49,705 results match your criteria Proteome Science [Journal]


In silico Leishmania proteome mining applied to identify drug target potential to be used to treat against visceral and tegumentary leishmaniasis.

J Mol Graph Model 2018 Nov 29;87:89-97. Epub 2018 Nov 29.

Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. Electronic address:

New therapeutic strategies against leishmaniasis are desirable, since the treatment against disease presents problems, such as the toxicity, high cost and/or parasite resistance. As consequence, new antileishmanial compounds are necessary to be identified, as presenting high activity against Leishmania, but low toxicity in mammalian hosts. In the present study, a Leishmania proteome mining strategy was developed, in order to select new drug targets with low homology to human proteins, but that are considered relevant for the parasite' survival. Read More

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November 2018
1 Read

Proteomic analysis of olfactory bulb suggests CACNA1E as a promoter of CREB signaling in microbiota-induced depression.

J Proteomics 2018 Dec 3. Epub 2018 Dec 3.

Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing 400016, China; Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing 400016, China; Department of Neurology, The First Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China. Electronic address:

Major depressive disorders impact approximately 17% of the population worldwide, whose high morbidity and considerable adversity have resulted in enormous social and economic burden. In addition, clinically depressed patients often show reduced volume of olfactory bulb (OB) and decreased olfactory sensitivity. Although mounting evidence conveyed that the gut microbiota may implicate the pathophysiology of major depressive disorder (MDD) via the microbe-gut-brain axis, knowledge about its distinctive molecular mechanism is rudimentary. Read More

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December 2018
2 Reads

Identification and Modulation of Microenvironment is Crucial for Effective MSC Therapy in Acute Lung Injury.

Am J Respir Crit Care Med 2018 Dec 6. Epub 2018 Dec 6.

The State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China, Critical Care Medicine, Guangzhou, Guangdong, China.

Rationale: There are controversial reports on applications of mesenchymal stromal cells (MSCs) in patients with acute respiratory distress syndrome (ARDS).

Objective: We hypothesized that lung microenvironment was the main determinant of beneficial versus detrimental effects of MSCs during ARDS.

Methods: Lung proteome was profiled in three models of injury induced by acid instillation and/or mechanical ventilation in mice. Read More

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December 2018
2 Reads

An efficient proteome-wide strategy for discovery and characterization of cellular nucleotide-protein interactions.

PLoS One 2018 6;13(12):e0208273. Epub 2018 Dec 6.

School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.

Metabolite-protein interactions define the output of metabolic pathways and regulate many cellular processes. Although diseases are often characterized by distortions in metabolic processes, efficient means to discover and study such interactions directly in cells have been lacking. A stringent implementation of proteome-wide Cellular Thermal Shift Assay (CETSA) was developed and applied to key cellular nucleotides, where previously experimentally confirmed protein-nucleotide interactions were well recaptured. Read More

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December 2018
1 Read

PPICurator: a tool for extracting comprehensive protein-protein interaction information.

Proteomics 2018 Dec 6:e1800291. Epub 2018 Dec 6.

State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing, 102206, P. R. China.

PPI extraction through biological literature curation has been widely employed for proteome analysis. There is a strong need for a tool that can assist researchers in extracting comprehensive PPI information through literature curation, which is critical in research on protein, e.g. Read More

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December 2018
3 Reads

The inner ear proteome of fish.

FEBS J 2018 Dec 6. Epub 2018 Dec 6.

The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville Campus, Victoria, Australia, 3010.

The mechanisms that underpin the formation, growth and composition of otoliths, the biomineralized stones in the inner ear of fish, are largely unknown, as only a few fish inner ear proteins have been reported. Using a partial transcriptome for the inner ear of black bream (Acanthopagrus butcheri), in conjunction with proteomic data, we discovered hundreds of previously unknown proteins in the otolith. This allowed us to develop hypotheses to explain the mechanisms of inorganic material supply and daily formation of growth bands. Read More

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December 2018

Annotation of the Giardia proteome through structure-based homology and machine learning.

Gigascience 2018 Dec 6. Epub 2018 Dec 6.

