Scope and method of study: To study the plant cell wall degradation process and changes in overall physiology during the growth of A. nidulans on sorghum stover at proteomic and genomic level, A. nidulans was grown on sorghum stover under solid-state culture conditions for 1, 2, 3, 5, 7 and 14 days. Semi-quantitative extracellular proteome analysis (1-D PAGE LC-MS/MS), whole genome microarray analysis, scanning and transmission electron microscopy, along with qualitative and quantitative analysis of extracellular hydrolytic enzyme activities, and analysis of the breakdown products by enzymes was used to study sorghum cell wall degradation by A. nidulans.Findings and conclusions: Based on analysis of chitin content, A. nidulans grew to be 4-5% of the total biomass in the culture. A hyphal mat developed on the surface of the sorghum by day one and as seen by scanning electron microscopy the hyphae enmeshed the sorghum particles by day 5. A total of 294 extracellular proteins were identified with ...

TY - JOUR. T1 - Copper exposure effects on yeast mitochondrial proteome. AU - Banci, Lucia. AU - Bertini, Ivano. AU - Ciofi-Baffoni, Simone. AU - DAlessandro, Annamaria. AU - Jaiswal, Deepa. AU - Marzano, Valeria. AU - Neri, Sara. AU - Ronci, Maurizio. AU - Urbani, Andrea. PY - 2011/10/1. Y1 - 2011/10/1. N2 - Mitochondria play an important role on the entire cellular copper homeostatic mechanisms. Alteration of cellular copper levels may thus influence mitochondrial proteome and its investigation represents an important contribution to the general understanding of copper-related cellular effects. In these study we have performed an organelle targeted proteomic investigation focusing our attention on the effect of non-lethal 1 mM copper concentration on Saccharomyces cerevisiae mitochondrial proteome. Functional copper effects on yeast mitochondrial proteome were evaluated by using both 2D electrophoresis (2-DE) and liquid chromatography coupled with tandem mass spectrometry. Proteomic data have ...

The last 30 years Enterococcus faecium has become an important nosocomial pathogen in hospitals worldwide. The aim of this study was to obtain insight in the cell surface proteome of E. faecium when grown in laboratory and clinically relevant conditions. Enterococcus faecium E1162, a clinical blood stream isolate, was grown ... read more until mid-log phase in brain heart infusion medium (BHI) with, or without 0.02% bile salts, Tryptic Soy Broth with 1% glucose (TSBg) and urine, and its cell surface was shaved using immobilized trypsin. Peptides were identified using MS/MS. Mapping against the translated E1162 whole genome sequence identified 67 proteins that were differentially detected in different conditions. In urine, 14 proteins were significantly more and nine proteins less abundant relative to the other conditions. Growth in BHI-bile and TSBg, revealed four and six proteins, respectively, which were uniquely present in these conditions while two proteins were uniquely present in both ...

The purpose of this study was to characterize the cell surface proteome of native compared to cultured equine retinal pigment epithelium (RPE) cells. The RPE plays an essential role in visual function and represents the outer blood-retinal barrier. We are investigating immunopathomechanisms of equine recurrent uveitis, an autoimmune inflammatory disease in horses leading to breakdown of the outer blood-retinal barrier and influx of autoreactive T-cells into affected horses vitrei. Cell surface proteins of native and cultured RPE cells from eye-healthy horses were captured by biotinylation, analyzed by high resolution mass spectrometry coupled to liquid chromatography (LC MS/MS), and the most interesting candidates were validated by PCR, immunoblotting and immunocytochemistry. A total of 112 proteins were identified, of which 84% were cell surface membrane proteins. Twenty-three of these proteins were concurrently expressed by both cell states, 28 proteins exclusively by native RPE cells. Among the

Time-Course Proteome Analysis Reveals the Dynamic Response of Cryptococcus gattii Cells to Fluconazole. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.

Human Plasma Proteome Analysis Following Endotoxin Challenge Identifies New Proteins that Contribute to Molecular Phenotype of Innate Immunity

phdthesis{be258743-7e2f-4e1a-b45d-bbfdaaa3d645, abstract = {Proteomics is expected to generate new insights into biological processes as well as identify novel biomarkers and therapeutic targets since most biological functions are transmitted through proteins. However, due to the complexity displayed by a proteome and inherent limitations associated with current methodologies, proteomic analyses often result in incomplete coverage and inconsistent measurements. Clearly, the development of novel high-performing proteomic platforms will be essential in order to successfully decipher the human proteome(s).,br/,,br, ,br/,,br, This thesis, based on four original papers denoted I to IV, describes the development and applicability of a novel proteomic technology platform entitled Global Proteome Survey (GPS) capable of transforming affinity proteomics into a global discovery engine. The GPS methodology combines the best features of affinity proteomics and mass spectrometry, and is based on using ...

Bifidobacterium animalis subsp. lactis BB-12 is a widely used probiotic strain associated with a variety of health-promoting traits. There is, however, only limited knowledge available regarding the membrane proteome and the proteins involved in oligosaccharide transport in BB-12. We applied two enrichment strategies to improve the identification of membrane proteins from BB-12 cultures grown on glucose and on xylo-oligosaccharides, the latter being an emerging prebiotic substrate recently reported to be fermented by BB-12. Our approach encompassed consecutive steps of detergent- and carbonate-treatment in order to generate inside-out membrane vesicles and to interfere with binding of membrane-associated proteins to the membrane, respectively. Proteins in the enriched membrane fraction and membrane-associated fraction were digested by lysyl endopeptidase and trypsin followed by peptide sequencing by LC-ESI-Q-TOF MS/MS. Ninety of a total of 248 identified unique proteins were predicted to possess ...

Fingerprint Dive into the research topics of The genome and structural proteome of an ocean siphovirus: A new window into the cyanobacterial mobilome. Together they form a unique fingerprint. ...

TY - JOUR. T1 - Testing the significance of microorganism identification by mass spectrometry and proteome database search. AU - Pineda, Fernando J.. AU - Lin, Jeffrey S.. AU - Fenselau, Catherine. AU - Demirev, Plamen A.. PY - 2000/8/15. Y1 - 2000/8/15. N2 - We derive and validate a simple statistical model that predicts the distribution of false matches between peaks in matrix-assisted laser desorption/ionization mass spectrometry data and proteins in proteome databases. The model allows us to calculate the significance of previously reported microorganism identification results. In particular, for Δm = ±1.5 Da, we find that the computed significance levels are sufficient to demonstrate the ability to identify microorganisms, provided the number of candidate microorganisms is limited to roughly three Escherichia coli-like or roughly 10 Bacillus subtilis-like microorganisms (in the sense of having roughly the same number of proteins per unit-mass interval). We conclude that, given the ...

TY - JOUR. T1 - Comparative proteome and peptidome analysis of the cephalic fluid secreted by Arapaima gigas (Teleostei Osteoglossidae) during and outside parental care. AU - Torati, Lucas S.. AU - Migaud, Hervé. AU - Doherty, Mary K.. AU - Siwy, Justyna. AU - Mullen, Willian. AU - Mesquita, Pedro E.C.. AU - Albalat, Amaya. N1 - ©2017 The Authors. PY - 2017/10/24. Y1 - 2017/10/24. N2 - Parental investment in Arapaima gigas includes nest building and guarding, followed by a care provision when a cephalic fluid is released from the parents head to the offspring. This fluid has presumably important functions for the offspring but so far its composition has not been characterised. In this study the proteome and peptidome of the cephalic secretion was studied in parental and non-parental fish using capillary electrophoresis coupled to mass spectrometry (CE-MS) and GeLC-MS/MS analyses. Multiple comparisons revealed 28 peptides were significantly different between males and parental males ...

