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https://www.readbyqxmd.com/read/28527949/microproteome-of-dentoalveolar-tissues
#1
Cristiane R Salmon, Ana Paula O Giorgetti, Adriana F Paes Leme, Romênia R Domingues, Tamara N Kolli, Brian L Foster, Francisco H Nociti
Proteomic analysis of extracellular matrices (ECM) of dentoalveolar tissues can provide insights into developmental, pathological, and reparative processes. However, targeted dissection of mineralized tissues, dental cementum (DC), alveolar bone (AB), and dentin (DE), presents technical difficulties. We demonstrate an approach combining EDTA decalcification and laser capture microdissection (LCM), followed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), to analyze proteome profiles of these tissues...
May 17, 2017: Bone
https://www.readbyqxmd.com/read/28526583/the-connexin-43-c-terminus-a-tail-of-many-tales
#2
REVIEW
Edward Leithe, Marc Mesnil, Trond Aasen
Connexins are chordate gap junction channel proteins that, by enabling direct communication between the cytosols of adjacent cells, create a unique cell signalling network. Gap junctional intercellular communication (GJIC) has important roles in controlling cell growth and differentiation and in tissue development and homeostasis. Moreover, several non-canonical connexin functions unrelated to GJIC have been discovered. Of the 21 members of the human connexin family, connexin 43 (Cx43) is the most widely expressed and studied...
May 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28524240/potential-serum-biomarkers-associated-with-mild-and-severe-leptospirosis-infection-a-cohort-study-in-the-malaysian-population
#3
Tan Xue Ting, Fairuz Binti Amran, Ravindran Thayan, Norazah Ahmad, Roslinda Jaafar, Rahimah Haron, Rafidah Abdullah, Sazwan Reezal Bin Shamsuddin, Nor Suhaila Binti Md Riffin, Puteri Shafinaz Abdul-Rahman
Leptospirosis is an emerging zoonotic infectious disease in Malaysia. The symptoms of leptospirosis vary from mild non-specific flu-like illness to a severe condition which is usually associated with serious complication and fatality. To study the protein expression profile of mild and severe leptospirosis, fifteen paired sera were collected from the patients who were mildly infected and following that progressed to severe stage. The proteome profiles of mild and severe cases were studied using 2DE analysis in combination with LC-MS/MS...
May 19, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28524201/a-computational-framework-for-distinguishing-direct-versus-indirect-interactions-in-human-functional-protein-protein-interaction-networks
#4
Suyu Mei, Erik K Flemington, Kun Zhang
Recognition of indirect interactions is instrumental to in silico reconstruction of signaling pathways and sheds light on the exploration of unknown physical paths between two indirectly interacting genes. However, very limited computational methods have explicitly exploited the indirect interactions with experimental evidence thus far. In this work, we attempt to distinguish direct versus indirect interactions in human functional protein-protein interaction (PPI) networks via a predictive l2-regularized logistic regression model built on the experimental data...
May 19, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28522639/definition-of-a-rack1-interaction-network-in-drosophila-melanogaster-using-swath-ms
#5
Lauriane Kuhn, Karim Majzoub, Evelyne Einhorn, Johana Chicher, Pompon Julien, Jean-Luc Imler, Philippe Hammann, Carine Meignin
Receptor for Activated C kinase 1 (RACK1) is a scaffold protein that has been found in association with several signaling complexes, and with the 40S subunit of the ribosome. Using the model organism Drosophila melanogaster, we recently showed that RACK1 is required at the ribosome for IRES-mediated translation of viruses. Here, we report a proteomic characterization of the interactome of RACK1 in Drosophila S2 cells. We carried out Label-Free quantitation using both Data-Dependent and Data-Independent Acquisition and observed a significant advantage for the Sequential Window Acquisition of all THeoretical fragment-ion spectra (SWATH) method both in terms of identification of interactants and quantification of low abundance proteins...