Walter & Eliza Hall Institute of Medical Research, Melbourne, Australia.

Background: Large-scale computational prediction of protein structures represents a cost-effective alternative to empirical structure determination with particular promise for non-model organisms and neglected pathogens. Conventional sequence-based tools are insufficient to annotate the genomes of such divergent biological systems. Conversely, protein structure tolerates substantial variation in primary amino acid sequence, and is thus a robust indicator of biochemical function. Read More

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December 2018
2 Reads

Tools for 3D Interactome Visualization.

J Proteome Res 2018 Dec 6. Epub 2018 Dec 6.

In cells, intra- and inter-molecular interactions of proteins confer function and the dynamic modulation of this interactome is critical to meet changing needs required to support life. Cross-linking and mass spectrometry (XL-MS) enable detection of both intra- and inter-molecular protein interactions in organelles, cells, tissues and organs. Quantitative XL-MS enables detection of interactome changes in cells due to environmental, phenotypic, pharmacological, or genetic perturbations. Read More

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December 2018
1 Read

Characterization of the Blister Fluid Proteome for Pediatric Burn Classification.

J Proteome Res 2018 Dec 6. Epub 2018 Dec 6.

Blister fluid (BF) is a novel and viable research matrix for burn injury study, which can reflect both systemic and local micro-environmental responses. The protein abundance in BF from different burn severities were initially observed using a 2D SDS-PAGE approach. Subsequently, a quantitative data independent acquisition (DIA) method - SWATHTM was employed to characterize the proteome of pediatric burn blister fluid. Read More

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December 2018
2 Reads

Implementation of clinical proteomics: A step closer to personalised medicine?

Authors:
Antonia Vlahou

Proteomics Clin Appl 2018 Dec 6:e1800088. Epub 2018 Dec 6.

Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, 11527, Athens, Greece.

The success of clinical proteomics, per definition, is ultimately defined by the clinical implementation of proteomics findings. Extensive research activity in the field, targeting especially biomarker discovery, has been conducted the past decades, with several studies suggesting a benefit from proteome based application in patient management. This viewpoint article discusses the current status in clinical proteomics with respect to implementation, (as evidenced by use of protein findings in drug labeling and patient stratification), and proposes specific action points for accelerating the biomarker validation process, placing special emphasis on the importance of data and resource sharing. Read More

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December 2018

Proteomics Analysis of Thermoplasma Quinone Droplets.

Proteomics 2018 Dec 5:e1800317. Epub 2018 Dec 5.

Department of Applied and Environmental Microbiology, National Agricultural Research and Innovation Centre, H-1022, Budapest, Hungary.

A novel type of lipid droplet/lipoprotein (LD/LP) particle from Thermoplasma acidophilum has been identified recently, and based on biochemical evidences it was named Thermoplasma Quinone Droplet (TaQD). The major components of TaQDs are menaquinones, and to some extent polar lipids, and the 153 amino acid long Ta0547 vitellogenin-N domain protein. In this paper we aimed to identify TaQD proteome components with 1D-SDS-PAGE/Lc-MS/MS and cross reference them with Edman degradation. Read More

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December 2018
1 Read

Identification of Saliva Proteins of Spider Mite Tetranychus evansi by Transcriptome and LC-MS/MS Analyses.

Proteomics 2018 Dec 5:e1800302. Epub 2018 Dec 5.

Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.

The spider mite Tetranychus evansi has a remarkable ability to suppress and manipulate plant defenses, which makes it an ideal model to investigate plant-herbivores interactions. In this study, we performed a de novo assembly of the transcriptome of T. evansi, and characterized the proteins in its secreted saliva by Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS). Read More

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December 2018
3 Reads

Examining Cellular Responses to Kinase Drug Inhibition Through Phosphoproteome Mapping of Substrates.

Methods Mol Biol 2019 ;1888:141-152

Department of Molecular Sciences, ARC Training Centre for Molecular Technology in the Food Industry, Macquarie University, Sydney, Australia.

