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proteomics review

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https://www.readbyqxmd.com/read/29226722/the-use-of-databases-data-mining-and-immunoinformatics-in-vaccinology-where-are-we
#1
Nagendra R Hegde, S Gauthami, H M Sampath Kumar, Jagadeesh Bayry
Vaccinology has evolved from a sub-discipline focussed on simplistic vaccine development based on antibody-mediated protection to a separate discipline involving epidemiology, host and pathogen biology, immunology, genomics, proteomics, structure biology, protein engineering, chemical biology, and delivery systems. Data mining in combination with bioinformatics has provided a scaffold linking all these disciplines to the design of vaccines and vaccine adjuvants. Areas covered: This review provides background knowledge on immunological aspects which have been exploited with informatics for the in silico analysis of immune responses and the design of vaccine antigens...
December 11, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/29224620/exploring-trichoderma-and-aspergillus-secretomes-proteomics-approaches-for-the-identification-of-enzymes-of-biotechnological-interest
#2
REVIEW
Nicholas de Mojana di Cologna, Diana Paola Gómez-Mendoza, Fabiana Fonseca Zanoelo, Giovana Cristina Giannesi, Nelciele Cavalieri de Alencar Guimarães, Leonora Rios de Souza Moreira, Edivaldo Ximenes Ferreira Filho, Carlos André Ornelas Ricart
Filamentous fungal secretomes comprise highly dynamic sets of proteins, including multiple carbohydrate active enzymes (CAZymes) which are able to hydrolyze plant biomass polysaccharides into products of biotechnological interest such as fermentable sugars. In recent years, proteomics has been used to identify and quantify enzymatic and non-enzymatic polypeptides present in secretomes of several fungi species. The resulting data have widened the scientific understanding of the way filamentous fungi perform biomass degradation and offered novel perspectives for biotechnological applications...
February 2018: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/29223801/the-external-face-of-candida-albicans-a-proteomic-view-of-the-cell-surface-and-the-extracellular-environment
#3
Ana Gil-Bona, Ahinara Amador-García, Concha Gil, Lucia Monteoliva
The cell surface and secreted proteins are the initial points of contact between Candida albicans and the host. Improvements in protein extraction approaches and mass spectrometers have allowed researchers to obtain a comprehensive knowledge of these external subproteomes. In this paper, we review the published proteomic studies that have examined C. albicans extracellular proteins, including the cell surface proteins or surfome and the secreted proteins or secretome. The use of different approaches to isolate cell wall and cell surface proteins, such as fractionation approaches or cell shaving, have resulted in different outcomes...
December 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29223644/functional-significance-of-o-glcnac-modification-in-regulating-neuronal-properties
#4
REVIEW
Hongik Hwang, Hyewhon Rhim
Post-translational modifications (PTMs) covalently modify proteins and diversify protein functions. Along with protein phosphorylation, another common PTM is the addition of O-linked β-N-acetylglucosamine (O-GlcNAc) to serine and/or threonine residues. O-GlcNAc modification is similar to phosphorylation in that it occurs to serine and threonine residues and cycles on and off with a similar time scale. However, a striking difference is that the addition and removal of the O-GlcNAc moiety on all substrates are mediated by the two enzymes regardless of proteins, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), respectively...
December 6, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/29220116/advances-in-microfluidics-applied-to-single-cell-operation
#5
REVIEW
Xudong Zhu, Ju Chu, Yonghong Wang
The field of microbiology has traditionally been concerned with and focused on studies at the population level. Microfluidic platforms have emerged as important tools for biology research at a small scale, even down to a single cell level. The spatial and temporal control of cells and stimuli transported by microfluidic channels in well-designed microsystems realized the studies of specific cells in a controlled microenvironment. The true cellular physiology responses, which were obtained mostly by inference from population-level data, could be revealed in this way...
