Spectral index for assessment of differential protein expression in shotgun proteomics

Detecting differentially expressed proteins is a key goal of proteomics. We describe a label-free method, the spectral index, for analyzing relative protein abundance in large-scale data sets derived from biological samples by shotgun proteomics. The spectral index is comprised of two biochemically plausible features: relative protein abundance (assessed by spectral counts) and the number of samples within a group with detectable peptides. We combined the spectral index with permutation analysis to establish confidence intervals for assessing differential protein expression in bronchoalveolar lavage fluid from cystic fibrosis and control subjects. Significant differences in protein abundance determined by the spectral index agreed well with independent biochemical measurements. When used to analyze simulated data sets, the spectral index outperformed four other statistical tests (Student's t-test, G-test, Bayesian t-test, and Significance Analysis of Microarrays) by correctly identifying the largest number of differentially expressed proteins. Correspondence analysis and functional annotation analysis indicated that the spectral index improves the identification of enriched proteins corresponding to clinical phenotypes. The spectral index is easily implemented and statistically robust, and its results are readily interpreted graphically. Therefore, it should be useful for biomarker discovery and comparisons of protein expression between normal and disease states.     

The role of the actin cytoskeleton in calcium signaling in starfish oocytes

Ca(2+) is the most universal second messenger in cells from the very first moment of fertilization. In all animal species, fertilized eggs exhibit massive mobilization of intracellular Ca(2+) to orchestrate the initial events of development. Echinoderm eggs have been an excellent model system for studying fertilization and the cell cycle due to their large size and abundance. In preparation for fertilization, the cell cycle-arrested oocytes must undergo meiotic maturation. Studies of starfish oocytes have shown that Ca(2+) signaling is intimately involved in this process. Our knowledge of the molecular mechanism of meiotic maturation and fertilization has expanded greatly in the past two decades due to the discovery of cell cycle-related kinases and Ca(2+)-mobilizing second messengers. However, the molecular details of their actions await elucidation of other cellular elements that assist in the creation and transduction of Ca(2+) signals. In this regard, the actin cytoskeleton, the receptors for second messengers and the Ca(2+)-binding proteins also require more attention. This article reviews the physiological significance and the mechanism of intracellular Ca2+ mobilization in starfish oocytes during maturation and fertilization.     

透明颤菌血红蛋白的研究进展及其在发酵工业中的应用

透明颤菌血红蛋白（Vitreoscilla Hemoglobin, VHb）是20世纪70年代后期发现的一种血红蛋白,该蛋白质能使透明颤菌在低氧的环境下生存,并保持较高的生长速率。随着其作用机理的深入研究,VHb在生物工程领域的应用越来越广泛。本文总结了近年来VHb的研究进展,包括蛋白结构、细胞定位、基因改组、作用机理等方面的研究,并概述了其在微生物发酵工业中的应用。     

Targeting tumors with LIGHT to generate metastasis-clearing immunity

Metastatic diseases cause the majority of morbidity and mortality of cancer patients. Established tumors form both physical and immunological barriers to limit immune detection and destruction. Current immunotherapy of vaccination and adoptive transfer shows limited effect at least in part due to the existing barriers in the tumors and depending on the knowledge of tumor antigens. Tumor necrosis factor (TNF) superfamily (TNFSF) member 14 (TNFSF14) LIGHT interacts with stromal cells, dendritic cells (DCs), NK cells, na?ve and activated T cells and tumor cells inside the tumor tissues via its two functional receptors, HVEM and lymphotoxin beta receptor (LTbetaR). Targeting tumor tissues with LIGHT leads to augmentation of priming, recruitment, and retention of effector cells at tumor sites, directly or indirectly, to induce strong anti-tumor immunity to inhibit the growth of primary tumors as well as eradicate metastases. Intratumor treatment would break tumor barriers and allow strong immunity against various tumors without defining tumor antigens. This review summarizes recent findings to support that LIGHT is a promising candidate for an effective cancer immunotherapy.     

Phosphorylation of Extracellular Signal-Regulated Kinases 1/2 Predominantly Enhanced in the Microglia of the Rat Spinal Cord Following Lipopolysaccharide Injection

The present study was initiated to investigate the role of extracellular signal-regulated kinases (ERK) 1/2 signaling pathway in the early response of spinal cord to systemic inflammation by using Western blotting and immunohistochemical techniques in a rat model intraperitoneally injected with 10 mg/kg of lipopolysaccharide (LPS). The results showed that there was a considerable amount of phosphorylated ERK 1/2 protein in the spinal cord of inflamed animals killed under pentobarbital anesthesia. The result of Western blotting showed that the phosphorylation level of ERK 1/2 in the spinal cord was increased at one hour; then 12 and 24 h after LPS injection the level decreased, while the total ERK 1/2 level seemed unchanged. The phosphorylated ERK 1/2 dominantly existed in the microglia cells of the gray matter of spinal cord, as demonstrated with double immunofluorescent staining 1 h after LPS injection. Collectively, the present results suggest that ERK signal pathway involve the cellular activation in the spinal cord following systemic inflammation, with ERK mainly in microglia. The increase of phosphorylation of ERK 1/2 in microglia of spinal cord after LPS injection implicates that ERK signaling pathway involves intracellular activity of microglia responding to the inflammation. Dan Zhou and Min Fei contributed equally to this work.     

