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https://www.readbyqxmd.com/read/29241110/design-synthesis-and-initial-evaluation-of-affinity-based-small-molecular-probe-for-detection-of-wdr5
#1
Wei-Lin Chen, Dong-Dong Li, Zhi-Hui Wang, Xiao-Li Xu, Xiao-Jin Zhang, Zheng-Yu Jiang, Xiao-Ke Guo, Qi-Dong You
WDR5, a subunit of the SET/MLL complex, plays critical roles in various biological progresses and are abnormally expressed in many cancers. Here we report the design, synthesis, and biochemical characterization of a new chemical tool to capture WDR5 protein. The probe is a biotinylated version of compound 30 that is a potent WDR5 inhibitor we previously reported. Importantly, the probe displayed high affinity to WDR5 protein in vitro binding potency and showed the ability in specifically and real time monitoring WDR5 protein...
November 28, 2017: Bioorganic Chemistry
https://www.readbyqxmd.com/read/29240760/novel-linear-motif-filtering-protocol-reveals-the-role-of-the-lc8-dynein-light-chain-in-the-hippo-pathway
#2
Gábor Erdős, Tamás Szaniszló, Mátyás Pajkos, Borbála Hajdu-Soltész, Bence Kiss, Gábor Pál, László Nyitray, Zsuzsanna Dosztányi
Protein-protein interactions (PPIs) formed between short linear motifs and globular domains play important roles in many regulatory and signaling processes but are highly underrepresented in current protein-protein interaction databases. These types of interactions are usually characterized by a specific binding motif that captures the key amino acids shared among the interaction partners. However, the computational proteome-level identification of interaction partners based on the known motif is hindered by the huge number of randomly occurring matches from which biologically relevant motif hits need to be extracted...
December 14, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29240604/potential-significance-of-peptidome-in-human-ovarian-cancer-for-patients-with-ascites
#3
Xiaohao Huang, Juan Zhou, Ranran Tang, Suping Han, Xue Zhou
OBJECTIVE: Ovarian cancer (OC) is one of the lethal gynecological malignancies. Most women affected by OC with malignant ascites will relapse. Peptidomics, as an emerging branch of proteomics, is more applied in screening of disease biomarkers, diagnosis, treatment, and monitoring. However, there is still little in-depth analysis about peptidomics study in OC with malignant ascites. METHODS: A comparative peptidomic profiling of ascites fluid between 6 OC patients and 6 benign gynecological conditions using liquid chromatography-tandem mass spectrometry was analyzed...
December 13, 2017: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/29240408/itraq-based-untargeted-quantitative-proteomic-approach-to-identify-change-of-the-plasma-proteins-by-salbutamol-abuse-in-beef-cattle
#4
Kai Zhang, Chaohua Tang, Xiaowei Liang, Qingyu Zhao, Junmin Zhang
Salbutamol, a selective β2-agonist, endangers the safety of animal products because of illegal use in food animals. In this study, an iTRAQ-based untargeted quantitative proteomic approach was applied to screen potential protein biomarkers in plasma of cattle before and after treatment with salbutamol for 21 days. A total of 62 plasma proteins were significantly affected by salbutamol treatment, which can be used as potential biomarkers to screen for the illegal use of salbutamol in beef cattle. Enzyme-linked immunosorbent assay measurements of five selected proteins demonstrated the reliability of iTRAQ-based proteomics in screening of candidate biomarkers among the plasma proteins...
December 14, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29240217/interdependence-of-free-zinc-changes-and-protein-complex-assembly-insights-into-zinc-signal-regulation
#5
Anna Kocyła, Justyna Adamczyk, Artur Krężel
Cellular zinc (Zn(ii)) is bound with proteins that are part of the proteomes of all domains of life. It is mostly utilized as a catalytic or structural protein cofactor, which results in a vast number of binding architectures. The Zn(ii) ion is also important for the formation of transient protein complexes with a Zn(ii)-dependent quaternary structure that is formed upon cellular zinc signals. The mechanisms by which proteins associate with and dissociate from Zn(ii) and the connection with cellular Zn(ii) changes remain incompletely understood...
