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https://www.readbyqxmd.com/read/28092656/influence-of-node-abundance-on-signaling-network-state-and-dynamics-analyzed-by-mass-cytometry
#1
Xiao-Kang Lun, Vito R T Zanotelli, James D Wade, Denis Schapiro, Marco Tognetti, Nadine Dobberstein, Bernd Bodenmiller
Signaling networks are key regulators of cellular function. Although the concentrations of signaling proteins are perturbed in disease states, such as cancer, and are modulated by drug therapies, our understanding of how such changes shape the properties of signaling networks is limited. Here we couple mass-cytometry-based single-cell analysis with overexpression of tagged signaling proteins to study the dependence of signaling relationships and dynamics on protein node abundance. Focusing on the epidermal growth factor receptor (EGFR) signaling network in HEK293T cells, we analyze 20 signaling proteins during a 1-h EGF stimulation time course using a panel of 35 antibodies...
January 16, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28092521/measuring-and-predicting-tag-importance-for-image-retrieval
#2
Shangwen Li, Sanjay Purushotham, Chen Chen, Yuzhuo Ren, C-C Jay Kuo
Textual data such as tags, sentence descriptions are combined with visual cues to reduce the semantic gap for image retrieval applications in today's Multimodal Image Retrieval (MIR) systems. However, all tags are treated as equally important in these systems, which may result in misalignment between visual and textual modalities during MIR training. This will further lead to degenerated retrieval performance at query time. To address this issue, we investigate the problem of tag importance prediction, where the goal is to automatically predict the tag importance and use it in image retrieval...
January 11, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28092269/analysis-of-microtubule-growth-dynamics-arising-from-altered-actin-network-structure-and-contractility-in-breast-tumor-cells
#3
Eleanor Ory, Lekhana Bhandary, Amanda Boggs, Kristi Chakrabarti, Joshua Parker, Wolfgang Losert, Stuart S Martin
The periphery of epithelial cells is shaped by opposing cytoskeletal physical forces generated predominately by two dynamic force generating systems - growing microtubule ends push against the boundary from the cell center, and the actin cortex contracts the attached plasma membrane. Here we investigate how changes to the structure and dynamics of the actin cortex alter the dynamics of microtubules. Current drugs target actin polymerization and contraction to reduce cell division and invasiveness; however, the impacts on microtubule dynamics remain incompletely understood...
January 16, 2017: Physical Biology
https://www.readbyqxmd.com/read/28092104/quantitative-proteomic-analysis-of-gingival-crevicular-fluids-from-deciduous-and-permanent-teeth
#4
Yumi Moriya, Takashi Obama, Toshihiro Aiuchi, Tomomi Sugiyama, Yumiko Endo, Yoko Koide, Emiko Noguchi, Motonori Ishizuka, Mitsuko Inoue, Hiroyuki Itabe, Matsuo Yamamoto
AIM: Gingivitis commonly progresses to periodontitis in permanent dentition but rarely in deciduous teeth. Little is known about the biochemical differences between gingiva of deciduous and permanent teeth. Here we compared the protein profiles of gingival crevicular fluids (GCF) from the gingiva of deciduous and permanent teeth. MATERIALS AND METHODS: Forty children with mixed dentition (Hellman's dental age IIIA) were selected and GCF samples were collected from deciduous cuspids and central incisors in the maxilla...
