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https://www.readbyqxmd.com/read/28743114/cervical-alpha-actinin-4-is-upregulated-in-women-with-threatened-preterm-labor-and-microbial-invasion-of-the-amniotic-cavity
#1
Teresa Cobo, Montse Palacio, Maribel Grande, Ana B Sánchez-García, Josep M Estanyol, Marta López, Jordi Bosch, Cristina Martí, Eduard Gratacós
OBJECTIVE: To characterize the proteome profile of women with threatened preterm labor (PTL) below 34;0 weeks with and without microbial invasion of the amniotic cavity (MIAC) using mass spectrometry in the amniotic fluid (AF) and Western blot analysis in the cervical mucus and the vaginal fluid. SUBJECTS AND METHODS: In the discovery phase, a case-control study including 8 women with MIAC and 7 without matched for gestational age at sampling was performed. Proteomic profile characterization was done using the LTQ VELOS Orbitrap mass spectrometer in the AF...
July 26, 2017: Fetal Diagnosis and Therapy
https://www.readbyqxmd.com/read/28742856/fit-for-genomic-and-proteomic-purposes-sampling-the-fitness-of-nucleic-acid-and-protein-derivatives-from-formalin-fixed-paraffin-embedded-tissue
#2
Anna Yakovleva, Jordan L Plieskatt, Sarah Jensen, Razan Humeida, Jonathan Lang, Guangzhao Li, Paige Bracci, Sylvia Silver, Jeffrey Michael Bethony
The demand for nucleic acid and protein derivatives from formalin-fixed paraffin-embedded (FFPE) tissue has greatly increased due to advances in extraction and purification methods, making these derivatives available for numerous genomic and proteomic platforms. Previously, DNA, RNA, microRNA (miRNA), or protein derived from FFPE tissue blocks were considered "unfit" for such platforms, as the process of tissue immobilization by FFPE resulted in cross-linked, fragmented, and chemically modified macromolecules...
2017: PloS One
https://www.readbyqxmd.com/read/28742844/control-of-runx-induced-repression-of-notch-signaling-by-mlf-and-its-partner-dnaj-1-during-drosophila-hematopoiesis
#3
Marion Miller, Aichun Chen, Vanessa Gobert, Benoit Augé, Mathilde Beau, Odile Burlet-Schiltz, Marc Haenlin, Lucas Waltzer
A tight regulation of transcription factor activity is critical for proper development. For instance, modifications of RUNX transcription factors dosage are associated with several diseases, including hematopoietic malignancies. In Drosophila, Myeloid Leukemia Factor (MLF) has been shown to control blood cell development by stabilizing the RUNX transcription factor Lozenge (Lz). However, the mechanism of action of this conserved family of proteins involved in leukemia remains largely unknown. Here we further characterized MLF's mode of action in Drosophila blood cells using proteomic, transcriptomic and genetic approaches...
July 25, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28742527/biotechnological-potential-of-insect-fatty-acid-modifying-enzymes
#4
Michal Tupec, Aleš Buček, Irena Valterová, Iva Pichová
There are more than one million described insect species. This species richness is reflected in the diversity of insect metabolic processes. In particular, biosynthesis of secondary metabolites, such as defensive compounds and chemical signals, encompasses an extraordinarily wide range of chemicals that are generally unparalleled among natural products from other organisms. Insect genomes, transcriptomes and proteomes thus offer a valuable resource for discovery of novel enzymes with potential for biotechnological applications...
July 25, 2017: Zeitschrift Für Naturforschung. C, A Journal of Biosciences
https://www.readbyqxmd.com/read/28742394/assessment-of-proteomic-measures-across-serious-psychiatric-illness
#5
S Charles Schulz, Shauna Overgaard, David J Bond, Rajesh Kaldate
The diagnoses of serious psychiatric illnesses, such as schizophrenia, schizoaffective disorder, and bipolar disorder, rely on the subjective recall and interpretation of often overlapping symptoms, and are not based on the objective pathophysiology of the illnesses. The subjectivity of symptom reporting and interpretation contributes to the delay of accurate diagnoses and limits effective treatment of these illnesses. Proteomics, the study of the types and quantities of proteins an organism produces, may offer an objective biological approach to psychiatric diagnosis...
