caenorhabditis elegans proteomics: Topics by WorldWideScience.org

P granules are non-membrane-bound organelles found in the germ-line cytoplasm throughout Caenorhabditis elegans development. Like their “germ granule” counterparts in...Full Text Available

2009-12-01

Global 'worming'

Lifespan extension induced by AMPK and calcineurin is mediated by CRTC-1 and CREB

A report on the 16th International Caenorhabditis elegans Meeting, Los Angeles, USA, 27 June-1 July 2007.

2007-01-01

A Mitochondrial Superoxide Signal Triggers Increased Longevity in Caenorhabditis elegans

Activating AMPK or inactivating calcineurin slows ageing in Caenorhabditis elegans^1,2...Full Text Available

2011-02-17

Zebrafish TRPA1 Channels are Required for Chemosensation but not for Thermosensation or Mechanosensory Hair Cell Function

The nuo-6 and isp-1 genes of C. elegans encode, respectively, subunits of complex I and III of the mitochondrial respiratory chain. Partial loss-of-function...Full Text Available

2010-12-01

Variable Pathogenicity Determines Individual Lifespan in Caenorhabditis elegans

Transient receptor potential (TRP) ion channels have been implicated in detecting chemical, thermal and mechanical stimuli in organisms ranging from mammals to Caenorhabditis elegans....Full Text Available

2008-10-01

The Dystrophin Complex Controls BK Channel Localization and Muscle Activity in Caenorhabditis elegans

A common property of aging in all animals is that chronologically and genetically identical individuals age at different rates. To unveil mechanisms that influence aging variability, we identified markers...Full Text Available

2011-04-01

The Caenorhabditis elegans Elongator Complex Regulates Neuronal ?-tubulin Acetylation

Genetic defects in the dystrophin-associated protein complex (DAPC) are responsible for a variety of pathological conditions including muscular dystrophy, cardiomyopathy, and vasospasm. Conserved DAPC...Full Text Available

2009-12-01

Stressed-Induced TMEM135 Protein Is Part of a Conserved Genetic Network Involved in Fat Storage and Longevity Regulation in Caenorhabditis elegans

Although acetylated α-tubulin is known to be a marker of stable microtubules in neurons, precise factors that regulate α-tubulin acetylation are, to date, largely unknown. Therefore,...Full Text Available

2010-01-01

Regulation of DAF-16-mediated Innate Immunity in Caenorhabditis elegans*

Disorders of mitochondrial fat metabolism lead to sudden death in infants and children. Although survival is possible, the underlying molecular mechanisms which enable this outcome have not yet been...Full Text Available

Purpose and regulation of stem cells: a systems-biology view from the Caenorhabditis elegans germ line

Activation of the innate immune system results in a rapid microbicidal response against microorganisms, which needs to be fine-tuned because uncontrolled immune responses can lead to infection and cancer,...Full Text Available

2009-12-18

PDP-1 Links the TGF-? and IIS Pathways to Regulate Longevity, Development, and Metabolism

Stem cells are expected to play a key role in the development and maintenance of organisms, and hold great therapeutic promises. However, a number of questions must be answered to achieve an...Full Text Available

2009-01-01

Membrane Efflux and Influx Modulate both Multidrug Resistance and Virulence of Klebsiella pneumoniae in a Caenorhabditis elegans Model?

The insulin/IGF-1 signaling (IIS) pathway is a conserved regulator of longevity, development, and metabolism. In Caenorhabditis elegans IIS involves activation of DAF-2 (insulin/IGF-1...Full Text Available

2011-04-01

A Decline in p38 MAPK Signaling Underlies Immunosenescence in Caenorhabditis elegans

Cross-resistance to cefoxitin (FOX), chloramphenicol (CMP), and quinolones (nalidixic acid [NAL]) related to a putative efflux system overexpression has recently been reported for Klebsiella...Full Text Available

2010-10-01

Disruption of the ATP-binding Cassette B7 (ABTM-1/ABCB7) Induces Oxidative Stress and Premature Cell Death in Caenorhabditis elegans*

The decline in immune function with aging, known as immunosenescence, has been implicated in evolutionarily diverse species, but the underlying molecular mechanisms are not understood. During aging...Full Text Available

2011-05-01

A Role for Set1/MLL-Related Components in Epigenetic Regulation of the Caenorhabditis elegans Germ Line

X-linked sideroblastic anemia with ataxia (XLSA/A) is a rare inherited disorder characterized by mild anemia and ataxia. XLSA/A is caused by mutations in the ABCB7 gene, which encodes...Full Text Available

2011-06-17

Proteome analysis of castor bean seeds

The methylation of lysine 4 of Histone H3 (H3K4me) is an important component of epigenetic regulation. H3K4 methylation is a consequence of transcriptional activity, but also has been shown to contribute...Full Text Available

2011-03-01

C. elegans as a model for stem cell biology

No abstract prepared.

