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Analytical Biochemistry

Lu Chen, Hui-Ting Lian, Xiang-Ying Sun, Bin Liu
A novel electrochemical sensor was presented for the determination of L-5-hydroxytryptophan (L-5-HTP) based on a graphene-chitosan molecularly imprinted film modified on the surface of glassy carbon electrode (GR-MIP/GCE). The morphology and composition of the imprinted film were observed in field emission scanning electron microscopy (FESEM), raman spectroscopy and fourier transform infrared (FTIR). The properties of the sensor were evaluated by electrochemical techniques. Under the optimal conditions, the peak currents of L-5-HIP were found to be linear in the concentration range of 0...
March 19, 2017: Analytical Biochemistry
Jing Zhao, Xinyue Liu, Anju Malhotra, Quanhong Li, Fuming Zhang, Robert J Linhardt
A novel method has been developed for the easy measurement of heparin's anticoagulant activity using surface plasmon resonance. The anticoagulant activity of target heparin was evaluated by measuring the competitive antithrombin III binding of analyte heparin in the solution phase and USP heparin immobilized on chip surface. Heparins, obtained from different animal sources, and low molecular weight heparins were analyzed. The results were reproducible and correlated well with the results of chromogenic assays (correlation coefficient r = 0...
March 18, 2017: Analytical Biochemistry
Xingping Wu, Ailin Zhu, Xiaowu Pang, Guiqin Xie, Xinbin Gu
We describe a simple method to accurately detect and quantify both Pten mutation and allele-specific loss using allele-specific PCR analysis. Our approach used a heterozygous genomic DNA with one wild-type and one mutant Pten allele as a reference at a single concentration to calculate the percent ratio of the wild-type Pten gene for the detection of allele-specific gene loss. With a standard curve, ratios from PCR data were used to quantitate the wild-type Pten allele copy number loss in tumor specimens. We demonstrate the utility of our approach to calculate allele-specific Pten loss during tumor progression and show that our approach generates quantitative data that are comparable to those obtained from digital droplet PCR...
March 17, 2017: Analytical Biochemistry
Dal-Hoe Koo, Bhupendra Singh, Jiming Jiang, Bernd Friebe, Bikarm S Gill, Paul D Chastain, Upender Manne, Hemant K Tiwari, Keshav K Singh
Somatic human cells contains thousands of copies of mitochondrial DNA (mtDNA). In eukaryotes, natural transfer of mtDNA into the nucleus generates nuclear mitochondrial DNA (NUMT) copies in eukaryotes. We name this phenomenon as "numtogenesis". Numtogenesis is a well-established evolutionary process reported in various sequenced eukaryotic genomes. We have established a molecular tool to rapidly detect and analyze NUMT insertions in whole genomes. To date, NUMT analyses depend on deep genome sequencing combined with comprehensive computational analyses of the whole genome...
March 17, 2017: Analytical Biochemistry
Alexander M Firsov, Elena A Kotova, Yuri N Antonenko
Membrane-permeabilizing activity of cytochrome c (cyt c) in the presence of hydrogen peroxide associated with its functioning as peroxidase is considered relevant to initiation of the mitochondrial pathway of apoptosis. Here, we present evidence that the choice of a fluorescent dye for measuring cyt c/H2O2-induced dye leakage from liposomes by fluorescence de-quenching is of major importance. The popular fluorescent marker 5(6)-carboxyfluorescein appeared highly susceptible to cyt c-mediated peroxidative destruction and therefore unsuitable for the leakage assay with cyt c/H2O2...
March 16, 2017: Analytical Biochemistry
Hey Young Yoon, Jong-In Hong
Sulfatases catalyze the hydrolysis of sulfate esters that are present in a range of biomolecules. This is an important step in several biological processes such as cellular degradation, hormone regulation, and cell signaling. We have developed a new activity-based sulfatase probe (probe 1) that generates a fluorescent N-methylisoindole upon hydrolysis by sulfatase. Because of the autoxidation of N-methylisoindole, the sulfatase activity was also tested under reducing conditions, containing either glutathione (GSH) or tris(2-carboxyethyl)phosphine (TCEP), exhibiting little change in kinetic parameters compared to non-reducing conditions...
March 16, 2017: Analytical Biochemistry
Chiaki Murakami, Satoru Mizuno, Sayaka Kado, Fumio Sakane
Phosphatidylcholine (PC)-specific phospholipase C (PC-PLC) hydrolyzes PC to generate the second messenger 1,2-diacylglycerol (DG) and phosphocholine. PC-PLC plays pivotal roles in inflammation, carcinogenesis, tumor progression, atherogenesis, and subarachnoid hemorrhage. Although the activity of PC-PLC in mammalian tissues was discovered approximately 40 years ago, neither the protein nor its gene has been identified. In the present study, we developed a non-radioactive enzyme activity assay for PC-PLC based on mass spectrometric detection of DG following HPLC separation...