Title: Amino Acid Sequence Database Suitable for the Protein and Proteome Analysis. VOLUME: 5 ISSUE: 4. Author(s):Takao Kawakami, Junko Ozaki, Kazuhiro Kondo, Shinji Sato and Harunobu Yunokawa. Affiliation:Clinical Proteome Center, Tokyo Medical University, Shinjuku Sumitomo Building 17th Floor, 2-6-1 Nishi Shinjuku, Shinjuku, Tokyo 163-0217, Japan.. Keywords:Alternative splicing, database search program, peptide identification, posttranslational processing, sequence annotation, sequence database, tandem mass spectrometry. Abstract: Amino acid sequence database is one of the essential components in the current proteomics with mass spectrometry. Protein identification routine as well as posttranslational modification analysis is based on correlation between the mass spectrometry data of peptides obtained from proteome and the entry sequences in the database. While different sequence databases are available from public resources for the correlation search, these primary sequence data can be ...

Like other DNA viruses, herpes simplex virus type 1 (HSV-1) replicates and proliferates in host cells continuously modulating the host molecular environment. Following a sophisticated temporal expression pattern, HSV-1 encodes at least 89 multifunctional proteins that interplay with and modify the host cell proteome. During the last decade, advances in mass spectrometry applications coupled to the development of proteomic separation methods have allowed to partially monitor the impact of HSV-1 infection in human cells. In this review, we discuss the current use of different proteome fractionation strategies to define HSV-1 targets in two major application areas: (i) viral-protein interactomics to decipher viral-protein interactions in host cells and (ii) differential quantitative proteomics to analyze the virally induced changes in the cellular proteome. Moreover, we will also discuss the potential application of high-throughput proteomic approaches to study global proteome dynamics and also post

2017 The Author(s). Rhizoctonia solani is a fungal pathogen causing substantial damage to many of the worlds largest food crops including wheat, rice, maize and soybean. Despite impacting global food security, little is known about the pathogenicity mechanisms employed by R. solani. To enable prediction of effectors possessing either broad efficacy or host specificity, a combined secretome was constructed from a monocot specific isolate, a dicot specific isolate and broad host range isolate infecting both monocot and dicot hosts. Secretome analysis suggested R. solani employs largely different virulence mechanisms to well-studied pathogens, despite in many instances infecting the same host plants. Furthermore, the secretome of the broad host range AG8 isolate may be shaped by maintaining functions for saprophytic life stages while minimising opportunities for host plant recognition. Analysis of possible co-evolution with host plants and in-planta up-regulation in particular, aided ...

TY - JOUR. T1 - Rapid identification of monospecific monoclonal antibodies using a human proteome microarray.. AU - Jeong, Jun Seop. AU - Jiang, Lizhi. AU - Albino, Edisa. AU - Marrero, Josean. AU - Rho, Hee Sool. AU - Hu, Jianfei. AU - Hu, Shaohui. AU - Vera, Carlos. AU - Bayron-Poueymiroy, Diane. AU - Rivera-Pacheco, Zully Ann. AU - Ramos, Leonardo. AU - Torres-Castro, Cecil. AU - Qian, Jiang. AU - Bonaventura, Joseph. AU - Boeke, Jef D.. AU - Yap, Wendy Y.. AU - Pino, Ignacio. AU - Eichinger, Daniel J.. AU - Zhu, Heng. AU - Blackshaw, Seth. PY - 2012/6. Y1 - 2012/6. N2 - To broaden the range of tools available for proteomic research, we generated a library of 16,368 unique full-length human ORFs that are expressible as N-terminal GST-His(6) fusion proteins. Following expression in yeast, these proteins were then individually purified and used to construct a human proteome microarray. To demonstrate the usefulness of this reagent, we developed a streamlined strategy for the production of ...

PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

The Human Cell chapters provide a knowledge-based analysis of the human cellular proteomes and an entry into the Human Protein Atlas from different perspectives. The Cell Atlas can be explored on the basis of the transcriptomes of a large panel of human cell lines. This includes the classification of genes with variable and stable expression across the panel. Furthermore, various spatiotemporal aspects of the human proteome can be explored, such as the organelle proteomes, the multilocalizing proteome and the proteome showing single-cell variation. The human proteome can further be explored based on the expression in different organelles and cellular structures. This enables the definition of organelle proteomes that indicates the distinct organelle structures and functions. Each separate chapter includes a description of a particular proteome and explorations of protein expression patterns, a complete list of proteins that build a proteome, as well as examples of detailed images ...

Carboxylate efflux from roots is a crucial and differential response of soybean genotypes to low phosphorus (P) stress. Exudation of carboxylic acids including oxalate, citrate, succinate and fumarate was induced under low P stress, particularly in P-efficient soybean genotypes. Enhancement of root length, surface area and volume further improved P acquisition under low P stress. To understand the molecular basis of carboxylate efflux under low P stress, the root proteome of contrasting genotypes (P-efficient: EC-232019 and P-inefficient: EC-113396) was compared. Among a total of 325 spots, 105 (32%) were differentially abundant proteins (DAPs) between sufficient (250 µM) and low P (4 µM) levels. Abundance of 44 (14%) proteins decreased by more than two-fold under low P stress, while 61 (19%) proteins increased by more than two-fold. Protein identification and annotation revealed that the DAPs were involved in a myriad of functions including carboxylic acid synthesis, carbohydrate, protein and lipid

In line with the aims of the Chromosome-centric Human Proteome Project (C-HPP) to completely annotate proteins of each chromosome and biology/disease driven HPP (B/D-HPP) to decipher their relation to diseases, we have generated a nonredundant catalogue of protein-coding genes for Chromosome 12 (Chr …

Our study showed for the first time the effect of the long term consumption of four dietary models, providing different quantity and quality of dietary lipids, on the whole proteome of peripheral blood mononuclear cells (PBMC) from patients with MetS. In this study, we analyzed separately the changes induced in the nuclear and cytoplasmic proteome after the long-term consumption of a high saturated fatty acid diet (HSFA), a high monounsaturated fatty acids-rich diet (HMUFA), a low-fat high carbohydrates diet (LFHCC) and a low-fat high carbohydrates diet supplemented with n-3 fatty acids (LFHCC n-3).. The proteins responding to the quantity and quality of dietary lipids identified in our study showed that dietary lipids regulate different biomechanisms directly involved in the etiology of MetS. This idea is supported by the relationship found between MetS parameters, mainly in changes in the TAG and glucose levels and several changes in the proteome. Long-term consumption of an HSFA diet leads to ...

