液后,房颤持续时间随实验天数增加而逐渐延长,DHA干预缩短房颤持续时间。与CTL组相比,AF组大鼠心房肌细胞复极50%时的动作电位时程（APD₅₀）和复极90%时的动作电位时程（APD₉₀）明显缩短,心房肌细胞TASK-1电流密度升高,蛋白表达升高（P<0.05）。与AF组相比,DHA+AF组大鼠心房肌细胞APD₅₀和APD₉₀明显延长,TASK-1电流密度和蛋白表达降低（P<0.05）。结论：DHA具有延长房颤大鼠心房肌细胞APD的作用,可能与其下调心房肌TASK-1蛋白的表达从而降低心房肌细胞TASK-1电流密度有关。     

Microvesicle-delivery miR-150 promotes tumorigenesis by up-regulating VEGF,and the neutralization of miR-150 attenuate tumor development

Tumor-associated macrophages (TAMs) mostly exhibit M2-like (alternatively activated) properties and play positive roles in angiogenesis and tumorigenesis. Vascular endothelial growth factor (VEGF) is a key angiogenic factor. During tumor development, TAMs secrete VEGF and other factors to promote angiogenesis; thus, anti-treatment against TAMs and VEGF can repress cancer development, which has been demonstrated in clinical trials and on an experimental level. In the present work, we show that miR-150 is an oncomir because of its promotional effect on VEGF. MiR-150 targets TAMs to up-regulate their secretion of VEGF in vitro. With the utilization of cell-derived vesicles, named microvesicles (MVs), we transferred antisense RNA targeted to miR-150 into mice and found that the neutralization of miR-150 down-regulates miR-150 and VEGF levels in vivo and attenuates angiogenesis. Therefore, we proposed the therapeutic potential of neutralizing miR-150 to treat cancer and demonstrated a novel, natural, microvesicle-based method for the transfer of nucleic acids.     

Altered Hypothalamic Signaling and Responses to Food Deprivation in Rats Fed a Low‐Carbohydrate Diet

Objective: To model how consuming a low‐carbohydrate (LC) diet influences food intake and body weight. Research Methods and Procedures: Food intake and body weight were monitored in rats with access to chow (CH), LC‐high‐fat (HF), or HF diets. After 8 weeks, rats received intracerebroventricular injections of a melanocortin agonist (melanotan‐II) and antagonist (SHU9119), and feeding responses were measured. At sacrifice, plasma hormones and hypothalamic expression of mRNA for proopiomelanocortin (POMC), melanocortin‐4 receptor, neuropeptide Y (NPY), and agouti related protein (AgRP) were assessed. A second set of rats had access to diet (chow or LC‐HF) for 4 weeks followed by 24 h food deprivation on two occasions, after which food intake and hypothalamic POMC, NPY, and AgRP mRNA expression were measured. Results: HF rats consumed more food and gained more weight than rats on CH or LC‐HF diets. Despite similar intakes and weight gains, LC‐HF rats had increased adiposity relative to CH rats. LC‐HF rats were more sensitive to melanotan‐II and less sensitive to SHU9119. LC‐HF rats had increased plasma leptin and ghrelin levels and decreased insulin levels, and patterns of NPY and POMC mRNA expression were consistent with those of food‐deprived rats. LC‐HF rats did not show rebound hyperphagia after food deprivation, and levels NPY, POMC, and AgRP mRNA expression were not affected by deprivation. Discussion: Our results demonstrate that an LC diet influences multiple systems involved in the controls of food intake and body weight. These data also suggest that maintenance on an LC‐HF diet affects food intake by reducing compensatory responses to food deprivation.     

转录病毒载体介导的稳定表达口蹄疫病毒3D基因的BHK21细胞系的建立

[目的]研究口蹄疫病毒RNA聚合酶在BHK-21细胞中的稳定表达状况,为研究RNA聚合酶生物学活性及其基囚工程疫苗研制提供科学依据.[方法]从重组质粒pMD18-T-3D扩增口蹄疫病毒3D基因,通过分子克隆技术构建莺组逆转录病毒表达载体pBPSTR1-3D.用pBPSTR1-3D和pVSV-G双质粒瞬时转染GP2-293包装细胞,收获重组逆转录病毒,然后感染BHK-21细胞,嘌呤霉素持续筛选12 d后获得阳性克隆,并用有限稀释法挑选单个阳性细胞克隆.[结果]应用PCR、RT-PCR技术可从体外反复传代的阳性细胞中扩增到3D基因,证实目的外源基因能转录并被稳定整合进宿主细胞基因组中.经SDS-PAGE、Western blot、间接免疫荧光检测到在不同代次的阳性细胞中有目的蛋白表达.[结论]本试验利用逆转录病毒载体介导的基因转移技术,将外源基因插入到靶细胞的基因组中,构建了稳定表达口蹄疫病毒RNA聚合酶的包装细胞系,为研究3D基因表达及其蛋白定位提供了方便,也为下一步研究RNA聚合酶生物学功能和疫苗研制提供了科学依据.     

