Current chemical genomics最新文献

{"title":"Investigation of Particulate Flow in a Channel by Application of CFD, DEM and LDA/PDA","authors":"M. Azimian, M. Lichti, H. Bart","doi":"10.2174/1874123101408010001","DOIUrl":"https://doi.org/10.2174/1874123101408010001","url":null,"abstract":"Hydroabrasion in particulate flows plays an important role in various industrial and natural processes. To predict the influence of it in a pipeline, channel or a fitting, it is essential to characterize the effects in a simple standardized geometry. An example to this is a pipe channel with a cylindrical obstacle adjusted inside the channel perpendicular to the flow direction. Results of flow field are generated by using the non-invasive Laser/Phase Doppler Anemometry (LDA/PDA) measurement technique. The velocity profiles of single phase and particulate flow from computational fluid dynamics (CFD) and discrete element method (DEM) simulations were validated by the LDA experimental data. The simulations were performed on the basis of Euler-Lagrange technique for both CFD and DEM. The measurements show that a Karman vortex field forms behind the obstacle and particles move inside this field with an average negative velocity of up to 25% of the fully developed velocity field. A comparison of CFD and DEM results with experimental data showed that in Karman velocity field, the CFD results fit better to the LDA measurements. In the fully developed flow region and also above and under the vortex field behind the obstacle, the DEM results match better with the LDA data.","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"8 1","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2014-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68052759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kinetic Models of Integrated Solidification and Cementation of Cement- formation Interface with New Method","authors":"J. Gu, P. Zhong, Wenzhen Qin, Haoyang Liu, Lifei Dong, Yijun Yang","doi":"10.2174/1874123101307010009","DOIUrl":"https://doi.org/10.2174/1874123101307010009","url":null,"abstract":"The isolation failure of cement-formation interface is an important and urgent problem in oil production, while an effective way to solve it is to realize the integrated solidification and cementation of cement-formation interface (ISC- CFI). In order to study the kinetics of ISCCFI with MTA (Mud Cake to Agglomerated Cake) method, the Diamond Dif- ferential Scanning Calorimetry Analyzer is adopted for experiments with dynamic method and isothermal method. The results show that there is a linear relationship between the solidification reaction temperature and the heating rate of ISC- CFI with MTA method. For the first exothermic peak, the initial temperature, peak tip temperature and final tem- perature are 53 °C, 69 °C and 83 °C respectively, and the apparent activation energy of solidification reaction is 44.39×10 -3 kJ·mol -1 , the natural logarithm of preexponential factor is 7.26, the solidification reaction order is 0.88. For the second exothermic peak, the initial temperature, peak tip temperature and final temperature are 83 °C, 92 °C and 114 °C respectively, and the apparent activation energy of solidification reaction is 99.14×10 -3 kJ·mol -1 , the natural logarithm of preexponential factor is 24.77, the solidification reaction order is 0.94. The maximum solidification reac- tion rates at 50 °C, 75 °C and 90 °C are 0.09×10 -3 s -1 , 0.27×10 -3 s -1 and 0.51×10 -3 s -1 respectively. The kinetic models of ISCCFI with MTA method under different temperatures are established. It provides a theoretical and technical support for the isolation improvement of cement-formation interface.","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"191 1","pages":"9-17"},"PeriodicalIF":0.0,"publicationDate":"2013-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68052746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The HaloTag: Improving Soluble Expression and Applications in Protein Functional Analysis.","authors":"Scott N Peterson,&nbsp;Keehwan Kwon","doi":"10.2174/1875397301206010008","DOIUrl":"https://doi.org/10.2174/1875397301206010008","url":null,"abstract":"<p><p>Technological and methodological advances have been critical for the rapidly evolving field of proteomics. The development of fusion tag systems is essential for purification and analysis of recombinant proteins. The HaloTag is a 34 KDa monomeric protein derived from a bacterial haloalkane dehalogenase. The majority of fusion tags in use today utilize a reversible binding interaction with a specific ligand. The HaloTag system is unique in that it forms a covalent linkage to its chloroalkane ligand. This linkage permits attachment of the HaloTag to a variety of functional reporters, which can be used to label and immobilize recombinant proteins. The success rate for HaloTag expression of soluble proteins is very high and comparable to maltose binding protein (MBP) tag. Furthermore, cleavage of the HaloTag does not result in protein insolubility that often is observed with the MBP tag. In the present report, we describe applications of the HaloTag system in our ongoing investigation of protein-protein interactions of the Y. pestis Type 3 secretion system on a custom protein microarray. We also describe the utilization of affinity purification/mass spectroscopy (AP/MS) to evaluate the utility of the Halo Tag system to characterize DNA binding activity and protein specificity.