The proteomic analysis of human blood and blood-derived products (e.g., plasma) offers an attractive avenue to translate research progress from the laboratory into the clinic. However, due to its unique protein composition, performing proteomics assays with plasma is challenging. Plasma proteomics has regained interest due to recent technological advances, but challenges imposed by both complications inherent to studying human biology (e.g., interindividual variability) and analysis of biospecimens (e.g., sample variability), as well as technological limitations remain. As part of the Human Proteome Project (HPP), the Human Plasma Proteome Project (HPPP) brings together key aspects of the plasma proteomics pipeline. Here, we provide considerations and recommendations concerning study design, plasma collection, quality metrics, plasma processing workflows, mass spectrometry (MS) data acquisition, data processing, and bioinformatic analysis. With exciting opportunities in studying human health and disease

Compartmentalization is a unique feature of eukaryotes that helps in maintaining cellular homeostasis not only in intra- and inter-organellar context, but also between the cells and the external environment. Plant cells are highly compartmentalized with a complex metabolic network governing various cellular events. The membranes are the most important constituents in such compartmentalization, and membrane-associated proteins play diverse roles in many cellular processes besides being part of integral component of many signaling cascades. To obtain valuable insight into the dynamic repertoire of membrane proteins, we have developed a proteome reference map of a grain legume, chickpea, using two-dimensional gel electrophoresis. MALDI-TOF/TOF and LC-ESI-MS/MS analysis led to the identification of 91 proteins involved in a variety of cellular functions viz., bioenergy, stress-responsive and signal transduction, metabolism, protein synthesis and degradation, among others. Significantly, 70% of the

A bottom-up label-free mass spectrometric proteomic strategy was used to analyse the protein profiles of the human embryonic secretome. Culture media samples used for embryonic culture of patients undergoing intracytoplasmic sperm injection cycles were selected as a test case for this exploratory proof-of-principle study. The media were stored after embryo transfer and then pooled into positive (n = 8) and negative (n = 8) implantation groups. The absolute quantitative bottom-up technique employed a multidimensional protein identification technology based on separation by nano-ultra-high pressure chromatography and identification via tandem nano-electrospray ionization mass spectrometry with data-independent scanning in a hydrid QqTOF mass spectrometer. By applying quantitative bottom-up proteomics, unique proteins were found exclusively in both the positive- and negative-implantation groups, which suggest that competent embryos express and secrete unique biomarker proteins into the surrounding ...

Enhanced qualitative and quantitative proteomic analysis using pSMART combines data dependent and data independent acquisition for improved results.

The small intestine is an important human organ that plays a central role in many physiological functions including digestion, absorption, secretion and defense. Duodenal pathologies include, for instance, the ulcer associated to Helicobacter Pylori infection, adenoma and, in genetically predisposed individuals, celiac disease. Alterations in the bowel reduce its capability to absorb nutrients, minerals and fat-soluble vitamins. Anemia and osteopenia or osteoporosis may develop as a consequence of vitamins malabsorption. Adenoma is a benign tumor that has the potential to become cancerous. Adult celiac disease patients present an overall risk of cancer that is almost twice than that found in the general population. These disease processes are not completely known. To date, a two dimensional (2D) reference map of proteins expressed in human duodenal tissue is not yet available: the aim of our study was to characterize the 2D protein map, and to identify proteins of duodenal mucosa of adult individuals

The nucleolus is the cellular organelle that manufactures ribosomes and plays a part in many vital process including cell-cycle regulation and senescence. Using the latest proteomics technologies, Andersen et al. have generated a comprehensive list of nucleolar proteins. Over 690 proteins were found in the in the nucleolar preparation, including Werners syndrome helicase and various regulatory proteins. The technology also allows analysis of changes in relative levels of proteins as a result of perturbing growth conditions with drugs. This paints a picture of a dynamic proteome: in effect there may be no definitive proteome for the nucleolus or any other organelle, rather there is a series of overlapping proteomes corresponding to different cell states. The nucleolus is a key organelle that coordinates the synthesis and assembly of ribosomal subunits and forms in the nucleus around the repeated ribosomal gene clusters. Because the production of ribosomes is a major metabolic activity, the function of

One of the constant challenges for proteomics is inadequate protein identification because of the interference of high abundance proteins (1). The challenge is particularly critical for plant proteomics analysis because of the prevalence of Rubisco (Ribulose-1,5-bisphosphate carboxylase oxygenase) in green tissue. As a major enzyme involved in carbon fixation, Rubisco consists of 30 to 50% of total plant protein from green tissues and causes less sensitivity, dynamic range, and protein identification of plant proteomics (2⇓-4). Influences of high abundance proteins like Rubisco affect both gel-based and shot-gun proteomics analysis. In one of the most popular shot-gun proteomics platforms with the data-dependent MS/MS acquisition, the peptides derived from the abundant proteins have more chance to be sampled by the MS instrument than the peptides from other functional proteins. Thus, the dynamic range and detection sensitivity will be sacrificed because of the prevalence of high abundance ...

Mass spectrometry (MS) - based proteomics allows the sensitive and accurate quantification of almost complete proteomes of complex biological fluids and tissues. At the moment, however, the routinely usage of MS-based proteomics is prevented and complicated by the very complex work flow comprising sample preparation, chromatography, MS measurement followed by data processing and evaluation. The new technologies, products and assays developed by Precision Proteomics could help enabling and establishing mass spectrometry (MS) - based proteomics in academic and pharmaceutical proteomics research as well as in clinical diagnostics.. ...

Fernandes, I., et al. Secretome Analysis Identifies Potential Virulence Factors of Diplodia corticola, a Fungal Pathogen Involved in Cork Oak (Quercus suber) Decline. Fungal Biotechnology. (118) 5-6, 516-523. 18/05/2014.. ...

TY - JOUR. T1 - Serological immunoreactivity against colon cancer proteome varies upon disease progression. AU - De Monte, Lucia. AU - Sanvito, Francesca. AU - Olivieri, Stefano. AU - Viganò, Fiammetta. AU - Doglioni, Claudio. AU - Frasson, Matteo. AU - Braga, Marco. AU - Bachi, Angela. AU - Dellabona, Paolo. AU - Protti, Maria Pia. AU - Alessio, Massimo. PY - 2008/2. Y1 - 2008/2. N2 - Sera from colon carcinoma patients were used to identify tumor-associated antigens (TAAs) by screening tumor proteome resolved by 2D electrophoresis. A panel of six TAAs eliciting a serological immune response in colorectal cancer was identified, showing a modification in antigen recognition by B cells in patients as a function of colon cancer progression. The expression of these proteins was either confined or increased in tumor as compared to normal mucosa.. AB - Sera from colon carcinoma patients were used to identify tumor-associated antigens (TAAs) by screening tumor proteome resolved by 2D electrophoresis. ...

1. Severity and Frequency of Proximal Tubule Injury Determines Renal Prognosis.. Takaori K, Nakamura J, Yamamoto S, Nakata H, Sato Y, Takase M, Nameta M, Yamamoto T, Economides AN, Kohno K, Haga H, Sharma K, Yanagita M.. J Am Soc Nephrol. 2015 Dec 23. pii: ASN.2015060647. [Epub ahead of print] PMID: 26701981. 2. The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling.. Habuka M, Fagerberg L, Hallström BM, Pontén F, Yamamoto T, Uhlen M.. PLoS One. 2015 Dec 22;10(12):e0145301. doi: 10.1371/journal.pone.0145301. eCollection 2015.. PMID: 26694548 Free PMC Article. 3. Leptin deficiency down-regulates IL-23 production in glomerular podocytes resulting in an attenuated immune response in nephrotoxic serum nephritis.. Goto K, Kaneko Y, Sato Y, Otsuka T, Yamamoto S, Goto S, Yamamoto K, Yamamoto T, Kawachi H, Madaio MP, Narita I.. Int Immunol. 2015 Nov 13. pii: dxv067. [Epub ahead of print] PMID: 26567290. 4. A proteomic glimpse into human ureter ...

Citation. Pieper, R., Gatlin, C. L., Makusky, A. J., Russo, P. S., Schatz, C. R., Miller, S. S., Su, Q., McGrath, A. M., Estock, M. A., Parmar, P. P., Zhao, M., Huang, S. T., Zhou, J., Wang, F., Esquer-Blasco, R., Anderson, N. L., Taylor, J., Steiner, S.. The Human Serum Proteome: Display of Nearly 3700 Chromatographically Separated Protein Spots on Two-dimensional Electrophoresis Gels and Identification of 325 Distinct Proteins. Proteomics. 2003 Jul 01; 3(7): 1345-64.. PubMed Citation. Abstract. Plasma, the soluble component of the human blood, is believed to harbor thousands of distinct proteins, which originate from a variety of cells and tissues through either active secretion or leakage from blood cells or tissues. The dynamic range of plasma protein concentrations comprises at least nine orders of magnitude. Proteins involved in coagulation, immune defense, small molecule transport, and protease inhibition, many of them present in high abundance in this body fluid, have been functionally ...