December 8, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/29218397/can-we-better-predict-the-biologic-behavior-of-incidental-ipmn-a-comprehensive-analysis-of-molecular-diagnostics-and-biomarkers-in-intraductal-papillary-mucinous-neoplasms-of-the-pancreas
#6
Kiara A Tulla, Ajay V Maker
PURPOSE: Predicting the biologic behavior of intraductal papillary mucinous neoplasm (IPMN) remains challenging. Current guidelines utilize patient symptoms and imaging characteristics to determine appropriate surgical candidates. However, the majority of resected cysts remain low-risk lesions, many of which may be feasible to have under surveillance. We herein characterize the most promising and up-to-date molecular diagnostics in order to identify optimal components of a molecular signature to distinguish levels of IPMN dysplasia...
December 7, 2017: Langenbeck's Archives of Surgery
https://www.readbyqxmd.com/read/29218272/blood-based-biomarkers-in-lung-cancer-prognosis-and-treatment-decisions
#7
REVIEW
Meng Xu-Welliver, David P Carbone
Despite recent advances, non-small cell lung cancer (NSCLC) remains a devastating disease with overall poor prognosis. Major contributing factors include obstacles to diagnosing the disease early in its course during the asymptomatic stage as well as diversity and complexity of its biology underlying tumorigenesis and tumor progression. Advances in molecularly targeted therapies which drives the development of personalized cancer care require precise and comprehensive understanding of tumor biology, not only at the time of diagnosis but also during treatment course and surveillance...
December 2017: Translational Lung Cancer Research
https://www.readbyqxmd.com/read/29218269/blood-based-biomarkers-for-precision-medicine-in-lung-cancer-precision-radiation-therapy
#8
REVIEW
Dirk De Ruysscher, Jianyue Jin, Tim Lautenschlaeger, Jin-Xiong She, Zhongxing Liao, Feng-Ming Spring Kong
Both tumors and patients are complex and models that determine survival and toxicity of radiotherapy or any other treatment ideally must take into account this variability as well as its dynamic state. The genetic features of the tumor and the host, and increasingly also the epi-genetic and proteomic characteristics, are being unraveled. Multiple techniques, including histological examination, blood sampling, measurement of circulating tumor cells (CTCs), and functional and molecular imaging, can be used for this purpose...
December 2017: Translational Lung Cancer Research
https://www.readbyqxmd.com/read/29216893/the-integration-of-chloroplast-protein-targeting-with-plant-developmental-and-stress-responses
#9
REVIEW
Lynn G L Richardson, Rajneesh Singhal, Danny J Schnell
The plastids, including chloroplasts, are a group of interrelated organelles that confer photoautotrophic growth and the unique metabolic capabilities that are characteristic of plant systems. Plastid biogenesis relies on the expression, import, and assembly of thousands of nuclear encoded preproteins. Plastid proteomes undergo rapid remodeling in response to developmental and environmental signals to generate functionally distinct plastid types in specific cells and tissues. In this review, we will highlight the central role of the plastid protein import system in regulating and coordinating the import of functionally related sets of preproteins that are required for plastid-type transitions and maintenance...
December 7, 2017: BMC Biology
https://www.readbyqxmd.com/read/29216742/redox-sensing-iron-sulfur-cluster-regulators
#10
Jason C Crack, Nick E Le Brun
SIGNIFICANCE: Iron-sulfur cluster proteins carry out a wide range of functions, including as regulators of gene transcription/translation in response to environmental stimuli. In all known cases, the cluster acts as the sensory module, where the inherent reactivity/fragility of iron-sulfur clusters towards small/redox active molecules is exploited to effect conformational changes that modulate binding to DNA regulatory sequences. This promotes an often substantial re-programming of the cellular proteome that enables the organism or cell to adapt to, or counteract, its changing circumstances...
