Journal of biochemical and biophysical methods最新文献

{"title":"Tribute to Stellan Hjertén","authors":"","doi":"10.1016/j.jprot.2007.11.014","DOIUrl":"https://doi.org/10.1016/j.jprot.2007.11.014","url":null,"abstract":"","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages vi-vii"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jprot.2007.11.014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136487925","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":"Novel method for preparation of the template DNA and selection of primers to differentiate the material rice cultivars of rice wine by PCR","authors":"Ken'ichi Ohtsubo,&nbsp;Keitaro Suzuki,&nbsp;Kazutomo Haraguchi,&nbsp;Sumiko Nakamura","doi":"10.1016/j.jbbm.2007.07.001","DOIUrl":"10.1016/j.jbbm.2007.07.001","url":null,"abstract":"<div><p>As many rice wine brewers label the name of the cultivar of the material rice, authentication technology is necessary. The problems are (1) decomposition of DNAs during the fermentation, (2) contamination of DNAs from microorganisms, (3) co-existence of PCR inhibitors, such as polyphenols. The present authors improved the PCR method by (1) lyophilizing and pulverizing the rice wine to concentrate DNAs, (2) decomposition of starches and proteins so as not to inhibit DNA extraction by the use of heat-resistant amylase and proteinase K, (3) purification of the template DNA by the combination of CTAB method and fractional precipitation by 70% EtOH. To prevent the amplification of microorganism's DNAs during PCR, the present authors selected the suitable plant-specific primers. It became possible to prepare the template DNAs for PCR from the rice wine. The sequences of the amplified DNAs by PCR were ascertained to be same with those of material rice. Mislabeling of material rice cultivar was detected by PCR using the commercial rice wine. It became possible to extract and purify the template DNAs for PCR from the rice wine and to differentiate the material rice cultivars by the PCR using the rice wine as a sample.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 1020-1028"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jbbm.2007.07.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26869806","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":"Evaluation of the ET-AAS and HG-AAS methods of selenium determination in vegetables","authors":"Ondrej Hegedűs ,&nbsp;Alžbeta Hegedűsová ,&nbsp;Silvia Šimková ,&nbsp;Vladimír Pavlík ,&nbsp;Klaudia Jomová","doi":"10.1016/j.jprot.2008.01.002","DOIUrl":"10.1016/j.jprot.2008.01.002","url":null,"abstract":"<div><p>ET-AAS and HG-AAS methods of selenium determination were compared and evaluated. The ET-AAS method has been followed with deuterium background correction and Zeeman background correction respectively. The following validation parameters were determined: accuracy (under repeatability conditions), trueness, calibration curve and linearity, limit of detection, limit of determination and combined standard uncertainty of the method. The HG-AAS method and the ET-AAS method with Zeeman correction were more suitable for the determination of low selenium concentrations in vegetables. The results were calculated by the standard addition method because of the strong matrix effect.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 1287-1291"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jprot.2008.01.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27266217","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":"Determination of the thermodynamics of carbonic anhydrase acid-unfolding by titration calorimetry","authors":"Lina Baranauskienė,&nbsp;Jurgita Matulienė,&nbsp;Daumantas Matulis","doi":"10.1016/j.jprot.2007.12.003","DOIUrl":"10.1016/j.jprot.2007.12.003","url":null,"abstract":"<div><p>The enthalpy of unfolding (Δ<em>_uH</em>) of carbonic anhydrase II was determined by titrating the protein with acid and measuring the heat using isothermal titration calorimetry (ITC) in the temperature range of 5 to 59 °C. By combining the ITC results with our previous findings by differential scanning calorimetry (DSC) in the temperature range of 39 to 72 °C, the Δ<em>_uH</em> dependence over a wide temperature range was obtained. The temperature dependence of the enthalpy displays significant curvature indicating that the heat capacity of unfolding (Δ<em>_uC_p</em>) is dependent on temperature. The <em>T</em>-derivative of Δ<em>_uC_p</em> was equal to 100<!