The prevalence of Th17 cells in patients with gastric cancer

Th17 cells have emerged as an important mediator in inflammatory and autoimmune diseases. However, recent studies suggest a potential impact of Th17 cells on tumor. The current study was designed to investigate the possible involvement of Th17 cells in gastric cancer. Compared with healthy volunteers, patients with gastric cancer had a higher proportion of Th17 cells in peripheral blood. Notably, the increased prevalence of Th17 cells was associated with clinical stage. In addition, increased populations of Th17 cells were present in tumor-draining lymph nodes with advanced disease. Furthermore, the mRNA expression levels of Th17-related factors (IL-17, IL-23p19, and RORC) in tumor tissues and the serum concentrations of IL-17 and IL-23 cytokines were significantly increased in patients with advanced gastric cancer. The results indicate that Th17 cells may contribute to gastric cancer pathogenesis.     

Adaptation of Arabidopsis to nitrogen limitation involves induction of anthocyanin synthesis which is controlled by the NLA gene

Plants can survive a limiting nitrogen (N) supply by developing a set of N limitation adaptive responses. However, the Arabidopsis nla (nitrogen limitation adaptation) mutant fails to produce such responses, and cannot adapt to N limitation. In this study, the nla mutant was utilized to understand further the effect of NLA on Arabidopsis adaptation to N limitation. Grown with limiting N, the nla mutant could not accumulate anthocyanins and instead produced an N limitation-induced early senescence phenotype. In contrast, when supplied with limiting N and limiting phosphorus (Pi), the nla mutants accumulated abundant anthocyanins and did not show the N limitation-induced early senescence phenotype. These results support the hypothesis that Arabidopsis has a specific pathway to control N limitation-induced anthocyanin synthesis, and the nla mutation disrupts this pathway. However, the nla mutation does not affect the Pi limitation-induced anthocyanin synthesis pathway. Therefore, Pi limitation induced the nla mutant to accumulate anthocyanins under N limitation and allowed this mutant to adapt to N limitation. Under N limitation, the nla mutant had a significantly down-regulated expression of many genes functioning in anthocyanin synthesis, and an enhanced expression of genes involved in lignin production. Correspondingly, the nla mutant grown with limiting N showed a significantly lower production of anthocyanins (particularly cyanidins) and an increase in lignin contents compared with wild-type plants. These data suggest that NLA controls Arabidopsis adaptability to N limitation by channelling the phenylpropanoid metabolic flux to the induced anthocyanin synthesis, which is important for Arabidopsis to adapt to N limitation.     

CDKA and CDKB kinases from Chlamydomonas reinhardtii are able to complement cdc28 temperature-sensitive mutants of Saccharomyces cerevisiae

Summary. Cyclin-dependent kinases (CDK) play a key role in coordinating cell division in all eukaryotes. We investigated the capability of cyclin-dependent kinases CDKA and CDKB from the green alga Chlamydomonas reinhardtii to complement a Saccharomyces cerevisiae cdc28 temperature-sensitive mutant. The full-length coding regions of algal CDKA and CDKB cDNA were amplified by RT-PCR and cloned into the yeast expression vector pYES-DEST52, yielding pYD52-CDKA and pYD52-CDKB. The S. cerevisiae cdc28-1N strain transformed with these constructs exhibited growth at 36 °C in inducing (galactose) medium, but not in repressing (glucose) medium. Microscopic observation showed that the complemented cells had the irregular cylindrical shape typical for G₂ phase-arrested cells when grown on glucose at 36 °C, but appeared as normal budded cells when grown on galactose at 36 °C. Sequence analysis and complementation tests proved that both CDKA and CDKB are functional CDC28/cdc2 homologs in C. reinhardtii. The complementation of the mitotic phenotype of the S. cerevisiae cdc28-1N mutant suggests a mitotic role for both of the kinases. Correspondence: K. Bišová, Laboratory of Cell Cycles of Algae, Institute of Microbiology, Academy of Sciences of the Czech Republic, 379 81 Třeboň, Czech Republic.