2008-07-01

SIP goes Proteomics - Elucidation of structure and function of microbial communities

We review the application of C. elegans as a model system to understand key aspects of stem cell biology. The only bona fide stem cells in C. elegans...Full Text Available

2010-05-01

Proteomics of Severe Traumatic Brain Injury: A Feasibility Study

Not Available

2009-06-01

1 2 3 4 5

Calcineurin may regulate multiple endocytic processes in C. elegans

Brain Injuries, Traumatic

2009-02-20

Mass spectrometry-based analysis of therapy-related changes in serum proteome patterns of patients with early-stage breast cancer

Full Text Available

2011-02-01

Proteomic strategies in multiple sclerosis and its animal models

BackgroundThe proteomics approach termed proteome pattern analysis has been shown previously to have potential in the detection and classification of breast cancer. Here we aimed...Full Text Available

Perinuclear P granules are the principal sites of mRNA export in adult C. elegans germ cells

The early and precise diagnosis, the prognosis, and the clinical management of multiple sclerosis, remain a considerable challenge. In recent years, the development of novel and powerful proteomic...Full Text Available

2007-10-16

Proteomic Functional Characterization of Bovine Stromal Vascular Cells from Omental, Subcutaneous and Intramuscular Adipose Depots

Germline-specific granules of unknown function are found in a wide variety of organisms, including C. elegans, where they are called P granules. P granules are cytoplasmic bodies...Full Text Available

2010-04-15

Protein profile changes in platelet concentrates according to storage and leukoreduction- analysis using proteomics technology

Full Text Available

2011-01-01

Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics

Full Text Available

2008-02-01

Simultaneous recognition and segmentation of cells: application in C.elegans

We review recent development in separations and mass spectrometric instrumentation for sensitive and high-throughput proteomic analyses. These efforts have been primarily focused on the development of high-efficiency (separation peak capacity of ~103) nanoscale liquid chromatography (nanoLC; e.g., flow rates extending down to ~20 nL/min at optimal separation linear velocities through narrow packed capillaries) in combination with advanced mass spectrometry (MS), including high sensitivity and high resolution Fourier transform ion cyclotron resonance (FTICR) MS. This technology enables MS analysis of low nanogram-level proteomic samples (i.e., nanoscale proteomics) with individual protein identification sensitivity at the low zeptomole-level. The resultant protein measurement dynamic range can reach 106 for nanogram-sized proteomic samples, while more abundant proteins can be detected from complex ...

2005-06-01

Use of DNA ladders for reproducible protein fractionation by SDS-PAGE for quantitative proteomics

Motivation: Automatic recognition of cell identities is critical for quantitative measurement, targeting and manipulation of cells of model animals at single-cell resolution. It has been...Full Text Available

2011-10-15

Proteomic Analysis of Seed Dormancy in Arabidopsis1[W

In proteomics, one-dimensional (1D) SDS-PAGE is widely used for protein fractionation prior to mass spectrometric analysis to enhance dynamic range of analysis and to improve identification...Full Text Available

2008-02-01

Proteome-wide Anti-HCV and Anti-HIV Antibody Profiling for Predicting and Monitoring Response to HCV Treatment in HIV Co-infected Patients

The mechanisms controlling seed dormancy in Arabidopsis (Arabidopsis thaliana) have been characterized by proteomics using the dormant (D) accession Cvi originating from the Cape Verde...Full Text Available

2006-12-01

Proteome of human colon cancer stem cells: A comparative analysis

We quantified antibody responses to the HCV proteome that are associated with sustained virologic response (SVR) in HIV/HCV co-infected patients treated with pegylated interferon and ribavirin....Full Text Available

2010-09-15

Molecular Architecture of the Centriole Proteome: The Conserved WD40 Domain Protein POC1 Is Required for Centriole Duplication and Length Control

AIM: To isolate and identify the biological characteristics of human colon cancer stem cells (SW1116 cells) and further study their proteome.METHODS: SW1116 cells were isolated and cultured with...Full Text Available

2011-03-14

Investigation of Early Protein Changes in the Urinary Bladder Following Partial Bladder Outlet Obstruction by Proteomic Approach

Centrioles are intriguing cylindrical organelles composed of triplet microtubules. Proteomic data suggest that a large number of proteins besides tubulin are necessary for the formation and maintenance...Full Text Available

2009-02-15

A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics

We investigated the pathophysiological mechanism by proteomic approach as a possible tool to detect the marker proteins to develop lower urinary tract symptoms following bladder outlet obstruction (BOO)....Full Text Available