March 14, 2017: Analytical Biochemistry
Mohammad Shahidul Makki, Nahid Akhtar, Tariq M Haqqi
Human chondrocytes accumulate an ECM-rich matrix by secreting matrix macromolecules during monolayer culture, which makes them difficult to transfect efficiently. Here we report a non-viral based protocol to transfect the primary human chondrocytes with high efficiency in suspension. Chondrocyte cultures were digested using Pronase and Collagenase and transfected in suspension. Transfection efficiencies of more than 80% were achieved routinely using the protocol described. The viability of siRNA transfected or un-transfected chondrocytes was not affected and resulted in 80-90% knockdown of the target mRNA levels...
March 14, 2017: Analytical Biochemistry
Danyang Ji, Hongqi Wang, Jia Ge, Lin Zhang, Jianjun Li, Dongmei Bai, Juan Chen, Zhaohui Li
In this work, an aptamer-based fluorescent strategy for label-free detection of ATP was developed by using Thioflavin T (ThT) as a fluorescence indicator, which can specifically bind with G-quadruplex DNAs to generate enhanced fluorescence intensity. In the absence of ATP, the folded structure of ATP aptamer allows the intercalation of ThT to produce strong fluorescence signal. However, upon ATP binding to the aptamer where ThT intercalated, the conformational change or distortion of the aptamer is large enough to cause much less intercalation of ThT and consequently drastic suppression of the fluorescence intensity...
March 14, 2017: Analytical Biochemistry
Maša Primec, Dušanka Mičetić-Turk, Tomaž Langerholc
Short-chain fatty acids (SCFAs) play a crucial role in maintaining homeostasis in humans, therefore the importance of a good and reliable SCFAs analytical detection has raised a lot in the past few years. The aim of this scoping review is to show the trends in the development of different methods of SCFAs analysis in feces, based on the literature published in the last eleven years in all major indexing databases. The search criteria included analytical quantification techniques of SCFAs in different human clinical and in vivo studies...
March 12, 2017: Analytical Biochemistry
Md Al Mehedi Hasan, Jinyan Li, Shamim Ahmad, Md Khademul Islam Molla
The carbonylation is found as an irreversible post-translational modification and considered a biomarker of oxidative stress. It plays major role not only in orchestrating various biological processes but also associated with some diseases such as Alzheimer's disease, diabetes, and Parkinson's disease. However, since the experimental technologies are costly and time-consuming to detect the carbonylation sites in proteins, an accurate computational method for predicting carbonylation sites is an urgent issue which can be useful for drug development...
March 9, 2017: Analytical Biochemistry
Aicheng Wang, Huimin Zhao, Xiaochi Chen, Bing Tan, Yaobin Zhang, Xie Quan
A sensitive, rapid and label-free colorimetric aptasensor for sulfadimethoxine (SDM) detection was developed based on the tunable peroxidase-like activity of graphene/nickel@palladium nanoparticle (Gr/Ni@Pd) hybrids. The addition of the SDM aptamer could inhibit the peroxidase-like catalytic activity of the hybrids. However, the target SDM and aptamer could be triggered tightly and recover the catalytic activity of the Gr/Ni@Pd hybrids. Due to the peroxidase-like catalytic activity, Gr/Ni@Pd could catalyze the decomposition of H2O2 with releasing hydroxyl radicals which further oxidized reagent 3, 3', 5, 5'-Tetramethylbenzidine (TMB) to oxTMB accompanied with a colorless-to-blue color change...
March 7, 2017: Analytical Biochemistry
Yun Wang, Qian Wang, Ai-Hua Wu, Zhen-Ping Hao, Xian-Jin Liu
Traditional ELISA methods of using animal immunity yield antibodies for detection Cry toxin. Not only is this incredibly harmful to the animals, but is also time-intensive. Here we developed a simple method to yield the recognition element. Using a critical selection strategy and immunoassay we confirmed a clone from the Ph.D-C7C phage library, which has displayed the most interesting Cry1Ab-binding characteristics examined in this study (Fig. 1). The current study indicates that isolating peptide is an alternative method for the preparation of a recognition element, and that the developed assay is a potentially useful tool for detecting Cry1Ab...
March 6, 2017: Analytical Biochemistry
Christine Nowak, Gomathinayagam Ponniah, Alyssa Neill, Hongcheng Liu
LC-MS peptide mapping is the most commonly used method to analyze protein modifications. The proteins are generally digested using trypsin at a slightly basic pH at 37 °C from several hours to overnight. Assay-induced artifacts can be generated during this procedure, potentially causing false-positive or false-negative results for a given modification. Unfortunately, for the analysis of succinimide, both false-negative and false-positive results can be generated within the same procedure. This study evaluates the stability of succinimide during the peptide mapping procedure and has demonstrated that up to 13% of pre-existing succinimide was lost during a 4 h trypsin digestion at pH 5...
