26,824 results match your criteria Analytical Biochemistry [Journal]


anti-EGFR capture mitigates EMT- and chemoresistance-associated heterogeneity in a resistance-profiling CTC platform.

Anal Biochem 2019 Feb 18. Epub 2019 Feb 18.

Cornell University, Ithaca, USA; Weill Cornell Medicine, New York, USA. Electronic address:

Capture and analysis of circulating tumor cells (CTCs) holds promise for diagnosing and guiding treatment of pancreatic cancer. To accurately monitor disease progression, capture platforms must be robust to processes that increase the phenotypic heterogeneity of CTCs. Most CTC-analysis technologies rely on the recognition of epithelial-specific markers for capture and identification, in particular the epithelial cell-adhesion molecule (EpCAM) and cytokeratin. Read More

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http://dx.doi.org/10.1016/j.ab.2019.02.003DOI Listing
February 2019

Sarkosyl: A milder detergent than SDS for identifying proteins with moderately high hyperstability using gel electrophoresis.

Anal Biochem 2019 Feb 16. Epub 2019 Feb 16.

Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. Electronic address:

Sodium dodecyl sulfate (SDS) is a detergent used as a strong denaturant of proteins in gel electrophoresis. It has previously been shown that certain hyperstable, also known as kinetically stable, proteins are resistant to SDS and thus require heating for their denaturation in the presence of SDS. Because of its high denaturing strength, relatively few proteins are resistant to SDS thereby limiting the current use of SDS-PAGE for identifying hyperstable degradation-resistant proteins. Read More

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http://dx.doi.org/10.1016/j.ab.2019.02.008DOI Listing
February 2019

Exosomes, new biomarkers in early cancer detection.

Anal Biochem 2019 Feb 15. Epub 2019 Feb 15.

Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran. Electronic address:

Exosomes are endosomal-derived vesicles, playing a major role in cell-to-cell communication. Multiple cells secret these vesicles to induce and inhibit different cellular and molecular pathways. Cancer-derived exosomes have been shown to affect development of cancer in different stages and contribute to the recruitment and reprogramming of both proximal and distal tissues. Read More

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http://dx.doi.org/10.1016/j.ab.2019.02.013DOI Listing
February 2019

Development of a sandwich enzyme-linked immunosorbent assay for the quantification of ponatinib in serum.

Anal Biochem 2019 Feb 13. Epub 2019 Feb 13.

Applied Life Science Department, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Kumamoto, 860-0082, Japan.

The tyrosine kinase inhibitor ponatinib is extensively metabolized in the body, and consequently the development of specific immunoassays for pharmacokinetic studies and therapeutic drug monitoring of ponatinib is challenging. If two antibodies simultaneously recognize the entire structure of ponatinib, they could be utilized to establish an ultra-specific sandwich immunoassay for ponatinib, free of any interference from ponatinib metabolites. In this study, we created two types of anti-ponatinib polyclonal antibodies that recognize two different ponatinib epitopes, and sandwiched almost all structural components of ponatinib in these two antibodies in order to develop an enzyme-linked immunosorbent assay (ELISA) technique not affected by any ponatinib metabolites. Read More

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http://dx.doi.org/10.1016/j.ab.2019.02.010DOI Listing
February 2019
2 Reads

Reduced levels of modified nucleosides in the urine of autistic children. Preliminary studies.

Anal Biochem 2019 Feb 13. Epub 2019 Feb 13.

Department of Chemistry, Institute of General and Ecological Chemistry, Lodz University of Technology, Lodz, Poland. Electronic address:

The aim of this study was to investigate and compare the levels of concentration of modified nucleosides in the urine of autistic and healthy children. The compounds have never been analyzed before. The levels of nucleosides in the urine of both groups were determined by validated high performance liquid chromatography coupled to mass spectrometry (LC-MS/MS) method using multiple reaction monitoring (MRM) mode. Read More

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http://dx.doi.org/10.1016/j.ab.2019.02.009DOI Listing
February 2019
1 Read

Ultrasound-enhanced scintillation proximity assay for rapid diagnostics.