2005-12-01

A Proteomic Analysis of Leaf Responses to Enhanced Ultraviolet-B Radiation in Two Rice (Oryza sativa L.) Cultivars Differing in UV Sensitivity

BackgroundIn current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences...Full Text Available

Natural variation in life history and aging phenotypes is associated with mitochondrial DNA deletion frequency in Caenorhabditis briggsae

Full Text Available

Review of recent proteomic applications in aquatic toxicology

BackgroundMutations that impair mitochondrial functioning are associated with a variety of metabolic and age-related disorders. A barrier to rigorous tests of the role of mitochondrial...Full Text Available

British Library Electronic Table of Contents (United Kingdom)

Abstract Over the last decade, the environmental sciences have witnessed an incredible movement towards the utilization of high-throughput molecular tools that are capable of detecting simultaneous changes of hundreds, and even thousands, of molecules and molecular components after exposure of organisms to different environmental stressors. These techniques have received a great deal of attention because they not only offer the potential to unravel novel mechanisms of physiological and toxic action but are also amenable to the discovery of biomarkers of exposure and effects. In this article, we review the state of knowledge of one of these tools in ecotoxicological research: proteomics. We summarize the state of proteomics research in fish, and follow with studies conducted with aquatic in...

2011-01-01

Systems medicine: the future of medical genomics and healthcare

Proteomic Analysis of Global Changes in Protein Expression During Exposure of Gamma Radiation in Bacillus sp. HKG 112 Isolated from Saline Soil

High-throughput technologies for DNA sequencing and for analyses of transcriptomes, proteomes and metabolomes have provided the foundations for deciphering the structure, variation and function of the...Full Text Available

1 2 3 4 5

HDL in humans with cardiovascular disease exhibits a proteomic signature

Full Text Available

Computational biology for ageing

BackgroundAlterations in protein composition and oxidative damage of high-density lipoprotein (HDL) have been proposed to impair the cardioprotective properties of...Full Text Available

2010-07-04

The Cell Non-Autonomous Nature of Electron Transport Chain-Mediated Longevity

High-throughput genomic and proteomic technologies have generated a wealth of publicly available data on ageing. Easy access to these data, and their computational analysis, is of great importance in...Full Text Available

2011-01-12

Regulation of life span by mitochondrial respiration: the HIF-1 and ROS connection

SummaryThe life span of C. elegans can be increased via reduced function of the mitochondria; however, the extent to which mitochondrial alteration in a single,...Full Text Available

2011-01-07

Modulation of lipid biosynthesis contributes to stress resistance and longevity of C. elegans mutants

A mild reduction in mitochondrial respiration extends the life span of many species, including C. elegans. We recently showed that hypoxia-inducible factor 1 (HIF-1) is required for...Full Text Available

Gene expression profiling of oxidative stress response of C. elegans aging defective AMPK mutants using massively parallel transcriptome sequencing

Many lifespan-modulating genes are involved in either generation of oxidative substrates and end-products, or their detoxification and removal. Among such metabolites, only lipoperoxides have the ability...Full Text Available

Biochemical analysis of PIFTC3, the Trypanosoma brucei ortholog of nematode DYF-13, reveals interactions with established and putative intraflagellar transport components

BackgroundA strong association between stress resistance and longevity in multicellular organisms has been established as many mutations that extend lifespan also show increased...Full Text Available

Absence of Ataxin-3 Leads to Enhanced Stress Response in C. elegans

DYF-13, originally identified in C. elegans within a collection of dye-filling chemosensory mutants, is one of several proteins that have been classified as putatively involved...Full Text Available

2010-10-01

A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical binding

Ataxin-3, the protein involved in Machado-Joseph disease, is able to bind ubiquitylated substrates and act as a deubiquitylating enzyme in vitro, and it has been involved in the modulation of protein...Full Text Available

High-throughput proteomics of breast carcinoma cells: a focus on FTICR-MS

BackgroundProteins may evolve through the recruitment and modification of discrete domains, and in many cases, protein action can be dissected at the domain level. PDZ domains are...Full Text Available

A systematic RNAi screen reveals involvement of endocytic pathway in neuronal dysfunction in a-synuclein transgenic C. elegans

Discovery of better biomarkers for diagnosis, prognosis, and therapy-response prediction is the most critical task of a scientific quest aimed at developing newly designed, tailor-made therapies for patients with cancer. Consequently, a proteome wide analysis, in addition to genomic studies, is an absolute requirement for a complete functional understanding of tumor biology. Ultra-sensitive, high-performance Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) currently holds an important role in fulfilling the demands of biomarker discovery. In this review, we describe the applicability of FTICR MS for breast cancer proteomics, particularly for the analysis of complex protein mixtures obtained from a limited number of cells typically available from clinical specimens.

