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Proteomes

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https://www.readbyqxmd.com/read/29762536/proteomics-of-human-retinal-pigment-epithelium-rpe-cells
#1
REVIEW
Sarka Beranova-Giorgianni, Francesco Giorgianni
Retinal pigment epithelium (RPE) are specialized, multifunctional cells in the retina that form a monolayer of cuboidal, polarized cells adjoining the photoreceptor cells. The RPE are a critical component of the blood-retinal barrier, and they play essential functional roles for maintenance of retinal homeostasis and for support and health of photoreceptors. Age-dependent, progressive dysfunction and death of RPE cells and the resultant loss of photoreceptors contribute significantly to the development and progression of age-related macular degeneration (AMD) and other retinal degenerative diseases...
May 15, 2018: Proteomes
https://www.readbyqxmd.com/read/29734680/the-use-of-proteomic-tools-to-address-challenges-faced-in-clonal-propagation-of-tropical-crops-through-somatic-embryogenesis
#2
REVIEW
Chiew Foan Chin, Hooi Sin Tan
In many tropical countries with agriculture as the mainstay of the economy, tropical crops are commonly cultivated at the plantation scale. The successful establishment of crop plantations depends on the availability of a large quantity of elite seedling plants. Many plantation companies establish plant tissue culture laboratories to supply planting materials for their plantations and one of the most common applications of plant tissue culture is the mass propagation of true-to-type elite seedlings. However, problems encountered in tissue culture technology prevent its applications being widely adopted...
May 4, 2018: Proteomes
https://www.readbyqxmd.com/read/29701723/integrated-chemometrics-and-statistics-to-drive-successful-proteomics-biomarker-discovery
#3
REVIEW
Anouk Suppers, Alain J van Gool, Hans J C T Wessels
Protein biomarkers are of great benefit for clinical research and applications, as they are powerful means for diagnosing, monitoring and treatment prediction of different diseases. Even though numerous biomarkers have been reported, the translation to clinical practice is still limited. This mainly due to: (i) incorrect biomarker selection, (ii) insufficient validation of potential biomarkers, and (iii) insufficient clinical use. In this review, we focus on the biomarker selection process and critically discuss the chemometrical and statistical decisions made in proteomics biomarker discovery to increase to selection of high value biomarkers...
April 26, 2018: Proteomes
https://www.readbyqxmd.com/read/29693629/a-proteomic-view-of-salmonella-typhimurium-in-response-to-phosphate-limitation
#4
Jiezhang Jiang, Kaiwen Yu, Linlu Qi, Yanhua Liu, Sen Cheng, Mei Wu, Zhen Wang, Jiaqi Fu, Xiaoyun Liu
Salmonella enterica serovar Typhimurium ( S. Typhimurium), an important foodborne pathogen, often encounters phosphate (Pi ) shortage both in the environment and inside host cells. To gain a global view on its physiological responses to Pi starvation, we performed proteomic profiling of S. Typhimurium upon the shift from Pi -rich to Pi -low conditions. In addition to the Pho regulon, many metabolic processes were up-regulated, such as glycolysis, pentose phosphate pathway, pyrimidine degradation, glycogen, and trehalose metabolism, allowing us to chart an overview of S...
April 25, 2018: Proteomes
https://www.readbyqxmd.com/read/29673200/surface-and-extracellular-proteome-of-the-emerging-pathogen-corynebacterium-ulcerans
#5
Miriam Bittel, Susanne Gastiger, Bushra Amin, Jörg Hofmann, Andreas Burkovski
Corynebacterium ulcerans is an emerging pathogen, which is increasingly recognized as an etiological agent of diphtheria, but can also evoke ulcers of the skin and systemic infections in humans. Besides man, the bacteria can colonize a wide variety of different animals, including cattle and pet animals, which might serve as a reservoir for human infections. In this study, surface-located proteins and the exoproteome of two Corynebacterium ulcerans strains were analyzed, since these may have key roles in the interaction of the pathogen with host cells...
