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low-throughput proteomics

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https://www.readbyqxmd.com/read/30092380/transcriptome-facilitated-proteomic-characterization-of-rear-fanged-snake-venoms-reveal-abundant-metalloproteinases-with-enhanced-activity
#1
Cassandra M Modahl, Seth E Frietze, Stephen P Mackessy
High-throughput technologies were used to identify venom gland toxin expression and to characterize the venom proteomes of two rear-fanged snakes, Ahaetulla prasina (Asian Green Vine Snake) and Borikenophis portoricensis (Puerto Rican Racer). Sixty-nine complete toxin-coding transcripts from 12 venom protein superfamilies (A. prasina) and 50 complete coding transcripts from 11 venom protein superfamilies (B. portoricensis) were identified in the venom glands. However, only 18% (A. prasina) and 32% (B. portoricensis) of the translated protein isoforms were detected in the proteome of these venoms...
August 6, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/30078316/a-surfactant-cocktail-aided-extraction-precipitation-on-pellet-digestion-sepod-strategy-enables-rapid-efficient-and-reproducible-sample-preparation-for-large-scale-quantitative-proteomics
#2
Shichen Shen, Bo An, Xue Wang, Shannon P Hilchey, Jun Li, Jin Cao, Yu Tian, Chenqi Hu, Liang Jin, Andrew Ng, Chengjian Tu, Miao Qu, Martin ZAnd, Jun Qu
For quantitative proteomics, efficient, robust, and reproducible sample preparation with high throughput is critical yet challenging, especially when large cohorts are involved, as is often required by clinical/pharmaceutical studies. We describe a rapid and straightforward surfactant cocktail-aided extraction/precipitation/on-pellet digestion(SEPOD) strategy to address this need. Prior to organic solvent precipitation and on-pellet digestion, SEPOD treats samples with a surfactant cocktail(SC) containing multiple non-ionic/anionic surfactants, which achieves: i)exhaustive/reproducible protein extraction, including membrane-bound proteins; ii)effective removal of detrimental non-protein matrix components(e...
August 5, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/30058389/applications-of-maldi-tof-mass-spectrometry-in-clinical-proteomics
#3
Viviana Greco, Cristian Piras, Luisa Pieroni, Maurizio Ronci, Lprenza Putignani, Paola Roncada, Andrea Urbani
The development of precision medicine requires advanced technologies to address the multifactorial disease stratification and to support personalized treatments. Among omics techniques, proteomics based on Mass Spectrometry (MS) is becoming increasingly relevant in clinical practice allowing a phenotypic characterization of the dynamic functional status of the organism. From this perspective, Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) MS is a suitable platform for providing a high-throughput support to clinics...
July 30, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/30047063/proteomics-of-vibrio-cholerae
#4
Ryszard A Zielke
Combining high-throughput mass spectrometry with isobaric tags for relative and absolute quantification (iTRAQ) allows for the identification and relative quantification of proteins from multiple samples. Furthermore, low-abundance proteins that are usually not detected can be enriched by using only the relevant fraction of the proteome, e.g., cytoplasmic, membrane proteins, or secreted proteins. Described here is a workflow for isolation and enrichment of secreted and membrane proteins that is compatible with mass spectrometry...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29936833/deciphering-the-functions-of-o-glcnac-glycosylation-in-the-brain-the-role-of-site-specific-quantitative-o-glcnacomics
#5
John W Thompson, Alexander W Sorum, Linda C Hsieh-Wilson
The dynamic posttranslational modification O-linked β- N-acetylglucosamine glycosylation (O-GlcNAcylation) is present on thousands of intracellular proteins in the brain. Like phosphorylation, O-GlcNAcylation is inducible and plays important functional roles in both physiology and disease. Recent advances in mass spectrometry (MS) and bioconjugation methods are now enabling the mapping of O-GlcNAcylation events to individual sites in proteins. However, our understanding of which glycosylation events are necessary for regulating protein function and controlling specific processes, phenotypes, or diseases remains in its infancy...