2017: Clinical Schizophrenia & related Psychoses
https://www.readbyqxmd.com/read/28742275/the-proteome-and-transcriptome-of-the-infectious-metacyclic-form-of-trypanosoma-brucei-define-quiescent-cells-primed-for-mammalian-invasion
#6
Romain Christiano, Nikolay G Kolev, Huafang Shi, Elisabetta Ullu, Tobias C Walther, Christian Tschudi
The infectious metacyclic forms of Trypanosoma brucei result from a complex development in the tsetse fly vector. When they infect mammals, they cause African sleeping sickness in humans. Due to scarcity of biological material and difficulties of the tsetse fly as an experimental system, very limited information is available concerning the gene expression profile of metacyclic forms. We used an in vitro system based on expressing the RNA binding protein 6 to obtain infectious metacyclics and determined their protein and mRNA repertoires by mass-spectrometry (MS) based proteomics and mRNA sequencing (RNA-Seq) in comparison to non-infectious procyclic trypanosomes...
July 25, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28742267/profiling-the-effects-of-short-time-course-cold-ischemia-on-tumor-protein-phosphorylation-using-a-bayesian-approach
#7
You Wu, Jeremy Gaskins, Maiying Kong, Susmita Datta
Phosphorylated proteins provide insight into tumor etiology and are used as diagnostic, prognostic, and therapeutic markers of complex diseases. However, pre-analytic variations, such as freezing delay after biopsy acquisition, often occur in real hospital settings and potentially lead to inaccurate results. The objective of this work is to develop statistical methodology to assess the stability of phosphorylated proteins under short-time cold ischemia. We consider a hierarchical model to determine if phosphorylation abundance of a protein at a particular phosphorylation site remains constant or not during cold ischemia...
July 25, 2017: Biometrics
https://www.readbyqxmd.com/read/28742213/derivatization-agents-for-electrochemical-detection-in-amino-acid-peptide-and-protein-separations-the-hidden-electrochemistry
#8
REVIEW
Tania Sierra, Agustin G Crevillen, Alberto Escarpa
In proteomics and clinical analysis, LIF and MS are the most used detectors coupled to separation techniques. MS offers good sensitivity and analyte identification ability but, as counterbalance, it is expensive and it needed background electrolytes compatible with mass spectrometers. LIF detection offers the highest sensitivity but, in general, proteins, peptides and amino acids are not fluorescents so it is necessary the use of fluorescence tags. This fact hindered the potential sensitivity of LIF detection due to the difficulty of labeling analytes at extremely low concentrations...
July 25, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28742153/reconstructing-the-regulatory-circuit-of-cell-fate-determination-in-yeast-mating-response
#9
Bin Shao, Haiyu Yuan, Rongfei Zhang, Xuan Wang, Shuwen Zhang, Qi Ouyang, Nan Hao, Chunxiong Luo
Massive technological advances enabled high-throughput measurements of proteomic changes in biological processes. However, retrieving biological insights from large-scale protein dynamics data remains a challenging task. Here we used the mating differentiation in yeast Saccharomyces cerevisiae as a model and developed integrated experimental and computational approaches to analyze the proteomic dynamics during the process of cell fate determination. When exposed to a high dose of mating pheromone, the yeast cell undergoes growth arrest and forms a shmoo-like morphology; however, at intermediate doses, chemotropic elongated growth is initialized...
July 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28742128/construction-and-characterization-of-the-korean-whole-saliva-proteome-to-determine-ethnic-differences-in-human-saliva-proteome
#10
Ha Ra Cho, Han Sol Kim, Jun Seo Park, Seung Cheol Park, Kwang Pyo Kim, Troy D Wood, Yong Seok Choi
As the first step to discover protein disease biomarkers from saliva, global analyses of the saliva proteome have been carried out since the early 2000s, and more than 3,000 proteins have been identified in human saliva. Recently, ethnic differences in the human plasma proteome have been reported, but such corresponding studies on human saliva in this aspect have not been previously reported. Thus, here, in order to determine ethnic differences in the human saliva proteome, a Korean whole saliva (WS) proteome catalogue indexing 480 proteins was built and characterized through nLC-Q-IMS-TOF analyses of WS samples collected from eleven healthy South Korean male adult volunteers for the first time...