April 17, 2018: Proteomes
https://www.readbyqxmd.com/read/29614738/molecular-pathophysiology-of-epithelial-barrier-dysfunction-in-inflammatory-bowel-diseases
#6
REVIEW
Jessica Y Lee, Valerie C Wasinger, Yunki Y Yau, Emil Chuang, Vijay Yajnik, Rupert Wl Leong
Over the years, the scientific community has explored myriads of theories in search of the etiology and a cure for inflammatory bowel disease (IBD). The cumulative evidence has pointed to the key role of the intestinal barrier and the breakdown of these mechanisms in IBD. More and more scientists and clinicians are embracing the concept of the impaired intestinal epithelial barrier and its role in the pathogenesis and natural history of IBD. However, we are missing a key tool that bridges these scientific insights to clinical practice...
March 31, 2018: Proteomes
https://www.readbyqxmd.com/read/29584711/proteomics-analysis-to-assess-the-role-of-mitochondria-in-brca1-mediated-breast-tumorigenesis
#7
Antonio Concolino, Erika Olivo, Laura Tammè, Claudia Vincenza Fiumara, Maria Teresa De Angelis, Barbara Quaresima, Valter Agosti, Francesco Saverio Costanzo, Giovanni Cuda, Domenica Scumaci
Mitochondria are the organelles deputed to energy production, but they are also involved in carcinogenesis, cancer progression, and metastasis, playing a role in altered energy metabolism in cancer cells. Mitochondrial metabolism is connected with several mitochondrial pathways such as ROS signaling, Ca2+ homeostasis, mitophagy, and mitochondrial biogenesis. These pathways are merged in an interactive super-network that seems to play a crucial role in cancer. Germline mutations of the BRCA1 gene account for 5-10% of breast cancers and confer a risk of developing the disease 10- to 20-fold much higher than in non-carriers...
March 27, 2018: Proteomes
https://www.readbyqxmd.com/read/29565292/association-of-proteomics-changes-with-al-sensitive-root-zones-in-switchgrass
#8
Mahesh Rangu, Zhujia Ye, Sarabjit Bhatti, Suping Zhou, Yong Yang, Tara Fish, Theodore W Thannhauser
In this paper, we report on aluminum (Al)-induced root proteomic changes in switchgrass. After growth in a hydroponic culture system supplemented with 400 μM of Al, plants began to show signs of physiological stress such as a reduction in photosynthetic rate. At this time, the basal 2-cm long root tips were harvested and divided into two segments, each of 1-cm in length, for protein extraction. Al-induced changes in proteomes were identified using tandem mass tags mass spectrometry (TMT-MS)-based quantitative proteomics analysis...
March 22, 2018: Proteomes
https://www.readbyqxmd.com/read/29561781/the-secretome-and-n-glycosylation-profiles-of-the-charophycean-green-alga-penium-margaritaceum-resemble-those-of-embryophytes
#9
Eliel Ruiz-May, Iben Sørensen, Zhangjun Fei, Sheng Zhang, David S Domozych, Jocelyn K C Rose
The secretome can be defined as the population of proteins that are secreted into the extracellular environment. Many proteins that are secreted by eukaryotes are N -glycosylated. However, there are striking differences in the diversity and conservation of N -glycosylation patterns between taxa. For example, the secretome and N -glycosylation structures differ between land plants and chlorophyte green algae, but it is not clear when this divergence took place during plant evolution. A potentially valuable system to study this issue is provided by the charophycean green algae (CGA), which is the immediate ancestors of land plants...
March 21, 2018: Proteomes
https://www.readbyqxmd.com/read/29495455/subcellular-proteomics-application-to-elucidation-of-flooding-response-mechanisms-in-soybean
#10
REVIEW
Setsuko Komatsu, Akiko Hashiguchi
Soybean, which is rich in protein and oil, is cultivated in several climatic zones; however, its growth is markedly decreased by flooding. Proteomics is a useful tool for understanding the flooding-response mechanism in soybean. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and during stress. Under flooding, proteins related to signaling, stress and the antioxidative system are increased in the plasma membrane; scavenging enzymes for reactive-oxygen species are suppressed in the cell wall; protein translation is suppressed through inhibition of proteins related to preribosome biogenesis and mRNA processing in the nucleus; levels of proteins involved in the electron transport chain are reduced in the mitochondrion; and levels of proteins related to protein folding are decreased in the endoplasmic reticulum...
