Towards standard protocols and guidelines for urine proteomics: a report on the Human Kidney and Urine Proteome Project (HKUPP) symposium and workshop, 6 October 2007, Seoul, Korea and 1 November 2007, San Francisco, CA, USA

The Human Kidney and Urine Proteome Project (HKUPP) was initiated in 2005 to promote proteomics research in the nephrology field, to better understand kidney functions as well as pathogenic mechanisms of kidney diseases, and to define novel biomarkers and therapeutic targets. This project was first approved in 2005 by the Human Proteome Organisation (HUPO) as a Kidney Disease Initiative under an umbrella of the HUPO Disease Biomarker Initiative (DBI), and more recently was approved as the HKUPP Initiative in 2007. Several sub-projects have been planned to achieve the ultimate goals. The most pressing is the establishment of "standard protocols and guidelines for urine proteome analysis". This sub-project had been extensively discussed during the first HKUPP symposium (during 6(th) HUPO Annual World Congress--October 2007, Seoul, Korea) and second workshop (during 40(th) American Society of Nephrology Renal Week--November 2007, San Francisco, CA, USA). Additional data and references have been collected after the symposium and workshop. An initial draft of standard protocols and guidelines for proteome analysis of non-proteinuric urine (urine protein excretion < or =150 mg/day) will soon be released as the first HKUPP product.     

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.     

The AOHUPO Membrane Proteomics Initiative, Fourth Workshop 22 June 2008, Cairns, Australia

The Fourth Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative (AOHUPO MPI) Workshop took place on 22 June 2008 in Cairns, Australia, with approximately 90 attendees from academia and industry. Participants from ten of the seventeen collaborating centres presented workshop papers. This was part of the pre-conference programme of the Joint Fourth Asian Oceania Human Proteome Organisation Conference and the Second Pacific Rim International Conference on Protein Structure.     

The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006

The plenary session of the Proteomics Standards Initiative of the Human Proteome Organisation provided an opportunity to update delegates on the progress of the work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO-PSI) to develop and implement standards in the field of proteomics. Significant advances have been made since the previous congress, with several of the interchange standards and minimal requirements documents being submitted for publication in the literature and being more widely adopted by both manufacturers and data repositories. An exciting development over the interim twelve months is the ongoing merger of the two existing mass spectrometry standards, the PSI mzData and Institute for Systems Biology mzXML, into a single product. This should be achieved by early in 2007.     

Frontiers in glycomics; bioinformatics and biomarkers in disease. September 11-13, 2006 Natcher Conference Center, NIH Campus, Bethesda, MD, USA

This is a short summary of a meeting entitled "The Frontiers in Glycomics; Bioinformatics and Biomarkers in Disease" which was jointly organized by the NIH Consortium for Functional Glycomics (CFG), Human Disease Glycomics/Proteome Initiative (HGPI), National Cancer Institute, National Institute of General Medical Sciences, Japan Society for the Promotion of Science and National Center for Research Resources held at the NIH Campus, Bethesda, MD, Natcher Conference Center in September 11-13, 2006.     

Correlation between Human Leukocyte Antigen Class II Alleles and HAI Titers Detected Post-Influenza Vaccination

Influenza is a major cause of morbidity and mortality. Despite vaccination, many elderly recipients do not develop a protective antibody response. To determine whether Human Leukocyte Antigen (HLA) alleles modulate seroprotection to influenza, a cohort of HLA class II-typed high-risk vaccine recipients was investigated. Haemagglutinin inhibition (HAI) titres were measured 14–40 days post-subunit vaccination. Seroprotection was defined as HAI titres reaching 40 or greater for all three vaccine strains. HLA-DRB1*04∶01 and HLA-DPB1*04∶01 alleles were detected at higher frequencies in seroprotected compared with non-seroprotected individuals. Thus, the presence of certain HLA class II alleles may determine the magnitude of antibody responses to influenza vaccination.     

The 2011 Human Liver Proteome Project (HLPP) Workshop September 5, 2011, Geneva, Switzerland

During the 10th HUPO Annual World Congress held in Geneva (Switzerland) from 4th to 7th September, a workshop on Human Liver Proteome Project (HLPP) Initiative took place. Four research groups presented their latest results from different ongoing projects. Later on, during the HLPP executive members' meeting, the status of current projects and the next possible steps to be taken were discussed.     

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.     

Automated DNA sequencing and the analysis of the human genome

The Human Genome Initiative is a complex, multifaceted, international effort to establish a massive data base of map and sequence information for humans and other organisms. The success of this initiative is dependent upon the development of new technologies for the analysis of genomes. In this paper, an overview of the Human Genome Initiative is presented, and the current status of efforts to automate large-scale DNA sequence analysis is reviewed.     