Anal Biochem 2019 Feb 13;570:51-55. Epub 2019 Feb 13.

Radioisotope Research Division, Korea Atomic Energy Research Institute (KAERI), Daejeon, 305-353, Republic of Korea.

Scintillation proximity assay (SPA) is a type of radioimmunoassay (RIA). We apply ultrasound enhancement to the general SPA. All assay procedures, including the antibody coating and radiolabeled antigen binding are achieved by simply mixing then standing for 5 min in an ultrasound chamber. Read More

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http://dx.doi.org/10.1016/j.ab.2019.02.011DOI Listing
February 2019

Methodological aspects of Universal immuno-PCR on standard tubes.

Anal Biochem 2019 Feb 12;570:56-61. Epub 2019 Feb 12.

Instituto de Salud y Ambiente Del Litoral ISAL, CONICET-UNL, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional Del Litoral, Ciudad Universitaria, Ruta Nacional N°168, km 472, CPA S3000ZAA, Santa Fe, Argentina. Electronic address:

One of the most used formats in inmuno-polymerase chain reaction (IPCR) is known as "Universal" IPCR (signal-generating complexes is based on conjugates of biotinylated DNA, biotinylated IgG and avidin). In the present study, we evaluated the utility of using mono- and bi-biotinylated DNA probes, pre-self-assembled DNA-neutravidin complex, blocking step and glutaraldehyde pretreatment of standard PCR tubes to improve the analytical performance of the hTSH-IPCR assay. The use of pre-self-assembled mono-biotinylated DNA-neutravidin complex enhances both the sensitivity and the reproducibility of the hTSH-IPCR assay, even without blocking step: hTSH-IPCR assay showed an improved limit of detection (LOD: 0. Read More

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http://dx.doi.org/10.1016/j.ab.2019.02.007DOI Listing
February 2019

Development and characterization of novel 2'-F-RNA aptamers specific to human total and glycated hemoglobins.

Anal Biochem 2019 Feb 8;570:43-50. Epub 2019 Feb 8.

Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.

Aptamers are short DNA and RNA fragments which bind their molecular targets with affinity and specificity comparable to those of antibodies. Here, we describe the selection of novel 2'-F-RNA aptamers against total human hemoglobin or its glycated form HbA1c. After SELEX and high-throughput sequencing of the enriched libraries, affinities and specificities of candidate aptamers and their truncated variants were examined by the solid-phase bioluminescent assay. Read More

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http://dx.doi.org/10.1016/j.ab.2019.02.004DOI Listing
February 2019
1 Read

Detection of phenol contamination in RNA samples and its impact on qRT-PCR results.

Anal Biochem 2019 Feb 8. Epub 2019 Feb 8.

Institute for Synthetic Microbiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, 40225, Germany.

Residual phenol, carried over from RNA purification, can alter RNA concentration measurements and is assumed to inhibit PCR. Here, we demonstrate that Impurities A260 values of spectral content profiling (SCP) UV/Vis measurements correlated with phenol concentration, whereas absorbance ratios of classical UV/Vis systems failed to reliably detect phenol in RNA samples. Phenol contamination led to over- or underestimation of RNA concentration on UV/Vis systems, whereas it had no influence on fluorometry quantification. Read More

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http://dx.doi.org/10.1016/j.ab.2019.02.002DOI Listing
February 2019

Pyruvate kinase from Geobacillus stearothermophilus displays an unusual preference for Mn in a cycling reaction.

Anal Biochem 2019 Feb 7;570:27-31. Epub 2019 Feb 7.

R&D Group, Diagnostics Dept., Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni-shi, Shizuoka, 410-2321, Japan.