July 10, 2018: Biochemistry
https://www.readbyqxmd.com/read/29900422/cell-free-synthesis-of-stable-isotope-labeled-internal-standards-for-targeted-quantitative-proteomics
#6
REVIEW
Ryohei Narumi, Keiko Masuda, Takeshi Tomonaga, Jun Adachi, Hiroki R Ueda, Yoshihiro Shimizu
High-sensitivity mass spectrometry approaches using selected reaction monitoring (SRM) or multiple reaction monitoring (MRM) methods are powerful tools for targeted quantitative proteomics-based investigation of dynamics in specific biological systems. Both high-sensitivity detection of low-abundance proteins and their quantification using this technique employ stable isotope-labeled peptide internal standards. Currently, there are various ways for preparing standards, including chemical peptide synthesis, cellular protein expression, and cell-free protein or peptide synthesis...
June 2018: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29881726/using-omics-to-understand-and-treat-pulmonary-vascular-disease
#7
REVIEW
Anna R Hemnes
Pulmonary arterial hypertension (PAH) is a devastating disease for which there is no cure. Presently this condition is differentiated from other diseases of the pulmonary vasculature by a practitioner's history, physical examination, and clinical studies with clinical markers of disease severity primarily guiding therapeutic choices. New technologies such as next generation DNA sequencing, high throughput RNA sequencing, metabolomics and proteomics have greatly enhanced the amount of data that can be studied efficiently in patients with PAH and other rare diseases...
2018: Frontiers in Medicine
https://www.readbyqxmd.com/read/29872746/proteomic-studies-on-lactic-acid-bacteria-a-review
#8
REVIEW
K Sri Vinusha, K Deepika, T Sudhakar Johnson, Ganesh K Agrawal, Randeep Rakwal
Probiotics are amongst the most common microbes in the gastro-intestinal tract of humans and other animals. Prominent among probiotics are Lactobacillus and Bifidobacterium . They offer wide-ranging health promoting benefits to the host which include reduction in pathological alterations, stimulation of mucosal immunity and interaction with mediators of inflammation among others. Proteomics plays a vital role in understanding biological functions of a cell. Proteomics is also slowly and steadily adding to the existing knowledge on role of probiotics...
July 2018: Biochemistry and Biophysics Reports
https://www.readbyqxmd.com/read/29868478/discovery-of-novel-and-clinically-relevant-markers-in-formalin-fixed-paraffin-embedded-esophageal-cancer-specimen
#9
Joe Abdo, Christopher S Wichman, Nicholas E Dietz, Pawel Ciborowski, John Fleegel, Sumeet K Mittal, Devendra K Agrawal
Due to the ineffectiveness of chemoradiation and targeted therapy in esophageal anticancer care and the subsequent low survival rates, we constructed a high throughput method to discover and investigate new markers with prognostic, diagnostic, and therapeutic clinical utility. This was accomplished by developing a quick, inexpensive, and dependable platform to simultaneously quantify thousands of proteins which subsequently revealed novel markers involved in the pathogenesis of esophageal adenocarcinoma (EAC) via discovery mass spectrometry paired with conservative biostatistics...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29843713/development-of-a-high-throughput-flexible-quantitative-suspension-array-assay-for-igg-against-multiple-plasmodium-falciparum-antigens
#10
Itziar Ubillos, Joseph J Campo, Alfons Jiménez, Carlota Dobaño
BACKGROUND: Antibody responses to Plasmodium falciparum play a critical role in disease control. Finding reliable IgG biomarkers of protection is complicated by a parasite proteome of over 5000 proteins, some with polymorphisms. Studies of anti-malarial naturally acquired and vaccine immunity would benefit from a standard high-throughput immunoassay to measure multiple antibodies. A multiplex quantitative suspension assay to measure antigen-specific IgGs was developed and its precision (reproducibility and repeatability), dynamic range, limits of detection and quantification, and non-specific binding to different P...
May 29, 2018: Malaria Journal
https://www.readbyqxmd.com/read/29778222/exploring-dinoflagellate-biology-with-high-throughput-proteomics
#11
REVIEW
David Morse, Sirius P K Tse, Samuel C L Lo
Dinoflagellates are notorious for their ability to form the harmful algal blooms known as "red tides," yet the mechanisms underlying bloom formation remain poorly understood. Despite recent advances in nucleic acid sequencing, which have generated transcriptomes from a wide range of species exposed to a variety of different conditions, measuring changes in RNA levels have not generally produced great insight into dinoflagellate cell biology or environmental physiology, nor do we have a thorough grasp on the molecular events underpinning bloom formation...