December 14, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/29239754/characterization-of-rhodococcus-sp-a5wh-isolated-from-a-high-altitude-andean-lake-to-unravel-the-survival-strategy-under-lithium-stress
#6
Carolina Belfiore, María V Curia, María E Farías
Lithium (Li) is widely distributed in nature and has several industrial applications. The largest reserves of Li (over 85%) are in the so-called "triangle of lithium" that includes the Salar de Atacama in Chile, Salar de Uyuni in Bolivia and Salar del Hombre Muerto in Argentina. Recently, the use of microorganisms in metal recovery such as copper has increased; however, there is little information about the recovery of lithium. The strain Rhodococcus sp. A5wh used in this work was previously isolated from Laguna Azul...
November 24, 2017: Revista Argentina de Microbiología
https://www.readbyqxmd.com/read/29239490/proteomic-changes-of-the-porcine-skeletal-muscle-in-response-to-chronic-heat-stress
#7
Yanjun Cui, Yue Hao, Jielei Li, Yanli Gao, Xianhong Gu
BACKGROUND: Heat stress (HS) has an adverse effect on meat quality; yet, the underlying molecular mechanisms altering meat quality due to muscle responses to stress remain unclear. Sixteen castrated male crossbreeds between Landrace × Yorkshire sows and Duroc boars (79.00 ± 1.50 kg body weight) were exposed to either thermal neutral (22 °C, n=8) or heat stress (30 °C, n=8) conditions for 3 weeks. Subsequently, the longissimus dorsi (LD) muscle of all pigs was assayed for meat quality parameters and proteome analysis...
December 14, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/29239171/thermoresponsive-arrays-patterned-via-photo-click-chemistry-smart-maldi-plate-for-protein-digest-enrichment-desalting-and-direct-ms-analysis
#8
Xiao Meng, Junjie Hu, Zhicong Chao, Ying Liu, Huangxian Ju, Quan Cheng
Sample desalting and concentrating is a crucial step prior to MALDI-MS analysis. Current sample pretreatment approaches require tedious fabrication and operation procedures, which are unamenable to high-throughput analysis and also result in sample loss. Here we report the development of a smart MALDI substrate for on-plate desalting, enrichment, and direct MS analysis of protein digests based on thermo-responsive, hydrophilic/hydrophobic transition of surface grafted poly(N-isopropylacrylamide) (PNIPAM) microarrays...
December 14, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29239132/translational-systems-pharmacology-studies-in-pregnant-women
#9
REVIEW
Sara K Quinney, Rakesh Gullapelli, David M Haas
Pregnancy involves rapid physiological adaptation and complex interplay between mother and fetus. New analytic technologies provide large amounts of genomic, proteomic, and metabolomics data. The integration of these data through bioinformatics, statistical, and systems pharmacology techniques can improve our understanding of the mechanisms of normal maternal physiologic changes and fetal development. New insights into the mechanisms of pregnancy-related disorders, such as preterm birth (PTB), may lead to the development of new therapeutic interventions and novel biomarkers...
December 14, 2017: CPT: Pharmacometrics & Systems Pharmacology
https://www.readbyqxmd.com/read/29239117/deep-omics
#10
Ngoc Hieu Tran, Xianglilan Zhang, Ming Li
Deep learning has revolutionized research in image processing, speech recognition, natural language processing, game playing, and will soon in proteomics and genomics. Through three examples in genomics, protein structure prediction, and proteomics, we demonstrate that deep learning is changing bioinformatics research, shifting from algorithm-centric to data-centric approaches. This article is protected by copyright. All rights reserved.