Previously, we developed a kinase cycling method using creatine kinase and pyruvate kinase (RMPK) both from rabbit muscle in the presence of an excess amount of ATP and IDP for the quantitative determination of substrate. To our surprise, the RMPK cycling reaction was 10-fold more efficient using Mn rather than Mg. Here, we investigated PK from Geobacillus stearothermophilus (GSPK) as an alternative source of enzyme. Read More

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http://dx.doi.org/10.1016/j.ab.2019.02.005DOI Listing
February 2019

Single-site phosphorylation within the His-tag sequence attached to a recombinant protein.

Anal Biochem 2019 Feb 5. Epub 2019 Feb 5.

Institut Pasteur, Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, C3BI USR 3756, Paris, France.

We report the observation of single-site phosphorylation in a His-tag sequence N-terminally attached to a recombinant protein (UVI31+) in vitro. This modification was detected at position 23 at a serine residue of the His-tag sequence encoded by the vector pET28a. Furthermore, the phosphorylated tag sequence was found to be dephosphorylated by the action of alkaline phosphatases. Read More

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http://dx.doi.org/10.1016/j.ab.2019.02.001DOI Listing
February 2019

Rapid time-resolved luminescence based screening of bacteria in urine with luminescence modulating biosensing phages.

Anal Biochem 2019 Feb 5;570:21-26. Epub 2019 Feb 5.

Medicity Research Laboratories and Laboratory of Biophysics, Institute of Biomedicine, Faculty of Medicine, University of Turku, Finland.

Urinary tract infections (UTIs) are a common problem worldwide. The most prevalent causative pathogen of UTI is Escherichia coli, focus of this study. The current golden standard for detecting UTI is bacterial culture, creating a major workload for hospital laboratories - cost-effective and rapid mass screening of patient samples is needed. Read More

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http://dx.doi.org/10.1016/j.ab.2019.01.011DOI Listing
February 2019

Surface plasmon resonance and cytotoxicity assays of drug efficacies predicted computationally to inhibit p53/MDM2 interaction.

Anal Biochem 2019 Mar 2;569:53-58. Epub 2019 Feb 2.

Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles, CA, 90032, USA. Electronic address:

Docking on the p53-binding site of murine double minute 2 (MDM2) by small molecules restores p53's tumor-suppressor function. We previously assessed 3244 FDA-approved drugs via "computational conformer selection" for inhibiting MDM2 and p53 interaction. Here, we developed a surface plasmon resonance method to experimentally confirm the inhibitory effects of the known MDM2 inhibitor, nutlin-3a, and two drug candidates predicted by our computational method. Read More

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http://dx.doi.org/10.1016/j.ab.2019.01.012DOI Listing

Direct and highly sensitive measurement of fluorescent molecules in bulk solutions using flow cytometry.

Anal Biochem 2019 Jan 30;570:32-42. Epub 2019 Jan 30.

Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, D-21073, Hamburg, Germany.

Utilizing flow cytometry to monitor progress of bulk biochemical reactions and concentration of chemical species normally relies on the utilization of cells carrying intrinsic fluorescence or modified beads. We present a method for a simple measurement of the fluorescent marker molecule fluorescein and GFPuv in bulk solutions with high sensitivity using a CytoFLEX flow cytometer and without the need for modified beads. Polystyrene beads were used to trigger measurements based on their high scatter signal, to detect the fluorescence signal from two different fluorophores present in the sample solution. Read More

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http://dx.doi.org/10.1016/j.ab.2019.01.006DOI Listing
January 2019

A simple fluorescent assay for the discovery of protein-protein interaction inhibitors.

Anal Biochem 2019 Mar 30;569:46-52. Epub 2019 Jan 30.

University of Nebraska Medical Center, Department of Biochemistry and Molecular Biology, 985870 Nebraska Medical Center, Omaha, NE, 68198-5870, USA; University of Nebraska Medical Center, The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, 986805 Nebraska Medical Center, Omaha, NE, 68198-6805, USA. Electronic address:

Due to the therapeutic potential of targeting protein-protein interactions (PPIs) there is a need for easily executed assays to perform high throughput screening (HTS) of inhibitors. We have developed and optimized an innovative and robust fluorescence-based assay for detecting PPI inhibitors, called FluorIA (Fluorescence-based protein-protein Interaction Assay). Targeting the PPI of RAD52 with replication protein A (RPA) was used as an example, and the FluorIA protocol design, optimization and successful application to HTS of large chemical libraries are described. Read More

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http://dx.doi.org/10.1016/j.ab.2019.01.010DOI Listing

Effects of incubation temperature and acetonitrile amount on microwave-assisted tryptic digestion of proteins.