2008-06-05

British Library Electronic Table of Contents (United Kingdom)

Mutations or multiplications in a-synuclein gene cause familial forms of Parkinson disease or dementia with Lewy bodies (LB), and the deposition of wild-type a-synuclein as LB occurs as a hallmark lesion of these disorders, collectively referred to as synucleinopathies, implicating a-synuclein in the pathogenesis of synucleinopathy. To identify modifier genes of a-synuclein-induced neurotoxicity, we conducted an RNAi screen in transgenic C. elegans (Tg worms) that overexpress human a-synuclein in a pan-neuronal manner. To enhance the RNAi effect in neurons, we crossed a-synuclein Tg worms with an RNAi-enhanced mutant eri-1 strain. We tested RNAi of 1673 genes related to nervous system or synaptic functions, and identified 10 genes that, upon knockdown, caused severe growth/motor abnormalit...

2008-01-01

Straightforward and de Novo Peptide Sequencing by MALDI-MS/MS Using a Lys-N Metalloendopeptidase*S?

Selective Enrichment of Azide-Containing Peptides from Complex Mixtures

In this work, we explore the potential of the metalloendopeptidase Lys-N for MALDI-MS/MS proteomics applications. Initially we digested a HEK293 cellular lysate with Lys-N and, for comparison, in parallel...Full Text Available

2009-04-01

Seasonal proteomic changes reveal molecular adaptations to preserve and replenish liver proteins during ground squirrel hibernation

A general method is described to sequester peptides containing azides from complex peptide mixtures, aimed at facilitating mass spectrometric analysis to study different aspects of proteome...Full Text Available

2009-07-01

Proteomic patterns analysis with multivariate calculations as a promising tool for prompt differentiation of early stage lung tissue with cancer and unchanged tissue material

Hibernators are unique among mammals in their ability to survive extended periods of time with core body temperatures near freezing and with dramatically reduced heart, respiratory, and metabolic rates...Full Text Available

2010-02-01

Proteomic approach with LCMS-IT-TOF identified an increase of Rab33B after transient focal cerebral ischemia in mice

BackgroundLung cancer diagnosis in tissue material with commonly used histological techniques is sometimes inconvenient and in a number of cases leads to ambiguous conclusions. Frequently...Full Text Available

Predicting Protein Post-translational Modifications Using Meta-analysis of Proteome Scale Data Sets*S?

BackgroundSeveral proteins are known to be markedly expressed in the brain during cerebral ischemia; however, the changes in protein profiles within the ischemic brain after an ischemic...Full Text Available

PRISM: A Data Management System for High-Throughput Proteomics

Protein post-translational modifications are an important biological regulatory mechanism, and the rate of their discovery using high throughput techniques is rapidly increasingly. To make use of this...Full Text Available

2009-02-01

MudPIT Analysis: Application to Human Heart Tissue

Advanced proteomic research efforts involving areas such as systems biology or biomarker discovery are enabled by the use of high level informatics tools that allow the effective analysis of large quantities of differing types of data originating from various studies. Performing such analyses on a large scale is not feasible without a computational platform that performs data processing and management tasks. Such a platform must be able to provide high-throughput operation while having sufficient flexibility to accommodate evolving data analysis tools and methodologies. The Proteomics Research Information Storage and Management System (PRISM) provides a platform that serves the needs of the accurate mass and time tag approach developed at PNNL. PRISM incorporates a diverse set of analysis tools and allows a wide range of operations to be incorporated by using a state machine that is accessible to independent, distributed computational nodes. ...

2006-03-01

Large-scale Analysis of Thermo-stable, Mammalian Proteins Provides Insights into the Intrinsically Disordered Proteome

Although two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) has been used as the standard proteomic approach for separating proteins in a complex mixture, this technique has many drawbacks....Full Text Available

2009-01-01

1 2 3 4 5

Individual Mycobacterium tuberculosis universal stress protein homologues are dispensable in vitro

Intrinsically disordered proteins are predicted to be highly abundant and play broad biological roles in eukaryotic cells. In particular, by virtue of their structural malleability and propensity...Full Text Available

2009-01-01

Identification of Host Proteins Associated with Retroviral Vector Particles by Proteomic Analysis of Highly Purified Vector Preparations?