This chapter provides a detailed description for mass spectrometry-based phosphoproteomics analysis. We describe sample preparation, phosphopeptide enrichment, mass spectrometry acquisition, label-free data analysis and statistical analysis. This technique can be employed to characterize cell signaling networks, and is particularly useful to monitor cellular responses to kinase drug inhibitors. Read More

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January 2019

Proteomic Profiling for Target Identification of Biologically Active Small Molecules Using 2D DIGE.

Methods Mol Biol 2019 ;1888:127-139

Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama, Japan.

Recent improvements in technologies such as omics analysis have enabled us to acquire a large amount of data regarding the biological changes in cells treated with bioactive small molecules. Using such data, a variety of profiling methods have been established for target identification of such bioactive compounds. In this chapter, we describe a proteomic profiling system, ChemProteoBase, based on proteome analysis using two-dimensional difference gel electrophoresis. Read More

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January 2019

Target Engagement of Small Molecules: Thermal Profiling Approaches on Different Levels.

Methods Mol Biol 2019 ;1888:73-98

Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.

The identification of protein targets and the elucidation of the molecular mechanism of action (MMoA) of bioactive small molecules are central goals of chemical biology. Many different techniques for target identification and engagement are developed, but none of them is generic. Here we describe one of these techniques-the cellular thermal shift assay (CETSA). Read More

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January 2019

Novel insights into molecular chaperone regulation of ribonucleotide reductase.

Curr Genet 2018 Dec 5. Epub 2018 Dec 5.

Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.

The molecular chaperones Hsp70 and Hsp90 bind and fold a significant proportion of the proteome. They are responsible for the activity and stability of many disease-related proteins including those in cancer. Substantial effort has been devoted to developing a range of chaperone inhibitors for clinical use. Read More

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December 2018

The plasma peptidome.

Clin Proteomics 2018 1;15:39. Epub 2018 Dec 1.

1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St, Toronto, ON Canada.

Background: It may be possible to discover new diagnostic or therapeutic peptides or proteins from blood plasma using LC-ESI-MS/MS to identify, with a linear quadrupole ion trap to identify, quantify and compare the statistical distributions of peptides cleaved ex vivo from plasma samples from different clinical populations.

Methods: A systematic method for the organic fractionation of plasma peptides was applied to identify and quantify the endogenous tryptic peptides from human plasma from multiple institutions by C18 HPLC followed nano electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) with a linear quadrupole ion trap. The endogenous tryptic peptides, or tryptic phospho peptides (i. Read More

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December 2018

Temporal proteomic profiling of postnatal human cortical development.

Transl Psychiatry 2018 Dec 5;8(1):267. Epub 2018 Dec 5.

Department of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS, Cambridge, UK.

Healthy cortical development depends on precise regulation of transcription and translation. However, the dynamics of how proteins are expressed, function and interact across postnatal human cortical development remain poorly understood. We surveyed the proteomic landscape of 69 dorsolateral prefrontal cortex samples across seven stages of postnatal life and integrated these data with paired transcriptome data. Read More

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December 2018
2 Reads

Novel and conventional approaches for the analysis of quantitative proteomic data are complementary towards the identification of seminal plasma alterations in infertile patients.

Mol Cell Proteomics 2018 Dec 5. Epub 2018 Dec 5.

Molecular Biology of Reproduction and Development, Human Genetics Unit, Faculty of Medicine, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), University of Barcelona, and Hospital Clinic, Spain

Our aim was to define seminal plasma proteome signatures of infertile patients categorized according to their seminal parameters using TMT-LC-MS/MS. To that extent, quantitative proteomic data was analyzed following two complementary strategies: (i) the conventional approach based on standard statistical analyses of relative protein quantification values; and (ii) a novel strategy focused on establishing stable-protein pairs. By conventional analyses, the abundance of some seminal plasma proteins was found to be positively correlated with sperm concentration. Read More

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December 2018

A Chemoproteomic Strategy for Direct and Proteome-wide Covalent Inhibitor Target-site Identification.

J Am Chem Soc 2018 Dec 6. Epub 2018 Dec 6.