Adaptation, Physiological; Animals; Cattle; Electrophoresis, Gel, Two-Dimensional; Energy Metabolism; Female; Gene Expression; Genotype; Mastitis, Bovine; Plant Proteins; Protein Interaction Maps; Proteome; Proteomics; Prototheca; Signal Transduction ...

Hypothesis:. Differences in the proteome concerning cell death pathways of glaucoma patients correspond to the differences in the mRNA expression of these patients.. Specific aims:. Characterization of the cellular proteome from human leukocytes of glaucoma patients compared to healthy controls and patients with Parkinsons disease.. Background:. Glaucoma is a worldwide leading cause of blindness. The key feature of this ocular neuropathy is characterized by an excavating optic nerve head. Loss of retinal ganglion cells is the final end point in blinding diseases of the optic nerve such as glaucoma. It is known that neuronal cell death in glaucoma occurs by an apoptotic mechanism. In earlier studies we could demonstrate that this cell death is reflected in circulating leukocytes by different parameters, like differential mRNA expression, and an increased fragmentation of the DNA. The differences in mRNA expression indicate a close relationship to cellular stress conditions and apoptotic events: ...

The focus of this article is to review the recent advances in proteome analysis of human body fluids, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, and amniotic fluid, as well as its applications to human …

Plasma biomarkers that reflect molecular states of the cardiovascular system are central for clinical decision making. Routinely used plasma biomarkers include troponins, natriuretic peptides, and lipoprotein particles, yet interrogate only a modest subset of pathways relevant to cardiovascular disease. Systematic profiling of a larger portion of circulating plasma proteins (the plasma proteome) will provide opportunities for unbiased discovery of novel markers to improve diagnostic or predictive accuracy. In addition, proteomic profiling may inform pathophysiological understanding and point to novel therapeutic targets. Obstacles for comprehensive proteomic profiling include the immense size and structural heterogeneity of the proteome, and the broad range of abundance levels, as well. Proteome-wide, untargeted profiling can be performed in tissues and cells with tandem mass spectrometry. However, applications to plasma are limited by the need for complex preanalytical sample preparation stages ...

Daphnia pulex (Water flea) is the first fully sequenced crustacean genome. The crustaceans and insects have diverged from a common ancestor. It is a model organism for studying the molecular makeup for coping with the environmental challenges. In the complete proteome, there are 30,550 putative proteins. However, about 10,000 of them have no known homologues. Currently, the UniProtoKB reports on 95% of the Daphnias proteins as putative and uncharacterized proteins. We have applied ProtoNet, an unsupervised hierarchical protein clustering method that covers about 10 million sequences, for automatic annotation of the Daphnias proteome. 98.7% (26,625) of the Daphnia full-length proteins were successfully mapped to 13,880 ProtoNet stable clusters, and only 1.3% remained unmapped. We compared the properties of the Daphnias protein families with those of the mouse and the fruitfly proteomes. Functional annotations were successfully assigned for 86% of the proteins. Most proteins (61%) were mapped to only

78069 avhandlingar från svenska högskolor och universitet. Avhandling: Advancing bioinformatics methods for in-depth proteome analysis based on high-resolution mass spectrometry.

Scientists at the Center for Proteome Analysis (CPA) in Odense, Denmark, have identified a natural protein that seems to protect the bodys insulin-producing beta cells from attack. Their approach is to analyze the thousands of gene products in cells and tissues, with special interest in galectin, a small protein that is vital in insulin dependent diabetes mellitus (IDDM). Every cell, no matter what tissue its in, carries the same full set of genetic information, the species genome. Now that genomic information is pouring in at a breathtaking pace, scientists are rushing to understand which proteins a particular type of cell synthesizes, how much the cell synthesizes, how cells modify proteins after synthesis and how all those proteins interact. This is the new science of proteomics. Among the first to realize the potential of proteomics, biologists Peter Mose Larsen and Stephen Fey founded CPA in 1997. And even today, when proteome centers are sprouting up everywhere, this research compound, ...

A wide range of state-of-the-art proteomics experiments are possible. These include, but are not limited, to intact mass determination, post-translational modification analysis, protein identification, and targeted (e.g. co-immunoprecipitation) or comprehensive (e.g. protein expression profiling) proteome analysis. Proteome analysis may employ a number of different isotope-labeling strategies enabling quantitative measurements on our high resolution discovery platforms (Orbitrap-Elite and Q-Exactive HF mass spectrometers) for deep proteome coverage or multiplexed targeted quantification on our triple quadrupole mass spectrometer (Xevo-TQS). Unique among regional cores is our ability to quantitatively analyze proteomes, phosphoproteomes, ubiquitylomes, and lysine acetylomes at a deep level through a process of serial enrichment. Under development are refinements of statistical and bioinformatic analyses of proteomic results. It is also possible to tailor sensitive and specific methods for ...

Lung cancer is the most common cause of cancer-related death worldwide, less than 7% of patients survive 10 years following diagnosis across all stages of lung cancer. Late stage of diagnosis and lack of effective and personalized medicine reflect the need for a better understanding of the mechanisms that underlie lung cancer progression. Quantitative proteomics provides the relative different protein abundance in normal and cancer patients which offers the information for molecular interactions, signaling pathways, and biomarker identification. Here we introduce both theoretical and practical applications in the use of quantitative proteomics approaches, with principles of current technologies and methodologies including gel-based, label free, stable isotope labeling as well as targeted proteomics. Predictive markers of drug resistance, candidate biomarkers for diagnosis, and prognostic markers in lung cancer have also been discovered and analyzed by quantitative proteomic analysis. Moreover,

Low abundant proteins make up about 1% of the entire human serum proteome, with the remaining 99% being comprised of only 22 proteins. It is therefore imperative to deplete the level of abundant proteins as an essential first step in the characterization of serum by MS analyses. Prefractionation approaches employing chromatographic adsorbents (e.g. anti-HSA antibodies, Cibacron Blue) have been used to remove abundant proteins such as albumin, however, these methods likely result in the removal of LMW species bound to albumin (10). We used centrifugal ultrafiltration employing Centriplus 30 (YM30) membrane ultrafilters to deplete abundant proteins such as albumin and enrich for LMW proteins. The method described here allows for the rapid and efficient removal of albumin and other highly abundant proteins while minimizing the concomitant loss of LMW components potentially bound to high abundant proteins. An earlier study by Georgiou et al. (21) reported that ultrafiltration failed to remove ...

Aspergillus fumigatus is a ubiquitously distributed filamentous fungus that has emerged as one of the most serious life-threatening pathogens in immunocompromised patients. The mechanisms for its pathogenicity are poorly understood. Here, we analyzed the proteome of dormant A. fumigatus conidia as the fungal entity having the initial contact with the host. Applying two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), we established a 2-D reference map of conidial proteins. By MALDI-TOF mass spectrometry, we identified a total number of 449 different proteins. We show that 57 proteins of our map are over-represented in resting conidia compared to mycelium. Enzymes involved in reactive oxygen intermediates (ROI) detoxification, pigment biosynthesis, and conidial rodlet layer formation were highly abundant in A. fumigatus spores and most probably account for their enormous stress resistance. Interestingly, pyruvate decarboxylase and alcohol dehydrogenase were detectable in dormant ...

