Proteomics Data Collection – 5th ProDaC Workshop 4 March 2009, Kolympari,Crete, Greece

The Proteomics Data Collection (ProDaC) consortium, a “Coordination Action” funded by the 6th EU Framework Programme, started in October 2006. Its aim was to facilitate the collection and distribution of proteomics data and the public availability of data sets from proteomics experiments. Within the consortium standard formats are created and tools are developed to allow extensive data collection within the proteomics community. An important part of ProDaC is the organization of workshops twice a year to inform about the consortium's progress and to stimulate communication between the ProDaC partners and between partners and interested members of the proteomics community. ProDaC ends on March 31, 2009. The most recent (and final) workshop was the 5th ProDaC workshop held on March 4, 2009 in Kolympari, Crete, Greece. The progress since the last meeting and an overall summary was presented by the work package coordinators and partners. Four external speakers presented talks about their work in relation to ProDaC.     

Proteomics Data Collection – 4th ProDaC Workshop 15 August 2008, Amsterdam,The Netherlands

ProDaC (Proteomics Data Collection), a “Coordination Action” within the 6^th EU framework programme, was created to support the collection, distribution and public availability of data from proteomics experiments. Within the consortium standards are created and maintained enabling an extensive data collection within the proteomics community. Important elements of ProDaC are workshops held twice a year to allow communication between the ProDaC partners and to report the ongoing progress. The most recent assembly was the 4^th ProDaC workshop on August 15^th, 2008, in Amsterdam, The Netherlands. It took place directly before the 7^th HUPO Annual World Congress (Human Proteome Organisation). Work package coordinators and partners presented the progress achieved since the last meeting. Additionally, an EU official presented funding opportunities for proteomics in the next EU framework programme and five external speakers presented talks about their work in relation to ProDaC.     

Proteomics Data Collection - 3rd ProDaC workshop April 22nd 2008, Toledo, Spain

The "Coordination Action" ProDaC (Proteomics Data Collection) - funded by the EU within the 6th framework programme - was created to support the dissemination, utilization and publication of proteomics data. Within this international consortium, standards are developed and maintained to support extensive data collection by the proteomics community. An important part of ProDaC are workshops organized on a regular basis (two per year) to allow discussions and communication between the ProDaC partners and to report on the progress of the project. The kick-off meeting took place in October 2006 in Long Beach, CA, USA. The 1st ProDaC workshop was held in Lyon, France (April 2007) and the 2nd in Seoul, Korea in October 2007. ProDaC organized the 3rd ProDaC workshop at the Beatriz Hotel, Toledo, on 22nd April, 2008, directly before the HUPO - PSI spring meeting (Human Proteome Organisation - Proteomics Standards Initiative). The work package coordinators presented talks about the progress achieved during the past six months. Additionally four external speakers presented their work on data conversion and data repositories. The concluding discussion session was chaired by the Journal's representative.     

Getting a grip on proteomics data – Proteomics Data Collection (ProDaC)

In proteomics, rapid developments in instrumentation led to the acquisition of increasingly large data sets. Correspondingly, ProDaC was founded in 2006 as a Coordination Action project within the 6th European Union Framework Programme to support data sharing and community‐wide data collection. The objectives of ProDaC were the development of documentation and storage standards, setup of a standardized data submission pipeline and collection of data. Ending in March 2009, ProDaC has delivered a comprehensive toolbox of standards and computer programs to achieve these goals.     

High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK

The Wellcome Trust Conference Centre at Hinxton, UK, was the meeting place of the 7th HUPO Brain Proteome Project Workshop entitled "High Performance Proteomics". It started on Wednesday, March 7, 2007 with a steering committee meeting followed by a two days series of talks dealing with the standardization and handling of tissues, body fluids as well as of proteomics data. The presentation and accompanying vivid discussions created a picture of actual strategies and standards in recent proteomics.     