Despite recent clinical successes for irreversible drugs, potential toxicities mediated by unpredictable modification of off-target cysteines represents a major hurdle for expansion of covalent drug programs. Understanding the proteome-wide binding profile of covalent inhibitors can significantly accelerate their development; however, current mass spectrometry strategies typically do not provide a direct, amino acid level readout of covalent activity for complex, selective inhibitors. Here we report the development of CITe-Id, a novel chemoproteomic approach that employs covalent pharmacologic inhibitors as enrichment reagents in combination with an optimized proteomic platform to directly quantify dose-dependent binding at cysteine-thiols across the proteome. Read More

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December 2018

Cysteine reactivity across the subcellular universe.

Curr Opin Chem Biol 2018 Nov 30;48:96-105. Epub 2018 Nov 30.

Department of Chemistry, Boston College, Chestnut Hill, MA 02467, United States. Electronic address:

Cysteine residues are concentrated at key functional sites within proteins, performing diverse roles in metal binding, catalysis, and redox chemistry. Chemoproteomic platforms to interrogate the reactive cysteinome have developed significantly over the past 10 years, resulting in a greater understanding of cysteine functionality, modification, and druggability. Recently, chemoproteomic methods to examine reactive cysteine residues from specific subcellular organelles have provided significantly improved proteome coverage and highlights the unique functionalities of cysteine residues mediated by cellular localization. Read More

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November 2018
2 Reads

Profiling of Methylglyoxal Blood Metabolism and Advanced Glycation End-Product Proteome Using a Chemical Probe.

ACS Chem Biol 2018 Dec 3. Epub 2018 Dec 3.

Department of Forensic Medicine , Aarhus University , Aarhus 8200 , Denmark.

Methylglyoxal (MG) is quantitatively the most important precursor to advanced glycation end-products (AGEs), and evidence is accumulating that it is also a causally linked to diabetes and aging related diseases. Living systems primarily reside on the glyoxalase system to detoxify MG into benign d-lactate. The flux to either glycation or detoxification, accordingly, is a key parameter for how well a system handles the ubiquitous glyoxal burden. Read More

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December 2018

Metabolic Signatures of Cystic Fibrosis Identified in Dried Blood Spots For Newborn Screening Without Carrier Identification.

J Proteome Res 2018 Dec 3. Epub 2018 Dec 3.

Cystic fibrosis (CF) is a complex multi-organ disorder that is among the most common fatal genetic diseases benefiting from therapeutic interventions early in life. Newborn screening (NBS) for pre-symptomatic detection of CF currently relies on a two-stage immunoreactive trypsinogen (IRT) and cystic fibrosis transmembrane conductance regulator (CFTR) mutation panel algorithm that is sensitive, but not specific for identifying affected neonates with a low positive predictive value. For the first time, we report the discovery of a panel of CF-specific metabolites from a single 3. Read More

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December 2018

Altered levels of focal adhesion and extracellular matrix-receptor interacting proteins were identified in Hailey-Hailey disease by quantitative iTRAQ proteome analysis.

J Cell Biochem 2018 Dec 3. Epub 2018 Dec 3.

Department of Dermatology, The Second Hospital of Xi'an Jiaotong University, Xi'an, China.

Benign chronic familial pemphigus or Hailey-Hailey disease (HHD, OMIM 169600) is a rare, autosomal dominant blistering skin disorder characterized by suprabasal cell separation (acantholysis) of the epidermis. To date, the proteomic changes in skin lesions from HHD patients has not been reported yet. In this study, a sample of skin lesions from HHD patients was collected for isobaric tags for relative and absolute quantitation to analyze proteome changes compared with unaffected individuals. Read More

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December 2018

Targeting of tail-anchored proteins to Trichomonas vaginalis hydrogenosomes.

Mol Microbiol 2018 Dec 1. Epub 2018 Dec 1.

Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic.

Tail-anchored (TA) proteins are membrane proteins that are found in all domains of life. They consist of an N-terminal domain that performs various functions and a single transmembrane domain (TMD) near the C-terminus. In eukaryotes, TA proteins are targeted to the membranes of mitochondria, the endoplasmic reticulum (ER), peroxisomes and in plants, chloroplasts. Read More

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December 2018

Proteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling .

mSystems 2018 Nov-Dec;3(6). Epub 2018 Nov 20.