Anal Biochem 2019 Mar 29;569:31-38. Epub 2019 Jan 29.

Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea. Electronic address:

The effects of incubation temperature and acetonitrile (ACN) amount on microwave-assisted tryptic digestion of horse skeletal muscle myoglobin (MYG) and bovine serum albumin (BSA) were investigated. Microwave-assisted tryptic digestion was performed on BSA or MYG solutions containing different amounts (0, 10, and 20%) of ACN for different times (10, 20, 30, 40, and 50 min) at different temperatures (25, 37, and 55 °C). Conventional overnight tryptic digestion was also conducted with gentle mixing at 37 °C for 16 h. Read More

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http://dx.doi.org/10.1016/j.ab.2019.01.009DOI Listing

Polydopamine-functionalized magnetic iron oxide for the determination of trace levels of lead in bovine milk.

Anal Biochem 2019 Jan 25;570:5-12. Epub 2019 Jan 25.

Faculty of Chemistry, K.N. Toosi University of Technology, Tehran, Iran. Electronic address:

In this work, a novel sorbent based on polydopamine-functionalized magnetic ferric oxide (FeO) was synthesized and applied for dispersive solid phase extraction of Pb(II) in bovine milk samples. The extracts were analyzed by flame atomic absorption spectrometry (FAAS). The sorbent was characterized with different analytical techniques (XRD, FT-IR, SEM, TEM, VSM and EDX). Read More

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http://dx.doi.org/10.1016/j.ab.2019.01.008DOI Listing
January 2019

An easily-performed high-throughput method for plant genomic DNA extraction.

Anal Biochem 2019 Mar 25;569:28-30. Epub 2019 Jan 25.

Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, 466001, China; Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou, 466001, China; Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, 453003, China. Electronic address:

Genomic DNA isolation is a crucial technique for researchers studying plant molecular biology. A current widely-used protocol for DNA extraction needs a pestle and mortal for each sample and consumes a large amount of liquid nitrogen in grinding the samples. Most high-throughput methods depend on expensive machines for tissue homogenization. Read More

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http://dx.doi.org/10.1016/j.ab.2019.01.007DOI Listing
March 2019
1 Read

EPAI-NC: Enhanced prediction of adenosine to inosine RNA editing sites using nucleotide compositions.

Anal Biochem 2019 Mar 18;569:16-21. Epub 2019 Jan 18.

Department of Computer Science and Engineering, United International University, Plot 2, United City, Madani Avenue, Satarkul, Badda, Dhaka, 1212, Bangladesh. Electronic address:

RNA editing process like Adenosine to Intosine (A-to-I) often influences basic functions like splicing stability and most importantly the translation. Thus knowledge about editing sites is of great importance in molecular biology. With the growth of known editing sites, machine learning or data centric approaches are now being applied to solve this problem of prediction of RNA editing sites. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00032697183112
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http://dx.doi.org/10.1016/j.ab.2019.01.002DOI Listing
March 2019
4 Reads

Acetonitrile-assisted enzymatic digestion can facilitate the bottom-up identification of proteins of cancer origin.

Anal Biochem 2019 Jan 17;570:1-4. Epub 2019 Jan 17.