SummaryMycobacterium tuberculosis has 10 universal stress proteins, whose function is unknown. However, proteomic and transcriptomic analyses have shown that a number...Full Text Available

2010-07-01

Identification of Cardiac Myosin-binding Protein C as a Candidate Biomarker of Myocardial Infarction by Proteomics Analysis*

The Moloney murine leukemia virus (MMLV) belongs to the Retroviridae family of enveloped viruses, which is known to acquire minute amounts of host cellular proteins both on the surface...Full Text Available

2008-02-01

Global Analysis of the General Stress Response of Bacillus subtilis

Acute myocardial infarction (AMI) is a common cause of death for which effective treatments are available provided that diagnosis is rapid. The current diagnostic gold standards are circulating cardiac...Full Text Available

2009-12-01

Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration

Gene arrays containing all currently known open reading frames of Bacillus subtilis were used to examine the general stress response of Bacillus. By proteomics, transcriptional...Full Text Available

2001-10-01

Conserved Alternative Splicing and Expression Patterns of Arthropod N-Cadherin

BackgroundThere is an ever increasing rate of data made available on genetic variation, transcriptomes and proteomes. Similarly, a growing variety of bioinformatic programs are becoming...Full Text Available

Analysis on the alterations of lens proteins by Vitex negundo in selenite cataract models

Metazoan development requires complex mechanisms to generate cells with diverse function. Alternative splicing of pre-mRNA not only expands proteomic diversity but also provides a means to regulate...Full Text Available

2009-04-01

A proteomic study of cMyc improvement of CHO culture

PurposeCataract is the leading cause of blindness and is associated with oxidative damage and protein modification in the lens. In the present study, we have employed proteomic and...Full Text Available

A genomic and proteomic investigation of the impact of preimplantation factor on human decidual cells

BackgroundThe biopharmaceutical industry requires cell lines to have an optimal proliferation rate and a high integral viable cell number resulting in a maximum volumetric recombinant...Full Text Available

Proteomic analysis of the shistosome tegument and its surface membranes

OBJECTIVEPreimplantation factor (PIF) is a novel, 15 amino acid peptide, secreted by viable embryos. This study aims to elucidate PIF’s effects in human endometrial...Full Text Available

2010-05-01

Scientific Electronic Library Online (English)

Abstract in english The tegument surface of the adult schistosome, bounded by a normal plasma membrane overlain by a secreted membranocalyx, holds the key to understanding how schistosomes evade host immune responses. Recent advances in mass spectrometry (MS), and the sequencing of the Schistosoma mansoni transcriptome/genome, have facilitated schistosome proteomics. We detached the tegument from the worm body and enriched its surface membranes by differential extraction, before subjecting t (more) he preparation to liquid chromatography-based proteomics to identify its constituents. The most exposed proteins on live worms were labelled with impearmeant biotinylation reagents, and we also developed methods to isolate the membranocalyx for analysis. We identified transporters for sugars, amino acids, inorganic ions and water, which confirm the importance of the tegument plasma membrane in nutrient acquisition and solute balance. Enzymes, ...

2006-10-01

Proteomic Analysis of Proteins Secreted by HepG2 Cells Treated with Butyl Benzyl Phthalate

British Library Electronic Table of Contents (United Kingdom)

Proteomic changes in proteins secreted by human hepatocellular carcinomas (HepG2) cells exposed to butyl benzyl phthalate (BBP) were evaluated. HepG2 cells were treated with three different concentrations of BBP (0, 10, or 25 ?M) for 24 or 48 h. Following incubation, the cells were subjected to proteomic analysis using two different pI ranges (4-7 and 6-9) and large-size two-dimensional gel electrophoresis. Results showed resolution of a total of 2776 protein spots. Of these, 29, including 19 upregulated and 10 downregulated proteins, were identified by electrospray ionization-mass spectrometry-mass spectrometry (ESI-MS/MS). Among these, the identities of cystatin C, Rho guanine nucleotide dissociation inhibitor, gelsolin, DEK protein, Raf kinase inhibitory protein, triose phosphate ...

2010-01-01

Proteomic analysis of sericin in Bombyx mori cocoons

British Library Electronic Table of Contents (United Kingdom)

Cocoon sericin plays an important role in the reeling of silk and serves as a valuable biomaterial in the field of biomedicine, skincare, and food industries; however, knowledge about cocoon sericin proteins has been limited. For a comprehensive study on sericin, cocoons of eight varieties of silkworm of different geographic origin and with varied cocoon color were analyzed utilizing proteomics and bioinformatics approaches. The electrophoresis pattern demonstrated some common protein bands for all silkworm varieties and distinctive protein bands for some of those examined in the present study. The Ser2 protein, a new Ser3 protein, and four other novel sericin proteins were identified in cocoons for the first time. Products of both Ser1 and Ser3 genes appear to be ubiquitous in the cocoon ...