Wallenberg Wood Science Center, Department of Biology and Biotechnology, Chalmers University of Technology, Gothenburg, Sweden.

Bacteria of the phylum are regarded as highly efficient carbohydrate metabolizers, but most species are limited to (semi)soluble glycans. The soil species Cytophaga hutchinsonii and Sporocytophaga myxococcoides have long been known as efficient cellulose metabolizers, but neither species conforms to known cellulolytic mechanisms. Both species require contact with their substrate but do not encode cellulosomal systems of cell surface-attached enzyme complexes or the polysaccharide utilization loci found in many other species. Read More

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November 2018

An Alliance of Gel-Based and Gel-Free Proteomic Techniques Displays Substantial Insight Into the Proteome of a Virulent and an Attenuated Strain.

Front Cell Infect Microbiol 2018 16;8:407. Epub 2018 Nov 16.

Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria.

The unicellular protozoan is notorious for being the causative agent of histomonosis, which can cause high mortality in turkeys and substantial production losses in chickens. The complete absence of commercially available curative strategies against the disease renders the devising of novel approaches a necessity. A fundamental step toward this objective is to understand the flagellate's virulence and attenuation mechanisms. Read More

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November 2018
2 Reads

The comparative biochemistry of viruses and humans: an evolutionary path towards autoimmunity.

Authors:
Darja Kanduc

Biol Chem 2018 Dec 3. Epub 2018 Dec 3.

Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, I-70124 Bari, Italy.

Analyses of the peptide sharing between five common human viruses (Borna disease virus, influenza A virus, measles virus, mumps virus and rubella virus) and the human proteome highlight a massive viral vs. human peptide overlap that is mathematically unexpected. Evolutionarily, the data underscore a strict relationship between viruses and the origin of eukaryotic cells. Read More

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December 2018
1 Read

The stop and go traffic regulating protein biogenesis: how translation kinetics control proteostasis.

J Biol Chem 2018 Nov 30. Epub 2018 Nov 30.

James Clark Center, Stanford University, United States.

Generating a functional proteome requires the ribosome to carefully regulate disparate co-translational processes that determine the fate of nascent polypeptides. With protein synthesis being energetically expensive, the ribosome must balance the costs of efficiently making a protein with those of properly folding it. Emerging as a primary means of regulating this trade-off are the non-uniform rates of translation elongation that define translation kinetics. Read More

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November 2018

Oncolytic adenovirus Delta-24-RGD induces a widespread glioma proteotype remodeling during autophagy.

J Proteomics 2018 Nov 29. Epub 2018 Nov 29.

Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain; IDISNA, Navarra Institute for Health Research, Pamplona, Spain; Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain. Electronic address:

Adenovirus Delta-24-RGD has shown a remarkable efficacy in a phase I clinical trial for glioblastoma. Delta-24-RGD induces autophagy in glioma cells, however, the molecular derangements associated with Delta-24-RGD infection remains poorly understood. Here, proteomics was applied to characterize the glioma metabolic disturbances soon after Delta-24-RGD internalization and late in infection. Read More

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November 2018

Comparative proteomics of Tobacco mosaic virus-infected Nicotiana tabacum plants identified major host proteins involved in photosystems and plant defence.

J Proteomics 2018 Nov 29. Epub 2018 Nov 29.

Department of Biological Sciences, National University of Singapore (NUS), 14 Science Drive 4, 117543, Singapore; Temasek Life Sciences Laboratory, 1 Research Link, 117604, Singapore; National University of Singapore Suzhou Research Institute, Suzhou, Jiangsu 215123, China. Electronic address:

Tobacco mosaic virus (TMV) is a positive single-stranded RNA virus. Its 5' end ORF codes for the replicase proteins, namely 126 kDa and 183 kDa, respectively. These proteins interact with many host proteins to form a virus replication complex (VRC). Read More

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November 2018

Isolinderalactone regulates the BCL-2/caspase-3/PARP pathway and suppresses tumor growth in a human glioblastoma multiforme xenograft mouse model.