February 27, 2018: Proteomes
https://www.readbyqxmd.com/read/29473895/the-gene-centric-content-management-system-and-its-application-for-cognitive-proteomics
#11
Ekaterina V Poverennaya, Alexander V Shargunov, Elena A Ponomarenko, Andrey V Lisitsa
The Human Proteome Project is moving into the next phase of creating and/or reconsidering the functional annotations of proteins using the chromosome-centric paradigm. This challenge cannot be solved exclusively using automated means, but rather requires human intelligence for interpreting the combined data. To foster the integration between human cognition and post-genome array a number of specific tools were recently developed, among them CAPER, GenomewidePDB, and The Proteome Browser (TPB). For the purpose of tackling the task of protein functional annotating the Gene-Centric Content Management System (GenoCMS) was expanded with new features...
February 23, 2018: Proteomes
https://www.readbyqxmd.com/read/29439554/pilot-study-on-mass-spectrometry-based-analysis-of-the-proteome-of-cd34%C3%A2-%C2%BAcd123%C3%A2-%C2%BA-progenitor-cells-for-the-identification-of-potential-targets-for-immunotherapy-in-acute-myeloid-leukemia
#12
Johannes R Schmidt, Elke Rücker-Braun, Katharina Heidrich, Malte von Bonin, Friedrich Stölzel, Christian Thiede, Jan M Middeke, Gerhard Ehninger, Martin Bornhäuser, Johannes Schetelig, Kristin Schubert, Martin von Bergen, Falk Heidenreich
Targeting of leukemic stem cells with specific immunotherapy would be an ideal approach for the treatment of myeloid malignancies, but suitable epitopes are unknown. The comparative proteome-level characterization of hematopoietic stem and progenitor cells from healthy stem cell donors and patients with acute myeloid leukemia has the potential to reveal differentially expressed proteins which can be used as surface-markers or as proxies for affected molecular pathways. We employed mass spectrometry methods to analyze the proteome of the cytosolic and the membrane fraction of CD34 and CD123 co-expressing FACS-sorted leukemic progenitors from five patients with acute myeloid leukemia...
February 12, 2018: Proteomes
https://www.readbyqxmd.com/read/29419792/revealing-subtle-functional-subgroups-in-class-a-scavenger-receptors-by-pattern-discovery-and-disentanglement-of-aligned-pattern-clusters
#13
Pei-Yuan Zhou, En-Shiun Annie Lee, Antonio Sze-To, Andrew K C Wong
A protein family has similar and diverse functions locally conserved as aligned sequence segments. Further discovering their association patterns could reveal subtle family subgroup characteristics. Since aligned residues associations (ARAs) in Aligned Pattern Clusters (APCs) are complex and intertwined due to entangled function, factors, and variance in the source environment, we have recently developed a novel method: Aligned Residue Association Discovery and Disentanglement (ARADD) to solve this problem...
February 8, 2018: Proteomes
https://www.readbyqxmd.com/read/29415455/proteome-profiling-of-diabetic-mellitus-patient-urine-for-discovery-of-biomarkers-by-comprehensive-ms-based-proteomics
#14
Yoshitoshi Hirao, Suguru Saito, Hidehiko Fujinaka, Shigeru Miyazaki, Bo Xu, Ali F Quadery, Amr Elguoshy, Keiko Yamamoto, Tadashi Yamamoto
Diabetic mellitus (DM) is a disease that affects glucose homeostasis and causes complications, such as diabetic nephropathy (DN). For early diagnosis of DN, microalbuminuria is currently one of the most frequently used biomarkers. However, more early diagnostic biomarkers are desired in addition to microalbuminuria. In this study, we performed comprehensive proteomics analysis of urine proteomes of diabetic mellitus patients without microalbuminuria and healthy volunteers to compare the protein profiles by mass spectrometry...
February 6, 2018: Proteomes
https://www.readbyqxmd.com/read/29401756/in-depth-proteomic-characterization-of-classical-and-non-classical-monocyte-subsets
#15
Víctor Segura, M Luz Valero, Laura Cantero, Javier Muñoz, Eduardo Zarzuela, Fernando García, Kerman Aloria, Javier Beaskoetxea, Jesús M Arizmendi, Rosana Navajas, Alberto Paradela, Paula Díez, Rosa Mª Dégano, Manuel Fuentes, Alberto Orfao, Andrés García Montero, Alba Garin-Muga, Fernando J Corrales, Manuel M Sánchez Del Pino
Monocytes are bone marrow-derived leukocytes that are part of the innate immune system. Monocytes are divided into three subsets: classical, intermediate and non-classical, which can be differentiated by their expression of some surface antigens, mainly CD14 and CD16. These cells are key players in the inflammation process underlying the mechanism of many diseases. Thus, the molecular characterization of these cells may provide very useful information for understanding their biology in health and disease. We performed a multicentric proteomic study with pure classical and non-classical populations derived from 12 healthy donors...