Source: Journal of Proteome Research - August 20, 2018 Category: Biochemistry Authors: Heeyoun Hwang, Ji Eun Jeong, Hyun Kyoung Lee, Ki Na Yun, Hyun Joo An, Bonghee Lee, Young-Ki Paik, Tae Seok Jeong, Gi Taek Yee, Jin Young Kim, Jong Shin Yoo Source Type: research. [ASAP] Transcriptional and Proteomic Analysis Revealed a Synergistic Effect of Aflatoxin M1 and Ochratoxin A Mycotoxins on the Intestinal Epithelial Integrity of Differentiated Human Caco-2 Cells ...

Background: Selection of patients to receive a primary prevention ICD is solely based on LV EF. Plasma biomarkers may compliment this but most have not been evaluated in predicting arrhythmic death. We determined whether plasma proteomic profiling could afford an unbiased, discovery based approach to identify novel biomarkers to predict cause specific event rates from SCA (arrhythmic death or defibrillation for VT/VF).. Methods: Plasma samples were obtained at entry in 203 patients in the PAREPET study. Proteomic profiling was performed in a subset of 10 patients with SCA vs. 10 survivors matched for EF (26%), age (66 years) and creatinine (1.4). We used a tandem affinity depletion method (IgY14-SuperMix) to reduce high- and medium- abundance plasma proteins, followed by extensive ion current based biomarker discovery. Plasma proteins were expressed as SCA/survivors.. Results: SCA developed 1016±735 days after sampling. Stringent cutoff criteria (0.3% peptide identification FDR ; ≥2 unique ...

NEW YORK (GenomeWeb) - A group from the Spanish National Cancer Research Centre has published a critique raising questions about two recent studies in which researchers generated the first relatively comprehensive maps of the human proteome.

Trypanosoma brucei is the causative agent of human African sleeping sickness and Nagana in cattle. In addition to being an important pathogen T. brucei has developed into a model system in cell biology. Using Stable Isotope Labelling of Amino acids in Cell culture (SILAC) in combination with mass spectrometry we determined the abundance of |1600 proteins in the long slender (LS), short stumpy (SS) mammalian bloodstream form stages relative to the procyclic (PC) insect-form stage. In total we identified 2645 proteins, corresponding to ~30% of the total proteome and for the first time present a comprehensive overview of relative protein levels in three life stages of the parasite. We can show the extent of pre-adaptation in the SS cells, especially at the level of the mitochondrial proteome. The comparison to a previously published report on monomorphic in vitro grown bloodstream and procyclic T. brucei indicates a loss of stringent regulation particularly of mitochondrial proteins in these cells when

Two serious nuclear accidents during the last quarter century (Chernobyl, 1986 and Fukushima, 2011) contaminated large agricultural areas with radioactivity. The database

PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

TY - JOUR. T1 - Surface Proteome Analysis and Characterization of Surface Cell Antigen (Sca) or Autotransporter Family of Rickettsia typhi. AU - Sears, Khandra T.. AU - Ceraul, Shane M.. AU - Gillespie, Joseph J.. AU - Allen, Edwin D.. AU - Popov, Vsevolod L.. AU - Ammerman, Nicole C.. AU - Rahman, M. Sayeedur. AU - Azad, Abdu F.. PY - 2012/8/1. Y1 - 2012/8/1. N2 - Surface proteins of the obligate intracellular bacterium Rickettsia typhi, the agent of murine or endemic typhus fever, comprise an important interface for host-pathogen interactions including adherence, invasion and survival in the host cytoplasm. In this report, we present analyses of the surface exposed proteins of R. typhi based on a suite of predictive algorithms complemented by experimental surface-labeling with thiol-cleavable sulfo-NHS-SS-biotin and identification of labeled peptides by LC MS/MS. Further, we focus on proteins belonging to the surface cell antigen (Sca) autotransporter (AT) family which are known to be involved ...

TY - JOUR. T1 - Survey of the camel urinary proteome by shotgun proteomics using a multiple database search strategy. AU - Alhaider, Abdulqader A.. AU - Bayoumi, Nervana. AU - Argo, Evelyn. AU - Gader, Abdel G. M. A.. AU - Stead, David A.. PY - 2012/11. Y1 - 2012/11. N2 - We report the first survey of the dromedary camel urinary proteome. Proteins retained from ultrafiltration of urine were analysed by GeLC-MS/MS (SDS-PAGE followed by LC-MS/MS). In the absence of a complete camel genome sequence, the number of protein identifications was maximised by searching three primary sequence databases: Swiss-Prot, alpaca and camel EST. This search strategy enabled the identification of 1274 peptide sequences, of which 735 were found in at least two independent samples. Functional annotations for proteins identified from alpaca and camel EST sequences were mapped from basic local alignment search tool (protein) searches. These 735 peptides, which included many novel sequences found only in the camel EST ...

Additional file 9: of Comparative proteomic analysis reveals a dynamic pollen plasma membrane protein map and the membrane landscape of receptor-like kinases and transporters important for pollen tube growth and interaction with pistils in rice

The recent explosion in available genomic and protein sequence information is providing a sequence infrastructure for the emerging field of proteomics. A major aspect of many proteomics strategies is the identification of proteins using an analytical fingerprint that can be used to search a sequence database. One common fingerprint is the tandem mass (MS/MS) spectrum of a peptide. Thus, an MS/MS spectrum can be algorithmically compared with predicted peptide spectra from a sequence database to identify the respective protein (1, 2). The digestion of intact protein mixtures followed by the direct analysis of the resulting peptides by capillary liquid chromatography-MS/MS has facilitated shotgun identification of protein mixtures without the need for prior sample fractionation (3). Combined with the recent development of capillary multidimensional liquid chromatography [multidimensional protein identification technology (MudPIT)], this approach is now capable of characterizing proteins ...

Purpose: Polymorphisms in tissue inhibitor of metalloproteinase 3 (TIMP3) have been associated with Sorsby fundus dystrophy (SFD) and age-related macular degeneration. Toward a molecular understanding of TIMP3 dysfunction, we pursued quantitative proteomic analyses of the retina and choroid from TIMP-3 knockout (KO) mice and knockin (KI) mice expressing the TIMP3 S156C mutation that causes SFD.. Methods: Soluble proteins from isolated retinas and choroid-containing posterior globes from TIMP3 KO mice (n = 5 mice), KI homozygotes (n = 5), KI heterozygotes (n = 4), and wild-type mice (n = 7) were quantified by iTRAQ technology. Protein was digested with trypsin, peptides labeled with iTRAQ tags, fractionated by strong cation exchange chromatography, and peptides were analyzed by LC MS/MS. Proteins were identified using the Swiss-Protein database and quantified using code written in R. Proteins quantified with ≥ 2 unique peptides/protein in ≥ 3 mice/strain were considered significantly altered ...

Alu elements are major contributors to lineage-specific new exons in primate and human genomes. Recent studies indicate that some Alu exons have high transcript inclusion levels or tissue-specific splicing profiles, and may play important regulatory roles in modulating mRNA degradation or translational efficiency. However, the contribution of Alu exons to the human proteome remains unclear and controversial. The prevailing view is that exons derived from young repetitive elements, such as Alu elements, are restricted to regulatory functions and have not had adequate evolutionary time to be incorporated into stable, functional proteins. We adopt a proteotranscriptomics approach to systematically assess the contribution of Alu exons to the human proteome. Using RNA sequencing, ribosome profiling, and proteomics data from human tissues and cell lines, we provide evidence for the translational activities of Alu exons and the presence of Alu exon derived peptides in human proteins

Title:iTRAQ-based Quantitative Proteomic Analysis of Dural Tissues Reveals Upregulated Haptoglobin to be a Potential Biomarker of Moyamoya Disease. VOLUME: 17 Author(s):Xiaojun Zhang, Lin Yin, Xiaofang Jia, Yujiao Zhang, Tiefu Liu and Lijun Zhang*. Affiliation:The 85th hospital of the Chinese Peoples Liberation Army, Shanghai 200052, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508. Keywords:Moyamoya disease, Dura mater, Proteomics, iTRAQ, Haptoglobin, Biomarker. Abstract:Background: Moyamoya disease (MMD) is a rare cerebrovascular disease with high rate of disability and mortality. Immune reactions has been implicated in the pathogenesis of MMD, however, the underlying ...