Cancer Lett 2018 Nov 29. Epub 2018 Nov 29.

Department of Korean Medical Science, School of Korean Medicine, Pusan National University, Yangsan, Gyeongnam, 50612, Republic of Korea; Korean Medical Science Research Center for Healthy-Aging, Pusan National University, Yangsan, Gyeongnam, 50612, Republic of Korea; Graduate Training Program of Korean Medicine for Healthy-Aging, Pusan National University, Yangsan, Gyeongnam, 50612, Republic of Korea. Electronic address:

Glioblastoma multiforme (GBM) is the most common malignant brain tumor, which remains incurable. Plant extracts are a potential source of potent anticancer medicines. In this study, we investigated the effect of isolinderalactone from Lindera aggregata on tumor growth using U-87 human glioblastoma cells. Read More

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November 2018
1 Read

Identification of novel vaccine candidates against cryptosporidiosis of neonatal bovines by reverse vaccinology.

Vet Parasitol 2018 Dec 12;264:74-78. Epub 2018 Nov 12.

Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Instituto de Patobiología Veterinaria, (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Argentina; Facultad de Ciencias exactas, químicas y naturales (FCEQN), Universidad de Morón, Morón, Argentina. Electronic address:

The apicomplexan protozoan Cryptosporidium parvum is an important causative agent of diarrhea of neonatal bovines. Vaccination has been proposed as an advantageous strategy against cryptosporidiosis of calves since besides protection against disease it has also the potential to prevent dissemination of infective oocysts into the environment. Antigens anchored to the parasite surface via glycosylphosphatidylinositol (GPI) are implicated in host cell attachment and invasion and represent promising vaccine candidates. Read More

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December 2018

Comparative proteomics identified immune response proteins involved in response to vaccination with heat-inactivated Mycobacterium bovis and mycobacterial challenge in cattle.

Vet Immunol Immunopathol 2018 Dec 29;206:54-64. Epub 2018 Oct 29.

SaBio, Instituto de Investigación en Recursos Cinegéticos IREC CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005 Ciudad Real, Spain; Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA.

There is an imperative need for effective control of bovine tuberculosis (BTB) on a global scale and vaccination of cattle may prove to be pivotal in achieving this. The oral and parenteral use of a heat-inactivated Mycobacterium bovis (M. bovis) vaccine has previously been found to confer partial protection against BTB in several species. Read More

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December 2018

Protein analysis of moro blood orange pulp during storage at low temperatures.

Food Chem 2019 Mar 23;277:75-83. Epub 2018 Oct 23.

Fundo de Defesa da Citricultura (Fundecitrus), Av. Adhemar P. Barros, Araraquara, São Paulo, Brazil; Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, Valencia, Spain. Electronic address:

A protein analysis in the pulp of Moro blood oranges (Citrus sinensis L. Osbeck) at the onset and after 30 days of storage at either 4 or 9 °C was performed. All differential proteins belonged to different functional classes (sugar, amino acid and secondary metabolism, defense, stress response, oxidative process, transport and cellular component biogenesis), displaying a differential accumulation in those Moro oranges kept at 9 versus 4 °C, and in those stored at 4 °C versus onset. Read More

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Nitrogen topdressing timing modifies the gluten quality and grain hardness related protein levels as revealed by iTRAQ.

Food Chem 2019 Mar 13;277:135-144. Epub 2018 Oct 13.

National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, PR China. Electronic address:

Nitrogen fertilization regimes significantly affect both grain quality and yield. Wheat plants were subjected to different application timing of topdressed nitrogen at the emergence of the top fifth (TL5), top third (TL3) and top first leaf (TL1), respectively. The iTRAQ (isobaric tag for relative and absolute quantitation) technology was adopted to obtain the complete proteome of wheat flour and to identify the differentially expressed proteins (DEPs) as regulated by nitrogen topdressing timing. Read More

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March 2019
1 Read

Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival.

Genome Med 2018 Dec 3;10(1):94. Epub 2018 Dec 3.

Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bldg.37/Room 3050B, Bethesda, MD, 20892-4258, USA.

