scholarly journals Functional Proteomic Profiling of Phosphodiesterases Using SeraFILE Separations Platform

2012 ◽  
Vol 2012 ◽  
pp. 1-8
Author(s):  
Amita R. Oka ◽  
Matthew P. Kuruc ◽  
Ketan M. Gujarathi ◽  
Swapan Roy
Keyword(s):  
Biomarker Discovery ◽  
Brain Homogenate ◽  
Disease Diagnosis ◽  
Bovine Brain ◽  
Tissue Cell ◽  
Kinetic Properties ◽  
Proteomic Profiling ◽  
Tissue Samples ◽  
Camp Hydrolysis ◽  
Few Data

Functional proteomic profiling can help identify targets for disease diagnosis and therapy. Available methods are limited by the inability to profile many functional properties measured by enzymes kinetics. The functional proteomic profiling approach proposed here seeks to overcome such limitations. It begins with surface-based proteome separations of tissue/cell-line extracts, using SeraFILE, a proprietary protein separations platform. Enzyme kinetic properties of resulting subproteomes are then characterized, and the data integrated into proteomic profiles. As a model, SeraFILE-derived subproteomes of cyclic nucleotide-hydrolyzing phosphodiesterases (PDEs) from bovine brain homogenate (BBH) and rat brain homogenate (RBH) were characterized for cAMP hydrolysis activity in the presence (challenge condition) and absence of cGMP. Functional profiles of RBH and BBH were compiled from the enzyme activity response to the challenge condition in each of the respective subproteomes. Intersample analysis showed that comparable profiles differed in only a few data points, and that distinctive subproteomes can be generated from comparable tissue samples from different animals. These results demonstrate that the proposed methods provide a means to simplify intersample differences, and to localize proteins attributable to sample-specific responses. It can be potentially applied for disease and nondisease sample comparison in biomarker discovery and drug discovery profiling.

Reverse Transcription–Polymerase Chain Reaction Assay for Species-Specific Detection of Bovine Central Nervous System Tissue in Meat and Meat Products

2003 ◽  
Vol 66 (4) ◽  
pp. 644-651 ◽  
Author(s):  
C. SEYBOLDT ◽  
A. JOHN ◽  
T. v. MUEFFLING ◽  
B. NOWAK ◽  
S. WENZEL
Keyword(s):  
Meat Products ◽  
Rflp Analysis ◽  
Brain Homogenate ◽  
Bovine Brain ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Tissue Samples ◽  
Polymerase Chain ◽  
Minced Meat ◽  
Cooked Meat

This paper reports the development of a reverse transcription–polymerase chain reaction (RT-PCR) assay coupled with restriction fragment length polymorphism (RFLP) analysis to specifically detect the glial fibrillary acidic protein (GFAP) mRNA of bovine central nervous system (CNS) tissue in minced meat and meat products. RNA extracted from bovine brain tissue and brain tissue from other mammals yielded a 168-bp CNS-specific signal after RT-PCR. The species specificity of the assay can be obtained by subsequent RFLP analysis of the amplified RT-PCR product. To determine the tissue specificity of the RT-PCR assay, various bovine tissues were analyzed. Bovine GFAP mRNA was detected in the brain and spinal cord, and these results are consistent with the reported large amounts of detectable protein in these tissues. Additionally, GFAP mRNA was present in skeletal muscle tissue samples and in some heart muscle tissue samples, but heat treatment of samples prior to extraction resulted in the loss of the non-CNS signals. To evaluate the stability and detectability of bovine GFAP mRNA in comminuted meat and in cooked meat products, mixtures containing bovine brain homogenate at concentrations of 0.5 to 5% were prepared and analyzed. The examination of minced meat with added bovine brain homogenate revealed GFAP mRNA RT-PCR signal stability for at least 7 days at a storage temperature of 4°C. In cooked meat products bovine GFAP mRNA signal was detectable for at least 35 days. Bovine brain homogenate at a concentration of 0.5% was successfully detected in all of the experiments conducted, and no false-negative results were obtained. It is concluded that bovine GFAP mRNA can serve as a sensitive and specific marker for bovine CNS tissue in minced meat and in pasteurized meat products.

scholarly journals Current Status and Future Perspectives about Molecular Biomarkers of Nasopharyngeal Carcinoma

Cancers ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 3490
Author(s):  
Pui Yan Siak ◽  
Alan Soo-Beng Khoo ◽  
Chee Onn Leong ◽  
Boon-Peng Hoh ◽  
Shiau-Chuen Cheah
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Biomarker Discovery ◽  
Southern China ◽  
Disease Diagnosis ◽  
Late Presentation ◽  
Dietary Factors ◽  
Current Status ◽  
Complex Nature ◽  
Epstein Barr Virus Infection ◽  
Potential Biomarker

