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Proteomes, Volume 2, Issue 1 (March 2014), Pages 1-153

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Editorial

Jump to: Research, Review

Open AccessEditorial Acknowledgement to Reviewers of Proteomes in 2013
Proteomes 2014, 2(1), 84; doi:10.3390/proteomes2010084
Received: 27 February 2014 / Accepted: 27 February 2014 / Published: 27 February 2014
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Abstract The editors of Proteomes would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2013. [...] Full article

Research

Jump to: Editorial, Review

Open AccessArticle Is Five Percent Too Small? Analysis of the Overlaps between Disorder, Coiled Coil and Collagen Predictions in Complete Proteomes
Proteomes 2014, 2(1), 72-83; doi:10.3390/proteomes2010072
Received: 31 October 2013 / Revised: 24 January 2014 / Accepted: 27 January 2014 / Published: 7 February 2014
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Abstract
Identification of intrinsic disorder in proteins and proteomes has revealed important novel aspects of protein function and interactions. However, it has been pointed out that several oligomeric fibrillar protein motifs such as coiled coils and collagen triple helical segments can also identified [...] Read more.
Identification of intrinsic disorder in proteins and proteomes has revealed important novel aspects of protein function and interactions. However, it has been pointed out that several oligomeric fibrillar protein motifs such as coiled coils and collagen triple helical segments can also identified as intrinsically disordered. This feature has not yet been investigated in more detail at the proteome level. The present work aims at the identification and quantification of such overlaps in full proteomes to assess their significance in large-scale studies of protein disorder. It was found that the percentage of cross-predicted residues is around 5% in the human proteome and is generally near that value in other metazoan ones but shows remarkable variation in different organisms. In particular, smaller proteomes are increasingly prone to such cross-predictions, thus, especially the analysis of viral proteomes requires the use of specific prediction tools. Full article
(This article belongs to the Special Issue Feature Paper 2013)

Review

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Open AccessReview High-Throughput Analysis of Plasma Hybrid Markers for Early Detection of Cancers
Proteomes 2014, 2(1), 1-17; doi:10.3390/proteomes2010001
Received: 26 November 2013 / Revised: 17 December 2013 / Accepted: 8 January 2014 / Published: 13 January 2014
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Abstract
Biomarkers for the early detection of cancer in the general population have to perform with high sensitivity and specificity in order to prevent the costs associated with over-diagnosis. There are only a few current tissue or blood markers that are recommended for [...] Read more.
Biomarkers for the early detection of cancer in the general population have to perform with high sensitivity and specificity in order to prevent the costs associated with over-diagnosis. There are only a few current tissue or blood markers that are recommended for generalized cancer screening. Despite the recognition that combinations of multiple biomarkers will likely improve their utility, biomarker panels are usually limited to a single class of molecules. Tissues and body fluids including plasma and serum contain not only proteins, DNA and microRNAs that are differentially expressed in cancers but further cancer specific information might be gleaned by comparing different classes of biomolecules. For example, the level of a certain microRNA might be related to the level of a particular protein in a cancer specific manner. Proteins might have cancer-specific post-translational modifications (e.g., phosphorylation or glycosylation) or lead to the generation of autoantibodies. Most currently approved biomarkers are glycoproteins. Autoantibodies can be produced as a host’s early surveillance response to cancer-specific proteins in pre-symptomatic and pre-diagnostic stages of cancer. Thus, measurement of the level of a protein, the level of its glycosylation or phosphorylation and whether autoantibodies are produced to it can yield multi-dimensional information on each protein. We consider specific proteins that show consistent cancer-specific changes in two or three of these measurements to be “hybrid markers”. We hypothesize these markers will suffer less variation between different individuals since one component can act to “standardize” the other measurement. As a proof of principle, a 180 plasma sample set consisting of 120 cases (60 colon cancers and 60 adenomas) and 60 controls were analyzed using our high-density antibody array for changes in their protein, IgG-complex and sialyl-Lewis A (SLeA) modified proteins. At p < 0.05, expression changes in 1,070 proteins, 49 IgG-complexes (11 present in the protein list) and 488 Lewis X-modified proteins (57 on the protein list) were observed. The biomarkers significant on both lists are potential hybrid markers. Thus, plasma hybrid markers have the potential to create a new class of early detection markers of cancers. Full article
(This article belongs to the Special Issue Proteomic Cancer Biomarkers in Human Biofluids)
Figures