Background: Transcriptome analysis of breast cancer discovered distinct disease subtypes of clinical significance. However, it remains a challenge to define disease biology solely based on gene expression because tumor biology is often the result of protein function. Here, we measured global proteome and transcriptome expression in human breast tumors and adjacent non-cancerous tissue and performed an integrated proteotranscriptomic analysis. Read More

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December 2018

Profiling the proteomic inflammatory state of human astrocytes using DIA mass spectrometry.

J Neuroinflammation 2018 Nov 30;15(1):331. Epub 2018 Nov 30.

Department of Internal Medicine Specialties, Faculty of Medicine, University of Geneva, 1 Rue Michel Servet, 1211, Geneva 4, Switzerland.

Background: Astrocytes are the most abundant cells in the central nervous system and are responsible for a wide range of functions critical to normal neuronal development, synapse formation, blood-brain barrier regulation, and brain homeostasis. They are also actively involved in initiating and perpetuating neuroinflammatory responses. However, information about their proteomic phenotypes under inflammation is currently limited. Read More

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November 2018

TomahaqCompanion: A tool for the creation and analysis of isobaric label based multiplexed targeted assays.

J Proteome Res 2018 Dec 3. Epub 2018 Dec 3.

Triggered by Offset, Multiplexed, Accurate mass, High resolution, and Absolute Quantitation (TOMAHAQ) is a recently introduced targeted proteomics method that combines peptide and sample multiplexing. TOMAHAQ assays enable sensitive and accurate multiplexed quantification by implementing an intricate data collection scheme that comprises multiple MSn scans, mass inclusion lists, and data-driven filters. Consequently, manual creation of TOMAHAQ methods can be time consuming and error prone while the resulting TOMAHAQ data may not be compatible with common mass spectrometry analysis pipelines. Read More

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December 2018

Integrated In Vivo Quantitative Proteomics and Nutrient Tracing Reveals Age-Related Metabolic Rewiring of Pancreatic β Cell Function.

Cell Rep 2018 Dec;25(10):2904-2918.e8

Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

Pancreatic β cell physiology changes substantially throughout life, yet the mechanisms that drive these changes are poorly understood. Here, we performed comprehensive in vivo quantitative proteomic profiling of pancreatic islets from juvenile and 1-year-old mice. The analysis revealed striking differences in abundance of enzymes controlling glucose metabolism. Read More

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December 2018
1 Read

Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata).

PLoS One 2018 5;13(12):e0204796. Epub 2018 Dec 5.

Department of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, China.

In the present study, we carried out an examination of the amino acid usage in the zebra finch (Taeniopygia guttata) proteome. We found that tRNA abundance, base composition, hydrophobicity and aromaticity, protein second structure, cysteine residue (Cys) content and protein molecular weight had significant impact on the amino acid usage of the zebra finch. The above factors explained the total variability of 22. Read More

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December 2018

Vegetable signatures derived from human urinary metabolomic data in controlled feeding studies.

J Proteome Res 2018 Dec 5. Epub 2018 Dec 5.

Examination of changes in urinary metabolomic profiles after vegetable ingestion may lead to new methods of assessing plant food intake. To this regard, we developed a proof-of-principle methodology to identify urinary metabolomic signatures for spinach, celery, and onion. Three feeding studies were conducted. Read More

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December 2018

RNA-binding proteomics reveals MATR3 interacting with lncRNA SNHG1 to enhance neuroblastoma progression.

J Proteome Res 2018 Dec 5. Epub 2018 Dec 5.

The interaction of long noncoding RNAs (lncRNAs) with one or more RNA-binding proteins (RBPs) are important to a plethora of cellular and physiological processes. The lncRNA SNHG1 was reported to be aberrantly expressed and associated with poor patient prognosis in several cancers, including neuroblastoma. However, the interacting RBPs and biological functions associated with SNHG1 in neuroblastoma remains unknown. Read More

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December 2018

Protein O-fucosyltransferase 2-mediated O-glycosylation of the adhesin MIC2 is dispensable for Toxoplasma gondii tachyzoite infection.

J Biol Chem 2018 Dec 4. Epub 2018 Dec 4.