January 16, 2017: Journal of Clinical Periodontology
https://www.readbyqxmd.com/read/28092049/rosette-assay-highly-customizable-dot-blot-for-sh2-domain-screening
#5
Khong Y Ng, Kazuya Machida
With a growing number of high-throughput studies, structural analyses, and availability of protein-protein interaction databases, it is now possible to apply web-based prediction tools to SH2 domain-interactions. However, in silico prediction is not always reliable and requires experimental validation. Rosette assay is a dot blot-based reverse-phase assay developed for the assessment of binding between SH2 domains and their ligands. It is conveniently customizable, allowing for low- to high-throughput analysis of interactions between various numbers of SH2 domains and their ligands, e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092034/expression-and-purification-of-sh2-domains-using-baculovirus-expression-system
#6
Mari Ogiue-Ikeda, Kazuya Machida
Recombinant proteins expressed in bacteria are sometimes insoluble, aggregated, and incorrectly folded. For those Src homology 2 (SH2) domains that are insoluble in bacteria, baculovirus-insect cell expression systems can be an alternative to produce soluble and functionally active proteins. We describe a protocol for cloning and purification of GST-tagged SH2 domains using the Bac-to-Bac baculovirus expression system.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092031/expression-and-production-of-sh2-domain-proteins
#7
Bernard A Liu, Mari Ogiue-Ikeda, Kazuya Machida
The Src Homology 2 (SH2) domain lies at the heart of phosphotyrosine signaling, coordinating signaling events downstream of receptor tyrosine kinases (RTKs), adaptors, and scaffolds. Over a hundred SH2 domains are present in mammals, each having a unique specificity which determines its interactions with multiple binding partners. One of the essential tools necessary for studying and determining the role of SH2 domains in phosphotyrosine signaling is a set of soluble recombinant SH2 proteins. Here we describe methods, based on a broad experience with purification of all SH2 domains, for the production of SH2 domain proteins needed for proteomic and biochemical-based studies such as peptide arrays, mass-spectrometry, protein microarrays, reverse-phase microarrays, and high-throughput fluorescence polarization (HTP-FP)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28091410/molecular-mechanisms-of-increased-heart-rate-in-shenxianshengmai-treated-bradycardia-rabbits
#8
Zhou-Ying Liu, Jian Huang, Na-Na Liu, Min Zheng, Tao Zhao, Bu-Chang Zhao, Yi-Min Wang, Jie-Lin Pu
BACKGROUND: The molecular mechanisms of Shenxianshengmai (SXSM), a traditional Chinese medicine, on bradycardia have been incompletely understood. The study tried to investigate the gene expression profile and proteomics of bradycardia rabbits' hearts after SXSM treatment. METHODS: Twenty-four adult rabbits were randomly assigned in four groups: sham, model, model plus SXSM treatment, and sham plus SXSM treatment groups. Heart rate was recorded in all rabbits. Then, total RNA of atria and proteins of ventricle were isolated and quantified, respectively...
2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28090804/choline-acetyltransferase-may-contribute-to-the-risk-of-tourette-syndrome-combination-of-family-based-analysis-and-case-control-study
#9
Xiuling Yang, Wenmiao Liu, Mingji Yi, Ru Zhang, Yinglei Xu, Zuzhou Huang, Shiguo Liu, Tang Li
OBJECTIVES: Twin and family analyses have revealed a genetic contribution to Tourette syndrome and postmortem studies have raised the intriguing possibility of a reduction in cholinergic interneuronsin TS patients. METHODS: We selected five tag SNPs (rs100824791, rs12264845, rs1880676, rs3793790 and rs3793798) of Choline Acetyltransferase (CHAT) from the Han Chinese population Hapmap database. Genotyping was conducted on 401 TS nuclear family trios and 405 control subjects...
January 16, 2017: World Journal of Biological Psychiatry
https://www.readbyqxmd.com/read/28090468/clinical-features-and-extraintestinal-manifestations-of-crohn-disease-in-children
#10
Young Ah Lee, Peter Chun, Eun Ha Hwang, Sang Wook Mun, Yeoun Joo Lee, Jae Hong Park
PURPOSE: The aim of this study was to investigate the clinical features and extraintestinal manifestations (EIMs) of Crohn disease (CD) in Korean pediatric patients. METHODS: The medical records of 73 children diagnosed with CD were retrospectively reviewed. Data regarding baseline demographic and clinical characteristics, including CD phenotype at diagnosis based on the Montreal classification, and clinical features and course of EIMs were investigated. RESULTS: Fifty-two (71...
December 2016: Pediatric Gastroenterology, Hepatology & Nutrition
https://www.readbyqxmd.com/read/28090346/a-gwas-follow-up-of-obesity-related-snps-in-sypl2-reveals-sex-specific-association-with-hip-circumference
#11
J de Toro-Martín, F Guénard, A Tchernof, Y Deshaies, L Pérusse, S Biron, O Lescelleur, L Biertho, S Marceau, M-C Vohl
OBJECTIVE: A novel single-nucleotide polymorphism (SNP) associated with morbid obesity was recently identified by exome sequencing. The purpose of this study was to follow up this low-frequency coding SNP located within the SYPL2 locus and associated with body mass index in order to reveal novel associations with obesity-related traits. METHODS: The body mass index-associated SNP (rs62623713 A>G [chr1:109476817/hg19]) and two tagging SNPs within the SYPL2 locus, rs9661614 T>C (chr1:109479215) and rs485660 G>A (chr1:109480810), were genotyped in the obesity (n = 3,017) and the infogene (n = 676) cohorts, which were further combined, leading to a larger cohort of 3,693 individuals...