Open AccessReview Respiratory Proteomics Today: Are Technological Advances for the Identification of Biomarker Signatures Catching up with Their Promise? A Critical Review of the Literature in the Decade 2004–2013
Proteomes 2014, 2(1), 18-52; doi:10.3390/proteomes2010018
Received: 15 October 2013 / Revised: 8 January 2014 / Accepted: 10 January 2014 / Published: 22 January 2014
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Abstract
To improve the knowledge on a variety of severe disorders, research has moved from the analysis of individual proteins to the investigation of all proteins expressed by a tissue/organism. This global proteomic approach could prove very useful: (i) for investigating the biochemical [...] Read more.
To improve the knowledge on a variety of severe disorders, research has moved from the analysis of individual proteins to the investigation of all proteins expressed by a tissue/organism. This global proteomic approach could prove very useful: (i) for investigating the biochemical pathways involved in disease; (ii) for generating hypotheses; or (iii) as a tool for the identification of proteins differentially expressed in response to the disease state. Proteomics has not been used yet in the field of respiratory research as extensively as in other fields, only a few reproducible and clinically applicable molecular markers, which can assist in diagnosis, having been currently identified. The continuous advances in both instrumentation and methodology, which enable sensitive and quantitative proteomic analyses in much smaller amounts of biological material than before, will hopefully promote the identification of new candidate biomarkers in this area. The aim of this report is to critically review the application over the decade 2004–2013 of very sophisticated technologies to the study of respiratory disorders. The observed changes in protein expression profiles from tissues/fluids of patients affected by pulmonary disorders opens the route for the identification of novel pathological mediators of these disorders. Full article
(This article belongs to the Special Issue Feature Paper 2013)
Open AccessReview Proteomic Applications in the Study of Human Mesenchymal Stem Cells
Proteomes 2014, 2(1), 53-71; doi:10.3390/proteomes2010053
Received: 4 December 2013 / Revised: 15 January 2014 / Accepted: 26 January 2014 / Published: 7 February 2014
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Abstract
Mesenchymal stem cells (MSCs) are undifferentiated cells with an unlimited capacity for self-renewal and able to differentiate towards specific lineages under appropriate conditions. MSCs are, a priori, a good target for cell therapy and clinical trials as an alternative to embryonic [...] Read more.
Mesenchymal stem cells (MSCs) are undifferentiated cells with an unlimited capacity for self-renewal and able to differentiate towards specific lineages under appropriate conditions. MSCs are, a priori, a good target for cell therapy and clinical trials as an alternative to embryonic stem cells, avoiding ethical problems and the chance for malignant transformation in the host. However, regarding MSCs, several biological implications must be solved before their application in cell therapy, such as safe ex vivo expansion and manipulation to obtain an extensive cell quantity amplification number for use in the host without risk accumulation of genetic and epigenetic abnormalities. Cell surface markers for direct characterization of MSCs remain unknown, and the precise molecular mechanisms whereby growth factors stimulate their differentiation are still missing. In the last decade, quantitative proteomics has emerged as a promising set of techniques to address these questions, the answers to which will determine whether MSCs retain their potential for use in cell therapy. Proteomics provides tools to globally analyze cellular activity at the protein level. This proteomic profiling allows the elucidation of connections between broad cellular pathways and molecules that were previously impossible to determine using only traditional biochemical analysis. However; thus far, the results obtained must be orthogonally validated with other approaches. This review will focus on how these techniques have been applied in the evaluation of MSCs for their future applications in safe therapies. Full article
(This article belongs to the Special Issue Feature Paper 2013)
Open AccessReview Transcription Factor Functional Protein-Protein Interactions in Plant Defense Responses
Proteomes 2014, 2(1), 85-106; doi:10.3390/proteomes2010085
Received: 30 October 2013 / Revised: 21 February 2014 / Accepted: 21 February 2014 / Published: 4 March 2014
Cited by 11 | PDF Full-text (1548 KB) | HTML Full-text | XML Full-text
Abstract
Responses to biotic stress in plants lead to dramatic reprogramming of gene expression, favoring stress responses at the expense of normal cellular functions. Transcription factors are master regulators of gene expression at the transcriptional level, and controlling the activity of these factors [...] Read more.
