Large-scale protein identification of human urine proteome by multi-dimensional LC and MS/MS

2007 ◽  
Vol 1 (6) ◽  
pp. 577-587 ◽  
Author(s):  
Yi-Ting Chen ◽  
Chao-Yun Tsao ◽  
Jen-Ming Li ◽  
Chih-Yen Tsai ◽  
Su-Feng Chiu ◽  
...  
2013 ◽  
Vol 113 (suppl_1) ◽  
Author(s):  
Xuan Guan ◽  
David L Mack ◽  
Claudia M Moreno ◽  
Fernando Santana ◽  
Charles E Murry ◽  
...  

Introduction: Human somatic cells can be reprogrammed into primitive stem cells, termed induced pluripotent stem cells (iPSCs). These iPSCs can be extensively expanded in vitro and differentiated into multiple functional cell types, enabling faithful preservation of individual’s genotype and large scale production of disease targeted cellular components. These unique cellular reagents thus hold tremendous potential in disease mechanism study, drugs screening and cell replacement therapy. Due to the genetic mutation of the protein dystrophin, many DMD patients develop fatal cardiomyopathy with no effective treatment. The underlying pathogenesis has not been fully elucidated. Hypothesis: We tested the hypothesis that iPSCs could be generated from DMD patients’ urine samples and differentiated into cardiomyocytes, recapitulating the dystrophic phenotype. Methods: iPSCs generation was achieved by introducing a lentiviral vector expressing Oct4, Sox2, c-Myc and Klf4 into cells derived from patient’s (n=1) and healthy volunteers’ (n=3) urine. Cardiomyocytes were derived by sequentially treating iPSCs with GSK3 inhibitor CHIR99021 and Wnt inhibitor IWP4. Differentiated cardiomyocytes were subjected to calcium imaging, electrophysiology recording, Polymerase Chain Reaction (PCR) analysis, and immunostaining. Results: iPSCs were efficiently generated from human urine samples and further forced to differentiate into contracting cardiomyocytes. PCR analysis and immunostaining confirmed the expression of a panel of cardiac markers. Both normal and patient iPSC derived cardiomyocytes exhibited spontaneous and field stimulated calcium transients (up to 2Hz), as well as action potentials with ventricular-like and nodal-like characteristics. Anti-dystrophin antibodies stained normal iPSC-derived cardiomyocyte membranes but did not react against DMD iPSC-derived cardiomyocytes. Conclusions: Cardiomyocytes can be efficiently generated from human urine, through the cellular reprogramming technology. DMD cardiomyocytes retained the patient’s genetic information and manifested a dystrophin-null phenotype. Functional assessments are underway to determine differences that may exist between genotypes.


2021 ◽  
Vol 12 ◽  
Author(s):  
Yuran Jia ◽  
Shan Huang ◽  
Tianjiao Zhang

DNA-binding protein (DBP) is a protein with a special DNA binding domain that is associated with many important molecular biological mechanisms. Rapid development of computational methods has made it possible to predict DBP on a large scale; however, existing methods do not fully integrate DBP-related features, resulting in rough prediction results. In this article, we develop a DNA-binding protein identification method called KK-DBP. To improve prediction accuracy, we propose a feature extraction method that fuses multiple PSSM features. The experimental results show a prediction accuracy on the independent test dataset PDB186 of 81.22%, which is the highest of all existing methods.


Author(s):  
Jia Hao ◽  
Duoxia Xu ◽  
Yangping Cao

Oil bodies (OBs) are micron- or submicron-sized sub-organelles widely found in plants seeds and nuts. The structure OBs is composed of a core of triglycerides covered by a phospholipid-protein layer, which ensures the stability of the OBs under extreme environmental conditions and further protects core lipids as energy reserves. As naturally pre-emulsified oil-in-water emulsions, OBs have been gradually applied to replace synthetically engineered oil droplets. In this paper, the recent research on the composition, extraction, stability, delivery system, digestion, food applications and future perspectives of plant OBs are reviewed. Recent studies have focused on the OBs surface protein identification and function, large-scale extraction techniques such as enzyme assisted, high pressure, ultrasound, and extrusion and the reconstituted OBs. Electrostatic deposition of polysaccharides significantly improves the stability of OBs emulsions. OBs emulsions have promising applications to encapsulate bioactive compounds, deliver targeted drugs, and prepare gels and edible functional films. The digestive behavior of OBs emulsions is similar to that of protein-stabilized emulsions, which can increase the satiety, effectively help reduce calorie intake and improve the bioavailability of functional factors. It has also promoted the development of simulated dairy, spices and meat products.


