Journal of biochemical and biophysical methods最新文献

{"title":"Role of chemical structure in stereoselective recognition of β-blockers by cyclodextrins in capillary zone electrophoresis","authors":"László Gagyi ,&nbsp;Árpád Gyéresi ,&nbsp;Ferenc Kilár","doi":"10.1016/j.jbbm.2007.10.004","DOIUrl":"https://doi.org/10.1016/j.jbbm.2007.10.004","url":null,"abstract":"<div><p>Most of the β-blocking drugs for treating diseases of the cardiovascular system are chiral aryloxy–propanolamine derivatives. Tipically, the <em>S</em>(−) enantiomers are more active than the <em>R</em>(+) enantiomers. Only some of them (for example timolol) are used as single enantiomers, the others are employed as racemates. For the determination of the enantiomeric purity of timolol European Pharmacopoeia prescribes an HPLC method using chiral stationary phase. However, the use of chiral capillary zone electrophoresis for the determination of the enantiomeric purity is of pharmaceutical interest. This study describes the application of various cyclodextrin derivatives, hydroxypropyl-β-cyclodextrin, randomly methylated β-cyclodextrin, sulphated β-cyclodextrin and sulphated α-cyclodextrin for the stereoselective analyses of β-blockers. Baseline separation was obtained for bopindolol, carvedilol, mepindolol, pindolol and alprenolol, while only partial separation was observed for sotalol, propranolol, oxprenolol, atenolol, bisoprolol, bupranolol, and metoprolol. The uneven molecular recognition of the enantiomers of the β-blockers, especially of the optical isomers of labetalol and nadolol, showed the importance of the chemical nature of the separators and the analytes.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 1268-1275"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jbbm.2007.10.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72221043","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":"Filtration performance of microporous ceramic supports","authors":"Aissa Belouatek ,&nbsp;Abdellah Ouagued ,&nbsp;Mustapha Belhakem ,&nbsp;Ahmed Addou","doi":"10.1016/j.jbbm.2007.08.004","DOIUrl":"10.1016/j.jbbm.2007.08.004","url":null,"abstract":"<div><p>The use of inorganic membranes in pollution treatment is actually limited by the cost of such membranes. Advantages of inorganic membranes are their chemical, thermal and pH properties. The purpose of this work was the development of microporous ceramic materials based on clay for liquid waste processing. The supports or ceramic filters having various compositions were prepared and thermally treated at 1100 °C. The results show that, at the temperature studied, porosity varied according to the support composition from 12% for the double-layered (ceramic) support to 47% for the activated carbon- filled support with a mean pore diameter between 0.8 and 1.3 μm, respectively. Volumes of 5 l of distilled water were filtered tangentially for 3 h under an applied pressure of 3.5 and 5.5 bar. The retention of tubular supports prepared was tested with molecules of varying size (Evans blue, NaCl and Sacharose). The study of the liquid filtration and flow through these supports showed that the retention rate depends on support composition and pore diameter, and solute molecular weight. The S1 support (mixture of barbotine and 1% (w/w) activated carbon) gave a flux for distilled water of 68 L/m² h while the double-layered support resulted in a flux of 8 L/m² h for the same solution at the pressure of 3.5 bar. At a pressure of 5.5 bar an increase in the distilled water flux through the various supports was observed. It was significant for the S1 support (230 L/m h).</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 1174-1179"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jbbm.2007.08.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41003600","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":"Continuous-flow complete-mixing system for assessing the effects of environmental factors on colony-level coral metabolism","authors":"Hiroyuki Fujimura ,&nbsp;Tomihiko Higuchi ,&nbsp;Kazuyo Shiroma ,&nbsp;Takemitsu Arakaki ,&nbsp;Asha Mansour Hamdun ,&nbsp;Yoshikatsu Nakano ,&nbsp;Tamotsu Oomori","doi":"10.1016/j.jprot.2008.01.014","DOIUrl":"10.1016/j.jprot.2008.01.014","url":null,"abstract":"<div><p>A small-scale chamber experimental system was designed to study the effects of temperature on colony-level coral metabolism. The system continuously supplies fresh seawater to the chamber, where it is mixed immediately and completely with the seawater already present. This continuous-flow complete-mixing system (CFCM system), in conjunction with theoretical equations, allows quantitative determination of chemical uptake and release rates by coral under controlled environmental conditions. We used the massive hermatypic coral <em>Goniastrea aspera</em> to examine variations in pH, total alkalinity, and total inorganic carbon for 16 days at 27 °C under controlled light intensities (300 and 0 µmol m^{−<!