December 14, 2017: Proteomics
https://www.readbyqxmd.com/read/29239102/serpinh1-overexpression-in-clear-cell-renal-cell-carcinoma-association-with-poor-clinical-outcome-and-its-potential-as-a-novel-prognostic-marker
#11
Yijun Qi, Yue Zhang, Zhiqiang Peng, Lei Wang, Kaizhen Wang, Duiping Feng, Junqi He, Junfang Zheng
Precision therapy for clear cell renal cell carcinoma (ccRCC) requires molecular biomarkers ascertaining disease prognosis. In this study, we performed integrated proteomic and transcriptomic screening in all four tumour-node-metastasis stages of ccRCC and adjacent normal tissues (n = 18) to investigate differentially expressed genes. Most identified differentially expressed genes revealed a strong association with transforming growth factor-β level and the epithelial-to-mesenchymal transition process. Of them, Serpin peptidase inhibitor clade H member 1 (SERPINH1) revealed the strongest association with poor prognosis and regulation on the expression levels of epithelial-to-mesenchymal transition markers...
December 14, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/29238340/commentary-proteomics-analysis-revealed-that-crosstalk-between-helicobacter-pylori-and-streptococcus-mitis-may-enhance-bacterial-survival-and-reduces-carcinogenesis
#12
COMMENT
https://www.readbyqxmd.com/read/29238335/treatment-with-cefotaxime-affects-expression-of-conjugation-associated-proteins-and-conjugation-transfer-frequency-of-an-inci1-plasmid-in-escherichia-coli
#13
Thea S B Møller, Gang Liu, Anders Boysen, Line E Thomsen, Freja L Lüthje, Sisse Mortensen, Jakob Møller-Jensen, John E Olsen
Horizontal gene transfer (HGT) is the major mechanism responsible for spread of antibiotic resistance. Antibiotic treatment has been suggested to promote HGT, either by directly affecting the conjugation process itself or by selecting for conjugations subsequent to DNA transfer. However, recent research suggests that the effect of antibiotic treatment on plasmid conjugation frequencies, and hence the spread of resistance plasmids, may have been overestimated. We addressed the question by quantifying transfer proteins and conjugation frequencies of a blaCTX-M-1 encoding IncI1 resistance plasmid in Escherichia coli MG1655 in the presence and absence of therapeutically relevant concentrations of cefotaxime (CTX)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29238329/relative-quantitative-proteomic-analysis-of-brucella-abortus-reveals-metabolic-adaptation-to-multiple-environmental-stresses
#14
Xiaodong Zai, Qiaoling Yang, Ying Yin, Ruihua Li, Mengying Qian, Taoran Zhao, Yaohui Li, Jun Zhang, Ling Fu, Junjie Xu, Wei Chen
Brucella spp. are facultative intracellular pathogens that cause chronic brucellosis in humans and animals. The virulence of Brucella primarily depends on its successful survival and replication in host cells. During invasion of the host tissue, Brucella is simultaneously subjected to a variety of harsh conditions, including nutrient limitation, low pH, antimicrobial defenses, and extreme levels of reactive oxygen species (ROS) via the host immune response. This suggests that Brucella may be able to regulate its metabolic adaptation in response to the distinct stresses encountered during its intracellular infection of the host...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29238284/functional-and-proteomic-analyses-reveal-that-scpbxv-is-involved-in-bacterial-growth-virulence-and-biofilm-formation-in-xanthomonas-campestris-pv-vesicatoria
#15
Hye-Jee Park, Sang-Wook Han
Segregation and condensation protein B (ScpB) is essential for replication and segregation in living organisms. Here, we reported the functions of ScpBXv (ScpB-like protein in Xanthomonas campestris pv. vesicatoria) using phenotypic and proteomic analyses. Growth of XcvΔscpBXv (ScpBXv knockout mutant) was reduced under both slow and fast growth conditions in rich medium, but comparable to this of the wild-type in plant-mimic conditions. Interestingly, the mutant was significantly less virulent than the wild-type in tomato, indicating that ScpBXv is involved in virulence...