February 5, 2018: Proteomes
https://www.readbyqxmd.com/read/29385081/disseminating-metaproteomic-informatics-capabilities-and-knowledge-using-the-galaxy-p-framework
#16
Clemens Blank, Caleb Easterly, Bjoern Gruening, James Johnson, Carolin A Kolmeder, Praveen Kumar, Damon May, Subina Mehta, Bart Mesuere, Zachary Brown, Joshua E Elias, W Judson Hervey, Thomas McGowan, Thilo Muth, Brook Nunn, Joel Rudney, Alessandro Tanca, Timothy J Griffin, Pratik D Jagtap
The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research...
January 31, 2018: Proteomes
https://www.readbyqxmd.com/read/29385730/evaluation-of-optimized-tube-gel-methods-of-sample-preparation-for-large-scale-plant-proteomics
#17
Thierry Balliau, Mélisande Blein-Nicolas, Michel Zivy
The so-called tube-gel method is a sample preparation protocol allowing for management of SDS for protein solubilization through in-gel protein trapping. Because of its simplicity, we assumed that once miniaturized, this method could become a standard for large scale experiments. We evaluated the performances of two variants of the miniaturized version of the tube-gel method based on different solubilization buffers (Tris-SDS or urea-SDS). To this end, we compared them to two other digestion methods: (i) liquid digestion after protein solubilization in the absence of SDS (liquid method) and (ii) filter-aided sample preparation (FASP)...
January 30, 2018: Proteomes
https://www.readbyqxmd.com/read/29364831/exploring-the-psoriatic-arthritis-proteome-in-search-of-novel-biomarkers
#18
REVIEW
Shalini M Mahendran, Vinod Chandran
Psoriatic arthritis (PsA) is an inflammatory arthritis which develops in up to one-third of patients suffering from the cutaneous disorder, psoriasis. The complex and heterogeneous nature of PsA renders it difficult to diagnose, leading to poor outcomes and, therefore, warrants an examination into soluble biomarkers, which may facilitate early detection of the disease. Protein biomarkers are a dynamic resource of pathophysiological information able to provide an immediate reflection of pathological changes caused by disease...
January 24, 2018: Proteomes
https://www.readbyqxmd.com/read/29342075/enrichment-and-identification-of-the-most-abundant-zinc-binding-proteins-in-developing-barley-grains-by-zinc-imac-capture-and-nano-lc-ms-ms
#19
Giuseppe Dionisio, Mohammad Nasir Uddin, Eva Vincze
Background: Zinc accumulates in the embryo, aleurone, and subaleurone layers at different amounts in cereal grains. Our hypothesis is that zinc could be stored bound, not only to low MW metabolites/proteins, but also to high MW proteins as well. Methods: In order to identify the most abundant zinc binding proteins in different grain tissues, we microdissected barley grains into (1) seed coats; (2) aleurone/subaleurone; (3) embryo; and (4) endosperm. Initial screening for putative zinc binding proteins from the different tissue types was performed by fractionating proteins according to solubility (Osborne fractionation), and resolving those via Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) followed by polyvinylidene fluoride (PVDF) membrane blotting and dithizone staining...
January 17, 2018: Proteomes
https://www.readbyqxmd.com/read/29286311/comparative-proteomics-analysis-of-urine-reveals-down-regulation-of-acute-phase-response-signaling-and-lxr-rxr-activation-pathways-in-prostate-cancer
#20
Katarina Davalieva, Sanja Kiprijanovska, Ivana Maleva Kostovska, Sotir Stavridis, Oliver Stankov, Selim Komina, Gordana Petrusevska, Momir Polenakovic
Detecting prostate cancer (PCa) using non-invasive diagnostic markers still remains a challenge. The aim of this study was the identification of urine proteins that are sufficiently sensitive and specific to detect PCa in the early stages. Comparative proteomics profiling of urine from patients with PCa, benign prostate hyperplasia, bladder cancer, and renal cancer, coupled with bioinformatics analysis, were performed. Statistically significant difference in abundance showed 20 and 85 proteins in the 2-D DIGE/MS and label-free LC-MS/MS experiments, respectively...
December 29, 2017: Proteomes
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