May 18, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28520934/the-smap1-2-proteins-of-the-crenarchaeon-sulfolobus-solfataricus-interact-with-the-exosome-and-stimulate-a-rich-tailing-of-transcripts
#6
Birgit Märtens, Linlin Hou, Fabian Amman, Michael T Wolfinger, Elena Evguenieva-Hackenberg, Udo Bläsi
The conserved Sm and Sm-like proteins are involved in different aspects of RNA metabolism. Here, we explored the interactome of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso) to shed light on their physiological function(s). Both, SmAP1 and SmAP2 co-purified with several proteins involved in RNA-processing/modification, translation and protein turnover as well as with components of the exosome involved in 3΄ to 5΄ degradation of RNA. In follow-up studies a direct interaction with the poly(A) binding and accessory exosomal subunit DnaG was demonstrated...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28514442/architecture-of-the-human-interactome-defines-protein-communities-and-disease-networks
#7
Edward L Huttlin, Raphael J Bruckner, Joao A Paulo, Joe R Cannon, Lily Ting, Kurt Baltier, Greg Colby, Fana Gebreab, Melanie P Gygi, Hannah Parzen, John Szpyt, Stanley Tam, Gabriela Zarraga, Laura Pontano-Vaites, Sharan Swarup, Anne E White, Devin K Schweppe, Ramin Rad, Brian K Erickson, Robert A Obar, K G Guruharsha, Kejie Li, Spyros Artavanis-Tsakonas, Steven P Gygi, J Wade Harper
The physiology of a cell can be viewed as the product of thousands of proteins acting in concert to shape the cellular response. Coordination is achieved in part through networks of protein-protein interactions that assemble functionally related proteins into complexes, organelles, and signal transduction pathways. Understanding the architecture of the human proteome has the potential to inform cellular, structural, and evolutionary mechanisms and is critical to elucidating how genome variation contributes to disease...
May 17, 2017: Nature
https://www.readbyqxmd.com/read/28503168/generation-and-comprehensive-analysis-of-host-cell-interactome-of-the-pa-protein-of-the-highly-pathogenic-h5n1-avian-influenza-virus-in-mammalian-cells
#8
Zhao Gao, Jiao Hu, Yanyan Liang, Qian Yang, Kun Yan, Dong Liu, Xiaoquan Wang, Min Gu, Xiaowen Liu, Shunlin Hu, Zenglei Hu, Huimou Liu, Wenbo Liu, Sujuan Chen, Daxin Peng, Xin-An Jiao, Xiufan Liu
Accumulating data have identified the important roles of PA protein in replication and pathogenicity of influenza A virus (IAV). Identification of host factors that interact with the PA protein may accelerate our understanding of IAV pathogenesis. In this study, using immunoprecipitation assay combined with liquid chromatography-tandem mass spectrometry, we identified 278 human cellular proteins that might interact with PA of H5N1 IAV. Gene Ontology annotation revealed that the identified proteins are highly associated with viral translation and replication...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28498392/the-flightless-i-protein-interacts-with-rna-binding-proteins-and-is-involved-in-the-genome-wide-mrna-post-transcriptional-regulation-in-lung-carcinoma-cells
#9
Cuihua Wang, Kezhi Chen, Shengyou Liao, Wei Gu, Xinlei Lian, Jing Zhang, Xuejuan Gao, Xiaohui Liu, Tong Wang, Qing-Yu He, Gong Zhang, Langxia Liu
The flightless I protein (FLII) belongs to the gelsolin family. Its function has been associated with actin remodeling, embryonic development, wound repair, and more recently with cancer. The structure of FLII is characterized by the N-terminal leucine-rich repeats (LRR) and C-terminal gesolin related repeated units that are both protein-protein inter-action domains, suggesting that FLII may exert its function by interaction with other proteins. Therefore, systematic study of protein interactions of FLII in cells is important for the understanding of FLII functions...
May 11, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28494922/analysis-of-jak-stat-signaling-pathway-genes-and-their-micrornas-in-the-intestinal-mucosa-of-genetically-disparate-chicken-lines-induced-with-necrotic-enteritis
#10
Anh Duc Truong, Deivendran Rengaraj, Yeojin Hong, Cong Thanh Hoang, Yeong Ho Hong, Hyun S Lillehoj
The JAK-STAT signaling pathway plays a key role in cytokine and growth factor activation and is involved in several cellular functions and diseases. The main objective of this study was to investigate the expression of candidate JAK-STAT pathway genes and their regulators and interactors in the intestinal mucosal layer of two genetically disparate chicken lines [Marek's disease (MD)-resistant line 6.3 and MD-susceptible line 7.2] induced with necrotic enteritis (NE). Through RNA-sequencing, we investigated 116 JAK-STAT signaling pathway-related genes that were significant and differentially expressed between the intestinal mucosa of the two lines compared with respective uninfected controls...