Nasopharyngeal carcinoma (NPC) is an epithelial malignancy that shows a remarkable ethnic and geographical distribution. It is one of the major public health problems in some countries, especially Southern China and Southeast Asia, but rare in most Western countries. Multifactorial interactions such as Epstein–Barr virus infection, individual’s genetic susceptibility, as well as environmental and dietary factors may facilitate the pathogenesis of this malignancy. Late presentation and the complex nature of the disease have led it to become a major cause of mortality. Therefore, an effective, sensitive, and specific molecular biomarker is urgently needed for early disease diagnosis, prognosis, and prediction of metastasis and recurrence after treatment. In this review, we discuss the recent research status of potential biomarker discovery and the problems that need to be explored further for better NPC management. By studying the aberrant pattern of these candidate biomarkers that promote NPC development and progression, we are able to understand the complexity of this malignancy better, hence positing our stands better towards strategies that may provide a way forward to the discovery of more reliable and specific biomarkers for diagnosis and targeted therapeutic development.

scholarly journals Next-Generation Biomarkers for Cholangiocarcinoma

Cancers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 3222
Author(s):  
Pedro M. Rodrigues ◽  
Arndt Vogel ◽  
Marco Arrese ◽  
Domingo C. Balderramo ◽  
Juan W. Valle ◽  
...  
Keyword(s):  
Biomarker Discovery ◽  
Tumor Development ◽  
Predictive Biomarkers ◽  
Disease Diagnosis ◽  
Future Research ◽  
Tumor Biopsy ◽  
Non Invasive ◽  
Tumor Stages ◽  
At Risk Populations ◽  
Early Tumor

The increasing mortality rates of cholangiocarcinoma (CCA) registered during the last decades are, at least in part, a result of the lack of accurate non-invasive biomarkers for early disease diagnosis, making the identification of patients who might benefit from potentially curative approaches (i.e., surgery) extremely challenging. The obscure CCA pathogenesis and associated etiological factors, as well as the lack of symptoms in patients with early tumor stages, highly compromises CCA identification and to predict tumor development in at-risk populations. Currently, CCA diagnosis is accomplished by the combination of clinical/biochemical features, radiological imaging and non-specific serum tumor biomarkers, although a tumor biopsy is still needed to confirm disease diagnosis. Furthermore, prognostic and predictive biomarkers are still lacking and urgently needed. During the recent years, high-throughput omics-based approaches have identified novel circulating biomarkers (diagnostic and prognostic) that might be included in large, international validation studies in the near future. In this review, we summarize and discuss the most recent advances in the field of biomarker discovery in CCA, providing new insights and future research directions.

Evidence of the three main clonalToxoplasma gondiilineages from wild mammalian carnivores in the UK

Parasitology ◽  
2013 ◽  
Vol 140 (14) ◽  
pp. 1768-1776 ◽  
Author(s):  
A. BURRELLS ◽  
P. M. BARTLEY ◽  
I. A. ZIMMER ◽  
S. ROY ◽  
A. C. KITCHENER ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Rflp Markers ◽  
Type I ◽  
Type Ii ◽  
Red Foxes ◽  
Mammal Species ◽  
Tissue Samples ◽  
Pcr Rflp ◽  
Few Data ◽  
The Uk

SUMMARYToxoplasma gondiiis a zoonotic pathogen defined by three main clonal lineages (types I, II, III), of which type II is most common in Europe. Very few data exist on the prevalence and genotypes ofT. gondiiin the UK. Wildlife can act as sentinel species forT. gondiigenotypes present in the environment, which may subsequently be transmitted to livestock and humans. DNA was extracted from tissue samples of wild British carnivores, including 99 ferrets, 83 red foxes, 70 polecats, 65 mink, 64 badgers and 9 stoats. Parasite DNA was detected using a nested ITS1 PCR specific forT. gondii, PCR positive samples were subsequently genotyped using five PCR–RFLP markers.Toxoplasma gondiiDNA was detected within all these mammal species and prevalence varied from 6·0 to 44·4% depending on the host. PCR–RFLP genotyping identified type II as the predominant lineage, but type III and type I alleles were also identified. No atypical or mixed genotypes were identified within these animals. This study demonstrates the presence of alleles for all three clonal lineages with potential for transmission to cats and livestock. This is the first DNA-based study ofT. gondiiprevalence and genotypes across a broad range of wild British carnivores.

scholarly journals Proteomic Identification and Quantification of Snake Venom Biomarkers in Venom and Plasma Extracellular Vesicles

Toxins ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 654
Author(s):  
Nicholas Kevin Willard ◽  
Emelyn Salazar ◽  
Fabiola Alejandra Oyervides ◽  
Cierra Siobhrie Wiebe ◽  
Jack Sutton Ocheltree ◽  
...  
Keyword(s):  
Extracellular Vesicles ◽  
Snake Venom ◽  
Biomarker Discovery ◽  
Bioinformatic Analysis ◽  
Disease Diagnosis ◽  
Systemic Circulation ◽  
Acid Oxidase ◽  
Amino Acid Oxidase ◽  
Proteomic Identification ◽  
Identification And Quantification