Institute of Analytical Chemistry of the Czech Academy of Sciences, Veveří 97, 602 00, Brno, Czech Republic. Electronic address:

The main objective of this study was to develop an effective in-gel trypsin digestion protocol using aqueous-acetonitrile solvent system to facilitate MS analysis and maximize the number of identified proteins from biological samples. The procedure, where 80% acetonitrile was present in the trypsin reaction mixture, increased the number of matched peptides, and allowed the identification of more proteins with higher coverage than the common digestion protocol. Vimentin, annexins, tubulin, actin, peptidyl-prolyl cis-trans isomerase or alpha-enolase are examples of important proteins that change during the progress cancer. Read More

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http://dx.doi.org/10.1016/j.ab.2019.01.004DOI Listing
January 2019
1 Read

A fluorescence-based activity assay for immobilized lipases in non-native media.

Anal Biochem 2019 Mar 17;569:22-27. Epub 2019 Jan 17.

Niederrhein University of Applied Sciences, Department of Chemistry, Adlerstr. 32, 47798, Krefeld, Germany. Electronic address:

A new method for the analysis of lipase activity in the immobilized state is developed. The fluorescence assay aims to quantify the potential of lipases for the application in organic solvents. As lipases are universally immobilized on polymeric carriers for the use in bioorganic synthesis, the assay includes an immobilization step on the walls of polymeric cuvettes. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00032697183110
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http://dx.doi.org/10.1016/j.ab.2019.01.005DOI Listing
March 2019
4 Reads

High-throughput Carbonyl Content Method of Therapeutic mAb using size-exclusion chromatography with ultraviolet and fluorescence detection.

Authors:
Yunyu Yi Li Zang

Anal Biochem 2019 Jan 14. Epub 2019 Jan 14.

Analytical Development, Biogen, Cambridge, MA, 02142, USA. Electronic address:

Monoclonal antibody (mAb), one of the major types of therapeutic proteins in the pharmaceutical industry, is predominantly manufactured using mammalian cell culture [1]. Oxidative stress, potentially present during cell culture process, may increase the protein carbonyl content in the mAb product, which was reported to positively correlate with aggregate burst rate during storage [2]. In order to monitor carbonyl content during mAb process development, we developed a high-throughput screening method for therapeutic mAbs using size-exclusion chromatography followed by ultraviolet and fluorescence detection (SEC-UV/FL), optimized from a fluorescein thiosemicarbazide (FTC) semi-microplate method. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.025DOI Listing
January 2019
1 Read

Enhanced protoplast assay by transfecting PCR-assembled gene expression cassettes with telomeric repeats and thiophosphate modifications.

Anal Biochem 2019 Mar 12;569:39-45. Epub 2019 Jan 12.

State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. Electronic address:

Transient expression assays are invaluable complements to the stable transgenic assay for studying gene functions by providing desirable time and labor efficiencies and high-throughput potential or circumventing technical difficulties of stable transgenic expression. The protoplast transient expression system is one of the mainstream transient expression assays used in plant research. Here, we developed a PCR amplicon-mediated protoplast transient (PROMPT) assay by using overlapping PCR assembled gene expression cassettes for Arabidopsis protoplast transfection without the need for time- and labor-consuming plasmid construction. Read More

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http://dx.doi.org/10.1016/j.ab.2019.01.003DOI Listing
March 2019
1 Read

The study of the constituents and source of toxicants in poisonous honey.

Anal Biochem 2019 Mar 9;569:10-15. Epub 2019 Jan 9.

Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Guangdong Provincial Public Laboratory of Analysis and Testing Technology, Guangdong Institute of Analysis, Guangzhou, 510070, Guangdong, China.

A novel method for non-target screening of toxicants in poisonous honey was established in this study. Poisonous honey and nontoxic honey were contrastive detected using liquid chromatography quadrupole-time-of-flight mass spectrometry and analyzed by Mass Profiler Professional Software. 4 poisonous alkaloids were screened out and confirmed by comparison with reference compounds. Read More

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http://dx.doi.org/10.1016/j.ab.2019.01.001DOI Listing
March 2019
1 Read

Simple protocol for sequence-specific detection of mixed-base nucleic acids using a smart probe with NABs.

Anal Biochem 2019 Mar 2;568:53-56. Epub 2019 Jan 2.

Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Saudi Arabia.