May 2017: Veterinary Immunology and Immunopathology
https://www.readbyqxmd.com/read/28488575/proteomics-analysis-of-bladder-cancer-invasion-targeting-eif3d-for-therapeutic-intervention
#11
Agnieszka Latosinska, Marika Mokou, Manousos Makridakis, William Mullen, Jerome Zoidakis, Vasiliki Lygirou, Maria Frantzi, Ioannis Katafigiotis, Konstantinos Stravodimos, Marie C Hupe, Maciej Dobrzynski, Walter Kolch, Axel S Merseburger, Harald Mischak, Maria G Roubelakis, Antonia Vlahou
Patients with advanced bladder cancer have poor outcomes, indicating a need for more efficient therapeutic approaches. This study characterizes proteomic changes underlying bladder cancer invasion aiming for the better understanding of disease pathophysiology and identification of drug targets. High resolution liquid chromatography coupled to tandem mass spectrometry analysis of tissue specimens from patients with non-muscle invasive (NMIBC, stage pTa) and muscle invasive bladder cancer (MIBC, stages pT2+) was conducted...
April 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/28487965/ho-1-ebp-interaction-alleviates-cholesterol-induced-hypoxia-through-the-activation-of-the-akt-and-nrf2-mtor-pathways-and-inhibition-of-carbohydrate-metabolism-in-cardiomyocytes
#12
Xiaohan Jin, Zhongwei Xu, Jin Cao, Rui Yan, Ruicheng Xu, Ruiqiong Ran, Yongqiang Ma, Wei Cai, Rong Fan, Yan Zhang, Xin Zhou, Yuming Li
Heme oxygenase-1 (HO-1) is an inducible and cytoprotective enzyme that provides a defense against oxidant damage. The present study screened 137 HO-1/interacting proteins using a profound co-immunoprecipitation (Co-IP) coupled with proteomics, and profiled the global HO-1 interactome network, including oxidative phosphorylation, endoplasmic reticulum and transport vesicle functions. Among these molecules, we observed that a novel interactor, emopamil-binding protein (EBP), is closely related to the cholesterol metabolism process...
June 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28485080/pelp1-a-key-mediator-of-estrogen-signaling-and-actions-in-the-brain
#13
REVIEW
Roshni Thakkar, Gangadhara Reddy Sareddy, Quanguang Zhang, Ruimin Wang, Ratna K Vadlamudi, Darrell Brann
Proline-, Glutamic acid-, and Leucine-rich Protein 1 (PELP1) is an estrogen receptor (ER) coregulator protein identified by our collaborative group. Work from our lab and others has shown that PELP1 is a scaffold protein that interacts with ERs, kinase signaling factors, as well as proteins involved in chromatin remodeling and DNA repair. Its role in mediating 17β-Estradiol (E2) signaling and actions has been heavily studied in cancer cells, but only recently has attention turned to its role in the brain. In this review, we discuss the tissue, cellular and subcellular localization of PELP1 in the brain...
May 9, 2017: Journal of Neuroendocrinology
https://www.readbyqxmd.com/read/28480880/intron-retention-is-regulated-by-altered-mecp2-mediated-splicing-factor-recruitment
#14
Justin J-L Wong, Dadi Gao, Trung V Nguyen, Chau-To Kwok, Michelle van Geldermalsen, Rob Middleton, Natalia Pinello, Annora Thoeng, Rajini Nagarajah, Jeff Holst, William Ritchie, John E J Rasko
While intron retention (IR) is considered a widely conserved and distinct mechanism of gene expression control, its regulation is poorly understood. Here we show that DNA methylation directly regulates IR. We also find reduced occupancy of MeCP2 near the splice junctions of retained introns, mirroring the reduced DNA methylation at these sites. Accordingly, MeCP2 depletion in tissues and cells enhances IR. By analysing the MeCP2 interactome using mass spectrometry and RNA co-precipitation, we demonstrate that decreased MeCP2 binding near splice junctions facilitates IR via reduced recruitment of splicing factors, including Tra2b, and increased RNA polymerase II stalling...
