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proteomics review

Manuel Mauricio Goez, Maria Constanza Torres-Madroñero, Sarah Röthlisberger, Edilson Delgado-Trejos
Various methods and specialized software programs are available for processing two-dimensional gel electrophoresis (2-DGE) images. However, due to the anomalies present in these images, a reliable, automated, and highly reproducible system for 2-DGE image analysis has still not been achieved. The most common anomalies found in 2-DGE images include vertical and horizontal streaking, fuzzy spots, and background noise, which greatly complicate computational analysis. In this paper, we review the preprocessing techniques applied to 2-DGE images for noise reduction, intensity normalization, and background correction...
February 20, 2018: Genomics, Proteomics & Bioinformatics
Heather L Martin, Robert Bedford, Sophie J Heseltine, Anna A Tang, Katarzyna Z Haza, Ajinkya Rao, Michael J McPherson, Darren C Tomlinson
Cancer is frequently characterised by dysregulation of the cellular signalling processes that govern proliferation, survival and attachment. Understanding such dysregulation continues to present a challenge given the importance of protein-protein interactions in intracellular processes. Exploring this protein-protein interactome requires novel tools capable of discriminating between highly homologous proteins, individual domains and post-translational modifications. This review examines the potential of scaffold-based binding proteins to fulfil these requirements...
February 20, 2018: New Biotechnology
Chi-Ming Wong, Lu Xu, Mabel Yin-Chun Yau
Alternative mRNA splicing is an important mechanism in expansion of proteome diversity by production of multiple protein isoforms. However, emerging evidence indicates that only a limited number of annotated protein isoforms by alternative splicing are detected, and the coding sequence of alternative splice variants usually is only slightly different from that of the canonical sequence. Nevertheless, mis-splicing is associated with a large array of human diseases. Previous reviews mainly focused on hereditary and somatic mutations in cis-acting RNA sequence elements and trans-acting splicing factors...
February 23, 2018: International Journal of Molecular Sciences
Catarina Bourgard, Letusa Albrecht, Ana C A V Kayano, Per Sunnerhagen, Fabio T M Costa
During the last decade, the vast omics field has revolutionized biological research, especially the genomics, transcriptomics and proteomics branches, as technological tools become available to the field researcher and allow difficult question-driven studies to be addressed. Parasitology has greatly benefited from next generation sequencing (NGS) projects, which have resulted in a broadened comprehension of basic parasite molecular biology, ecology and epidemiology. Malariology is one example where application of this technology has greatly contributed to a better understanding of Plasmodium spp...
2018: Frontiers in Cellular and Infection Microbiology
Shruti Nagaraja, Serge Ankri
During its life cycle, the unicellular parasite Entamoeba histolytica is challenged by a wide variety of environmental stresses, such as fluctuation in glucose concentration, changes in gut microbiota composition, and the release of oxidative and nitrosative species from neutrophils and macrophages. The best mode of survival for this parasite is to continuously adapt itself to the dynamic environment of the host. Our ability to study the stress-induced responses and adaptive mechanisms of this parasite has been transformed through the development of genomics, proteomics or metabolomics (omics sciences)...
2018: Frontiers in Cellular and Infection Microbiology
Klára Kosová, Pavel Vítámvás, Milan O Urban, Ilja T Prášil, Jenny Renaut
HIGHLIGHTS: Major environmental and genetic factors determining stress-related protein abundance are discussed.Major aspects of protein biological function including protein isoforms and PTMs, cellular localization and protein interactions are discussed.Functional diversity of protein isoforms and PTMs is discussed. Abiotic stresses reveal profound impacts on plant proteomes including alterations in protein relative abundance, cellular localization, post-transcriptional and post-translational modifications (PTMs), protein interactions with other protein partners, and, finally, protein biological functions...
2018: Frontiers in Plant Science
A Lawan, F F A Jesse, U H Idris, M N Odhah, M Arsalan, N A Muhammad, K R Bhutto, Innocent Damudu Peter, G A Abraham, A H Wahid, M L Mohd-Azmi, M Zamri-Saad
Innumerable Escherichia coli of animal origin are identified, which are of economic significance, likewise, cattle, sheep and goats are the carrier of enterohaemorrhagic E. coli, which are less pathogenic, and can spread to people by way of direct contact and through the contamination of foodstuff or portable drinking water, causing serious illness. The immunization of ruminants has been carried out for ages and is largely acknowledged as the most economical and maintainable process of monitoring E. coli infection in ruminants...