--> <!-->2} s^{−<!--> <!-->1}). We confirmed the stability of the CFCM system with respect to coral photosynthetic and calcification fluxes. In addition, we obtained daily photosynthetic and calcification rates at different temperatures (27 °C, 29 °C, 31 °C, and 33 °C). When seawater temperature was raised from 31 °C to 33 °C, the gross primary production rate (<em>P</em>_gross) decreased 29.5%, and the calcification rate (<em>G</em>) decreased 85.7% within 2 days. The CFCM system allows quantitative evaluation of coral colony chemical release and uptake rates, and metabolism.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 865-872"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jprot.2008.01.014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27359655","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":"Utilization of fluorescence tracer in hyperinsulinemic–euglycemic clamp test in mice","authors":"Fei Ye,&nbsp;Rongya Tao,&nbsp;Weina Cong,&nbsp;Jinying Tian,&nbsp;Qian Liu","doi":"10.1016/j.jprot.2008.01.003","DOIUrl":"10.1016/j.jprot.2008.01.003","url":null,"abstract":"<div><p>The hyperinsulinemic–euglycemic clamp test is considered to be a gold standard for the evaluation of insulin sensitivity. Here, a new version of the clamp test that used the fluorescence tracer 2-NBDG was tested. C57BL/6J mice were induced insulin resistant (IR) with a high-calorie diet. Rosiglitazone was administrated to IR mice and diabetic <em>db/db</em> mice. Insulin resistance was estimated with the oral glucose tolerance test (OGTT), the insulin tolerance test (ITT), the serum insulin level and the homeostasis model assessment of insulin resistance (HOMA-IR), and then confirmed by the hyperinsulinemic–euglycemic clamp test with 2-NBDG. The 2-NBDG content was measured by the fluorescence intensity. The characteristics of insulin resistance were shown remarkably with the increased values of serum insulin and HOMA-IR in IR mice, and with the results from OGTT and ITT in both IR and <em>db/db</em> mice. In the hyperinsulinemic–euglycemic clamp test, the glucose infusion rate and amount of 2-NBDG taken up into the liver, adipose, and skeletal muscle were decreased significantly in IR mice and <em>db/db</em> mice, respectively. The clearing rates of 2-NBDG from the circulation were much slower in both mouse models. All markers were reversed significantly by rosiglitazone treatment. The results indicate that with the fluorescence tracer 2-NBDG, the hyperinsulinemic–euglycemic clamp test can be used to estimate insulin sensitivity <em>in vivo</em>.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 978-984"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jprot.2008.01.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27334089","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":"A simple spectrophotometric streptavidin–biotin binding assay utilizing biotin-4-fluorescein","authors":"Mark J. Waner,&nbsp;David P. Mascotti","doi":"10.1016/j.jbbm.2007.06.001","DOIUrl":"10.1016/j.jbbm.2007.06.001","url":null,"abstract":"<div><p>A new assay for biotin binding capacity of Streptavidin (SA) is presented in this work. The assay is based on the large decrease in the extinction coefficient at 493 nm that accompanies binding of biotin-4-fluorescein (B4F) to SA. This decrease is attributed to formation of a charge transfer complex between the B4F-donor and one or more SA residues. We show that one may observe the stoichiometric binding via monitoring the absorbance at 493 nm using either SA or B4F as the titrant. The sensitivity of the assay is at the lower end of similar fluorimetric and photometric assays. Though the sensitivity is not substantially lower than other comparable techniques, this assay allows one added flexibility in working range and instrumentation, since the same stock solutions may be used for this new photometric assay or the fluorescence assay for which this ligand was first developed.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 873-877"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jbbm.2007.06.