Factors affecting somatic embryogenesis in anther cultures of Chinese pink <Emphasis Type="Italic">(Dianthus chinensis</Emphasis> L<Emphasis Type="Italic">.)</Emphasis>

In this study, we aimed to maximize the rates of somatic embryogenesis achievable in anther cultures of Chinese pink (Dianthus chinensis L.) (2n = 2x = 30). The genotype of the donor plant was found to be a major factor in determining the success rate. Conditions imposed during anther culture (notably medium composition and light conditions) and pretreatments (namely, cold, heat, and mannitol incubations) were also found to influence somatic embryo induction. For example, the highest levels of embryogenic callus induction were achieved when the donor buds had been cold pretreated and the subsequent anther culture was maintained in darkness. Furthermore, there appeared to be an interaction of genotype with culture conditions. Thus, in cultures of the cultivar (cv.) ‘Carpet’, the highest rates of embryogenesis were obtained when the anthers had received a 5-d heat-shock, but such a thermal treatment did not generally produce a significant effect. Likewise, a 3-d mannitol pretreatment was optimal only for the cross-hybrid line ‘HC’. Assessment of the ploidy of the plants regenerated from the anther cultures revealed both diploid and tetraploid plants. Histological and cytological observations showed that all of these (both from n-pollen and 2n-pollen lines) derived from anther wall cells. Spontaneous chromosome doubling was inferred to have occurred during the embryogenic callus culture period.     

Pattern analysis in landscape ecology: progress, challenges and outlook

Landscape pattern indices or landscape metrics, an important means in landscape pattern analysis, has resulted in the prosperity of landscape ecology. However, landscape pattern analysis was criticized recently for its poor correlation with ecological processes. In this paper, the current situation and challenges in landscape pattern analysis was elaborated, and the future of landscape pattern analysis was discussed. We believe that the landscape metrics is still the main method in spatial pattern analysis, and is important for landscape ecology. However, there are 3 challenges in landscape pattern analysis: (1) how to develop new methods by integrating explicit ecological sense in landscape pattern analysis? (2) How to link landscape pattern and ecological processes? (3) How to apply the theory of “matrix-patch-corridor” to practice? In future, 5 issues are to be addressed: (1) to develop a methodology to describe landscape pattern in a dynamic manner; (2) to explore the ecological sense of landscape pattern using a series of landscape metrics; (3) to develop new methods for landscape pattern analysis related to ecological processes; (4) to conduct landscape pattern analysis at multi-dimensions; (5) to explain the relationship between landscape pattern and ecological processes by multi-scale pattern analysis.     

Proteins responding to drought and high-temperature stress in <Emphasis Type="Italic">Populus </Emphasis>× <Emphasis Type="Italic">euramericana</Emphasis> cv. ‘74/76’

Proteomic analysis provides a powerful method of studying plant responses to stress at the protein level. In order to study stress-responsive molecular mechanisms for Populus × euramericana cv. ‘74/76’, one of the most important forest plantation tree species in subtropical and temperate regions, we analyzed the response of 2-year-old cuttings of P. × euramericana cv. ‘74/76’ to drought and high temperature using two-dimensional gel electrophoresis. More than 1,000 reproducible leaf proteins were detected in the controls and treatments, and 26 proteins were found to change notably in abundance. We identified 13 proteins affected by drought stress and 11 proteins affected by high temperature. These proteins are mainly involved in photosynthesis such as ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit and putative photosystem I reaction center subunit II precursor, and detoxification (manganese superoxide dismutase and methionine sulfoxide reductase A). Furthermore, the level of the photosynthesis proteins affected greatly by the imposed stress conditions was consistent with the observed noticeable decrease in net photosynthesis rate. These studies provides a fundamental data for future research on responses to drought and high temperature, two major factors limiting the growth of forest trees during summer under recent climatic warming.     

Cu2+对离体培养猪腺垂体细胞GH分泌的影响

目的：研究铜离子（Cu2＋）对离体培养猪腺垂体细胞生长激素（GH）分泌的影响。方法：试验选取32-35日龄仔猪腺垂体细胞,于10%小牛血清的Dulbecco MEM培养液（DMEM）中离体培养48 h。之后用含不同浓度Cu2＋（0 mg/L、0.025 mg/L、0.1 mg/L、0.4 mg/L、1.6 mg/L）的无小牛血清DMEM培养液培养36 h,于12 h、24 h、36 h收集细胞培养液,用Linco公司的试剂盒及放射免疫法测定培养液中GH浓度。结果：铜离子离体培养腺垂体细胞24 h,0.025 mg/L、0.1 mg/L、0.4 mg/L组培养液中GH浓度均高于0 mg/L组,其中0.1 mg/L组与0 mg/L组差异显著（P〈0.05）。结论：铜离子可促进离体培养猪腺垂体细胞分泌GH。     

由簇毛麦V染色体引起的小麦-簇毛麦染色体代换系、易位系中线粒体蛋白质组的变化(简报)

线粒体是需氧生物中的一种半自主性细胞器.在能量代谢中,它起了一个关键的作用,柠檬酸循环、电子传递和氧化磷酸化过程均在线粒体内完成.线粒体具有高度的生物化学和遗传上的独立性.含有DNA和核糖核蛋白体.负责合成生物体内2%-5%的蛋白质[1].线粒体DNA具有自身复制能力,控制着众多的遗传性状.在植物中广泛存在的细胞质雄性不育则被认为是由线粒体基因组控制的性状[2].