2011-01-01

Proteomic analysis of apoptosis induction in human lung cancer cells by recombinant MVL

British Library Electronic Table of Contents (United Kingdom)

Lung cancer is still difficult to treat by current chemotherapeutic procedures. We recently found that MVL, an anti-HIV lectin from blue-green algae Microcystis viridis, also has antitumor activity. The objective of this study was to investigate apoptosis-inducing activity of recombinant MVL (R-MVL) and proteomic changes in A549 cells, and to identify the molecular pathways responsible for the anti-cancer action of R-MVL. We found that R-MVL induces A549 cells apoptosis in a dose-dependent manner by using MTT assay, fluorescent microscope (FM) and flow cytometry (FCM), and the IC50 was calculated to be 24.12??g/ml. Subsequently, 7 altered proteins in R-MVL-treated A549 cells were identified, including upregulated aldehyde dehydrogenase 1 and ?-actin, and five downregulated proteins: heat s...

2011-01-01

Preliminary crystallographic analysis of a possible transcription factor encoded by the mimivirus L544 gene

British Library Electronic Table of Contents (United Kingdom)

Mimivirus is the prototype of a new family (the Mimiviridae) of nucleocytoplasmic large DNA viruses (NCLDVs), which already include the Poxviridae, Iridoviridae, Phycodnaviridae and Asfarviridae. Mimivirus specifically replicates in cells from the genus Acanthamoeba. Proteomic analysis of purified mimivirus particles revealed the presence of many subunits of the DNA-directed RNA polymerase II complex. A fully functional pre-transcriptional complex appears to be loaded in the virions, allowing mimivirus to initiate transcription within the host cytoplasm immediately upon infection independently of the host nuclear apparatus. To fully understand this process, a systematic study of mimivirus proteins that are predicted (by bioinformatics) or suspected (by proteomic analysis) to be involved in...

2011-01-01

Gel-based proteomics of liver cancer progression in rat.

Concentration and Preservation of Very Low Abundance Biomarkers in Urine, such as Human Growth Hormone (hGH), by Cibacron Blue F3G-A Loaded Hydrogel Particles

A significant challenge in proteomics biomarker research is to identify the changes that are of highest diagnostic interest, among the many unspecific aberrations associated with disease burden and inflammation. In the present study liver tissue specimens (n=18) from six experimental stages were collected from the resistant hepatocyte (RH) rat model of liver cancer and analyzed by 2D DIGE. The study included triplicates of regenerating liver, control "sham-operated" liver, three distinct premalignant stages and hepatomas. Out of 81 identified proteins two-thirds were differentially abundant in rat hepatomas compared to control rat liver and, secondly, the majority of proteins were also changed in precursor stages. This underscores the importance of adequate control samples in explorative cancer biomarker research. We confirm several proteomic changes previously identified in human hepatocellular carcinoma (HCC) and we identify novel candidate ...

2011-06-06

Data Merging for Integrated Microarray and Proteomic Analysis

Urine is a potential source of diagnostic biomarkers for detection of diseases, and is a very attractive means of non-invasive biospecimen collection. Nonetheless, proteomic measurement in urine...Full Text Available

2008-12-01

Omic Approaches in Environmental Issues

The functioning of even a simple system is much more complicated than the sum of its genes, proteins and metabolites. A premise of systems biology is that molecular profiling will lead to the discovery and characterization of important disease pathways. However, as multiple levels of effector pathway regulation appear to be the norm rather than the exception, a significant challenge presented by high-throughput genomics and proteomics technologies is to extract the biological implications of complex data. Thus, integration of heterogeneous types of data generated from diverse global technology platforms represents the first challenge in developing the necessary foundational databases needed for predictive modeling of cell and tissue responses. Given the apparent difficulty in defining the correspondence between gene expression and protein abundance measured in several systems to date, how do we make sense of these data and design the next experiment? In this ...

2006-05-10

British Library Electronic Table of Contents (United Kingdom)

Biomonitoring requires the application of batteries of different biomarkers, as environmental contaminants induce multiple responses in organisms that are not necessarily correlated. Omic technologies were proposed as an alternative to conventional biomarkers since these techniques quantitatively monitor many biological molecules in a high-throughput manner and thus provide a general appraisal of biological responses altered by exposure to contaminants. As the studies using omic technologies increase, it is becoming clear that any single omic approach may not be sufficient to characterize the complexity of ecosystems. This work aims to provide a preliminary working scheme for the use of combined transcriptomic and proteomic methodologies in environmental biomonitoring. There are difficulti...

2011-01-01

Study of Nitrate Stress in Desulfovibrio vulgaris Hildenborough Using iTRAQ Proteomics

Translational bioinformatics and healthcare informatics: computational and ethical challenges.