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"6 ","pages":"8-17"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/da/37/TOCHGENJ-6-8.PMC3480702.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31018186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HaloTag® Platform: From Proteomics to Cellular Analysis and Animal Imaging.","authors":"Mei Cong","doi":"10.2174/1875397301206010006","DOIUrl":"https://doi.org/10.2174/1875397301206010006","url":null,"abstract":"From in vitro proteomic protein analysis to in vivo animal models, various protein tagging systems are designed to provide useful functionalities. Commonly used affinity tags for protein purification and capture include GST, c-myc, metal ion affinity tag His6Tag, immuno-affinity FLAG tag, and maltose binding protein (MBP) tag [1-4]. For cellular imaging analysis, fluorescent proteins have served as markers for protein localization, translocation, interactions, and conformational change [5, 6]. However, in addition to the limited functionality, these protein fusion tags are further limited in that they cannot be used for in vivo animal models. Instead, bioluminescence, near-infrared (NIR) /IR800, Mag-netic Resonance Imaging (MRI), positron emission tomography (PET), and single-photon emission tomography (SPECT) are used to detect protein markers in vivo [7, 8]. Due to limited capabilities for individual tags, studies involving multiple analytical methods often require the use of more than one tag and multiple genetic constructions. \u0000 \u0000HaloTag® technology provides an efficient way to use a single tag readily reconfigured to meet the needs of different applications, from in vitro protein purification to cellular protein complex analysis, and in animal models. SNAP-tag and CLIP-tag provide similar synthetic fluorophores with switchable spectroscopic properties to visualize biochemical activities in living cells [9, 10]. The HaloTag® technology possesses two distinct moieties: the HaloTag® reporter protein and the HaloTag ligand. The HaloTag reporter protein is fused to the N- or C-terminus of a protein of interest (POI). The reporter is a monomeric, 34 KDa engineered protein developed from a rare bacterial hydrolase. There is no endogenous equivalent in eukaryotic cells, and like most bacterial reporter/tag systems, it has extremely low background. \u0000 \u0000In this special issue, Dr. Encell et al. [11] describe the design and molecular evolution of the HaloTag® reporter system. Using directed mutagenesis, the binding kinetics was significantly improved for the initial version of the reporter HaloTag2 by opening up the chloroalkane binding pocket. Random mutagenesis was then used to further evolve HaloTag® together with its linker sequence into a more soluble and stable variant, HaloTag7, which is suitable for applications across mammalian and bacterial cells as well as in vitro. The chloroalkane ligand is the second component in the HaloTag® technology platform and it can covalently bind to HaloTag® protein. Chloroalkane ligands can carry many different functional groups including i) solid surface for protein immobilization and display that can be used for protein purification, interaction analysis and display of antigens; and ii) fluorescent dyes for protein quantification, gel labeling, and cellular imaging analysis. Also in this special edition, Drs. Urh and Rosenberg [12] provide a comprehensive review of the HaloTag® technology platform and its wide r","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"6 ","pages":"6-7"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/80/12/TOCHGENJ-6-6.PMC3480685.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31018184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Dual Reporter Splicing Assay Using HaloTag-containing Proteins.","authors":"Koichi Oshima,&nbsp;Takahiro Nagase,&nbsp;Kohsuke Imai,&nbsp;Shigeaki Nonoyama,&nbsp;Megumi Obara,&nbsp;Tomoyuki Mizukami,&nbsp;Hiroyuki Nunoi,&nbsp;Hirokazu Kanegane,&nbsp;Futoshi Kuribayashi,&nbsp;Shin Amemiya,&nbsp;Osamu Ohara","doi":"10.2174/1875397301206010027","DOIUrl":"https://doi.org/10.2174/1875397301206010027","url":null,"abstract":"<p><p>To evaluate the effects of genetic variations on mRNA splicing, we developed a minigene-based splicing assay using reporter genes encoding luciferase and the multifunctional HaloTag protein. In addition to conventional RT-PCR analysis, splicing events can be monitored in this system using two parameters: luciferase activity and signals derived from HaloTag-containing proteins bound to a fluorescent ligand following SDS-PAGE. The luciferase activity reflects the accumulated amounts of successfully spliced HaloTag-luciferase fusion products, whereas the amounts and sizes of HaloTag-containing proteins provide quantitative insights into precursor, correctly spliced, and aberrantly spliced mRNA species. Preliminary experiments confirmed that the dual reporter minigene assay can provide estimates of overall splicing efficiency based on the levels of protein products. We then used the minigene assay to analyze a case of chronic granulomatous disease that was caused by a G>C mutation at position +5 in the 5'-splice donor site of intron 5 of the CYBB gene. We found that the G>C mutation affected CYBB mRNA splicing by changing a delicate balance of splicing efficiencies of introns 4, 5, and 6.