--> <!-->±<!--> <!-->30 J/(mol<!--> <!-->×<!--> <!-->K²), with the result that the Δ<em>_uC_p</em> is equal to 15.8 kJ/(mol<!--> <!-->×<!--> <!-->K) at 5 °C, 19.0 kJ/(mol<!--> <!-->×<!--> <!-->K) at 37 °C and 21.8 kJ/(mol<!--> <!-->×<!--> <!-->K) at 64 °C. The enthalpy of unfolding is zero at 17 °C. At lower temperatures, the Δ<em>_uH</em> becomes exothermic.</p><p>This method of determining protein unfolding thermodynamics using acid-ITC, significantly widens the accessible <em>T</em>-range, provides direct estimate of the thermodynamic parameters at physiological temperature, and gives further insight into the third <em>T</em>-derivative of the Gibbs free energy of unfolding.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 1043-1047"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jprot.2007.12.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27247821","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 novel FluoroChrome ImmunoAssay — (FCIA). The role of molecular environment upon molecular structure exemplified by constriction of a flourescence-photochrome flanked by two proteins","authors":"Oren Chen,&nbsp;Robert Glaser,&nbsp;Gertz I. Likhtenshtein","doi":"10.1016/j.jbbm.2007.07.007","DOIUrl":"10.1016/j.jbbm.2007.07.007","url":null,"abstract":"<div><p>A rapid, sensitive, and quantitative novel immunoassay [FluoroChrome ImmunoAssay, FCIA] technique was developed which auspiciously combines both the high sensitivity of fluorescence measurements with the high specificity of an antibody. As opposed to existing immunoassays, FCIA is performed without separation of antibody-bound haptens from those that are free, and utilizes fluorescence measurements from widely available standard commercial fluorimeters. FCIA is based on the hypothesis that an appropriately designed stilbene-antigen analogue probe will suffer considerable steric hindrance to <em>trans-cis</em> photoisomerization when bound within the combined constraints of both an antibody binding site and a second globular protein. Specifically, an appropriately designed 2,4–dinitrophenyl-hapten derivative of fluorescent <em>trans</em>-4,4′-diaminostilbene (DAS), was squeezed between two large globular proteins: lysozyme (Lys) from one side, and anti-2,4,6-trinitrophenyl antibody (antiTNP) from the other side, in order to provide the desired constricted environment to restrict <em>trans/cis</em>-stibene isomerization within the antiTNP-DNP-DAS-Lys adduct. As was theoretically predicted and then experimentally verified, the <em>trans-cis</em> photoisomerization rate for the bound probe was found to be markedly inhibited, compared to that expected for the free probe in solution. The fluorescence-photochrome labeled probe was competitively displaced from the antiTNP binding site in the presence of the picric acid hapten, and photoisomerization then commenced to produce the fluorescence-silent <em>cis</em>-stilbene diastereomer. The process of association and dissociation of a hapten-antibody complex was readily monitored by the fluorescence technique in the presence of both antibody-bound and free haptens.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 1073-1079"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jbbm.2007.07.007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27010667","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":"Enantioselectivity of potentiometric sensors with application of different mechanisms of chiral discrimination","authors":"Marzena Kaniewska ,&nbsp;Tomasz Sikora ,&nbsp;Ritu Kataky ,&nbsp;Marek Trojanowicz","doi":"10.1016/j.jbbm.2007.09.006","DOIUrl":"10.1016/j.jbbm.2007.09.006","url":null,"abstract":"<div><p>In the recent years, numerous successful applications of various chiral selectors in high performance separation methods have generated an increasing interest in the application of some of these compounds as electroactive species in potentiometric sensors. The objective of this work was to examine the enantioselectivy of several different sensors employing substituted cyclodextrins, example antibiotic teicoplanin and electrodeposited conductive polymers for various chiral analytes. Varying degrees of enantioselectivity were found for the ion-selective electrodes examined, depending on the chiral selector used and the target analyte.