Department of Microbiology and Immunology, University of Melbourne, Australia.

Toxoplasma gondii is a ubiquitous, obligate intracellular eukaryotic parasite that causes congenital birth defects, disease in immunocompromised individuals, and blindness. Protein glycosylation plays an important role in the infectivity and evasion of immune responses of many eukaryotic parasites and is also of great relevance to vaccine design. Here, we demonstrate that micronemal protein 2 (MIC2), a motility-associated adhesin of T. Read More

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December 2018

Urinary proteome analysis of acute hypercoagulable state in rat model induced by ε-aminocaproic acid.

Biomed Pharmacother 2018 Dec 1;110:275-284. Epub 2018 Dec 1.

Beijing Key Lab of Genetic Engineering and Biotechnology, College of Life Sciences, Beijing Normal University, Xinwai St 19, Haidian District, Beijing, 100875, China.

The hypercoagulable state occurs in a group of prothrombotic disorders associated with an increased risk for thromboembolic events, but it is difficult to diagnose due to the lack of available biomarkers. This study aimed to investigate systematic changes of urinary proteome in acute hypercoagulable state induced by certain antifibrinolytics. To reduce the effects of both genetic and environmental factors on the urinary proteome, we used a rat model of acute hypercoagulable state induced by an antifibrinolytic agent ε-aminocaproic acid, resembling human hypercoagulable state. Read More

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December 2018
1 Read

Comparative proteomic study of dog and human saliva.

PLoS One 2018 4;13(12):e0208317. Epub 2018 Dec 4.

Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand.

Saliva contains many proteins that have an important role in biological process of the oral cavity and is closely associated with many diseases. Although the dog is a common companion animal, the composition of salivary proteome and its relationship with that of human are unclear. In this study, shotgun proteomics was used to compare the salivary proteomes of 7 Thai village dogs and 7 human subjects. Read More

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December 2018
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An update on the moFF Algorithm for label-free quantitative proteomics.

J Proteome Res 2018 Dec 4. Epub 2018 Dec 4.

moFF is a modular and operating system independent tool for quantitative analysis of label-free mass-spectrometry based proteomics data. The moFF workflow, comprising matching-between-runs and apex quantification, can be applied to any upstream search engine's output, along with the corresponding Thermo or mzML raw file. We here present moFF 2. Read More

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December 2018
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msCRUSH: fast tandem mass spectral clustering using locality sensitive hashing.

J Proteome Res 2018 Dec 4. Epub 2018 Dec 4.

Large-scale proteomics projects often generate massive and highly redundant tandem mass spectra(MS/MS). Spectral clustering algorithms can reduce the redundancy in these datasets, and thus speed up database searching for peptide identification, a major bottleneck for proteomic data analysis. The key challenge of spectral clustering is to reduce the redundancy in the MS/MS spectra data, while retaining sufficient sensitivity to identify peptides from the clustered spectra. Read More

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December 2018

Multi-omics and temporal dynamics profiling reveal disruption of central metabolism in on bismuth treatment.

Chem Sci 2018 Oct 25;9(38):7488-7497. Epub 2018 Jul 25.

School of Chemistry , Sun Yat-sen University , Guangzhou , 510275 , P. R. China . Email:

Integration of multi-omics enables uncovering cellular responses to stimuli or the mechanism of action of a drug at a system level. Bismuth drugs have long been used for the treatment of infection and their antimicrobial activity was attributed to dysfunction of multiple proteins based on previous proteome-wide studies. Herein, we investigated the response of to a bismuth drug at transcriptome and metabolome levels. Read More

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October 2018

Proteomic Analysis of Plasmodesmata From Cell Suspension Cultures in Relation With Callose Biosynthesis.

Front Plant Sci 2018 19;9:1681. Epub 2018 Nov 19.

Division of Glycoscience, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.

Plasmodesmata are channels that link adjacent cells in plant tissues through which molecular exchanges take place. They are involved in multiple processes vital to plant cells, such as responses to hormonal signaling or environmental challenges including osmotic stress, wounding and pathogen attack. Despite the importance of plasmodesmata, their proteome is not well-defined. Read More

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November 2018
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