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"6 ","pages":"27-37"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/38/8f/TOCHGENJ-6-27.PMC3486960.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31034323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Vivo Fluorescent Labeling of Tumor Cells with the HaloTag® Technology.","authors":"Jen-Chieh Tseng,&nbsp;Hélène A Benink,&nbsp;Mark G McDougall,&nbsp;Isabel Chico-Calero,&nbsp;Andrew L Kung","doi":"10.2174/1875397301206010048","DOIUrl":"https://doi.org/10.2174/1875397301206010048","url":null,"abstract":"<p><p>Many fluorescent sensors are currently available for in vitro bio-physiological microscopic imaging. The ability to label cells in living animals with these fluorescent sensors would help translate some of these assays into in vivo applications. To achieve this goal, the first step is to establish a method for selectively labeling target cells with exogenous fluorophores. Here we tested whether the HaloTag® protein tagging system provides specific labeling of xenograft tumors in living animals. After systemic delivery of fluorophore-conjugated ligands, we performed whole animal planar fluorescent imaging to determine uptake in tag-expressing HCT116 xenografts. Our results demonstrate that HaloTag ligands containing red or near-infrared fluorophores have enhanced tumor uptake and are suitable for non-invasive in vivo imaging. Our proof-of-concept results establish feasibility for using HaloTag technology for bio-physiological imaging in living animals.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"6 ","pages":"48-54"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/76/a8/TOCHGENJ-6-48.PMC3480697.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31018188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of RNA aptamer and its ligand binding assay on microchip electrophoresis.","authors":"Ken-Ichi Ohno,&nbsp;Chikara Nakata,&nbsp;Yoshihiro Sano,&nbsp;Fumiko Nishikawa,&nbsp;Satoshi Nishikawa,&nbsp;Hidetoshi Arakawa","doi":"10.2174/1875397301206010001","DOIUrl":"https://doi.org/10.2174/1875397301206010001","url":null,"abstract":"<p><p>Microchip electrophoresis (ME) coupled with fluorescence detection was used to estimate the binding activity of aptamer in each systematic evolution of ligands by exponential enrichment (SELEX) round for a target molecule. This approach is a non-radioisotopic, rapid and simple platform, and electrophoretic separation appears to be an effective technique for aptamers of oligonucleotide molecules. We tried to obtain gonadotropin-specific RNA aptamer by the above approach. As a result, the peaks of aptamers based on the conformational differences between them were separated and detected on the electropherograms. Moreover, the intensity of peak of unbound aptamer was decreased with progression through the SELEX rounds, suggesting that RNA aptamer with high affinity was obtained by the proposed method.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"6 ","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2174/1875397301206010001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30424676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-Throughput Multiplexed Quantitation of Protein Aggregation and Cytotoxicity in a Huntington's Disease Model.","authors":"Steven A Titus,&nbsp;Noel Southall,&nbsp;Juan Marugan,&nbsp;Christopher P Austin,&nbsp;Wei Zheng","doi":"10.2174/1875397301206010079","DOIUrl":"https://doi.org/10.2174/1875397301206010079","url":null,"abstract":"<p><p>A hallmark of Huntington's disease is the presence of a large polyglutamine expansion in the first exon of the Huntingtin protein and the propensity of protein aggregation by the mutant proteins. Aberrant protein aggregation also occurs in other polyglutamine expansion disorders, as well as in other neurodegenerative diseases including Parkinson's, Alzheimer's, and prion diseases. However, the pathophysiological role of these aggregates in the cell death that characterizes the diseases remains unclear. Identification of small molecule probes that modulate protein aggregation and cytotoxicity caused by aggregated proteins may greatly facilitate the studies on pathogenesis of these diseases and potentially lead to development of new therapies. Based on a detergent insoluble property of the Huntingtin protein aggregates, we have developed a homogenous assay to rapidly quantitate the levels of protein aggregates in a cellular model of Huntington's disease. The protein aggregation assay has also been multiplexed with a protease release assay for the measurement of cytotoxicity resulting from aggregated proteins in the same cells. Through a testing screen of a compound library, we have demonstrated that this multiplexed cytotoxicity and protein aggregation assay has ability to identify active compounds that prevent cell death and/or modulate protein aggregation in cells of the Huntington's disease model. Therefore, this multiplexed screening approach is also useful for development of high-throughput screening assays for other neurodegenerative diseases involving protein aggregation.