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 1261-1267"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jbbm.2007.09.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27079909","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 new erythrose 4-phosphate dehydrogenase coupled assay for transketolase","authors":"Christina Naula,&nbsp;Vincent P. Alibu,&nbsp;Janice M. Brock,&nbsp;Nicola J. Veitch,&nbsp;Richard J.S. Burchmore,&nbsp;Michael P. Barrett","doi":"10.1016/j.jprot.2007.11.002","DOIUrl":"10.1016/j.jprot.2007.11.002","url":null,"abstract":"<div><p>The standard assay for transketolase (E.C 2.2.1.1) has depended upon the use of <span>d</span>-xylulose 5-phosphate as the ketose donor substrate since the production of <span>d</span>-glyceraldehyde 3-phosphate can be readily coupled to a reaction that consumes NADH allowing the reaction to be followed spectrophotometrically. Unfortunately, commercial supplies of <span>d</span>-xylulose 5-phosphate recently became unavailable. In this article we describe the coupling of a transketolase reaction (using <em>Leishmania mexicana</em> transketolase) that converts <span>d</span>-fructose 6-phosphate to <span>d</span>-erythrose 4-phosphate. <span>d</span>-Erythrose 4-phosphate can then be converted to 4-phosphate <span>d</span>-erythronate using erythrose-4-phosphate dehydrogenase (E.C 1.2.1.72), a reaction that reduces NAD⁺ to NADH and can be easily followed spectrophotometrically. <span>d</span>-Ribose 5-phosphate and <span>d</span>-glyceraldehyde 3-phosphate can both be used as ketol acceptor substrates in the reaction although <span>d</span>-ribose 5-phosphate is also a substrate for the coupling enzyme.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 1185-1187"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jprot.2007.11.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41049242","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 efficient cloning of DNA fragments by a method based on uracil-DNA glycosylase and endonuclease IV","authors":"Jingli Hou,&nbsp;Xipeng Liu,&nbsp;Yan Zheng,&nbsp;Jianhua Liu","doi":"10.1016/j.jbbm.2007.07.006","DOIUrl":"10.1016/j.jbbm.2007.07.006","url":null,"abstract":"<div><p><span>We introduced a novel method to clone random DNA fragments independent of ligation reaction. The method involves the generation of long protruding ends on PCR amplification DNA. Both oligonucleotides<span> used for the amplification of the vector DNA carried one uracil<span> residue at the tenth position from the 5′ end and this made the creation of the 3′ protruding ends of linearized vector possible by uracil-DNA glycosylase (UDG) and endonuclease IV (Endo IV). 76 groups of annealed oligonucleotides that had ten-nucleotides protruding at 3′-end, which were complementary to those at 3′-end of the linearized vector, were designed. The linearized vector and the annealed oligonucleotide were mixed together to transform </span></span></span><em>E.coli</em> directly without ligation reaction. The number of the clone that grew on the plates had been demonstrated to reach 1<!--> <!-->×<!--> <!-->10⁵ transformants/μg and 96.1% of transformants harbored the cloned fragments. From the results of transformation, we can confirm that the efficiency of the creation of 3′ protruding ends in our method is high and our cloning method is benefit to produce recombinants easily and efficiently.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 1196-1198"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jbbm.2007.07.