In higher plants, chloroplasts are the site for the photosynthetic reactions, converting solar energy to chemical energy. Within the chloroplast the thylakoid membrane network encloses the soluble lumen compartment. Until recently the knowledge of the lumen composition and function was limited, but a more profound understanding of the thylakoid lumen content is gradually emerging. The discovery that the thylakoid lumen contains numerous enzymes, besides the already known proteins directly involved or associated with the photosynthetic reactions, have changed the view on this compartment.. The first part of the thesis the lumen proteome maps of Arabidopsis and spinach were resolved. These two proteome maps showed good correlation and the same protein groups were represented in the two proteomes. Thirty eight proteins were identified and in combination with an in silico prediction for the proteome it was estimated that at least 80 different proteins are lumen located.. The second part was to ...

400 Quantitative proteome analysis of tongue squamous cell carcinoma was performed by using laser capture microdissection (LCM) and mass spectrometry. LCM allowed for the one-step procurement of homogeneous populations of normal/tumor epithelial cells from tissue sections. The protein expression profiles of dissected normal/cancer cells were examined using a quantitative proteomics approach based on stable isotope labeling and liquid chromatography-mass spectrometry (LC-MS). Both protein extracts were reduced, alkylated and digested with trypsin. The resulting peptides were labeled with iTRAQ 114 and 117 reagents, respectively. Both labeled peptides were then combined and analyzed simultaneously by nanoflow LC-QTOF MS for protein identification and quantitation. A total of 115 proteins were found to be differentially expressed, including 37 up-regulated (1.2-3 fold change) and 78 down-regulated (1.2-4 fold change) proteins in human tongue cancer tissue. A number of proteins altered at their ...

Fingerprint Dive into the research topics of High-throughput quantitative proteomic analysis of dengue virus type 2 infected A549 cells. Together they form a unique fingerprint. ...

Salt stress is a major abiotic stress that accounts for huge agricultural losses worldwide, which in turn threaten food security and sustainable agriculture. Salt triggers the excessive production of reactive oxygen species (ROS) which accumulate to levels that become toxic to plants, resulting in cell death and reduced plant growth. Part of the plants mechanisms to counteract ROS-induced cell death involves the scavenging ability of the antioxidant defense system to maintain redox homeostasis. Gallic acid (GA) is an antioxidant that has been shown to reduce salt-induced ROS in legume plants. However, its effects on wheat plants have not been elucidated. This study thus investigated the role of exogenous GA (250 μM) on the physiological responses and antioxidant system of wheat plants under salt stress (150 mM). In addition, this study also investigated how GA and salt stress influenced changes in the membrane proteome of wheat plants using LC-MS proteomic analysis ...

TY - JOUR. T1 - Quantitative proteomics analysis of human endothelial cell membrane rafts. T2 - Evidence of MARCKS and MRP regulation in the sphingosine 1-phosphate-induce barrier enhancement. AU - Guo, Yurong. AU - Singleton, Patrick A.. AU - Rowshan, Austin. AU - Gucek, Marjan. AU - Cole, Robert N.. AU - Graham, David R.M.. AU - Van Eyk, Jennifer E.. AU - Garcia, Joe G.N.. PY - 2007/4/1. Y1 - 2007/4/1. N2 - Endothelial cell barrier dysfunction results in the increased vascular permeability observed in inflammation, tumor metastasis, angiogenesis, and atherosclerosis. Sphingosine 1-phosphate (S1P), a biologically active phosphorylated lipid growth factor released from activated platelets, enhances the endothelial cell barrier integrity in vitro and in vivo. To begin to identify the molecular mechanisms mediating S1P induced endothelial barrier enhancement, quantitative proteomics analysis (iTRAO™) was performed on membrane rafts isolated from human pulmonary artery endothelial cells in the ...

Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose ...

PubMedID: 24599148 | Modulation of neuronal proteome profile in response to Japanese encephalitis virus infection. | PloS one | 3/6/2014

Aneuploidy causes severe developmental defects and is a near universal feature of tumor cells. Despite its profound effects, the cellular processes affected by aneuploidy are not well characterized. Here, we examined the consequences of aneuploidy on the proteome of aneuploid budding yeast strains. We show that although protein levels largely scale with gene copy number, subunits of multi-protein complexes are notable exceptions. Posttranslational mechanisms attenuate their expression when their encoding genes are in excess. Our proteomic analyses further revealed a novel aneuploidy-associated protein expression signature characteristic of altered metabolism and redox homeostasis. Indeed aneuploid cells harbor increased levels of reactive oxygen species (ROS). Interestingly, increased protein turnover attenuates ROS levels and this novel aneuploidy-associated signature and improves the fitness of most aneuploid strains. Our results show that aneuploidy causes alterations in metabolism and redox ...

Altered proteome profiles have been reported in both postmortem brain tissues and body fluids of subjects with Alzheimer disease (AD), but their broad relationships with AD pathology, amyloid pathology, and tau-related neurodegeneration have not yet been fully explored. Using a robust automated MS-based proteomic biomarker discovery workflow, we measured cerebrospinal fluid (CSF) proteomes to explore their association with well-established markers of core AD pathology. Cross-sectional analysis was performed on CSF collected from 120 older community-dwelling adults with normal (n = 48) or impaired cognition (n = 72). LC-MS quantified hundreds of proteins in the CSF. CSF concentrations of β-amyloid 1-42 (Aβ1-42), tau, and tau phosphorylated at threonine 181 (P-tau181) were determined with immunoassays. First, we explored proteins relevant to biomarker-defined AD. Then, correlation analysis of CSF proteins with CSF markers of amyloid pathology, neuronal injury, and tau hyperphosphorylation (i.e., Aβ1-42

Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, GermanyCologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, GermanySystems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany ...

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Purpose: : To investigate human cornea proteome. The human cornea is composed of several layers interacting in a complex manner and possessing specific functions, like eye protection and optical clearness. Only few proteomic studies of mammalian cornea have been performed leading to the identification of less than 200 proteins in human corneas. Methods: : The present study explores the proteome of the intact normal human cornea using a shot-gun nanoLC-MS/MS strategy and an LTQ Orbitrap mass spectrometer. Results: : A total of 2070 distinct corneal proteins were identified from five human cornea samples, which represents a 14-fold improvement in the number of proteins identified so far for human cornea. Network and gene ontology analyses were used to determine biological pathways specific of the human cornea. They allowed the identification of subnetworks of putative importance for corneal diseases, like a redox regulation and oxidative stress network constituted of aldehyde and alcohol ...

Proteomic profiling and mass spectrometry - posted in Protein and Proteomics: Hello All! Two-dimensional polyacrylamide gel electrophoresis remains a very popular option for global proteomic profiling for its accessibility and low cost. 2-DE has notable drawbacks relative to shotgun proteomics (insufficient resolving power results in multiple proteins per spot, not well-suited to membrane proteins, follow-up by tandem protein mass spectrometry required to ID proteins, etc.). However, t...