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"6 ","pages":"79-86"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/74/04/TOCHGENJ-6-79.PMC3551243.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31183573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HaloTag, a Platform Technology for Protein Analysis.","authors":"Marjeta Urh, Martin Rosenberg","doi":"10.2174/1875397301206010072","DOIUrl":"10.2174/1875397301206010072","url":null,"abstract":"<p><p>Understanding protein function and interaction is central to the elucidation of biological processes. Systematic analysis of protein interactions have shown that the eukaryotic proteome is highly interconnected and that biological function frequently depends on the orchestrated action of many proteins. Perturbation of these functions or interactions can lead to various disease states and pharmacologic intervention can result in corrective therapies. The fact that proteins rarely act in isolation, but rather comprise complex machines that stably and/or transiently interact with many different partners at different times, demands the need for robust tools that allow comprehensive global analyses of these events. Here we describe a powerful protein fusion technology, the HaloTag platform, and how it enables the study of many facets of protein biology by offering a broad choice of applications. We review the development of the key aspects of the technology and it's performance in both in vitro and in vivo applications. In particular, we focus on HaloTag's multifunctional utility in protein imaging, protein isolation and display, and in the study of protein complexes and interactions. We demonstrate it's potential to help elucidate important facets of proteomic biology across complex biological systems at the biochemical, cell-based and whole animal level.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"6 ","pages":"72-8"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/9c/e3/TOCHGENJ-6-72.PMC3480824.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31101134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a dehalogenase-based protein fusion tag capable of rapid, selective and covalent attachment to customizable ligands.","authors":"Lance P Encell,&nbsp;Rachel Friedman Ohana,&nbsp;Kris Zimmerman,&nbsp;Paul Otto,&nbsp;Gediminas Vidugiris,&nbsp;Monika G Wood,&nbsp;Georgyi V Los,&nbsp;Mark G McDougall,&nbsp;Chad Zimprich,&nbsp;Natasha Karassina,&nbsp;Randall D Learish,&nbsp;Robin Hurst,&nbsp;James Hartnett,&nbsp;Sarah Wheeler,&nbsp;Pete Stecha,&nbsp;Jami English,&nbsp;Kate Zhao,&nbsp;Jacqui Mendez,&nbsp;Hélène A Benink,&nbsp;Nancy Murphy,&nbsp;Danette L Daniels,&nbsp;Michael R Slater,&nbsp;Marjeta Urh,&nbsp;Aldis Darzins,&nbsp;Dieter H Klaubert,&nbsp;Robert F Bulleit,&nbsp;Keith V Wood","doi":"10.2174/1875397301206010055","DOIUrl":"https://doi.org/10.2174/1875397301206010055","url":null,"abstract":"<p><p>Our fundamental understanding of proteins and their biological significance has been enhanced by genetic fusion tags, as they provide a convenient method for introducing unique properties to proteins so that they can be examinedin isolation. Commonly used tags satisfy many of the requirements for applications relating to the detection and isolation of proteins from complex samples. However, their utility at low concentration becomes compromised if the binding affinity for a detection or capture reagent is not adequate to produce a stable interaction. Here, we describe HaloTag® (HT7), a genetic fusion tag based on a modified haloalkane dehalogenase designed and engineered to overcome the limitation of affinity tags by forming a high affinity, covalent attachment to a binding ligand. HT7 and its ligand have additional desirable features. The tag is relatively small, monomeric, and structurally compatible with fusion partners, while the ligand is specific, chemically simple, and amenable to modular synthetic design. Taken together, the design features and molecular evolution of HT7 have resulted in a superior alternative to common tags for the overexpression, detection, and isolation of target proteins.</p>","PeriodicalId":88232,"journal":{"name":"Current chemical genomics","volume":"6 ","pages":"55-71"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2174/1875397301206010055","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31127021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}