December 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/29238198/oral-microbiome-and-peri-implant-diseases-where-are-we-now
#16
REVIEW
Rafał Pokrowiecki, Agnieszka Mielczarek, Tomasz Zaręba, Stefan Tyski
Peri-implant infective diseases (PIIDs) in oral implantology are commonly known as peri-implant mucositis (PIM) and periimplantitis (PI). While PIM is restricted to the peri-implant mucosa and is reversible, PI also affects implant-supporting bone and, therefore, is very difficult to eradicate. PIIDs in clinical outcome may resemble gingivitis and periodontitis, as they share similar risk factors. However, recent study in the field of proteomics and other molecular studies indicate that PIIDs exhibit significant differences when compared to periodontal diseases...
2017: Therapeutics and Clinical Risk Management
https://www.readbyqxmd.com/read/29237681/plasma-proteomics-for-epidemiology-increasing-throughput-with-standard-flow-rates
#17
Xiaoke Yin, Ferheen Baig, Eloi Haudebourg, Richard T Blankley, Tejas Gandhi, Sebastian Müller, Lukas Reiter, Helmut Hinterwirth, Raimund Pechlaner, Sotirios Tsimikas, Peter Santer, Johann Willeit, Stefan Kiechl, Joseph L Witztum, Anthony Sullivan, Manuel Mayr
BACKGROUND: Mass spectrometry is selective and sensitive, permitting routine quantification of multiple plasma proteins. However, commonly used nanoflow liquid chromatography (LC) approaches hamper sample throughput, reproducibility, and robustness. For this reason, most publications using plasma proteomics to date are small in study size. METHODS AND RESULTS: Here, we tested a standard-flow LC mass spectrometry (MS) method using multiple reaction monitoring for the application to large epidemiological cohorts...
December 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/29237571/identification-of-genes-related-to-proliferative-diabetic-retinopathy-through-rwr-algorithm-based-on-protein-protein-interaction-network
#18
Jian Zhang, Yan Suo, Min Liu, Xun Xu
Proliferative diabetic retinopathy (PDR) is one of the most common complications of diabetes and can lead to blindness. Proteomic studies have provided insight into the pathogenesis of PDR and a series of PDR-related genes has been identified but are far from fully characterized because the experimental methods are expensive and time consuming. In our previous study, we successfully identified 35 candidate PDR-related genes through the shortest-path algorithm. In the current study, we developed a computational method using the random walk with restart (RWR) algorithm and the protein-protein interaction (PPI) network to identify potential PDR-related genes...
December 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29237567/integrated-metabolomics-and-proteomics-analysis-of-hippocampus-in-a-rat-model-of-depression
#19
Yuqing Zhang, Shuai Yuan, Juncai Pu, Lining Yang, Xinyu Zhou, Lanxiang Liu, Xiaofeng Jiang, Hanping Zhang, Teng Teng, Lu Tian, Peng Xie
Major depressive disorder (MDD) is a prevalent and serious mental disorder with high rates of suicide and disability. However, the underlying pathogenesis of MDD is complicated and remains largely unclear. An integrated analysis of multiple types of omics data may improve comprehensive understanding of the entire molecular mechanism of MDD. In this study, we applied an integrated analysis of gas chromatography/mass spectrometry (GC-MS)-based metabolomics and isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics to investigate changes in the hippocampus in the chronic unpredictable mild stress (CUMS) rat model of depression...
December 10, 2017: Neuroscience
https://www.readbyqxmd.com/read/29237455/molecular-and-histological-effects-of-mr-guided-pulsed-focused-ultrasound-to-the-rat-heart
#20
Kee W Jang, Tsang-Wei Tu, Matthew E Nagle, Bobbi K Lewis, Scott R Burks, Joseph A Frank
BACKGROUND: Image-guided high intensity focused ultrasound has been used as an extracorporeal cardiac pacing tool and to enhance homing of stem cells to targeted tissues. However, molecular changes in the myocardium after sonication have not been widely investigated. Magnetic-resonance (MR)-guided pulsed focused ultrasound (pFUS) was targeted to the rat myocardium over a range of pressures and the microenvironmental and histological effects were evaluated over time. METHODS: Eight-to-ten-week-old Sprague-Dawley rats received T2-weighted MR images to target pFUS to the left ventricular and septum without cardiac or respiratory gating...
December 13, 2017: Journal of Translational Medicine
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