International Symposium on High Performance Proteomics 2007: a contribution to Proteomics May 14-16, 2007 Dortmund, Germany

The symposium High Performance Proteomics was held in Dortmund on May 14-16, 2007, to celebrate the opening of the Zentrum für Angewandte Proteomik as well as the 6(th) anniversary of the German Human Brain Proteome Project. It offered an outstanding opportunity to obtain a broad overview about all fields of proteomics and related fields, combining the expertise of biochemists, physicians, bioinformatics, mathematicians and other researchers in Life Sciences. The main topics were the presentation of state-of-the-art proteomics technologies as well as possible transfer models for industrial applications. An accompanying industrial exhibition, as well as a discussion panel, offered the possibility to get in contact with colleagues and potential industrial partners. A visit to the former colliery Zeche Zollern and the social event at the Harenberg City-Center with an excellent view around Dortmund also left time for further communication between the more than 200 attendees.     

Report of the 9th HLPP Workshop October 2007, Seoul, Korea

The Human Liver Proteome Project is one of the Human Proteome Initiatives launched by Human Proteome Organization (HUPO). Major achievements of the project have been obtained under the efforts of international collaboration with all the participants since it was formally proposed in 2002. Its updated progresses were presented in the latest workshop held in conjunction with the sixth HUPO World Congress in October, 2007, Seoul, Korea. Furthermore, four topics related to the project as well as other initiatives were lively discussed among all the attendees.     

Cardiovascular Initiative of the Human Proteome Organisation, 5th Workshop October 2007, Seoul, Korea

The Cardiovascular Initiative (CVI) of the Human Proteome Organisation (HUPO) held its fifth workshop prior to the Sixth Annual HUPO World Congress in Seoul, Korea in October 2007. The objectives of this report are as follows: to trace the (relatively brief) history of the CVI for those who may not be acquainted with it; to highlight lectures given by members of the CVI during this Workshop; and to make the community aware of the aims of this Initiative, including collaborative projects currently under consideration.     

Tackling Quantitation: A Report on the Annual Spring Workshop of the HUPO‐PSI 28–30 March 2010, Seoul,South Korea

The annual Spring Workshop of the HUPO‐PSI took place in Korea, where the Mass Spectrometry and Protein Separations groups joined forces to tackle the issue of the consistent reporting of quantitative proteomic data generated by mass‐spectrometry‐based technologies. A preliminary mzQuantML schema was drafted which, when completed and tested, will complement the existing mzIdentML schema for reporting protein identifications. The Molecular Interactions group concentrated on the implementations of the PSICQUIC (PSI Common Query InterfaCe) service that allows users to simultaneously query interaction data across multiple participating resources. Work was also undertaken to update the MIAPE guidelines, in response to feedback from the editors of a number of proteomic journals.     

Applications in brain proteomics: 8(th) HUPO Brain Proteome Project Workshop 7 October 2007, Seoul, Korea

What are the current approaches in brain proteomics? Can we combine different, but complementary study designs to obtain better results concerning brain diseases? What are the neuro‐hotspots, especially in Korea? These were some of the questions the participants of the 8^th HUPO Brain Proteome Project Workshop tried to answer prior to the 6^th HUPO World Congress in Seoul, Korea. Around 100 scientists came together during the afternoon of 7 October, 2007, to discuss and to catch up on the latest results and strategies concerning Huntington's disease, glioblastoma and standardization.     

Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA

The theme of the third annual Spring workshop of the HUPO-PSI was "proteomics and beyond" and its underlying goal was to reach beyond the boundaries of the proteomics community to interact with groups working on the similar issues of developing interchange standards and minimal reporting requirements. Significant developments in many of the HUPO-PSI XML interchange formats, minimal reporting requirements and accompanying controlled vocabularies were reported, with many of these now feeding into the broader efforts of the Functional Genomics Experiment (FuGE) data model and Functional Genomics Ontology (FuGO) ontologies.     