Responses to biotic stress in plants lead to dramatic reprogramming of gene expression, favoring stress responses at the expense of normal cellular functions. Transcription factors are master regulators of gene expression at the transcriptional level, and controlling the activity of these factors alters the transcriptome of the plant, leading to metabolic and phenotypic changes in response to stress. The functional analysis of interactions between transcription factors and other proteins is very important for elucidating the role of these transcriptional regulators in different signaling cascades. In this review, we present an overview of protein-protein interactions for the six major families of transcription factors involved in plant defense: basic leucine zipper containing domain proteins (bZIP), amino-acid sequence WRKYGQK (WRKY), myelocytomatosis related proteins (MYC), myeloblastosis related proteins (MYB), APETALA2/ ETHYLENE-RESPONSIVE ELEMENT BINDING FACTORS (AP2/EREBP) and no apical meristem (NAM), Arabidopsis transcription activation factor (ATAF), and cup-shaped cotyledon (CUC) (NAC). We describe the interaction partners of these transcription factors as molecular responses during pathogen attack and the key components of signal transduction pathways that take place during plant defense responses. These interactions determine the activation or repression of response pathways and are crucial to understanding the regulatory networks that modulate plant defense responses. Full article
(This article belongs to the Special Issue Plant Proteomics) Print Edition available
Open AccessReview Potentiality of Soybean Proteomics in Untying the Mechanism of Flood and Drought Stress Tolerance
Proteomes 2014, 2(1), 107-127; doi:10.3390/proteomes2010107
Received: 17 November 2013 / Revised: 26 February 2014 / Accepted: 27 February 2014 / Published: 7 March 2014
Cited by 8 | PDF Full-text (808 KB) | HTML Full-text | XML Full-text
Abstract
Dissecting molecular pathways at protein level is essential for comprehensive understanding of plant stress response mechanism. Like other legume crops, soybean, the world’s most widely grown seed legume and an inexpensive source of protein and vegetable oil, is also extremely sensitive to [...] Read more.
Dissecting molecular pathways at protein level is essential for comprehensive understanding of plant stress response mechanism. Like other legume crops, soybean, the world’s most widely grown seed legume and an inexpensive source of protein and vegetable oil, is also extremely sensitive to abiotic stressors including flood and drought. Irrespective of the kind and severity of the water stress, soybean exhibits a tight control over the carbon metabolism to meet the cells required energy demand for alleviating stress effects. The present review summarizes the major proteomic findings related to changes in soybean proteomes in response to flood and drought stresses to get a clear insight into the complex mechanisms of stress tolerance. Furthermore, advantages and disadvantages of different protein extraction protocols and challenges and future prospects of soybean proteome study are discussed in detail to comprehend the underlying mechanism of water stress acclimation. Full article
(This article belongs to the Special Issue Plant Proteomics) Print Edition available
Open AccessReview Dynamic New World: Refining Our View of Protein Structure, Function and Evolution
Proteomes 2014, 2(1), 128-153; doi:10.3390/proteomes2010128
Received: 17 December 2013 / Revised: 12 February 2014 / Accepted: 20 February 2014 / Published: 7 March 2014
Cited by 1 | PDF Full-text (665 KB) | HTML Full-text | XML Full-text
Abstract
Proteins are crucial to the functioning of all lifeforms. Traditional understanding posits that a single protein occupies a single structure (“fold”), which performs a single function. This view is radically challenged with the recognition that high structural dynamism—the capacity to be extra [...] Read more.
Proteins are crucial to the functioning of all lifeforms. Traditional understanding posits that a single protein occupies a single structure (“fold”), which performs a single function. This view is radically challenged with the recognition that high structural dynamism—the capacity to be extra “floppy”—is more prevalent in functional proteins than previously assumed. As reviewed here, this dynamic take on proteins affects our understanding of protein “structure”, function, and evolution, and even gives us a glimpse into protein origination. Specifically, this review will discuss historical developments concerning protein structure, and important new relationships between dynamism and aspects of protein sequence, structure, binding modes, binding promiscuity, evolvability, and origination. Along the way, suggestions will be provided for how key parts of textbook definitions—that so far have excluded membership to intrinsically disordered proteins (IDPs)—could be modified to accommodate our more dynamic understanding of proteins. Full article
(This article belongs to the Special Issue Feature Paper 2013)

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