December 2016: Obesity Science & Practice
https://www.readbyqxmd.com/read/28090276/overexpression-of-recombinant-human-teriparatide-rhpth-1-34-in-escherichia-coli-an-innovative-gene-fusion-approach
#12
Nahid Bakhtiari, Zahra Amini Bayat, Sepideh Sagharidouz, Mohsen Vaez
BACKGROUND: Parathyroid hormone is an 84-amino acid peptide secreted by the parathyroid glands. Its physiological role is maintenance of normal serum calcium level and bone remodeling. Biological activity of this hormone is related to N-terminal 1-34 amino acids. The recombinant form of hormone (1-34) has been approved for treatment of osteoporosis from 2002. In this study, a novel fusion partner has been developed for preparation of high yield recombinant 1-34 amino acids of hPTH. METHODS: Novel nucleotide cassette designed encoding a chimeric fusion protein comprising of a fusion partner consisting of a His-tag in N-terminal, 53 amino acids belong to Escherichia coli (E...
January 2017: Avicenna Journal of Medical Biotechnology
https://www.readbyqxmd.com/read/28090034/evaluation-of-sub-surface-penetration-and-bonding-durability-of-self-etching-primer-systems-to-er-yag-laser-treated-cervical-dentin
#13
Zhengdi He, Lingling Chen, Yasushi Shimada, Junji Tagami, Shuangchen Ruan
This study aimed to investigate self-etching bonding systems penetrating in sub-surface dentin layer after Er:YAG laser irradiation and micro-shear bonding durability over a period of 1 year. Dentin slices obtained from extracted human third molars were prepared. Two self-etching adhesive systems were evaluated: Clearfil SE Bond and Clearfil Tri-S Bond. Specimens were tested for micro-shear bond strength with one of the following treatments: Er:YAG laser irradiation and 600-grit silicon paper polishing at 24 h, 7 days, 6 months and 1 year...
January 13, 2017: Dental Materials Journal
https://www.readbyqxmd.com/read/28089946/identification-by-pcr-signature-tagged-mutagenesis-of-attenuated-salmonella-pullorum-mutants-and-corresponding-genes-in-a-chicken-embryo-model
#14
Shizhong Geng, Qin Tian, Rongxian Guo, Yang Jiao, Paul Barrow, Chao Yin, Yaonan Wang, Haopeng Geng, Zhiming Pan, Xinan Jiao
A key feature of the fowl-specific pathogen Salmonella Pullorum is its vertical transmission to progeny via the egg. In this study, PCR signature-tagged mutagenesis identified nine genes of a strain of S. Pullorum that contributed to survival in the chicken embryo during incubation. The genes were involved in invasion, cell division, metabolism and bacterial defence. The competition index in vivo and in vitro together with a virulence evaluation for chicken embryos of all nine mutant strains confirmed their attenuation...
January 12, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28089900/the-rs4238326-polymorphism-in-aldh1a2-gene-potentially-associated-with-non-post-traumatic-knee-osteoarthritis-susceptibility-a-two-stage-population-based-study
#15
Minjie Chu, Xiaoyue Zhu, Chunli Wang, Jiesheng Rong, Yidan Wang, Shengyu Wang, Baifen Xing, Yuchun Tao, Xun Zhuang, Liying Jiang
OBJECTIVE: A recent genome-wide association study reported significant associations of genetic variants within the ALDH1A2 gene with osteoarthritis (OA) of the hand in European populations. However, these findings have not been well generalized to other joints, or to other populations. METHODS: We performed a two-stage population-based case-control study including 196 non-post traumatic knee OA cases and 442 controls in the first stage and independent 143 non-post traumatic knee OA cases and 238 controls in the second stage in a Chinese population by genotyping 8 tagging polymorphisms in ALDH1A2...