December 7, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/29215602/proteomic-contributions-to-medicinal-plant-research-from-plant-metabolism-to-pharmacological-action
#11
REVIEW
Akiko Hashiguchi, Jingkui Tian, Setsuko Komatsu
Herbal medicine is a clinical practice of utilizing medicinal plant derivatives for therapeutic purposes. It has an enduring history worldwide and plays a significant role in the fight against various diseases. Herbal drug combinations often exhibit synergistic therapeutic action compared with single-constituent dosage, and can also enhance the cytotoxicity induced by chemotherapeutic drugs. To explore the mechanism underlying the pharmacological action of herbs, proteomic approaches have been applied to the physiology of medicinal plants and its effects on animals...
December 7, 2017: Proteomes
https://www.readbyqxmd.com/read/29210173/direct-and-indirect-approaches-to-identify-drug-modes-of-action
#12
REVIEW
Lindsay B Tulloch, Stefanie K Menzies, Ross P Coron, Matthew D Roberts, Gordon J Florence, Terry K Smith
Phenotypic assays are becoming increasingly more common among drug discovery practices, expanding drug target diversity as lead compounds identified through such screens are not limited to known targets. While increasing diversity is beneficial to the drug discovery process and the fight against disease, the unknown modes of action of new lead compounds can hamper drug discovery as, in most cases, the process of lead compound optimization is made difficult due to the unknown nature of the target; blindly changing substituents can prove fruitless due to the inexhaustible number of potential combinations, and it is therefore desirable to rapidly identify the targets of lead compounds developed through phenotypic screening...
December 6, 2017: IUBMB Life
https://www.readbyqxmd.com/read/29209607/a-perspective-on-extracellular-vesicles-proteomics
#13
REVIEW
Livia Rosa-Fernandes, Victória Bombarda Rocha, Victor Corasolla Carregari, Andrea Urbani, Giuseppe Palmisano
Increasing attention has been given to secreted extracellular vesicles (EVs) in the past decades, especially in the portrayal of their molecular cargo and role as messengers in both homeostasis and pathophysiological conditions. This review presents the state-of-the-art proteomic technologies to identify and quantify EVs proteins along with their PTMs, interacting partners and structural details. The rapid growth of mass spectrometry-based analytical strategies for protein sequencing, PTMs and structural characterization has improved the level of molecular details that can be achieved from limited amount of EVs isolated from different biological sources...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/29209284/the-sit-and-wait-hypothesis-in-bacterial-pathogens-a-theoretical-study-of-durability-and-virulence
#14
Liang Wang, Zhanzhong Liu, Shiyun Dai, Jiawei Yan, Michael J Wise
The intriguing sit-and-wait hypothesis predicts that bacterial durability in the external environment is positively correlated with their virulence. Since its first proposal in 1987, the hypothesis has been spurring debates in terms of its validity in the field of bacterial virulence. As a special case of the vector-borne transmission versus virulence tradeoff, where vector is now replaced by environmental longevity, there are only sporadic studies over the last three decades showing that environmental durability is possibly linked with virulence...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29209209/nonribosomal-peptides-from-marine-microbes-and-their-antimicrobial-and-anticancer-potential
#15
REVIEW
Shivankar Agrawal, Debabrata Acharya, Alok Adholeya, Colin J Barrow, Sunil K Deshmukh
Marine environments are largely unexplored and can be a source of new molecules for the treatment of many diseases such as malaria, cancer, tuberculosis, HIV etc. The Marine environment is one of the untapped bioresource of getting pharmacologically active nonribosomal peptides (NRPs). Bioprospecting of marine microbes have achieved many remarkable milestones in pharmaceutics. Till date, more than 50% of drugs which are in clinical use belong to the nonribosomal peptide or mixed polyketide-nonribosomal peptide families of natural products isolated from marine bacteria, cyanobacteria and fungi...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29209003/prostate-cancer-diagnosis-and-characterization-with-mass-spectrometry-imaging
#16
REVIEW
Annika Kurreck, Lindsey A Vandergrift, Taylor L Fuss, Piet Habbel, Nathalie Y R Agar, Leo L Cheng
BACKGROUND: Prostate cancer (PCa), the most common cancer and second leading cause of cancer death in American men, presents the clinical challenge of distinguishing between indolent and aggressive tumors for proper treatment. PCa presents significant alterations in metabolic pathways that can potentially be measured using techniques like mass spectrometry (MS) or MS imaging (MSI) and used to characterize PCa aggressiveness. MS quantifies metabolomic, proteomic, and lipidomic profiles of biological systems that can be further visualized for their spatial distributions through MSI...