The response of Desulfovibrio vulgaris Hildenborough (DvH),a sulphate-reducing bacterium, to nitrate stress was examined usingquantitative proteomic analysis. DvH was stressed with 105 m M sodiumnitrate(NaNO3), a level that caused a 50 percent inhibition in growth.The protein profile of stressed cells was compared with that of cellsgrown in the absence of nitrate using the iTRAQ peptide labellingstrategy and tandem liquid chromatography separation coupled with massspectrometry (quadrupoletime-of-flight) detection. A total of 737 uniqueproteins were identified by two or more peptides, representing 22 percentof the total DvH proteome and spanning every functional category. Theresults indicate that this was a mild stress, as proteins involved incentral metabolism and the sulphate reduction pathway were unperturbed.Proteins involved in the nitrate reduction pathway increased. Increasesseen in transport systems for proline, glycine^ ...

2006-10-12

1 2 3 4 5

The discovery and development of proteomic safety biomarkers for the detection of drug-induced liver toxicity

Exponentially growing biological and bioinformatics data sets present a challenge and an opportunity for researchers to contribute to the understanding of the genetic basis of phenotypes. Due to breakthroughs in microarray technology, it is possible to simultaneously monitor the expressions of thousands of genes, and it is imperative that researchers have access to the clinical data to understand the genetics and proteomics of the diseased tissue. This technology could be a landmark in personalized medicine, which will provide storage for clinical and genetic data in electronic health records (EHRs). In this paper, we explore the computational and ethical challenges that emanate from the intersection of bioinformatics and healthcare informatics research. We describe the current situation of the EHR and its capabilities to store clinical and genetic data and then discuss the Genetic Information Nondiscrimination Act. Finally, we posit that the synergy obtained from ...

2009-09-16

British Library Electronic Table of Contents (United Kingdom)

Biomarkers are biometric measurements that provide critical quantitative information about the biological condition of the animal or individual being tested. In drug safety studies, established toxicity biomarkers are used along with other conventional study data to determine dose-limiting organ toxicity, and to define species sensitivity for new chemical entities intended for possible use as human medicines. A continuing goal of drug safety scientists in the pharmaceutical industry is to discover and develop better trans-species biomarkers that can be used to determine target organ toxicities for preclinical species in short-term studies at dose levels that are some multiple of the intended human dose and again later in full development for monitoring clinical trials at lower therapeutic ...

2010-01-01

Pigpen, a nuclear coiled body component protein, is involved in angiogenesis

British Library Electronic Table of Contents (United Kingdom)

We previously reported that puromycin-insensitive leucyl-specific aminopeptidase (PILSAP) is required for vascular endothelial growth factor (VEGF)- and basic fibroblast growth factor (bFGF)-induced angiogenesis and for endothelial differentiation from embryonic stem (ES) cells via the aminopeptidase activity of PILSAP. In this study, we searched for molecules that function during angiogenesis with PILSAP. We performed proteome analysis of nuclear extracts from embryoid bodies (EBs) made from ES cells transfected with mutant PILSAP lacking aminopeptidase activity and mock EBs. We identified pigpen, a 67-kDa nuclear coiled body component protein. Immunoprecipitation and western blotting demonstrated the binding of PILSAP and pigpen in endothelial cells (ECs), and this interaction was enhanc...

2010-01-01

Mapping Equivalence for Symbolic Sequences: Theory and Applications

CERN Document Server

Processing of symbolic sequences represented by mapping of symbolic data into numerical signals is commonly used in various applications. It is a particularly popular approach in genomic and proteomic sequence analysis. Numerous mappings of symbolic sequences have been proposed for various applications. It is unclear however whether the processing of symbolic data provides an artifact of the numerical mapping or is an inherent property of the symbolic data. This issue has been long ignored in the engineering and scientific literature. It is possible that many of the results obtained in symbolic signal processing could be a byproduct of the mapping and might not shed any light on the underlying properties embedded in the data. Moreover, in many applications, conflicting conclusions may arise due to the choice of the mapping used for numerical representation of symbolic data. In this paper, we present a novel framework for the analysis of the equivalence of the ...

2009-01-01

MGV: a generic graph viewer for comparative omics data

British Library Electronic Table of Contents (United Kingdom)

Motivation: High-throughput transcriptomics, proteomics and metabolomics methods have revolutionized our knowledge of biological systems. To gain knowledge from comparative omics studies, strong data integration and visualization features are required. Knowledge gained from these studies is often available in the form of graphs, and their visualization is especially useful in a wide range of systems biology topics, including pathway analysis, interaction networks or gene models. Especially, it is necessary to compare biological models with measured data. This allows the identification of new models and new insights into existing ones. Results: We present MGV, a versatile generic graph viewer for multiomics data. MGV is integrated into Mayday (Battke et al., 2010). It extends Maydays visual...