March 6, 2017: Analytical Biochemistry
Yuan Liu, Manman Lin, Xifeng Zhang, Xiaodan Hu, Jieru Lin, Jia Hao, Dan He, Xiao Zhang, Chongxin Xu, Jianfeng Zhong, Yajing Xie, Cunzheng Zhang, Xianjin Liu
Soluble anti-bovine serum albumin (BSA) single-chain variable fragments (scFvs) were expressed in E. Coli. HB2151. The antigen-binding equilibrium dissociation constant of the scFvs was determined to be 2.9 × 10(-8) M by surface plasmon resonance analysis. A competitive ELISA for the detection of BSA was developed using the antibody fragment above. The limits of detection (I10) and I50 were 0.002 and 0.74 μg/ml respectively, with a recovery between 87.8 and 119.2% in spiked milk samples. The assay has the potential to be used to detect concentration of BSA in milk or other matrix instead of the ELISA based on traditional antibodies...
March 6, 2017: Analytical Biochemistry
Rivo Presentini
A quantitative spectrophotometric method has been developed for the analysis of N-hydroxysulfosuccinimide (sulfo-NHS), a chromophore with a maximum absorbance at 268 nm. The extinction coefficients were determined between pH 6.0 and 8.0 and found to vary in a nonlinear manner. This spectrophotometric profile is not present in its esters which however release an equimolar amount of sulfo-NHS when they react with nucleophilic groups or hydrolyze in aqueous solution. This fact facilitates the determination in solution of the concentration and purity of bis(sulfosuccinimidyl) suberate (BS3) used as a model, as well as the examination of hydrolysis and aminolysis half-lives in different reaction conditions, these parameters being valuable in optimization of the use of the active esters...
March 6, 2017: Analytical Biochemistry
Yuan-Yuan Xue, Wen-Tao Zhang, Meng-Yue Zhang, Li-Zhi Liu, Wen-Xin Zhu, Ling-Zhi Yan, Jing Wang, Yan-Ru Wang, Jian-Long Wang, Dao-Hong Zhang
Microfluidic paper-based analytical devices (μPADs) have a significant potential in developing portable and disposable point-of-care testing (POCT). Herein, a facile, rapid, cost-effective and environment friendly strategy for μPADs fabrication is proposed. Specifically, the substrate paper was hydrophobized by coating with trimethoxysilane (TOS), and then the selected area was hydrophilized by treating with surfactant. The whole fabrication process was implemented within 7 min, with no need for complex pre-treatment, high-temperature and special equipment...
March 3, 2017: Analytical Biochemistry
Teraya Donaldson, Luisa Iozzino, Lindsay J Deacon, Hilbert Billones, Alessio Ausili, Sabato D'Auria, Jonathan D Dattelbaum
The Thermotoga maritima arginine-binding protein (TmArgBP) has been modified to create a reagentless fluorescent protein biosensor. Two design methods for biosensor construction are compared: 1) solvent accessibility of environmentally-sensitive probes and 2) fluorescence deactivation due to photo-induced electron transfer (PET). Nine single cysteine TmArgBP mutants were created and labeled with three different environmentally sensitive fluorescent probes. These mutants demonstrated limited changes in fluorescence emission upon the addition of arginine...
March 1, 2017: Analytical Biochemistry
L Kuchar, J Sikora, M E Gulinello, H Poupetova, A Lugowska, V Malinova, H Jahnova, B Asfaw, J Ledvinova
Acid sphingomyelinase deficiency (ASMd, Niemann-Pick disease A/B) and Niemann-Pick type C disease (NPC) share core clinical symptoms. Initial diagnostic discrimination of these two rare lysosomal storage diseases is thus difficult. As sphingomyelin accumulates in ASMd as well as NPC, lysosphingomyelin (sphingosylphosphorylcholine) and its m/z 509 analog were suggested as biomarkers for both diseases. Herein we present results of simultaneous LC-ESI-MS/MS measurements of lysosphingomyelin and lysosphingomyelin 509 in plasma and dried blood spots (DBS) collected from ASMd and NPC patients and suggest that the plasma but not DBS levels of the two analytes allow differential biochemical screening of ASMd and NPC...
March 1, 2017: Analytical Biochemistry
Dong-Mei Liu, Jun-Li Yang, Wei Ha, Juan Chen, Yan-Ping Shi
In the present study, pressure mediated microanalysis (PMMA), a fast, convenient and efficient capillary electrophoresis (CE) method was developed for studying enzyme kinetics of tyrosinase and inhibition kinetics of kojic acid, a model inhibitor of tyrosinase. The enzymatic reaction conditions and CE conditions were optimized in order to obtain high enzyme activity and short analysis time. By PMMA, only the product could be detected at 475 nm, and no voltage was applied to separate the product from the reaction mixture thus greatly simplifying the optimization procedure...
March 1, 2017: Analytical Biochemistry
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