The global exploration of snakebites requires the use of quantitative omics approaches to characterize snake venom as it enters into the systemic circulation. These omics approaches give insights into the venom proteome, but a further exploration is warranted to analyze the venom-reactome for the identification of snake venom biomarkers. The recent discovery of extracellular vesicles (EVs), and their critical cellular functions, has presented them as intriguing sources for biomarker discovery and disease diagnosis. Herein, we purified EV’s from the snake venom (svEVs) of Crotalus atrox and C. oreganus helleri, and from plasma of BALB/c mice injected with venom from each snake using EVtrap in conjunction with quantitative mass spectrometry for the proteomic identification and quantification of svEVs and plasma biomarkers. Snake venom EVs from C. atrox and C. o. helleri were highly enriched in 5′ nucleosidase, L-amino acid oxidase, and metalloproteinases. In mouse plasma EVs, a bioinformatic analysis for revealed upregulated responses involved with cytochrome P450, lipid metabolism, acute phase inflammation immune, and heat shock responses, while downregulated proteins were associated with mitochondrial electron transport, NADH, TCA, cortical cytoskeleton, reticulum stress, and oxidative reduction. Altogether, this analysis will provide direct evidence for svEVs composition and observation of the physiological changes of an envenomated organism.

scholarly journals Accelerated Protein Biomarker Discovery from FFPE tissue samples using Single-shot, Short Gradient Microflow SWATH MS

2019 ◽  
Author(s):  
Rui Sun ◽  
Christie Hunter ◽  
Chen Chen ◽  
Weigang Ge ◽  
Nick Morrice ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Biomarker Discovery ◽  
Single Shot ◽  
Protein Biomarkers ◽  
Differential Abundance ◽  
Tissue Samples ◽  
Peptide Precursors ◽  
High Consistency ◽  
Method R ◽  
Acquisition Method

ABSTRACTWe report and evaluated a microflow, single-shot, short gradient SWATH MS method intended to accelerate the discovery and verification of protein biomarkers in clinical specimens. The method uses 15-min gradient microflow-LC peptide separation, an optimized SWATH MS window configuration and OpenSWATH software for data analysis.We applied the method to a cohort 204 of FFPE prostate tissue samples from 58 prostate cancer patients and 10 prostatic hyperplasia patients. Altogether we identified 27,976 proteotypic peptides and 4,043 SwissProt proteins from these 204 samples. Compared to a reference SWATH method with 2-hour gradient the accelerated method consumed only 27% instrument time, quantified 80% proteins and showed reduced batch effects. 3,800 proteins were quantified by both methods in two different instruments with relatively high consistency (r = 0.77). 75 proteins detected by the accelerated method with differential abundance between clinical groups were selected for further validation. A shortlist of 134 selected peptide precursors from the 75 proteins were analyzed using MRM-HR, exhibiting high quantitative consistency with the 15-min SWATH method (r = 0.89) in the same sample set. We further verified the capacity of these 75 proteins in separating benign and malignant tissues (AUC = 0.99) in an independent prostate cancer cohort (n=154).Overall our data show that the single-shot short gradient microflow-LC SWATH MS method achieved about 4-fold acceleration of data acquisition with reduced batch effect and a moderate level of protein attrition compared to a standard SWATH acquisition method. Finally, the results showed comparable ability to separate clinical groups.

Proteomic Profiling for Colorectal Cancer Biomarker Discovery

2018 ◽  
pp. 241-269 ◽  
Author(s):  
Paula Álvarez-Chaver ◽  
Loretta De Chiara ◽  
Vicenta Soledad Martínez-Zorzano
Keyword(s):  
Colorectal Cancer ◽  
Biomarker Discovery ◽  
Cancer Biomarker ◽  
Proteomic Profiling

scholarly journals Perspectives for metabolomics in testosterone replacement therapy

2012 ◽  
Vol 215 (1) ◽  
pp. 3-16 ◽  
Author(s):  
Robin Haring
Keyword(s):  
Replacement Therapy ◽  
Biomarker Discovery ◽  
Clinical Symptoms ◽  
Late Onset ◽  
Disease Diagnosis ◽  
Deficiency Syndrome ◽  
Testosterone Replacement ◽  
Testosterone Replacement Therapy ◽  
Age Related ◽  
Pubmed Database

Testosterone is the major circulating androgen in men but exhibits an age-related decline in the ageing male. Late-onset hypogonadism or androgen deficiency syndrome (ADS) is a ‘syndromic’ disorder including both a persistent low testosterone serum concentration and major clinical symptoms, including erectile dysfunction, low libido, decreased muscle mass and strength, increased body fat, decreased vitality or depressed mood. Given its unspecific symptoms, treatment goals and monitoring parameters, this review will outline the various uncertainties concerning the diagnosis, therapy and monitoring of ADS to date. Literature was identified primarily through searches for specific investigators in the PubMed database. No date or language limits were applied in the literature search for the present review. The current state of research, showing that metabolomics is starting to have an impact not only on disease diagnosis and prognosis but also on drug treatment efficacy and safety monitoring, will be presented, and the application of metabolomics to improve the clinical management of ADS will be discussed. Finally, the scientific opportunities presented by metabolomics and other -omics as novel and promising tools for biomarker discovery and individualised testosterone replacement therapy in men will be explored.

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