EBioMedicine ◽  
2017 ◽  
Vol 18 ◽  
pp. 300-310 ◽  
Author(s):  
Wenchuan Leng ◽  
Xiaotian Ni ◽  
Changqing Sun ◽  
Tianyuan Lu ◽  
Anna Malovannaya ◽  
...  

Author(s):  
Haipeng Wang

Protein identification (sequencing) by tandem mass spectrometry is a fundamental technique for proteomics which studies structures and functions of proteins in large scale and acts as a complement to genomics. Analysis and interpretation of vast amounts of spectral data generated in proteomics experiments present unprecedented challenges and opportunities for data mining in areas such as data preprocessing, peptide-spectrum matching, results validation, peptide fragmentation pattern discovery and modeling, and post-translational modification (PTM) analysis. This article introduces the basic concepts and terms of protein identification and briefly reviews the state-of-the-art relevant data mining applications. It also outlines challenges and future potential hot spots in this field.


Urine ◽  
2019 ◽  
pp. 9-24
Author(s):  
Xiaolian Xiao ◽  
Lili Zou ◽  
Wei Sun

2020 ◽  
Vol 24 ◽  
pp. 219-231 ◽  
Author(s):  
Yitayal Addis Alemayehu ◽  
Seyoum Leta Asfaw ◽  
Tadesse Alemu Terfie

Author(s):  
Bradford William Hesse

The presence of large-scale data systems can be felt, consciously or not, in almost every facet of modern life, whether through the simple act of selecting travel options online, purchasing products from online retailers, or navigating through the streets of an unfamiliar neighborhood using global positioning system (GPS) mapping. These systems operate through the momentum of big data, a term introduced by data scientists to describe a data-rich environment enabled by a superconvergence of advanced computer-processing speeds and storage capacities; advanced connectivity between people and devices through the Internet; the ubiquity of smart, mobile devices and wireless sensors; and the creation of accelerated data flows among systems in the global economy. Some researchers have suggested that big data represents the so-called fourth paradigm in science, wherein the first paradigm was marked by the evolution of the experimental method, the second was brought about by the maturation of theory, the third was marked by an evolution of statistical methodology as enabled by computational technology, while the fourth extended the benefits of the first three, but also enabled the application of novel machine-learning approaches to an evidence stream that exists in high volume, high velocity, high variety, and differing levels of veracity. In public health and medicine, the emergence of big data capabilities has followed naturally from the expansion of data streams from genome sequencing, protein identification, environmental surveillance, and passive patient sensing. In 2001, the National Committee on Vital and Health Statistics published a road map for connecting these evidence streams to each other through a national health information infrastructure. Since then, the road map has spurred national investments in electronic health records (EHRs) and motivated the integration of public surveillance data into analytic platforms for health situational awareness. More recently, the boom in consumer-oriented mobile applications and wireless medical sensing devices has opened up the possibility for mining new data flows directly from altruistic patients. In the broader public communication sphere, the ability to mine the digital traces of conversation on social media presents an opportunity to apply advanced machine learning algorithms as a way of tracking the diffusion of risk communication messages. In addition to utilizing big data for improving the scientific knowledge base in risk communication, there will be a need for health communication scientists and practitioners to work as part of interdisciplinary teams to improve the interfaces to these data for professionals and the public. Too much data, presented in disorganized ways, can lead to what some have referred to as “data smog.” Much work will be needed for understanding how to turn big data into knowledge, and just as important, how to turn data-informed knowledge into action.


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