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26863046","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":"An electrochemical sensor for determination of calcium dobesilate based on PoPD/MWNTs composite film modified glassy carbon electrode","authors":"Xiuhua Zhang,&nbsp;Shimin Wang,&nbsp;Li Jia,&nbsp;Zuxun Xu,&nbsp;Yu Zeng","doi":"10.1016/j.jbbm.2007.10.002","DOIUrl":"10.1016/j.jbbm.2007.10.002","url":null,"abstract":"<div><p>A poly-<em>o</em>-phenylenediamine and multi-wall carbon nanotubes composite (PoPD/MWNTs) modified glassy carbon electrode (GCE) was prepared by in situ electropolymerization using an ionic surfactant as the supporting electrolyte. The morphology of the resulting PoPD/MWNTs composite was characterized by TEM and the electrochemical properties of the modified electrode were characterized by cyclic voltammetry. The electrochemical behavior of calcium dobesilate on PoPD/MWNTs modified electrode was also investigated. The large current response of calcium dobesilate on PoPD/MWNTs modified electrode is probably caused by the synergistic effect of the electrocatalytic property of PoPD and MWNTs. The reductive peak current increased linearly with the concentration of calcium dobesilate in the range of 0.1–1.0 μmol/L and 4.0–400 μmol/L by square wave adsorptive stripping voltammetry, respectively. The detection limit (three times the signal blank/slope) was 0.035 μmol/L. The modified electrode could eliminate the interference of dopamine, norepinephrine and epinephrine at 100-, 90- and 70-fold concentration of 1.0 μmol/L calcium dobesilate, respectively. The proposed modified electrode provides a new promising and alternative way to detect calcium dobesilate.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 1203-1209"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jbbm.2007.10.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41019681","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":"Importance of probe location for quantitative comparison of signal intensities among genes in microarray analysis","authors":"Rei Kakuhata ,&nbsp;Masahiro Watanabe ,&nbsp;Takenori Yamamoto ,&nbsp;Eriko Obana ,&nbsp;Naoshi Yamazaki ,&nbsp;Masatoshi Kataoka ,&nbsp;Toshihiko Ooie ,&nbsp;Yoshinobu Baba ,&nbsp;Tomoshige Hori ,&nbsp;Yasuo Shinohara","doi":"10.1016/j.jprot.2007.12.005","DOIUrl":"10.1016/j.jprot.2007.12.005","url":null,"abstract":"<div><p>In our previous studies, we demonstrated that expression levels of genes determined by Agilent oligoarray system, code G4130A, could be quantitatively evaluated by spike-in of synthetic full-length mRNAs as standards [Kakuhata R, Watanabe M, Yamamoto T, Akamine R, Yamazaki N, Kataoka M, et al. Possible utilization of in vitro synthesized mRNAs specifically expressed in certain tissues as standards for quantitative evaluation of the results of microarray analysis, J Biochem Biophys Methods 2007;70:755–60]. However, in its successor version (Agilent oligo array system, code G4131F), which was established to enable gene expression analysis over a much wider dynamic range, multiple probes are often utilized for evaluation of expression levels of individual genes; and they showed markedly distinct signal intensities. This result indicates that the observed signal intensities in this new version seemed not to simply reflect the transcript levels of individual genes. To understand the factors influencing the signal intensities of probes, we characterized the properties of the probes used in this new array system and the cRNAs formed during the labeling process. Analysis of cRNAs in the reaction mixture, which were hybridized with the arrays, revealed that the cRNAs were not fully transcribed under the conditions used. For this reason, probes located at the 5′ side of the message were found to give lower signals than those at the 3′ end; and the observed signal intensities were dependent upon the location of probes in the mRNA. Analysis of the correlation between signal intensities and locations on mRNAs for larger numbers of probes also supported the idea that probe location is one of the major determinants of signal intensities of probes in microarray analysis.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 926-931"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jprot.2007.12.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27235963","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":"Investigation of coenzyme Q biosynthesis in human fibroblast and HepG2 cells","authors":"Michael Tekle ,&nbsp;Mikael Turunen ,&nbsp;Gustav Dallner ,&nbsp;Tadeusz Chojnacki ,&nbsp;Ewa Swiezewska","doi":"10.1016/j.jbbm.2007.08.003","DOIUrl":"10.1016/j.jbbm.2007.08.003","url":null,"abstract":"<div><p>Coenzyme Q (CoQ) deficiency occurs in genetic disorders, during aging and various diseases. Diagnosis requires skin fibroblasts in tissue culture. [³H]Mevalonate incorporation was appropriate to measure the rate of CoQ synthesis in fibroblasts and hepatoblastoma cells. [¹⁴C]<em>p</em>-Hydroxybenzoate had limited permeability, but it could be increased with Fugene and cyclodextrin. Inhibition of decaprenyl-4-hydroxybenzoate transferase results in the accumulation of decaprenyl diphosphate, an indicator of enzyme deficiency. Also, analysis of the corresponding mRNAs in this case is useful. <em>In vitro</em> assays to measure <em>trans</em>-prenyltransferase and decaprenyl-4-hydroxybenzoate transferase activities are not available. Neither measurement of methyltransferases is reliable in human cells. <em>In vitro</em> reconstruction of CoQ synthesis, in opposite to cholesterol synthesis, proved to be unsuccessful. Thus, the biochemical characterization of the CoQ biosynthetic system in human cells is restricted to a few reliable analytical procedures.