February 19, 2018: Microbial Pathogenesis
G T Tsangaris, A K Anagnostopoulos
Pediatric brain tumors (PBTs) are the most common solid malignancies in childhood and continue to pose a serious burden to modern societies. Existing treatments impose debilitating effects on the developing child, highlighting the need for molecularly targeted treatments with reduced toxicity, and the necessity of markers that reliably assess efficacy of, and tumor response to targeted-therapies of PBTs. On this regard advances in technologies of protein identification and quantification, the large-scale, high-throughput investigation of the proteome, as well the newly-emerging field of "proteogenomics" aim to further our knowledge towards understanding the molecular pathophysiology of PBTs...
February 19, 2018: Journal of Proteomics
Yang Chun-Li, Cai Yu-Chun, Chen Jia-Xu
Babesia parasites are obligate intracellular apicomplexan protozoa and important pathogens causing babesiosis of humans and animals. They have conserved subcellular structures and invasion mechanism. Rhoptry-associated proteins, which are released into the host cell, are considered to be the key molecules of invasion and replication of parasites in the host cell and are immunosuppressive factors of the host cell mediated immunity in the stage of parasitophorous vacuole (PV) formation. The knowledge about rhoptry-associated proteins has made a great progress with the development of genomics and proteomics, so we review the research progress in rhoptry-associated proteins of different Babesia including Babesia bovis , B...
March 22, 2017: Zhongguo Xue Xi Chong Bing Fang Zhi za Zhi, Chinese Journal of Schistosomiasis Control
Rhian Lauren Preece, Sung Yeon Sarah Han, Sabine Bahn
Major depressive disorder (MDD) and bipolar disorder (BD) are leading causes of disability worldwide, yet many people remain undiagnosed, are misdiagnosed, and/or ineffectively treated. Diagnosis relies on the clinical assessment of symptoms, and there is currently no molecular or brain-imaging diagnostic test available. Identifying and validating protein biomarkers could provide a more accurate and objective means of diagnosis. Areas covered: Proteomics is a powerful tool that enables the identification and quantification of novel candidate biomarkers of disease...
February 22, 2018: Expert Review of Proteomics
Tania J Lupoli, Julien Vaubourgeix, Kristin Burns-Huang, Ben Gold
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains one of the world's deadliest infectious diseases and urgently requires new antibiotics to treat drug-resistant strains and to decrease the duration of therapy. During infection, Mtb encounters numerous stresses associated with host immunity, including hypoxia, reactive oxygen and nitrogen species, mild acidity, nutrient starvation, and metal sequestration and intoxication. The Mtb proteostasis network, composed of chaperones, proteases, and a eukaryotic-like proteasome, provides protection from stresses and chemistries of host immunity by maintaining the integrity of the mycobacterial proteome...
February 21, 2018: ACS Infectious Diseases
Bilal Khalil, Dmytro Morderer, Phillip L Price, Feilin Liu, Wilfried Rossoll
The development, maturation, and maintenance of the mammalian nervous system rely on complex spatiotemporal patterns of gene expression. In neurons, this is achieved by the expression of differentially localized isoforms and specific sets of mRNA-binding proteins (mRBPs) that regulate RNA processing, mRNA trafficking, and local protein synthesis at remote sites within dendrites and axons. There is growing evidence that axons contain a specialized transcriptome and are endowed with the machinery that allows them to rapidly alter their local proteome via local translation and protein degradation...
February 17, 2018: Brain Research
H Kočová Vlčková, V Pilařová, P Svobodová, J Plíšek, F Švec, L Nováková
Chromatographic methods have become popular in clinical analysis in both routine and research laboratories. The purpose of this review article is to provide an overview of the current state of chromatographic methods, i.e., high-performance liquid chromatography (HPLC), gas chromatography (GC), and supercritical fluid chromatography (SFC), in clinical analysis. The aspects related to method sensitivity, selectivity, analysis time, and throughput have been discussed in detail. Adequate solutions to improve these features have also been presented...