2017: PloS One
https://www.readbyqxmd.com/read/28742123/molecular-and-maldi-tof-identification-of-ticks-and-tick-associated-bacteria-in-mali
#11
Adama Zan Diarra, Lionel Almeras, Maureen Laroche, Jean-Michel Berenger, Abdoulaye K Koné, Zakaria Bocoum, Abdoulaye Dabo, Ogobara Doumbo, Didier Raoult, Philippe Parola
Ticks are considered the second vector of human and animal diseases after mosquitoes. Therefore, identification of ticks and associated pathogens is an important step in the management of these vectors. In recent years, mass spectrometry of the laser disorder / matrix assisted ionization (MALDI-TOF MS) has been reported as a promising method for the identification of arthropods including ticks. The objective of this study was to improve the conditions for the preparation of tick samples for their identification by MALDI-TOF MS from field-collected ethanol-stored Malian samples and to evaluate the capacity of this technology to distinguish infected and uninfected ticks...
July 24, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28742074/untargeted-screening-for-novel-autoantibodies-with-prognostic-value-in-first-episode-psychosis
#12
A Zandian, L Wingård, H Nilsson, E Sjöstedt, D X Johansson, D Just, C Hellström, M Uhlén, J M Schwenk, A Häggmark-Månberg, O Norbeck, B Owe-Larsson, P Nilsson, M A A Persson
Immunological and inflammatory reactions have been suggested to have a role in the development of schizophrenia, a hypothesis that has recently been supported by genetic data. The aim of our study was to perform an unbiased search for autoantibodies in patients with a first psychotic episode, and to explore the association between any seroreactivity and the development of a Diagnostic and Statistical Manual of Mental Disorders, fourth edition (DSM-IV) disorder characterized by chronic or relapsing psychotic symptoms...
July 25, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28741728/ebi2-contributes-to-the-induction-of-thymic-central-tolerance-in-mice-by-promoting-rapid-motility-of-medullary-thymocytes
#13
Sanghee Ki, Hiran M Thyagarajan, Zicheng Hu, Jessica N Lancaster, Lauren I R Ehrlich
Maturing thymocytes enter the thymic medulla, where they encounter numerous self-antigens presented by antigen presenting cells (APCs). Those thymocytes that are strongly self-reactive undergo either negative selection or diversion into the regulatory T cell lineage. Although the majority of the proteome is expressed in the medulla, many self-antigens are expressed by only a minor fraction of medullary APCs; thus, thymocytes must efficiently enter the medulla and scan APCs to ensure central tolerance. Chemokine receptors promote lymphocyte migration, organization within tissues, and interactions with APCs in lymphoid organs...
July 25, 2017: European Journal of Immunology
https://www.readbyqxmd.com/read/28741388/comparative-proteomic-analysis-of-the-effect-of-the-four-herb-chinese-medicine-anbp-on-promoting-mouse-skin-wound-healing
#14
Li Chen, Qian Hou, Zhong-Zhi Zhou, Mei-Rong Li, Ling-Zhi Zhong, Xiang-Dong Deng, Zi-Ying Zhu, Zhong-Yi Cheng, Jun Zhu, Cong-Lian Xiang, Wen-Jun He, Xiao-Bing Fu
Traditional Chinese medicine has great potential to improve wound healing. ANBP, the mixture of 4 Chinese herbs- Agrimoniapilosa, Nelumbonucifera, Boswelliacarteri, and Pollen typhae-is effective in trauma treatment while its mechanism is still elusive. In this study, quantitative proteomics and bioinformatics analyses were performed to decipher the possible roles of ANBP in accelerated wound healing of mouse skin. Among all 3171 identified proteins, 90, 71, 80, and 140 proteins were found to be differently expressed in 6 hours, 3 days, 7 days, and 14 days ANBP-treated tissues compared with corresponding control tissues, respectively...
July 1, 2017: International Journal of Lower Extremity Wounds
https://www.readbyqxmd.com/read/28741358/combining-de-novo-peptide-sequencing-algorithms-a-synergistic-approach-to-boost-both-identifications-and-confidence-in-bottom-up-proteomics
#15
Bernhard Blank-Landeshammer, Laxmikanth Kollipara, Karsten Biß, Markus Pfenninger, Sebastian Malchow, Konstantin Shuvaev, René P Zahedi, Albert Sickmann
Complex mass spectrometry based proteomics datasets are mostly analyzed by protein database-searches. While this approach performs considerably well for sequenced organisms, direct inference of peptide sequences from tandem mass spectra, i.e. de novo peptide sequencing, oftentimes is the only way to obtain information when protein databases are absent. However, available algorithms suffer from drawbacks such as lack of validation and often high rates of false positive hits (FP). Here we present a simple method of combining results from commonly available de novo peptide sequencing algorithms, which in conjunction with minor tweaks in data acquisition ensues lower empirical FDR compared to the analysis using single algorithms...
