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Proteomes

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https://www.readbyqxmd.com/read/29933573/proteomic-analysis-of-histone-variants-and-their-ptms-strategies-and-pitfalls
#1
REVIEW
Sara El Kennani, Marion Crespo, Jérôme Govin, Delphine Pflieger
Epigenetic modifications contribute to the determination of cell fate and differentiation. The molecular mechanisms underlying histone variants and post-translational modifications (PTMs) have been studied in the contexts of development, differentiation, and disease. Antibody-based assays have classically been used to target PTMs, but these approaches fail to reveal combinatorial patterns of modifications. In addition, some histone variants are so similar to canonical histones that antibodies have difficulty distinguishing between these isoforms...
June 21, 2018: Proteomes
https://www.readbyqxmd.com/read/29933572/editorial-for-special-issue-2017-plant-proteomics
#2
EDITORIAL
Elisabeth Jamet, Véronique Santoni
No abstract text is available yet for this article.
June 21, 2018: Proteomes
https://www.readbyqxmd.com/read/29865292/large-scale-proteomic-data-and-network-based-systems-biology-approaches-to-explore-the-plant-world
#3
Dario Di Silvestre, Andrea Bergamaschi, Edoardo Bellini, PierLuigi Mauri
The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification...
June 3, 2018: Proteomes
https://www.readbyqxmd.com/read/29843395/potential-alternative-strategy-against-drug-resistant-tuberculosis-a-proteomics-prospect
#4
REVIEW
Divakar Sharma, Deepa Bisht, Asad U Khan
Mycobacterium tuberculosis is one of the deadliest human pathogen of the tuberculosis diseases. Drug resistance leads to emergence of multidrug-resistant and extremely drug resistant strains of M. tuberculosis . Apart from principal targets of resistance, many explanations have been proposed for drug resistance but some resistance mechanisms are still unknown. Recently approved line probe assay (LPA) diagnostics for detecting the resistance to first and second line drugs are unable to diagnose the drug resistance in M...
May 28, 2018: Proteomes
https://www.readbyqxmd.com/read/29799446/proteomic-analysis-of-aphid-resistant-and-sensitive-rose-rosa-hybrida-cultivars-at-two-developmental-stages
#5
Sowbiya Muneer, Hai Kyoung Jeong, Yoo Gyeong Park, Byoung Ryong Jeong
The rose is one the most commercially grown and costly ornamental plants because of its aesthetic beauty and aroma. A large number of pests attack its buds, flowers, leaves, and stem at every growing stage due to its high sugar content. The most common pest on roses are aphids which are considered to be the major cause for product loss. Aphid infestations lead to major changes in rose plants, such as large and irregular holes in petals, intact leaves and devouring tissues. It is hypothesized that different cut rose cultivars would have different levels of sensitivity or resistance to aphids, since different levels of infestation are observed in commercially cut rose production greenhouses...
May 25, 2018: Proteomes
https://www.readbyqxmd.com/read/29786648/utilizing-optimized-tools-to-investigate-ptm-crosstalk-identifying-potential-ptm-crosstalk-of-acetylated-mitochondrial-proteins
#6
Henrick Horita, Andy Law, Kim Middleton
Post-translational modification (PTM) crosstalk is recognized as a major cell-regulatory mechanism, and studies of several proteins have validated the premise that PTMs work in concert. Previous work by our group investigated the potential PTM crosstalk on proteins in the EGFR-Ras-c-Fos axis by utilizing a comprehensive set of PTM reagents termed Signal-Seeker toolkits. In this study, these tools were used to investigate the potential PTM crosstalk that occurs in acetylated mitochondrial proteins in response to a mitochondrial stress-inducing agent hydrogen peroxide (H₂O₂)...
May 22, 2018: Proteomes
https://www.readbyqxmd.com/read/29786634/virophages-and-their-interactions-with-giant-viruses-and-host-cells
#7
REVIEW
Haitham Sobhy
Virophages are small dsDNA viruses that were first isolated in association with some giant viruses (GVs), and then found in metagenomics samples. They encode about 20⁻34 proteins. Some virophages share protein similarity with Maverick/Polinton transposons or are considered as a provirophage, whereas about half of the protein's repertoire remain of unknown function. In this review, we aim to highlight the current understanding of the biology of virophages, as well as their interactions with giant viruses and host cells...
May 22, 2018: Proteomes
https://www.readbyqxmd.com/read/29762536/proteomics-of-human-retinal-pigment-epithelium-rpe-cells
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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