December 5, 2017: Prostate Cancer and Prostatic Diseases
https://www.readbyqxmd.com/read/29208216/clinical-veterinary-proteomics-techniques-and-approaches-to-decipher-the-animal-plasma-proteome
#17
REVIEW
P Ghodasara, P Sadowski, N Satake, S Kopp, P C Mills
Over the last two decades, technological advancements in the field of proteomics have advanced our understanding of the complex biological systems of living organisms. Techniques based on mass spectrometry (MS) have emerged as powerful tools to contextualise existing genomic information and to create quantitative protein profiles from plasma, tissues or cell lines of various species. Proteomic approaches have been used increasingly in veterinary science to investigate biological processes responsible for growth, reproduction and pathological events...
December 2017: Veterinary Journal
https://www.readbyqxmd.com/read/29204749/phosphorylation-of-pyridoxal-5-phosphate-enzymes-an-intriguing-and-neglected-topic
#18
REVIEW
Giada Rossignoli, Robert S Phillips, Alessandra Astegno, Marta Menegazzi, Carla Borri Voltattorni, Mariarita Bertoldi
Pyridoxal 5'-phosphate (PLP)-dependent enzymes catalyze a wide range of reactions of amino acids and amines, with the exception of glycogen phosphorylase which exhibits peculiar both substrate preference and chemical mechanism. They represent about 4% of the gene products in eukaryotic cells. Although structure-function investigations regarding these enzymes are copious, their regulation by post-translational modifications is largely unknown. Protein phosphorylation is the most common post-translational modification fundamental in mediating diverse cellular functions...
December 4, 2017: Amino Acids
https://www.readbyqxmd.com/read/29204145/molecular-signatures-of-immunity-and-immunogenicity-in-infection-and-vaccination
#19
REVIEW
Mariëlle C Haks, Barbara Bottazzi, Valentina Cecchinato, Corinne De Gregorio, Giuseppe Del Giudice, Stefan H E Kaufmann, Antonio Lanzavecchia, David J M Lewis, Jeroen Maertzdorf, Alberto Mantovani, Federica Sallusto, Marina Sironi, Mariagrazia Uguccioni, Tom H M Ottenhoff
Vaccinology aims to understand what factors drive vaccine-induced immunity and protection. For many vaccines, however, the mechanisms underlying immunity and protection remain incompletely characterized at best, and except for neutralizing antibodies induced by viral vaccines, few correlates of protection exist. Recent omics and systems biology big data platforms have yielded valuable insights in these areas, particularly for viral vaccines, but in the case of more complex vaccines against bacterial infectious diseases, understanding is fragmented and limited...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29204080/genomics-of-metal-stress-mediated-signalling-and-plant-adaptive-responses-in-reference-to-phytohormones
#20
REVIEW
Anurakti Shukla, Sudhakar Srivastava, Penna Suprasanna
Introduction: As a consequence of a sessile lifestyle, plants often have to face a number of life threatening abiotic and biotic stresses. Plants counteract the stresses through morphological and physiological adaptations, which are imparted through flexible and well-coordinated network of signalling and effector molecules, where phytohormones play important role. Hormone synthesis, signal transduction, perception and cross-talks create a complex network. Omics approaches, which include transcriptomics, genomics, proteomics and metabolomics, have opened new paths to understand such complex networks...
December 2017: Current Genomics
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