The minimum information about a proteomics experiment (MIAPE).

Both the generation and the analysis of proteomics data are now widespread, and high-throughput approaches are commonplace. Protocols continue to increase in complexity as methods and technologies evolve and diversify. To encourage the standardized collection, integration, storage and dissemination of proteomics data, the Human Proteome Organization's Proteomics Standards Initiative develops guidance modules for reporting the use of techniques such as gel electrophoresis and mass spectrometry.

Past and present course of cardioprotection against ischemia-reperfusion injury.

Despite tremendous advances in cardiovascular research and clinical therapy, ischemic heart disease remains the leading cause of serious morbidity and mortality in western society and is growing in developing countries. For the past 5 decades, many scientists have studied the pathophysiology of myocardial ischemia-reperfusion (I/R) injury leading to infarction. With the exception of reperfusion therapy, attempts to salvage the myocardium during an acute myocardial infarction showed disappointing results in directly decreasing infarct size.

Mammalian proteasome subpopulations with distinct molecular compositions and proteolytic activities.

The proteasome-dependent protein degradation participates in multiple essential cellular processes. Modulation of proteasomal activities may alter cardiac function and disease phenotypes. However, cardiovascular studies reported thus far have yielded conflicting results.

Exploring proteasome complexes by proteomic approaches.

The ubiquitin proteasome system (UPS) represents a major pathway for intracellular protein degradation. Proteasome dependent protein quality control participates in cell cycle, immune response and apoptosis. Therefore, the UPS is in focus of therapeutic investigations and the development of pharmaceutical agents.

Publication Committee meeting. HUPO 5th annual World Congress. Long Beach, CA, USA 30 October 2006.

This meeting brought together delegates from industry, academia and the publishing houses to facilitate discussions on the level of support from the journals for the use of standardised data formats and their interest in the creation of a network of proteomics repositories collaborating on a coordinated data curation effort. Discussions centred on how best to structure interactions between journals, databases and researchers to improve accessibility to data, and facilitate comparisons between datasets.

A membrane receptor for retinol binding protein mediates cellular uptake of vitamin A.

Vitamin A has diverse biological functions. It is transported in the blood as a complex with retinol binding protein (RBP), but the molecular mechanism by which vitamin A is absorbed by cells from the vitamin A-RBP complex is not clearly understood. We identified in bovine retinal pigment epithelium cells STRA6, a multitransmembrane domain protein, as a specific membrane receptor for RBP.

Cardiovascular proteomics: tools to develop novel biomarkers and potential applications.

Proteomics is the new systems biological approach to the study of proteins and protein variation on a large scale as a result of biological processes and perturbations. The field is undergoing a dramatic transformation, owing to the completion and annotation of the human genome as well as technological advances to study proteins on a large scale. The new science of proteomics can potentially yield novel biomarkers reflecting cardiovascular disease, establish earlier detection strategies, and monitor responses to therapy.

Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Proteomics approaches to the systems biology of cardiovascular diseases.

Proteins play a central role in a systems view of biologic processes. This review provides an overview of proteomics from a systems perspective. We survey the key tools and methodologies used, present examples of how these are currently being used in the systems biology context, and discuss future directions.

Protein degradation by the 26S proteasome system in the normal and stressed myocardium.

The 26S proteasome is a multicatalytic threonine protease complex responsible for degradation of the majority of proteins in eukaryotic cells. In the last two decades, the ubiquitin proteasome system (UPS) has been increasingly recognized as an integral component in numerous biologic processes including cell proliferation, adaptation to stress, and cell death. The turnover of intracellular proteins inevitably affects the contributions of these molecules to cellular networks and pathways in any given tissue or organ, including the myocardium.

HUPO Publications Committee Meeting: 21 April 2006, San Francisco, CA, USA.

This meeting was convened with the aim of bringing together representatives from scientific journals, granting authorities, software and instrumentation manufacturers, data producers and database providers to discuss the implementation and adoption of the HUPO-PSI data standards and how these can be best used to support the publication and dissemination of proteomics data. The current status of data formats and reporting requirements was reviewed and the attendees agreed that the use of data standards was essential as the field of proteomics grows and matures.

Mapping the murine cardiac 26S proteasome complexes.

The importance of proteasomes in governing the intracellular protein degradation process has been increasingly recognized. Recent investigations indicate that proteasome complexes may exist in a species- and cell-type-specific fashion. To date, despite evidence linking impaired protein degradation to cardiac disease phenotypes, virtually nothing is known regarding the molecular composition, function, or regulation of cardiac proteasomes.