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26949320","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":"Optimized HPLC method for tramadol and O-desmethyl tramadol determination in human plasma","authors":"Augustin Curticapean,&nbsp;Daniela Muntean,&nbsp;Manuela Curticapean,&nbsp;Maria Dogaru,&nbsp;Camil Vari","doi":"10.1016/j.jprot.2008.01.012","DOIUrl":"10.1016/j.jprot.2008.01.012","url":null,"abstract":"<div><p>The optimized method for HPLC determination of tramadol and its metabolite <em>O</em>-desmethyl tramadol in human plasma using sotalol as internal standard has been developed and validated by a new approach. The determination by fluorescence detection was performed on re-eluted solution, obtained after liquid–liquid extraction with ethyl acetate of the three analytes from plasma. The chromatographic separation of tramadol under a gradient elution was achieved at a temperature of 15 °C with a RP-18 column, guarded by a C18 precolumn. The mobile phase was a mixed aqueous solution containing ortho-phosphoric acid, triethylamine, acetonitrile and methanol in a complex gradient mode. The quantitative determination of tramadol was performed at different successive pairs of excitation/emission wavelengths (200/300 nm, 200/295 nm, 212/305 nm) with lower limits of quantification: LLOQ<!--> <!-->=<!--> <!-->4.078 ng/ml for tramadol, respectively LLOQ<!--> <!-->=<!--> <!-->3.271 ng/ml for <em>O</em>-desmethyl tramadol. For the LLOQ limits, were calculated the values of the coefficient of variation and difference between mean and the nominal concentration. For tramadol analyte they were CV%<!--> <!-->=<!--> <!-->5.147% and bias%<!--> <!-->=<!--> <!-->−<!--> <!-->7.273% in the intra-days and CV%<!--> <!-->=<!--> <!-->4.894% and bias%<!--> <!-->=<!--> <!-->0.836% in the between-days assay, respectively for the metabolite <em>O</em>-desmethyl tramadol they were CV%<!--> <!-->=<!--> <!-->11.517% and bias%<!--> <!-->=<!--> <!-->0.337% in the intra-days and CV%<!--> <!-->=<!--> <!-->6.41% and bias%<!--> <!-->=<!--> <!-->3.259% in the between-days assay.</p><p>In addition, the stabilities of the analytes were verified in different conditions. Both, tramadol and its metabolite proved to be stable in plasma for four weeks, frozen at −<!--> <!-->20 °C, but also for 48 h at 15 °C in the re-eluted solution after liquid–liquid extraction.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 1304-1312"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jprot.2008.01.012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27369032","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":"Dispensing an enzyme-conjugated solution into an ELISA plate by adapting ink-jet printers","authors":"Luca Lonini ,&nbsp;Dino Accoto ,&nbsp;Silvia Petroni ,&nbsp;Eugenio Guglielmelli","doi":"10.1016/j.jbbm.2007.05.003","DOIUrl":"10.1016/j.jbbm.2007.05.003","url":null,"abstract":"<div><p>The rapid and precise delivery of small volumes of bio-fluids (from picoliters to nanoliters) is a key feature of modern bioanalytical assays. Commercial ink-jet printers are low-cost systems which enable the dispensing of tiny droplets at a rate which may exceed 10⁴ Hz per nozzle. Currently, the main ejection technologies are piezoelectric and bubble-jet. We adapted two commercial printers, respectively a piezoelectric and a bubble-jet one, for the deposition of immunoglobulins into an ELISA plate. The objective was to perform a comparative evaluation of the two classes of ink-jet technologies in terms of required hardware modifications and possible damage on the dispensed molecules. The hardware of the two printers was modified to dispense an enzyme conjugate solution, containing polyclonal rabbit anti-human IgG labelled with HRP in 7 wells of an ELISA plate. Moreover, the ELISA assay was used to assess the functional activity of the biomolecules after ejection. ELISA is a common and well-assessed technique to detect the presence of particular antigens or antibodies in a sample. We employed an ELISA diagnostic kit for the qualitative screening of anti-ENA antibodies to verify the ability of the dispensed immunoglobulins to bind the primary antibodies in the wells. Experimental tests showed that the dispensing of immunoglobulins using the piezoelectric printer does not cause any detectable difference on the outcome of the ELISA test if compared to manual dispensing using micropipettes. On the contrary, the thermal printhead was not able to reliably dispense the bio-fluid, which may mean that a surfactant is required to modify the wetting properties of the liquid.</p></div>","PeriodicalId":15257,"journal":{"name":"Journal of biochemical and biophysical methods","volume":"70 6","pages":"Pages 1180-1184"},"PeriodicalIF":0.0,"publicationDate":"2008-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jbbm.2007.05.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26794786","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}