May 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/28479977/the-foundations-of-plant-intelligence
#15
REVIEW
Anthony Trewavas
Intelligence is defined for wild plants and its role in fitness identified. Intelligent behaviour exhibited by single cells and systems similarity between the interactome and connectome indicates neural systems are not necessary for intelligent capabilities. Plants sense and respond to many environmental signals that are assessed to competitively optimize acquisition of patchily distributed resources. Situations of choice engender motivational states in goal-directed plant behaviour; consequent intelligent decisions enable efficient gain of energy over expenditure...
June 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/28478905/plant-rna-interactome-capture-revealing-the-plant-rbpome
#16
Marcel Bach-Pages, Alfredo Castello, Gail M Preston
The application of RNA interactome capture to plants has enabled comprehensive determination of the plant RNA-binding proteome and the identification of novel families of RNA-binding proteins (RBPs). The technique is providing insight into the evolution of the eukaryotic repertoire of RBPs and will enhance prospects for engineering RBPs to improve crop traits.
May 3, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28477369/snx27-interactome-in-t-lymphocytes-identifies-zo-2-dynamic-redistribution-at-the-immune-synapse
#17
María Tello-Lafoz, Gonzalo Martínez-Martínez, Cristina Rodríguez-Rodríguez, Juan Pablo Albar, Morgan Huse, Severine Gharbi, Isabel Merida
T lymphocyte recognition of antigens leads to the formation of a highly organized structure termed immune synapse (IS) by analogy with the nervous synapse. Sorting nexin 27 (SNX27) controls the endosomal traffic of PDZ domain-interacting proteins, and its alteration is associated with impaired synaptic function and neurological diseases. In T lymphocytes SNX27-positive vesicles polarize to the IS, the identity of SNX27 interactors in these conditions nonetheless remains unknown. Here we used proteomics to analyze the SNX27 interactome purified from IS-forming T cells, and confirmed the conserved nature of the SNX27/WASH/retromer association in hematopoietic cells...
May 6, 2017: Traffic
https://www.readbyqxmd.com/read/28473845/pancreatic-islet-protein-complexes-and-their-dysregulation-in-type-2-diabetes
#18
Helle Krogh Pedersen, Valborg Gudmundsdottir, Søren Brunak
Type 2 diabetes (T2D) is a complex disease that involves multiple genes. Numerous risk loci have already been associated with T2D, although many susceptibility genes remain to be identified given heritability estimates. Systems biology approaches hold potential for discovering novel T2D genes by considering their biological context, such as tissue-specific protein interaction partners. Pancreatic islets are a key T2D tissue and many of the known genetic risk variants lead to impaired islet function, hence a better understanding of the islet-specific dysregulation in the disease-state is essential to unveil the full potential of person-specific profiles...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28469556/integrative-analysis-of-brain-region-specific-shank3-interactomes-for-understanding-the-heterogeneity-of-neuronal-pathophysiology-related-to-shank3-mutations
#19
Yeunkum Lee, Hyojin Kang, Bokyoung Lee, Yinhua Zhang, Yoonhee Kim, Shinhyun Kim, Won-Ki Kim, Kihoon Han
Recent molecular genetic studies have identified 100s of risk genes for various neurodevelopmental and neuropsychiatric disorders. As the number of risk genes increases, it is becoming clear that different mutations of a single gene could cause different types of disorders. One of the best examples of such a gene is SHANK3, which encodes a core scaffold protein of the neuronal excitatory post-synapse. Deletions, duplications, and point mutations of SHANK3 are associated with autism spectrum disorders, intellectual disability, schizophrenia, bipolar disorder, and attention deficit hyperactivity disorder...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28465432/different-phosphoisoforms-of-rna-polymerase-ii-engage-the-rtt103-termination-factor-in-a-structurally-analogous-manner
#20
Corey M Nemec, Fan Yang, Joshua M Gilmore, Corinna Hintermair, Yi-Hsuan Ho, Sandra C Tseng, Martin Heidemann, Ying Zhang, Laurence Florens, Audrey P Gasch, Dirk Eick, Michael P Washburn, Gabriele Varani, Aseem Z Ansari
The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcription. Signature phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of the CTD engage specific "readers." Whereas phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. Here, we identify a role for phospho-Thr4 in transcription termination at noncoding small nucleolar RNA (snoRNA) genes...
May 2, 2017: Proceedings of the National Academy of Sciences of the United States of America
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