Regulation of murine cardiac 20S proteasomes: role of associating partners.

Our recent studies have provided a proteomic blueprint of the 26S proteasome complexes in the heart, among which 20S proteasomes were found to contain cylinder-shaped structures consisting of both alpha and beta subunits. These proteasomes exhibit a number of features unique to the myocardium, including striking differences in post-translational modifications (PTMs) of individual subunits and novel PTMs that have not been previously reported. To date, mechanisms contributing to the regulation of this myocardial proteolytic core system remain largely undefined; in particular, little is known regarding PTM-dependent regulation of cardiac proteasomes.

Gene delivery to the spinal cord: comparison between lentiviral, adenoviral, and retroviral vector delivery systems.

Viral gene delivery for spinal cord injury (SCI) is a promising approach for enhancing axonal regeneration and neuroprotection. An understanding of spatio-temporal transgene expression in the spinal cord is essential for future studies of SCI therapies. Commonly, intracellular marker proteins (e.

Nerve conduit filled with GDNF gene-modified Schwann cells enhances regeneration of the peripheral nerve.

A recombinant retrovirus vector containing the glial cell line-derived neurotrophic factor (GDNF) gene was constructed and transfected into Schwann cells (SCs) to investigate the possibility of GDNF transfection and functional expression of transfected SCs, including GDNF secretion and its mRNA expression. We found that transfection of the GDNF gene into SCs led to significantly enhanced expression of GDNF mRNA. The rate of GDNF secretion by GDNF-SCs was also increased.

A functional annotation of subproteomes in human plasma.

The data collected by Human Proteome Organization's Plasma Proteome Pilot project phase was analyzed by members of our working group. Accordingly, a functional annotation of the human plasma proteome was carried out. Here, we report the findings of our analyses.

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.

The murine cardiac 26S proteasome: an organelle awaiting exploration.

Multiprotein complexes have been increasingly recognized as essential functional units for a variety of cellular processes, including the protein degradation system. Selective degradation of proteins in eukaryotes is primarily conducted by the ubiquitin proteasome system. The current knowledge base, pertaining to the proteasome complexes in mammalian cells, relies largely upon information gained in the yeast system, where the 26S proteasome is hypothesized to contain a 20S multiprotein core complex and one or two 19S regulatory complexes.

Cardiovascular-related proteins identified in human plasma by the HUPO Plasma Proteome Project pilot phase.

Proteomic profiling of accessible bodily fluids, such as plasma, has the potential to accelerate biomarker/biosignature development for human diseases. The HUPO Plasma Proteome Project pilot phase examined human plasma with distinct proteomic approaches across multiple laboratories worldwide. Through this effort, we confidently identified 3020 proteins, each requiring a minimum of two high-scoring MS/MS spectra.

Functional recovery in traumatic spinal cord injury after transplantation of multineurotrophin-expressing glial-restricted precursor cells.

Demyelination contributes to the physiological and behavioral deficits after contusive spinal cord injury (SCI). Therefore, remyelination may be an important strategy to facilitate repair after SCI. We show here that rat embryonic day 14 spinal cord-derived glial-restricted precursor cells (GRPs), which differentiate into both oligodendrocytes and astrocytes, formed normal-appearing central myelin around axons of cultured DRG neurons and had enhanced proliferation and survival in the presence of neurotrophin 3 (NT3) and brain-derived neurotrophin factor (BDNF).

PKCepsilon activation augments cardiac mitochondrial respiratory post-anoxic reserve--a putative mechanism in PKCepsilon cardioprotection.

Modest cardiac-overexpression of constitutively active PKCepsilon (aPKCepsilon) in transgenic mice evokes cardioprotection against ischemia. As aPKCepsilon interacts with mitochondrial respiratory-chain proteins we hypothesized that aPKCepsilon modulates respiration to induce cardioprotection. Using isolated cardiac mitochondria wild-type and aPKCepsilon mice display similar basal mitochondrial respiration, rate of ATP synthesis and adenosine nucleotide translocase (ANT) functional content.

Poly(epsilon-caprolactone) polyurethane and its shape-memory property.

A series of segmented poly(epsilon-caprolactone) polyurethanes (PCLUs) were prepared from poly(epsilon-caprolactone) (PCL) diol, 2,4-toluene diisocyanate and ethylene glycol. The molecular weight (M(n)) of PCL was 500-10,000, and the soft-to-hard molar ratio was 1:2 to 1:6. Their shape-memory behaviors were investigated as a function of PCL molecular weight, PCLU composition, and thermal/mechanical history.