2nd BSPR London Regional Meeting and 6th Annual Imperial Proteomics Day. November 2007, Imperial College London, London, UK

The 2(nd) BSPR London Regional Meeting held at Imperial College London focused on nanoproteomics and single cell proteomics, the solutions to many of the technical challenges in proteomics and protein based molecular diagnostics. This one day meeting included presentations from leading scientists within and outside of Imperial College who share a common interest in novel solutions for the identification and characterization of proteins from a single cell. The conclusion was that nanomaterials are delivering enhanced reagents and have been tested at the proof-of-concept level, but have yet to be incorporated into routine proteomic workflows.     

Ten Years of Standardizing Proteomic Data: A Report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA

The Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) was established in 2002 with the aim of defining community standards for data representation in proteomics and facilitating data comparison, exchange and verification. Over the last 10 years significant advances have been made, with common data standards now published and implemented in the field of both mass spectrometry and molecular interactions. The 2012 meeting further advanced this work, with the mass spectrometry groups finalising approaches to capturing the output from recent developments in the field, such as quantitative proteomics and SRM. The molecular interaction group focused on improving the integration of data from multiple resources. Both groups united with a guest work track, organized by the HUPO Technology/Standards Committee, to formulate proposals for data submissions from the HUPO Human Proteome Project and to start an initiative to collect standard experimental protocols.     

A novel synthetic compound, (Z)-5-(3-hydroxy-4-methoxybenzylidene)-2-iminothiazolidin-4-one (MHY773) inhibits mushroom tyrosinase

As part of continued efforts for the development of new tyrosinase inhibitors, (Z)-5-(substituted benzylidene)-2-iminothiazolidin-4-one derivatives (1a – 1l) were rationally synthesized and evaluated for their inhibitory potential in vitro. These compounds were designed and synthesized based on the structural attributes of a β-phenyl-α,β-unsaturated carbonyl scaffold template. Among these compounds, (Z)-5-(3-hydroxy-4-methoxybenzylidene)-2-iminothiazolidin-4-one (1e, MHY773) exhibited the greatest tyrosinase inhibition (IC₅₀ = 2.87 μM and 8.06 μM for monophenolase and diphenolase), and outperformed the positive control, kojic acid (IC₅₀ = 15.59 and 31.61 μM). The kinetic and docking studies demonstrated that MHY773 interacted with active site of tyrosinase. Moreover, a melanin quantification assay demonstrated that MHY773 attenuates α-melanocyte-stimulating hormone (α-MSH) and 3-isobutyl-1-methylxanthine (IBMX)-induced melanin contents in B16F10 melanoma cells. Taken together, these data suggest that MHY773 suppressed the melanin production via the inhibition of tyrosinase activity. MHY773 is a promising for the development of effective pharmacological and cosmetic agents for skin-whitening.     

TGD1, -2, and -3 proteins involved in lipid trafficking form ATP-binding cassette (ABC) transporter with multiple substrate-binding proteins

Members of the ATP-binding cassette (ABC) transporter family are essential proteins in species as diverse as archaea and humans. Their domain architecture has remained relatively fixed across these species, with rare exceptions. Here, we show one exception to be the trigalactosyldiacylglycerol 1, 2, and 3 (TGD1, -2, and -3) putative lipid transporter located at the chloroplast inner envelope membrane. TGD2 was previously shown to be in a complex of >500 kDa. We demonstrate that this complex also contains TGD1 and -3 and is very stable because it cannot be broken down by gentle denaturants to form a "core" complex similar in size to standard ABC transporters. The complex was purified from Pisum sativum (pea) chloroplast envelopes by native gel electrophoresis and examined by mass spectrometry. Identified proteins besides TGD1, -2, or -3 included a potassium efflux antiporter and a TIM17/22/23 family protein, but these were shown to be in separate high molecular mass complexes. Quantification of the complex components explained the size of the complex because 8-12 copies of the substrate-binding protein (TGD2) were found per functional transporter.     