TY - GEN. T1 - The human saliva proteome. T2 - Advances in Global Health Through Sensing Technologies 2015. AU - Griffin, Timothy J. PY - 2015/1/1. Y1 - 2015/1/1. N2 - Among the different biomolecules found in human saliva, proteins are among the most prominent. Proteins carry out many vital roles in saliva, from enzymatic catalysis to structure. Proteins also have great potential as diagnostic biomarkers, which can be easily collected using non-invasive methods. In order to catalog salivary proteins, and determine those with diagnostic potential for human disease and other health conditions, mass spectrometry-based proteomic technologies have been used over the last decade or more. Using these conventional technologies, several thousand proteins have been identified in whole saliva, with numerous studies identifying proteins with diagnostic promise for a variety of health conditions. In addition, these technologies have been used to identify proteins expressed by microbial communities in human ...

Cardiac function is thought to play a central role in determining thermal optima and tolerance limits in teleost fishes. Investigating proteomic responses to temperature in cardiac tissues may provide insights into mechanisms supporting the thermal plasticity of cardiac function. Here, we utilized a global proteomic analysis to investigate changes in cardiac protein abundance in response to temperature acclimation (transfer from 13°C to 9, 19 and 26°C) in a eurythermal goby, Gillichthys mirabilis. Proteomic data revealed 122 differentially expressed proteins across acclimation groups, 37 of which were identified using tandem mass-spectrometry. These 37 proteins are involved in energy metabolism, mitochondrial regulation, iron homeostasis, cytoprotection against hypoxia, and cytoskeletal organization. Compared with the 9 and 26°C groups, proteins involved in energy metabolism increased in 19°C-acclimated fish, indicating an overall increase in the capacity for ATP production. Creatine kinase

Post-translational modifications (PTMs) of transcription factors alter interactions with co-regulators and epigenetic modifiers. For example, members of the C/EBP transcription factor family are extensively methylated on arginine and lysine residues in short, conserved, modular domains, implying modification-dependent cofactor docking. Here we describe array peptide screening (APS), a systematic and differential approach to detect PTM-dependent interactions in the human proteome using chemically synthesized, biotinylated peptides coupled to fluorophore-labeled streptavidin. Peptides with and without a modified residue are applied in parallel to bacterial expression libraries in an arrayed format. Interactions are detected and quantified by laser scanning to reveal proteins that differentially bind to nonmodified or modified peptides. We have previously used this method to investigate the effect of arginine methylation of C/EBPβ peptides. The method enables determination of PTM-dependent transcription

Eukaryotic cells replicate by a complex series of evolutionarily conserved events that are tightly regulated at defined stages of the cell division cycle. Progression through this cycle involves a large number of dedicated protein complexes and signaling pathways, and deregulation of this process is implicated in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites and their dynamics. Co-regulated proteins and phosphorylation sites were grouped according to their cell cycle kinetics and compared to publicly available messenger RNA microarray data. Most detected phosphorylation sites and more than 20% of all quantified proteins showed substantial regulation, mainly in mitotic cells. Kinase-motif analysis revealed global activation during S phase of the DNA damage response network, which was mediated by ...

Proteome analysis of bronchoalveolar lavage fluids reveals host and fungal proteins highly expressed during invasive pulmonary aspergillosis in mice and humans:

In this study, we had applied a comprehensive serum proteomics strategy to look for important differential proteins in serum based on AIH mouse model and patients serum. And totally 9 altered proteins were identified in AIH mice serum by 2-DE. Two upregulated proteins, C3 and A2M, were validated in the serum of AIH patients by a targeted iTRAQ analysis. And furthermore, serum level of C3 and A2M was generally higher in 34 cases of AIH patients than normal persons by ELISA detection. From mouse models to clinical AIH sera, the integrated serum proteomics investigation can overcome discrepancy in samples and tools, which is a translational medical viewpoint to look for the molecules associated with AIH.. Serum proteome contains the proteins not only from the liver, small intestine synthesis such as albumin, but also millions of species of immunoglobulin. The serum proteome holds the promise of a reform in disease diagnosis and therapeutic monitoring provided that major challenges in proteomics ...

The Schey lab is interested in both method/instrument development in proteomics analysis as well as in applications of state-of-the-art proteomics technologies in the study of development and disease. Method development/technology projects include methods for integral membrane protein analysis, tandem mass spectrometry of intact proteins (top-down proteomics), spatially-resolved proteomics analysis, and quantitative proteomics. The major area of application is human lens protein modifications and protein-protein interactions. Other areas of interest are: proteomics analysis of heart valve development, and invertebrate (shrimp and oyster) innate immunity. Integral membrane proteins play key roles in signaling, transport, and adhesion, yet they remain difficult to analyze using conventional proteomics methods. Our lab has developed methods to analyze integral membrane proteins and membrane associated proteins including their modifications. In addition, we have developed methods for membrane proteome

Infections by are a major cause of morbidity and mortality worldwide, often causing community-acquired pneumonia, otitis media and also bacteremia and meningitis. Studies on are mainly focused on its virulence or capacity to evade the host immune system, but little is known about the injury caused in lungs during a pneumococcal infection. Herein we investigated this issue comparing the proteome profile of lungs from infected mice with control mice by means of difference gel electrophoresis (DIGE) technology. In order to obtain reliable results three biological replicas were used, and four technical replicas were carried out in each biological replica. Proteomic comparison was performed at two time points: 24 and 48 h post infection. A total of 91 proteins were identified with different abundance. We found important changes in the protein profiles during pneumococcal infection mainly associated with regulation of vesicle-mediated transport, wound healing, and cytoskeleton organization. In ...

Phosphorus deficiency limits plant growth and development. To better understand the mechanisms behind how maize responds to phosphate stress, we compared the proteome analysis results of two groups of maize leaves that were treated separately with 1,000 µM (control, +P) and 5 µM of KH2PO4 (intervention group, −P) for 25 days. In total, 1,342 protein spots were detected on 2-DE maps and 15.43% had changed (P|0.05; ≥1.5-fold) significantly in quantity between the +P and −P groups. These proteins are involved in several major metabolic pathways, including photosynthesis, carbohydrate metabolism, energy metabolism, secondary metabolism, signal transduction, protein synthesis, cell rescue and cell defense and virulence. The results showed that the reduction in photosynthesis under low phosphorus treatment was due to the down-regulation of the proteins involved in CO2 enrichment, the Calvin cycle and the electron transport system. Electron transport and photosynthesis restrictions resulted in a large

Recent improvements in quantitative proteomics approaches, including Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS), permit reproducible large-scale protein measurements across diverse cohorts. Together with genomics, transcriptomics, and other technologies, transomic data sets can be generated that permit detailed analyses across broad molecular interaction networks. Here, we examine mitochondrial links to liver metabolism through the genome, transcriptome, proteome, and metabolome of 386 individuals in the BXD mouse reference population. Several links were validated between genetic variants toward transcripts, proteins, metabolites, and phenotypes. Among these, sequence variants in Cox7a2l alter its proteins activity, which in turn leads to downstream differences in mitochondrial supercomplex formation. This data set demonstrates that the proteome can now be quantified comprehensively, serving as a key complement to transcriptomics, genomics, and metabolomics--a ...

Split-root systems (SRS) have many applications in plant sciences, but their implementation, depending on the experimental design, can be difficult and time-consuming. Additionally, the system is not exempt from limitations, since the time required for the establishment of the SRS imposes a limit to how early in plant development experiments can be performed. Here, we optimized and explained in detail a method for establishing a SRS in young Arabidopsis thaliana seedlings, both in vitro and in soil. We found that the partial de-rooting minimized the recovery time compared to total de-rooting, thus allowing the establishment of the split-root system in younger plants. Analysis of changes in the Arabidopsis leaf proteome following the de-rooting procedure highlighted the distinct metabolic alterations that totally and partially de-rooted plants undergo during the healing process. This system was also validated for its use in drought experiments, as it offers a way to apply water-soluble compounds to

Sodium Laurate, a Novel Protease- and Mass Spectrometry-Compatible Detergent for Mass Spectrometry-Based Membrane Proteomics. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.