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 909-917"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jbbm.2007.08.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27032216","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":"Benchmarking protein classification algorithms via supervised cross-validation","authors":"Attila Kertész-Farkas ,&nbsp;Somdutta Dhir ,&nbsp;Paolo Sonego ,&nbsp;Mircea Pacurar ,&nbsp;Sergiu Netoteia ,&nbsp;Harm Nijveen ,&nbsp;Arnold Kuzniar ,&nbsp;Jack A.M. Leunissen ,&nbsp;András Kocsor ,&nbsp;Sándor Pongor","doi":"10.1016/j.jbbm.2007.05.011","DOIUrl":"10.1016/j.jbbm.2007.05.011","url":null,"abstract":"<div><p>Development and testing of protein classification algorithms are hampered by the fact that the protein universe is characterized by groups vastly different in the number of members, in average protein size, similarity within group, etc. Datasets based on traditional cross-validation (<em>k</em>-fold, leave-one-out, etc.) may not give reliable estimates on how an algorithm will generalize to novel, distantly related subtypes of the known protein classes. Supervised cross-validation, i.e., selection of test and train sets according to the known subtypes within a database has been successfully used earlier in conjunction with the SCOP database. Our goal was to extend this principle to other databases and to design standardized benchmark datasets for protein classification. Hierarchical classification trees of protein categories provide a simple and general framework for designing supervised cross-validation strategies for protein classification. Benchmark datasets can be designed at various levels of the concept hierarchy using a simple graph-theoretic distance. A combination of supervised and random sampling was selected to construct reduced size model datasets, suitable for algorithm comparison. Over 3000 new classification tasks were added to our recently established protein classification benchmark collection that currently includes protein sequence (including protein domains and entire proteins), protein structure and reading frame DNA sequence data. We carried out an extensive evaluation based on various machine-learning algorithms such as nearest neighbor, support vector machines, artificial neural networks, random forests and logistic regression, used in conjunction with comparison algorithms, BLAST, Smith-Waterman, Needleman-Wunsch, as well as 3D comparison methods DALI and PRIDE. The resulting datasets provide lower, and in our opinion more realistic estimates of the classifier performance than do random cross-validation schemes. A combination of supervised and random sampling was used to construct model datasets, suitable for algorithm comparison.</p><p>The datasets are available at <span>http://hydra.icgeb.trieste.it/benchmark</span><svg><path></path></svg>.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 1215-1223"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jbbm.2007.05.011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26807453","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":"Reactivity of histidine and lysine side-chains with diethylpyrocarbonate — A method to identify surface exposed residues in proteins","authors":"Aleš Hnízda ,&nbsp;Jiří Šantrůček ,&nbsp;Miloslav Šanda ,&nbsp;Martin Strohalm ,&nbsp;Milan Kodíček","doi":"10.1016/j.jbbm.2007.07.004","DOIUrl":"10.1016/j.jbbm.2007.07.004","url":null,"abstract":"<div><p>The chemical modification of amino acid side-chains followed by mass spectrometric detection can reveal at least partial information about the 3-D structure of proteins. In this work we tested diethylpyrocarbonate, as a common histidyl modification agent, for this purpose. Appropriate conditions for the reaction and detection of modified amino acids were developed using angiotensin II as a model peptide. We studied the modification of several model proteins with a known spatial arrangement (insulin, cytochrome c, lysozyme and human serum albumin). Our results revealed that the surface accessibility of residues is a necessary, although in itself insufficient, condition for their reactivity; the microenvironment of side-chains and the dynamics of protein structure also affect the ability of residues to react. However the detection of modified residues can be taken as proof of their surface accessibility, and of direct contact with solvent molecules.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 1091-1097"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jbbm.2007.07.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26951432","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}