February 20, 2018: Analyst
Julie P I Welburn, A Arockia Jeyaprakash
Protein kinases are major regulators of mitosis, with over 30% of the mitotic proteome phosphorylated on serines, threonines and tyrosines. The human genome encodes for 518 kinases that have a structurally conserved catalytic domain and includes about a dozen of cell division specific ones. Yet each kinase has unique structural features that allow their distinct substrate recognition and modes of regulation. These unique regulatory features determine their accurate spatio-temporal activation critical for correct progression through mitosis and are exploited for therapeutic purposes...
2018: Frontiers in Cell and Developmental Biology
Delia Goletti, Meng-Rui Lee, Jann-Yuan Wang, Nicholas Walter, Tom H M Ottenhoff
Tuberculosis (TB) remains a devastating disease, yet despite its enormous toll on global health, tools to control TB are insufficient and often outdated. TB Biomarkers (TB-BM) would constitute extremely useful tools to measure infection status and predict outcome of infection, vaccination or therapy. There are several types of TB-BM: Correlate of Infection; Correlate of TB Disease; Correlate of Increased Risk of Developing Active TB Disease; Correlate of the Curative Response to Therapy; and Correlate of Protection (CoP)...
February 18, 2018: Respirology: Official Journal of the Asian Pacific Society of Respirology
Nathan Basisty, Jesse G Meyer, Birgit Schilling
Progressive loss of proteostasis is a hallmark of aging that is marked by declines in various components of proteostasis machinery, including: autophagy, ubiquitin-mediated degradation, protein synthesis, and others. While declines in proteostasis have historically been observed as changes in these processes, or as bulk changes in the proteome, recent advances in proteomic methodologies have enabled the comprehensive measurement of turnover directly at the level of individual proteins in vivo. These methods, which utilize a combination of stable-isotope labeling, mass spectrometry, and specialized software analysis, have now been applied to various studies of aging and longevity...
February 17, 2018: Proteomics
Rout George Kerry, Gyana Prakash Mahapatra, Sushmita Patra, Santi Lata Sahoo, Chinmay Pradhan, Bijaya Kumar Padhi, Jyoti Ranjan Rout
Minerals or trace elements in small amount are essential nutrients for every plant, but when the internal concentration exceeds the threshold, these essential elements do create phytotoxicity. Plant responses to elemental stresses are very common due to different anthropogenic activities; however it is a complex phenomenon with individual characteristics for various species. To cope up with the situation, a plant produces a group of strategies both in proteomic and genomic level to overcome it. Controlling the metal stress is known to activate a multigene response resulting in the changes in various proteins, which directly affects almost all biological processes in a living cell...
February 16, 2018: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
Nathan P Manes, Aleksandra Nita-Lazar
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples...
February 13, 2018: Journal of Proteomics
Willem Johan van den Brink, Semra Palic, Isabelle Köhler, Elizabeth Cunera Maria de Lange
Despite substantial research carried out over the last decades, it remains difficult to understand the wide range of pharmacological effects of dopaminergic agents. The dopaminergic system is involved in several neurological disorders, such as Parkinson's disease and schizophrenia. This complex system features multiple pathways implicated in emotion and cognition, psychomotor functions and endocrine control through activation of G protein-coupled dopamine receptors. This review focuses on the system-wide effects of dopaminergic agents on the multiple biochemical and endocrine pathways, in particular the biomarkers (i...
February 15, 2018: Pharmaceutical Research
Stefan A Arnold, Shirley A Müller, Claudio Schmidli, Anastasia Syntychaki, Luca Rima, Mohamed Chami, H Stahlberg, Kenneth N Goldie, T Braun
This review compares and discusses conventional versus miniaturized specimen preparation methods for transmission electron microscopy (EM). The progress brought by direct electron detector cameras, software developments and automation have transformed transmission cryo-electron microscopy (cryo-EM) and made it an invaluable high-resolution structural analysis tool. In contrast, EM specimen preparation has seen very little progress in the last decades and is now one of the main bottlenecks in cryo-EM. Here, we discuss the challenges faced by specimen preparation for single particle EM, highlight current developments, and show the opportunities resulting from the advanced miniaturized and microfluidic sample grid preparation methods described, such as visual proteomics and time-resolved cryo-EM studies...
February 14, 2018: Proteomics
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