May 2018: Harmful Algae
https://www.readbyqxmd.com/read/29660691/proteomic-analysis-of-liquid-biopsy-from-tumor-draining-vein-indicates-that-high-expression-of-exosomal-ecm1-is-associated-with-relapse-in-stage-i-iii-colon-cancer
#12
Sandra Santasusagna, Isabel Moreno, Alfons Navarro, Joan J Castellano, Francisco Martinez, Raquel Hernández, Carmen Muñoz, Mariano Monzo
BACKGROUND: The analysis of exosomes in blood obtained from the tumor-draining mesenteric vein (MV) can identify tumor biomarkers before they reach target organs and form the premetastatic niche where circulating tumor cells can anchor. Our group has recently shown that microRNAs in plasma from the MV-but not the peripheral vein (PV)-have been related to liver metastases in colon cancer (CC) patients. Here we examine the exosomal protein cargo in plasma from the MV and paired PV in 31 CC patients...
June 2018: Translational Oncology
https://www.readbyqxmd.com/read/29608558/high-throughput-interaction-screens-illuminate-the-role-of-c-di-amp-in-cyanobacterial-nighttime-survival
#13
Benjamin E Rubin, TuAnh Ngoc Huynh, David G Welkie, Spencer Diamond, Ryan Simkovsky, Emily C Pierce, Arnaud Taton, Laura C Lowe, Jenny J Lee, Scott A Rifkin, Joshua J Woodward, Susan S Golden
The broadly conserved signaling nucleotide cyclic di-adenosine monophosphate (c-di-AMP) is essential for viability in most bacteria where it has been studied. However, characterization of the cellular functions and metabolism of c-di-AMP has largely been confined to the class Bacilli, limiting our functional understanding of the molecule among diverse phyla. We identified the cyclase responsible for c-di-AMP synthesis and characterized the molecule's role in survival of darkness in the model photosynthetic cyanobacterium Synechococcus elongatus PCC 7942...
April 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29588628/a-robust-mass-spectrometry-method-for-rapid-profiling-of-erythrocyte-ghost-membrane-proteomes
#14
Haddy K S Fye, Paul Mrosso, Lesley Bruce, Marie-Laëtitia Thézénas, Simon Davis, Roman Fischer, Gration L Rwegasira, Julie Makani, Benedikt M Kessler
Background: Red blood cell (RBC) physiology is directly linked to many human disorders associated with low tissue oxygen levels or anemia including chronic obstructive pulmonary disease, congenital heart disease, sleep apnea and sickle cell anemia. Parasites such as Plasmodium spp. and phylum Apicomplexa directly target RBCs, and surface molecules within the RBC membrane are critical for pathogen interactions. Proteomics of RBC membrane 'ghost' fractions has therefore been of considerable interest, but protocols described to date are either suboptimal or too extensive to be applicable to a larger set of clinical cohorts...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29544527/white-paper-by-the-society-for-csf-analysis-and-clinical-neurochemistry-overcoming-barriers-in-biomarker-development-and-clinical-translation
#15
REVIEW
Charlotte E Teunissen, Markus Otto, Sebastiaan Engelborghs, Sanna-Kaisa Herukka, Sylvain Lehmann, Piotr Lewczuk, Alberto Lleó, Armand Perret-Liaudet, Hayrettin Tumani, Martin R Turner, Marcel M Verbeek, Jens Wiltfang, Henrik Zetterberg, Lucilla Parnetti, Kaj Blennow
Body fluid biomarkers have great potential for different clinical purposes, including diagnosis, prognosis, patient stratification and treatment effect monitoring. This is exemplified by current use of several excellent biomarkers, such as the Alzheimer's disease cerebrospinal fluid (CSF) biomarkers, anti-neuromyelitis optica antibodies and blood neurofilament light. We still, however, have a strong need for additional biomarkers and several gaps in their development and implementation should be filled. Examples of such gaps are i) limited knowledge of the causes of neurological diseases, and thus hypotheses about the best biomarkers to detect subclinical stages of these diseases; ii) the limited success translating discoveries obtained by e...