July 25, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28741346/occurrence-state-and-molecular-structure-analysis-of-extracellular-proteins-with-implications-to-the-dewaterability-of-waste-activated-sludge
#16
Boran Wu, Bing-Jie Ni, Kristine Horvat, Liyan Song, Xiaoli Chai, Xiaohu Dai, Devinder Mahajan
The occurrence state and molecular structure of extracellular proteins were analyzed to reveal the influencing factors on the water-holding capacities of protein-like substances in waste activated sludge (WAS). The gelation process of extracellular proteins verified that advanced oxidation processes (AOPs) for WAS dewaterability improvement eliminated the water affinity of extracellular proteins and prevented these macromolecules to form stable colloidal aggregation. Isobaric tags for relative and absolute quantitation proteomics identified that most of extracellular proteins were originally derived from intracellular part and the proteins originally located at extracellular part were mainly membrane-associated...
July 25, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28741290/biochemical-characterization-of-lysine-acetylation-of-tyrosyl-trna-synthetase-in-escherichia-coli
#17
Sumana Venkat, Caroline Gregory, Qinglei Gan, Chenguang Fan
Aminoacyl-tRNA synthetases (AARSs) play essential roles in protein synthesis. As a member of the AARS family, the tyrosyl-tRNA synthetase (TyrRS) in Escherichia coli has been shown to be acetylated at multiple lysine residues by proteomic studies. However, these putative acetylation targets have not been biochemically characterized yet. In this study, we applied the genetic code expansion strategy to site-specifically incorporate Nε-acetyl-L-lysine into selected positions of TyrRS for in vitro characterization...
July 24, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28741221/optimization-and-application-of-a-biotinylation-method-for-quantification-of-plasma-membrane-expression-of-transporters-in-cells
#18
Vineet Kumar, Tot Bui Nguyen, Beáta Tóth, Viktoria Juhasz, Jashvant D Unadkat
Quantitative proteomics, using LC-MS/MS, is increasingly used to quantify drug transporters present in tissues and cells. Most of these investigations quantify total transporter expression in the cells by utilizing a total membrane fraction, not only the plasma membrane. Here, we report development and optimization of a biotinylation method to quantify protein expression of transporters in the plasma membrane of cells. The Pierce cell surface isolation protocol was optimized for plasma membrane isolation. Incubation of OATP1B1-expressing CHO cells with 0...
July 24, 2017: AAPS Journal
https://www.readbyqxmd.com/read/28741142/proteomic-expression-changes-in-large-cerebral-arteries-after-experimental-subarachnoid-hemorrhage-in-rat-are-regulated-by-the-mek-erk1-2-pathway
#19
Anne H Müller, Alistair V G Edwards, Martin R Larsen, Janne Nielsen, Karin Warfvinge, Gro K Povlsen, Lars Edvinsson
Subarachnoid hemorrhage (SAH) is a serious clinical condition where leakage of blood into the subarachnoid space causes an acute rise in intracranial pressure and reduces cerebral blood flow, which may lead to delayed cerebral ischemia and poor outcome. In experimental SAH, we have previously shown that the outcome can be significantly improved by early inhibition of the MAPK/ERK kinase/extracellular signal-regulated kinase (MEK/ERK1/2) pathway. The aim of this study was to apply mass spectrometry to investigate the overall late effects of experimental SAH on cerebrovascular protein expression...
July 24, 2017: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/28741036/network-based-subcellular-proteomics-in-monocyte-membrane-revealed-novel-candidate-genes-involved-in-osteoporosis
#20
Y Zeng, L Zhang, W Zhu, H He, H Sheng, Q Tian, F-Y Deng, L-S Zhang, H-G Hu, H-W Deng
In this study, label-free-based quantitative subcellular proteomics integrated with network analysis highlighted several candidate genes including P4HB, ITGB1, CD36, and ACTN1 that may be involved in osteoporosis. All of them are predicted as significant membrane proteins with high confidence and enriched in bone-related biological process. The results were further verified in transcriptomic and genomic levels. INTRODUCTION: Osteoporosis is a metabolic bone disease mainly characterized by low bone mineral density (BMD)...
July 24, 2017: Osteoporosis International
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