Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anti-coagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics.med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay-based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.     

The Effects of Using Trehalose as a Carbon Source on the Proliferation of Phalaenopsis and Doritaenopsis Protocorm-Like-Bodies

In this communication, the effects of trehalose and culture system on protocorm-like body (PLB) growth were investigated. PLB derived from Phalaenopsis and Doritaenopsis cultivars, which were grown on solidified trehalose amended NP medium showed higher proliferation rate than on NP medium containing sucrose. For P. ‘Hwa Feng Red Jewel’ and Dtp. ‘Mount Beauty×Su’s Red Lip’, the proliferation rates on solidified trehalose media were almost two times higher than those on sucrose media after 8-week culture. However, Knudson C (KC) medium did not reveal the similar results between trehalose and sucrose. In liquid culture system, both trehalose amended NP and KC media brought about better results than sucrose containing media for PLB proliferation. For culture system test, solidified media showed higher proliferation rate than liquid media under the same medium composition. Roller bottles were more suitable than flask-shaking cultures in liquid systems for PLB proliferation.     

Response of osteoblasts to low fluid shear stress is time dependent

The process of mechanotransduction of bone, the conversion of a mechanical stimulus into a biochemical response, is known to occur in osteoblasts in response to fluid shear stress. In order to understand the reaction of osteoblasts to various times of flow perfusion, osteoblasts were seeded on three-dimensional scaffolds, and cultured in the following conditions: continuous flow perfusion, intermittent flow perfusion, and static condition. We collected samples on day 4, 8 and 12 for analysis. Osteoblast proliferation was demonstrated by cell proliferation and scanning electron microscopy assay. Additionally, the expression of known markers of differentiation, including alkaline phosphatase and osteocalcin, were tested by qRT-PCR and alkaline phosphatase activity assay, and the deposition of calcium was used as an indicator of mineralization demonstrated by calcium content assay. The results supported that low fluid shear stress plays an important role in the activation of osteoblasts: enhance cell proliferation, increase calcium deposition, and promote the expression of osteoblastic markers. Furthermore, the continuous flow perfusion is a more favorable environment for the initiation of osteoblast activity compared with intermittent flow perfusion. Therefore, the force and time of fluid shear stress are important parameters for osteoblast activation.     

mal62 基因高表达对工业面包酵母发酵力的影响

【目的】构建高麦芽糖利用能力的面包酵母菌株,以期提高面包酵母在不加糖面团中的发酵力,增加经济效益的同时减少成本消耗。【方法】克隆工业面包酵母BY-14的麦芽糖酶基因mal62,以PGK1强启动子和终止子为调控元件,以酵母-大肠穿梭型质粒Yep-C为载体,构建重组表达质粒Yep-CPM,并转化酿酒酵母(Saccharomyces cerevisiae)BY-14,经筛选鉴定获得酵母转化子BYCPM。进行转化子的酶活力、mal62基因表达水平及发酵力测定,检测目的基因的功能性表达。【结果】工业酵母转化子BYCPM的最大麦芽糖酶活力比对照菌提高15%-52%,发酵力提高40%,比发酵力提高5.6%。【结论】转化子BYCPM具有更高的麦芽糖酶活力和更强的抗葡萄糖阻遏能力。并且在不加糖面团中,转化子具有更高的发酵力,可以在更短的时间内获得更大的产气量且消耗更少的碳源。     

可溶性肿瘤坏死因子受体II-脂联素球部融合蛋白的真核表达及生物学活性检测

本研究设计和构建了一种人肿瘤坏死因子受体II胞外区与人脂联素球部的融合基因sTNFRII-gAD,且相应的融合蛋白在哺乳动物细胞BHK-21S的无血清培养体系中实现了表达,并对该融合蛋白进行了初步鉴定。首先,用RT-PCR方法从人的外周血淋巴细胞总RNA中扩增人肿瘤坏死因子II型受体胞外区基因片段,与脂联素球部基因片段融合,克隆至pAAV2neo表达载体中,构建成pAAV2neo-sTNFRII-gAD。随后,用pAAV2neo-sTNFRII-gAD转染BHK-21S细胞获得G418抗性细胞BHK-21S/pAAV2neo-sTNFRII-gAD;然后,将原来含有血清的培养液换成无血清的化学成分限定的培养液,细胞从贴壁培养方式转换成悬浮培养方式;最后,收集BHK-21S/pAAV2neo-sTNFRII-gAD无血清悬浮培养24h后的培养上清,进行sTNFRII-gAD融合蛋白的鉴定分析。酶切鉴定和测序结果显示,所构建的pAAV2neo-sTNFRII-gAD质粒结构正确,sTNFRII-gAD序列与预期一致;分别用抗人肿瘤坏死因子受体II和抗人脂联素球部的单克隆抗体检测pAAV2neo-sTNFRII-gAD瞬时转染的BHK-21S细胞,免疫荧光呈现阳性;免疫印迹分析在pAAV2neo-sTNFRII-gAD稳定转染的BHK-21S细胞上清中检测到sTNFRII-gAD融合蛋白的表达,并以单体、三聚体和三聚体以上的多聚体形式存在。活性测定结果表明,sTNFRII-gAD融合蛋白具有显著抑制TNFα杀伤L929细胞的活性。因此,本研究为下一步大量制备sTNFRII-gAD融合蛋白用于体内外功能研究提供了良好基础。     

Systematic Evaluation of Protein Sequence Filtering Algorithms for Proteoform Identification Using Top‐Down Mass Spectrometry

Complex proteoforms contain various primary structural alterations resulting from variations in genes, RNA, and proteins. Top‐down mass spectrometry is commonly used for analyzing complex proteoforms because it provides whole sequence information of the proteoforms. Proteoform identification by top‐down mass spectral database search is a challenging computational problem because the types and/or locations of some alterations in target proteoforms are in general unknown. Although spectral alignment and mass graph alignment algorithms have been proposed for identifying proteoforms with unknown alterations, they are extremely slow to align millions of spectra against tens of thousands of protein sequences in high throughput proteome level analyses. Many software tools in this area combine efficient protein sequence filtering algorithms and spectral alignment algorithms to speed up database search. As a result, the performance of these tools heavily relies on the sensitivity and efficiency of their filtering algorithms. Here, we propose two efficient approximate spectrum‐based filtering algorithms for proteoform identification. We evaluated the performances of the proposed algorithms and four existing ones on simulated and real top‐down mass spectrometry data sets. Experiments showed that the proposed algorithms outperformed the existing ones for complex proteoform identification. In addition, combining the proposed filtering algorithms and mass graph alignment algorithms identified many proteoforms missed by ProSightPC in proteome‐level proteoform analyses.