2011-01-01

Identification of prostate cancer antigens by automated high-throughput filter immunoscreening

British Library Electronic Table of Contents (United Kingdom)

There is a need for earlier and more accurate cancer diagnostics as well as new targets for cancer immunotherapy. To this end, it is important to identify sets of tumour antigens specific for different cancer forms. Several methods that identify potential tumour antigens in an arrayed and high-throughput format have been developed during the last years of SEREX (serological identification of antigens by recombinant expression cloning) related research. Such techniques may hold the potential to describe the complete immunogenic part of the cancer proteome, also called the cancer immunoproteome.We have developed a powerful platform for automated serological high-throughput filter screening of tumour cDNA libraries. The screening format of this method is 18,000 single cDNAs clones, which is s...

2008-01-01

Proving Stabilization of Biological Systems

Proteomic Profiling of Mesenchymal Stem Cell Responses to Mechanical Strain and TGF-B1

We describe an efficient procedure for proving stabilization of biological systems modeled as qualitative networks or genetic regulatory networks. For scalability, our procedure uses modular proof techniques, where state-space exploration is applied only locally to small pieces of the system rather than the entire system as a whole. Our procedure exploits the observation that, in practice, the form of modular proofs can be restricted to a very limited set. For completeness, our technique falls back on a non-compositional counterexample search. Using our new procedure, we have solved a number of challenging published examples, including: a 3-D model of the mammalian epidermis; a model of metabolic networks operating in type-2 diabetes; a model of fate determination of vulval precursor cells in the C. elegans worm; and a model of pair-rule regulation during segmentation in the Drosophila embryo. Our results show many orders of magnitude speedup in cases where ...

2011-01-01

Systems Biology Approach in Chlamydomonas Reveals Connections between Copper Nutrition and Multiple Metabolic Steps[C][W][OA

Mesenchymal stem cells (MSCs) are a potential source of smooth muscle cells (SMCs) for constructing tissue-engineered vascular grafts. However, the details of how specific combinations of vascular microenvironmental factors regulate MSCs are not well understood. Previous studies have suggested that both mechanical stimulation with uniaxial cyclic strain and chemical stimulation with transforming growth factor {beta}1 (TGF-{beta}1) can induce smooth muscle markers in MSCs. In this study, we investigated the combined effects of uniaxial cyclic strain and TGF-{beta}1 stimulation on MSCs. By using a proteomic analysis, we found differential regulation of several proteins and genes, such as the up-regulation of TGF-{beta}1-induced protein ig-h3 (BGH3) protein levels by TGF-{beta}1 and up-regulation of calponin 3 protein level by cyclic strain. At the gene expression level, BGH3 was induced by TGF-{beta}1, but calponin 3 was not significantly regulated by mechanical ...

2009-10-12

What, why, and when we image: considerations for diagnostic imaging and clinical research in the Children's Oncology Group

In this work, we query the Chlamydomonas reinhardtii copper regulon at a whole-genome level. Our RNA-Seq data simulation and analysis pipeline validated a 2-fold cutoff and 10 RPKM (reads per kilobase of mappable length per million mapped reads) (~1 mRNA per cell) to reveal 63 CRR1 targets plus another 86 copper-responsive genes. Proteomic and immunoblot analyses captured 25% of the corresponding proteins, whose abundance was also dependent on copper nutrition, validating transcriptional regulation as a major control mechanism for copper signaling in Chlamydomonas. The impact of copper deficiency on the expression of several O2-dependent enzymes included steps in lipid modification pathways. Quantitative lipid profiles indicated increased polyunsaturation of fatty acids on thylakoid membrane digalactosyldiglycerides, indicating a global impact of copper deficiency on the photosynthetic apparatus. Discovery of a putative plastid copper chaperone and a membrane ...

2011-04-01

Global Molecular Characterization of the Chromate Stress Response in Shewanella oneidensis MR-1: Identification of a Putative DNA-Binding Response Regulator and Azoreductase Involved in Cr(VI) Detoxification

Success in improving treatment outcomes in childhood cancer has been achieved almost exclusively through multicenter and multidisciplinary clinical and applied research over several decades. While biologically rational as well as empirical approaches have led to combination chemotherapy and multimodality approaches to therapy, which have given rise to evidence-based practice standards, similar scientific rigor has not always been as evidently applied to modalities utilized to assess initial disease burden and, more important, response to investigational approaches to therapy. As the empirical approach to therapeutic advances has likely maximized its benefit, future progress will require translation of biologic discovery most notably from the areas of genomics and proteomics. Hence, attempts to improve efficacy of therapy will require a parallel effort to minimize collateral damage of future therapeutic approaches, and such a parallel approach will mandate the ...

2009-02-15