2-12烷基-6-甲氧基环己基-2,5-二烯-1,4-二酮(DMDD)抗弥漫大B淋巴瘤的作用及机制*

目的:探讨2-12烷基-6-甲氧基环己基-2,5-二烯-1,4-二酮(DMDD)抗弥漫大B淋巴瘤(DLBCL)的作用及分子机制。方法:动物实验取4周龄BALB/C小鼠,分5组,20只/组,腹股沟注射DLBCL细胞株OCI-LY19细胞1 × 10⁷ cells/ml 每只0.1 ml,两天后分别灌胃0、1、5、25、125 mg/kg剂量的DMDD,1次/2天,给药的第18日,杀10只小鼠,取瘤组织称重,记录剩余小鼠的生存期。细胞实验取OCI-LY19细胞加入96孔培养板,每孔100 μl 1×10⁵ cells/ml,分别加入100 μl DMDD使其终浓度分别为0、1、5、25和125 μmol/L,作用0、24、48和72 h,设三复孔,MTS法检测细胞增殖活性;根据细胞增殖实验结果,选择0 μmol/L、5 μmol/L和25 μmol/L的DMDD作为后续用药浓度作用OCI-LY19细胞24 h,流式细胞仪分析凋亡率,hoechst染色观察细胞核型,JC-1染色观察线粒体膜电位,LDH释放实验评估药物细胞毒性,qPCR、Western blot分析基因转录和表达水平。结果:动物实验表明:与0 mg/kg用药组比,1～125 mg/kg DMDD能抑制小鼠瘤组织生长并延长其生存期(P＜0.01)。细胞实验表明:DMDD用药组OCI-LY19细胞增殖活性明显降低、凋亡水平显著增加(P＜0.01),细胞核出现碎裂、凝集和凋亡小体及线粒体膜电位下降,LDH释放率显著增加(P＜0.01),细胞内caspase-3和bax基因的转录表达和IκBα的磷酸化水平显著上调,bcl-2、bcl-xL、jak2和stat3基因的转录和蛋白表达水平明显受抑(P＜0.01)。结论:DMDD通过抑制JAK2/STAT3和NF-κB信号通路中JAK2、STAT3和p-IκBα的表达,下调BCL-2/BAX、活化Caspase-3,最终激活OCI-LY19细胞线粒体凋亡的内源性通路而促进了DLBCL细胞凋亡,抑制了OCI-LY19细胞增殖,具有抗DLBCL的作用。     

Synthesis and biological evaluation of indole-based,anti-cancer agents inspired by the vascular disrupting agent 2-(3′-hydroxy-4′-methoxyphenyl)-3-(3″,4″,5″-trimethoxybenzoyl)-6-methoxyindole (OXi8006)

The discovery of a 2-aryl-3-aroyl indole-based small-molecule inhibitor of tubulin assembly (referred to as OXi8006) inspired the design, synthesis, and biological evaluation of a series of diversely functionalized analogues. In the majority of examples, the pendant 2-aryl ring contained a 3-hydroxy-4-methoxy substitution pattern, and the fused aryl ring featured a 6-methoxy group. Most of the variability was in the 3-aroyl moiety, which was modified to incorporate methoxy (33–36), nitro (25–27), halogen (28–29), trifluoromethyl (30), or trifluoromethoxy (31–32) functionalities. In two analogues (34 and 36), the methoxy substitution pattern in the fused aryl ring varied, while in another derivative (35) the phenolic moiety was translocated from the pendant 2-aryl ring to position-7 of the fused aryl ring. Each of the compounds were evaluated for their cytotoxicity (in vitro) against the SK-OV-3 (ovarian), NCI-H460 (lung), and DU-145 (prostate) human cancer cell lines and for their ability to inhibit tubulin assembly. Four of the compounds (30, 31, 35, 36) proved to be potent inhibitors of tubulin assembly (IC₅₀ <5 μM), and three of these compounds (31, 35, 36) were strongly cytotoxic against the three cancer cell lines. The most active compound (36) in this series, which incorporated a methoxy group at position-7, was comparable in terms of inhibition of tubulin assembly and cytotoxicity to the lead compound OXi8006.