Future Directions for Research on Human–Animal Interaction in an Aging Population

ABSTRACT

This final paper in the thematic issue, “Human–Animal Interaction and Healthy Human Aging,” highlights and distills key points from the series of papers and provides recommendations for improving and expanding Human–Animal Interaction (HAI) research into healthy human aging. This paper also focuses on translating research to practice and discussing important practical issues related to pet ownership or interaction with companion animals among older adults, and makes specific recommendations for researchers, caregivers, and professionals working with older adults. In addition to issues related to the human side of the equation, we make recommendations for protecting and insuring the health and wellbeing of the animals involved.     

GST-HAI-1融合蛋白的表达及抗人HAI-1单克隆抗体的制备

制备抗人肝细胞生长因子激活物抑制因子（HAI-1）单克隆抗体,为对HAI-1进行进一步的研究打下基础。将人HAI-1 cDNA分段克隆,构建GST-HAI-1融合蛋白原核表达载体,转化大肠杆菌后加IPTG诱导融合蛋白表达,经制备型SDS-PAGE法分离表达的GST-HAI-1融合蛋白,通过割胶、电洗脱回收融合蛋白,并以此为抗原免疫BALB/c小鼠,应用细胞融合技术制备产生抗人HAI-1单克隆抗体的杂交瘤,以ELISA、Western blot和免疫组织化学染色进行鉴定。最终获得抗人HAI-1单克隆抗体杂交瘤细胞株ZMC6,产生的单克隆抗体可特异性地与表达的GST-HAI-1融合蛋白反应,并可识别大肠组织中的膜型及脱落型HAI-1蛋白。该单克隆抗体的制备成功,为深入研究HAI-1的功能提供了有力工具。     

BK antibody and virus-specific IgM responses in renal transplant recipients,patients with malignant disease,and healthy people.

Haemagglutination-inhibition (HAI) antibodies to BK virus, including BK-virus-specific IgM, were determined before and after renal transplantation in 20 patients, in 57 patients with malignant disease, and in 66 healthy controls, Before transplantation 11 of the renal transplant recipients were seronegative, but eight later serocconverted, two before and six after transplantation. Twenty of the patients with malignant disease and 22 controls were also seronegative. The geometric mean titre of BK HAI antibodies was significantly higher among transplanted patients (1/180) than among controls (1/90). BK-virus-specific IgM antibody was detected in seven renal transplant recipients, six patients with malignant disease, and 13 healthy controls. In transplant recipients BK-virus-specific IgM antibody usually persisted throughout the duration of the study, and studies on controls from whom second serum samples were available suggested that they too had persistent BK-virus-specific IgM responses. The geometric mean titre of BK-virus-specific IgM HAI antibody was significantly greater in post-transplantation sera (1/223) than in control sera (1/28). The specificity of the detection of BK-virus-specific IgM HAI antibody was confirmed by direct visualisation of antibody by immune electron microscopy. The persistence of BK-virus-specific IgM suggested that BK virus continued to provide an antigenic stimulus. Nevertheless, there was no obvious association between the serological findings and any clinical features, and prospective studies will be needed to elucidate any such association.     

Changes in specific activities of peroxidase, chitinase and phenylalanine ammonia-lyase and phenolic content in cucumber leaves inoculated with Podosphaera fusca, the causal agent of powdery mildew

In this investigation, the effects of powdery mildew disease [caused by Podosphaera fusca (syn. Sphaerotheca fuliginea)] on specific activities of several defense-related enzymes and phenolic content were studied in cucumber leaves. Spore suspension of the fungus was sprayed on cucumber (cv. Super Dominus) plants in greenhouse and leaves from both inoculated and non-inoculated control plants were sampled at 0, 24, 48, 72 and 144 hours after inoculation (HAI). Spore germination and tissue colonization of P. fusca were microscopically studied on the inoculated surface of leaf samples. Further, Phenolic content (PHE) and specific activities of peroxidase (POX), chitinase (CHI) and phenylalanine ammonia-lyase (PAL) were spectrophotometrically measured in leaf extracts. Time-course of disease progress on the leaf surface showed that maximum spore germination occurred within 24 HAI and host penetration and disease development process began during 24-48 HAI. Evaluation of enzyme activities showed that POX specific activity in inoculated plants significantly increased at 72 HAI onwards and reached 2.5 times of that of control at 144 HAI. CHI specific activity showed a transient reduction in inoculated plants between 48-72 HAI and thereafter increased significantly in relation to control. PAL specific activity in inoculated plants was not significantly different from that of control. PHE in inoculated plants showed a significant increase compared to control at 48 HAI and thereafter. Comparison of time-course of disease progress with changes in enzyme activities indicated that POX activity had an increasing trend during disease progress whereas CHI activity showed a transient decrease at the early stages and then increased during the later stages of infection: PAL activity did not show any changes during the infection and PHE increased at the early stages of infection process and remained constant at rest of the time.     

Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain

The role of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) is to produce and release community-accepted reporting requirements, interchange formats and controlled vocabularies for mass spectrometry proteomics and related technologies such as gel electrophoresis, column chromatography and molecular interactions. A number of significant advances were made at this workshop, with the new MS standard, mzML, being finalised prior to release on 1(st) June 2008 and analysisXML, which will allow protein and peptide identifications and post-translational modifications to be captured, being prepared to enter the review process this summer. The accompanying controlled vocabularies are continuing to evolve and a number of standards papers are now being finalised prior to publication.     

HUPO 2011: The new Cardiovascular Initiative - integrating proteomics and cardiovascular biology in health and disease

A newly reorganized HUPO Cardiovascular Initiative was announced at the HUPO 2011 Cardiovascular Initiative Workshop at Geneva. The new initiative is now part of the biology- and disease-driven component of the HUPO Human Proteome Project (B/D-HPP). Here we report the recent achievements and future directions of the initiative, and offer a perspective on the present challenges of cardiovascular proteomics and its integration with the cardiovascular biology community at large.     

Fully human,HLA-DR-specific monoclonal antibodies efficiently induce programmed death of malignant lymphoid cells

The Human Combinatorial Antibody Library (HuCAL) was screened for antibodies specific to human leukocyte antigen-DR (HLA-DR) that induce programmed death of lymphoma/leukemia cells expressing the target antigen. The active Fab fragments were affinity-matured, and engineered to IgG(4) antibodies of sub-nanomolar affinity. The antibodies exhibited potent in vitro tumoricidal activity on several lymphoma and leukemia cell lines and on chronic lymphocytic leukemia patient samples. They were also active in vivo in xenograft models of non-Hodgkin lymphoma. Cell death occurred rapidly, without the need for exogenous immunological effector mechanisms, and was selective to activated/tumor-transformed cells. Although the expression of HLA-DR on normal hematopoietic cells is a potential safety concern, the antibodies caused no long-lasting hematological toxicity in primates, in vivo. Such monoclonal antibodies offer the potential for a novel therapeutic approach to lymphoid malignancies.     

The quantitation of rabies-specific antibodies. III. A comparative evaluation of modified counter immunoelectrophoresis, haemagglutination inhibition and serum neutralization titres of human sera

The rabies-specific antibodies of 73 serum samples from vaccinated humans were determined by the modified counter immunoelectrophoresis (MCIE), and the haemagglutination inhibition test (HAI) by using the conventional serum neutralization test (SN) as a yard-stick. Both MCIE and HAI were found to be sensitive and specific for the estimation of rabies antibodies. In general, the unitages obtained by the MCIE and SN showed statistically insignificant differences (P greater than 0.05) and the correlation coefficient between the two methods was 0.697 (P less than 0.05). Although the unitage of the sera detected by HAI tests was lower by a factor of 0.155 from the unitage of SN tests, there was statistically insignificant differences between the two techniques (P greater than 0.05) with a correlation coefficient of 0.556 (P less than 0.05).     

Implementing Data Standards: A report on the HUPOPSI Workshop September 2009, Toronto,Canada

The plenary session of the Proteomics Standards Initiative of the Human Proteome Organisation at the 8th Annual HUPO World Congress updated the delegates on the current status of the ongoing work of this group. The mass spectrometry group reviewed the progress of mzML since its release last year and detailed new work on providing a common format for SRM/MRM transition lists (TraML). The implementation of mzIdentML, for describing the output of proteomics search engines, was outlined and the release of a new web service PSICQUIC, which allows users to simultaneously search multiple interaction databases, was announced. Finally, the audience participated in a lively debate, discussing both the benefits of these standard formats and issues with their adoption and use in a research environment.     

Managing the Data Explosion A Report on the HUPO‐PSI Workshop August 2008, Amsterdam,The Netherlands

The plenary session of the Proteomics Standards Initiative (PSI) of the Human Proteome Organisation at the 7^th annual HUPO world congress updated the delegates on the current status of the ongoing work of this group. The release of the new MS interchange format, mzML, was formally announced and delegates were also updated on the advances in the area of molecular interactions, protein separations, proteomics informatics and also on PEFF, a common sequence database format currently under review in the PSI documentation process. Community input on this initiative was requested. Finally, the impact these new data standards are having on the data submission process, which increasingly is an integral part of the publication process, was reviewed and discussed.