March 15, 2018: Alzheimer's Research & Therapy
https://www.readbyqxmd.com/read/29522462/venomics-accelerated-cone-snail-venom-peptide-discovery
#16
REVIEW
S W A Himaya, Richard J Lewis
Cone snail venoms are considered a treasure trove of bioactive peptides. Despite over 800 species of cone snails being known, each producing over 1000 venom peptides, only about 150 unique venom peptides are structurally and functionally characterized. To overcome the limitations of the traditional low-throughput bio-discovery approaches, multi-omics systems approaches have been introduced to accelerate venom peptide discovery and characterisation. This "venomic" approach is starting to unravel the full complexity of cone snail venoms and to provide new insights into their biology and evolution...
March 9, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29501168/a-review-of-nanoscale-lc-esi-for-metabolomics-and-its-potential-to-enhance-the-metabolome-coverage
#17
REVIEW
Andrew J Chetwynd, Arthur David
Liquid chromatography-electrospray ionisation-mass spectrometry (LC-ESI-MS) platforms are widely used to perform high throughput untargeted profiling of biological samples for metabolomics-based approaches. However, these LC-ESI platforms usually favour the detection of metabolites present at relatively high concentrations because of analytical limitations such as ion suppression, thus reducing overall sensitivity. To counter this issue of sensitivity, the latest in terms of analytical platforms can be adopted to enable a greater portion of the metabolome to be analysed in a single analytical run...
May 15, 2018: Talanta
https://www.readbyqxmd.com/read/29499399/cancer-cells-biomineralize-ionic-gold-into-nanoparticles-microplates-via-secreting-defense-proteins-with-specific-gold-binding-peptides
#18
Ajay Vikram Singh, Timotheus Jahnke, Vimal Kishore, Byung-Wook Park, Madu Batuwangala, Joachim Bill, Metin Sitti
Cancer cells have the capacity to synthesize nanoparticles (NPs). The detailed mechanism of this process is not very well documented. We report the mechanism of biomineralization of aqueous gold chloride into NPs and microplates in the breast-cancer cell line MCF7. Spherical gold NPs are synthesized in these cells in the presence of serum in the culture media by the reduction of HAuCl4 . In the absence of serum, the cells exhibit gold microplate formation through seed-mediate growth albeit slower reduction...
April 15, 2018: Acta Biomaterialia
https://www.readbyqxmd.com/read/29467300/high-throughput-metabolomic-analysis-predicts-mode-of-action-of-uncharacterized-antimicrobial-compounds
#19
Mattia Zampieri, Balazs Szappanos, Maria Virginia Buchieri, Andrej Trauner, Ilaria Piazza, Paola Picotti, Sébastien Gagneux, Sonia Borrell, Brigitte Gicquel, Joel Lelievre, Balazs Papp, Uwe Sauer
Rapidly spreading antibiotic resistance and the low discovery rate of new antimicrobial compounds demand more effective strategies for early drug discovery. One bottleneck in the drug discovery pipeline is the identification of the modes of action (MoAs) of new compounds. We have developed a rapid systematic metabolome profiling strategy to classify the MoAs of bioactive compounds. The method predicted MoA-specific metabolic responses in the nonpathogenic bacterium Mycobacterium smegmatis after treatment with 62 reference compounds with known MoAs and different metabolic and nonmetabolic targets...
February 21, 2018: Science Translational Medicine
https://www.readbyqxmd.com/read/29454799/identification-of-genomic-variants-causing-sperm-abnormalities-and-reduced-male-fertility
#20
REVIEW
Jeremy F Taylor, Robert D Schnabel, Peter Sutovsky
Whole genome sequencing has identified millions of bovine genetic variants; however, there is currently little understanding about which variants affect male fertility. It is imperative that we begin to link detrimental genetic variants to sperm phenotypes via the analysis of semen samples and measurement of fertility for bulls with alternate genotypes. Artificial insemination (AI) bulls provide a useful model system because of extensive fertility records, measured as sire conception rates (SCR). Genetic variants with moderate to large effects on fertility can be identified by sequencing the genomes of fertile and subfertile or infertile sires identified with high or low SCR as adult AI bulls or yearling bulls that failed Breeding Soundness Evaluation...
July 2018: Animal Reproduction Science
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