Organeller proteomics can be an emerging technology that is critical in determining the cellular transmission transduction pathways. available literature, and databases focusing on detailed comparative analysis of NPs and their functions in order to understand how flower nucleus works. The evaluate also shed light on the current status of flower nuclear proteome and discusses the future prospect. analyses. Custom NP databases, for example, yeast-NPD1, human-NPD2, with that of candida, fruit-fly and animal (human being, rat, and mouse; Table ?Table11). The in investigating the nuclear proteomes of SCH 54292 inhibitor available species were the extensive literature search, availability of relevant databases (human being, mouse, rat and plant, TIGR, UniProt and Swissprot) and (Varma and Mishra, 2011), model vegetation (Abdalla et al., 2010; Abdalla and Rafudeen, 2012), and chickpea (Pandey et al., 2006, 2008). The beautiful results from these evaluations claim that until just 1868 NPs are ...

Dietary fish oil (DFO) has been identified as a micronutrient supplement with the potential to improve musculoskeletal health in old age. Few data are available for effects of DFO on muscle contractility, despite the significant negative impact of muscle weakness on age-related health outcomes. Accordingly, the effects of a DFO intervention on the contractile function and proteomic profile of adult and aged in an animal model of aging were investigated. This preliminary study evaluated 14 adult (8 months) and 12 aged (22 months) male, Sprague-Dawley rats consuming a DFO-supplemented diet or a control diet for 8 weeks (7 adult and 6 aged/dietary group). Animal weight, food intake and grip strength were assessed at the start and end of the FO intervention. In situ force and contractile properties were measured in the medial gastrocnemius muscle following the intervention and muscles were processed for 2-D gel electrophoresis and proteomic analysis via liquid chromatography with tandem mass spectrometry,

Sequence searching (5) revealed that 14 of the 39 calmodulin-binding proteins contain a motif whose consensus is (I/L)QXXK(K/X)GB, where X is any residue and B is a basic residue (Fig. 2B). A related sequence in myosins, IQXXXXKXXXR, has been shown previously to bind calmodulin (18). Thus, we demonstrate that the domain is found in many calmodulin-binding proteins. Presumably the other targets that lack this motif have other calmodulin-binding sequences (10).. In addition to the calmodulin-binding targets, we also identified one protein, Pyc1p, that bound Cy3-labeled streptavidin. Pyc1p encodes a pyruvate carboxylase 1 homolog that contains a highly conserved biotin attachment region (19). Thus, as predicted by its sequence, Pyc1p is biotinylated in vivo. With appropriate detection assays, we expect that proteome chips can identify many types of posttranslational modification of proteins.. To test whether proteome chips could be used to identify activities that might not be accessible by other ...

Proteomic studies of respiratory disorders have the potential to identify protein biomarkers for diagnosis and disease monitoring. Utilisation of sensitive quantitative proteomic methods creates opportunities to determine individual patient proteomes. The aim of the current study was to determine if quantitative proteomics of bronchial biopsies from asthmatics can distinguish relevant biological functions and whether inhaled glucocorticoid treatment affects these functions. Endobronchial biopsies were taken from untreated asthmatic patients (n = 12) and healthy controls (n = 3). Asthmatic patients were randomised to double blind treatment with either placebo or budesonide (800 μg daily for 3 months) and new biopsies were obtained. Proteins extracted from the biopsies were digested and analysed using isobaric tags for relative and absolute quantitation combined with a nanoLC-LTQ Orbitrap mass spectrometer. Spectra obtained were used to identify and quantify proteins. Pathways analysis was performed

Proteomic studies of respiratory disorders have the potential to identify protein biomarkers for diagnosis and disease monitoring. Utilisation of sensitive quantitative proteomic methods creates opportunities to determine individual patient proteomes. The aim of the current study was to determine if quantitative proteomics of bronchial biopsies from asthmatics can distinguish relevant biological functions and whether inhaled glucocorticoid treatment affects these functions. Endobronchial biopsies were taken from untreated asthmatic patients (n = 12) and healthy controls (n = 3). Asthmatic patients were randomised to double blind treatment with either placebo or budesonide (800 μg daily for 3 months) and new biopsies were obtained. Proteins extracted from the biopsies were digested and analysed using isobaric tags for relative and absolute quantitation combined with a nanoLC-LTQ Orbitrap mass spectrometer. Spectra obtained were used to identify and quantify proteins. Pathways analysis was performed

Biosci Rep. 2021 Apr 30;41(4):BSR-20180067_EOC. doi: 10.1042/BSR-20180067_EOC.. NO ABSTRACT. PMID:33786578 , DOI:10.1042/BSR-20180067_EOC. ...

Creative Proteomics is the proteomics division of CD Inc, an integrated CRO company that provides a full range of drug development services, including Molecular Biology, Biochemistry, Systems Biology, Organic Chemistry, Genomics, Bioinformatics, Structural Biology, Preclinical and Clinical studies. Creative Proteomics specializes in a full range of services to support various proteome-related researches from identification of single proteins to large-scale proteomic studies. We have one of the most advanced proteomics platforms in the world and our staff scientists are experienced proteomics professionals. Our proteome analysis platform provides protein separation, characterization, identification and quantification services, featured with high throughput and super-sensitivity. In addition, analyses of protein post-translational modifications such as phosphorylation and glycosylation are available. Creative Proteomics is staffed by specialists who are extensively experienced in handling hard-to

Identification of disease markers in serum represents a very important problem, but it is rather challenging due to the composition complexity and the large dynamic range of proteins in human sera, which makes direct comparative analyses of serum proteomic data between diseased and control samples exceedingly difficult [1, 2]. What can possibly alleviate the problem is to carry out such comparative analyses among a group of candidate protein markers rather than searching through the whole serum proteome in blind. The candidate markers could be suggested by differential analyses based on microarray gene expression or proteomic data of diseased versus control tissues [3]. The basic idea is to first identify genes or proteins with abnormal expression patterns in diseased versus control tissues, which represents a substantially simpler problem other than direct comparative proteomic analyses of serum marker identification, and then determine if the abnormally expressed proteins may possibly get ...

Among components of the translational machinery, ribonucleoside modifications on tRNAs are emerging as critical regulators of cell physiology and stress response. Here, we demonstrate highly coordinated behavior of the repertoire of tRNA modifications of Plasmodium falciparum throughout the intra-erythrocytic developmental cycle (IDC). We observed both a synchronized increase in 22 of 28 modifications from ring to trophozoite stage, consistent with tRNA maturation during translational up-regulation, and asynchronous changes in six modifications. Quantitative analysis of ~2,100 proteins across the IDC revealed that up- and down-regulated proteins in late but not early stages have a marked codon bias that directly correlates with parallel changes in tRNA modifications and enhanced translational efficiency. We thus propose a model in which tRNA modifications modulate the abundance of stage-specific proteins by enhancing translation efficiency of codon-biased transcripts for critical genes. These ...

Reverse-phase protein arrays (RPPA) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and to develop novel cancer therapies. To facilitate community-based investigation of the large-scale protein expression data generated by this platform, we have developed a user-friendly, open-access bioinformatic resource, The Cancer Proteome Atlas (TCPA, http://tcpaportal.org), which contains two separate web applications.

Rationale: Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts. Objective: The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine. Methods and results: We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10 924 proteins in ...