January 12, 2017: Osteoarthritis and Cartilage
https://www.readbyqxmd.com/read/28089881/two-step-chromatographic-purification-of-glutathione-s-transferase-tagged-human-papillomavirus-type-16-e6-protein-and-its-application-for-serology
#16
Mei Ling Xu, Seung Cheol Kim, Hyoung Jin Kim, Woong Ju, Yun Hwan Kim, Hong-Jin Kim
Human papillomavirus (HPV) E6 protein is an oncoprotein with a pivotal role in cervical carcinogenesis. Expression and purification of HPV E6 from Escherichia coli (E. coli) has been difficult because of its strong hydrophobicity even when expressed as a fusion protein with glutathione S-transferase (GST). There has been no protocol suggested for purifying GST-tagged HPV E6 protein with high purity so far. Herein, we provide efficient protocol for purifying GST-HPV16 E6 protein for the first time. In the current study, the GST-tagged protein was expressed in E...
January 9, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28089880/a-combined-approach-for-enhancing-the-stability-of-recombinant-cis-dihydrodiol-naphthalene-dehydrogenase-from-pseudomonas-putida-g7-allowed-for-the-structural-and-kinetic-characterization-of-the-enzyme
#17
Débora Maria Abrantes Costa, Mariana Amalia Figueiredo Costa, Samuel Leite Guimarães, Juliana Barbosa Coitinho, Stefanya Velásquez Gómez, Tiago Antônio da Silva Brandão, Ronaldo Alves Pinto Nagem
The second enzyme of the naphthalene degradation pathway in Pseudomonas putida G7 is NahB, a dehydrogenase that converts cis-1,2-dihydroxy-1,2-dihydronaphthalene to 1,2-dihydroxynaphthalene. We report the cloning, optimization of expression, purification, kinetic studies and preliminary structural characterization of the recombinant NahB. The nahB gene was cloned into a T7 expression vector and the enzyme was overexpressed in Escherichia coli Rosetta (DE3) as an N-terminal hexa-histidine-tagged protein (6xHis-NahB)...
January 9, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28089718/cathelicidin-antimicrobial-peptide-from-alligator-mississippiensis-has-antibacterial-activity-against-multi-drug-resistant-acinetobacter-baumanii-and-klebsiella-pneumoniae
#18
Stephanie M Barksdale, Evelyn J Hrifko, Monique L van Hoek
Alligator mississippiensis (American alligator), a member of order Crocodilia, lives in bacteria-laden environments but is not often known to succumb to bacterial infections. Their serum has been shown to have antibacterial activity beyond that of human serum, and it is believed that this activity is partially due to cationic antimicrobial peptides (CAMPs). CAMPs are produced by many organisms as part of the innate immune system. CAMPs are attractive possible therapies against multi-drug resistant bacteria, such as those found in biofilm-infected war wounds, because they seldom cause genetic resistance in bacteria and are effective against antibiotic resistant bacteria...
January 12, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28088451/efficient-sortase-mediated-n-terminal-labeling-of-tev-protease-cleaved-recombinant-proteins
#19
Kwabena Sarpong, Ron Bose
A major challenge in attaching fluorophores or other handles to proteins is the availability of a site-specific labeling strategy that provides stoichiometric modification without compromising protein integrity. We developed a simple approach that combines TEV protease cleavage, sortase modification and affinity purification to N-terminally label proteins. To achieve stoichiometrically-labeled protein, we included a short affinity tag in the fluorophore-containing peptide for post-labeling purification of the modified protein...
January 11, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28088444/feeding-recombinant-e-coli-with-gst-mbmktx-fusion-protein-increases-the-fecundity-and-lifespan-of-caenorhabditis-elegans
#20
Jie Xu, Yajie Jiang, Lu Wan, Qi Wang, Zebo Huang, Yongmei Liu, Yingliang Wu, Zongyun Chen, Xin Liu
Scorpion venom could be a useful treatment for a variety of diseases, such as cancer, epilepsy and analgesia. BmKTX is a polypeptide extracts from scorpion venom (PESV), which have attracted much attention from researchers in recent years. mBmKTX is a mutant polypeptide according to the amino acid sequence of BmKTX. We expressed it with the vector pGEX-4T-1 in Escherichia coli, and Caenorhabditis elegans were used as the animal model and fed with the strains. In this study, the expression of pGEX-mBmKTX was analyzed by SDS-PAGE, and GST-mBmKTX purified from pGEX-mBmKTX as a glutathione S-transferase (GST)-tagged fusion protein is approximately 30kDa...
January 11, 2017: Peptides
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