A fluorescent smart probe (SP) was used to detect a mixed-base ribonucleic acids sequence. While the SP presents excellent sensitivity for the target, it gives subtle discrimination between the perfect target sequence and several mismatch sequences. Its sequence-specificity for the target was greatly enhanced by using nucleic acid blockers (NABs), which are unlabeled, non-fluorescent hairpin oligonucleotides that are perfectly complementary to those mismatch sequences. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.024DOI Listing
March 2019
1 Read

Linking (Pyr)apelin-13 pharmacokinetics to efficacy: Stabilization and measurement of a high clearance peptide in rodents.

Anal Biochem 2019 Mar 31;568:41-50. Epub 2018 Dec 31.

Drug Discovery, Bristol-Myers Squibb Company, Princeton, NJ, 08543-5400, USA.

Apelin, the endogenous ligand for the APJ receptor, has generated interest due to its beneficial effects on the cardiovascular system. Synthesized as a 77 amino acid preproprotein, apelin is post-translationally cleaved to a series of shorter peptides. Though (Pyr)apelin-13 represents the major circulating form in plasma, it is highly susceptible to proteolytic degradation and has an extremely short half-life, making it challenging to quantify. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.022DOI Listing
March 2019
4 Reads

Simultaneous isotope dilution quantification and metabolic tracing of deoxyribonucleotides by liquid chromatography high resolution mass spectrometry.

Anal Biochem 2019 Mar 31;568:65-72. Epub 2018 Dec 31.

AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104, USA. Electronic address:

Quantification of cellular deoxyribonucleoside mono- (dNMP), di- (dNDP), triphosphates (dNTPs) and related nucleoside metabolites are difficult due to their physiochemical properties and widely varying abundance. Involvement of dNTP metabolism in cellular processes including senescence and pathophysiological processes including cancer and viral infection make dNTP metabolism an important bioanalytical target. We modified a previously developed ion pairing reversed phase chromatography-mass spectrometry method for the simultaneous quantification and C isotope tracing of dNTP metabolites. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.023DOI Listing
March 2019
2 Reads

Synthetic phosphopeptides: From spike-in standards to affinity tools for protein-protein interaction studies.

Anal Biochem 2019 Mar 28;568:73-77. Epub 2018 Dec 28.

Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany. Electronic address:

Synthetic isotope labeled phosphopeptides are valuable tools for the quantification and validation of phosphoproteome data. Here, we report that the same set of phosphopeptides, which are used as spike-in standards, can be successfully applied for identification of stimulus specific protein-protein interactions mediated by the respective phosphorylation sites. As a proof-of-concept, binding of two γH2AX (pS139) phosphosite specific interaction partners, MDC1 and 53BP1, was confirmed and elevated binding affinity was revealed in response to ionizing radiation. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.018DOI Listing
March 2019
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Enzymatic glutaredoxin-dependent method to determine glutathione and protein S-glutathionylation using fluorescent eosin-glutathione.

Anal Biochem 2019 Mar 28;568:24-30. Epub 2018 Dec 28.

Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177, Stockholm, Sweden. Electronic address:

Glutathione is an abundant low-molecular-weight thiol, up to 10 mM in mammalian cells, and exists in three major forms: reduced sulphydryl (GSH), glutathione disulfide (GSSG) or bound to Cys residues in proteins (PSSG). The ratio GSH/GSSG has been used as an indicator of the cells redox level but this parameter can also be estimated by the quantification of PSSG. In fact, PSSGs have the advantage of being more stable than GSSG. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.021DOI Listing
March 2019
2 Reads

A comparison of methods for effective differentiation of the frozen-thawed 3T3-L1 cells.

Anal Biochem 2019 Mar 27;568:57-64. Epub 2018 Dec 27.

Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China. Electronic address:

The differentiation efficiency of 3T3-L1 preadipocytes is an essential factor affecting studies on cellular mechanisms associated with obesity, diabetes, and related disorders. Differentiation of 3T3-L1 cells is commonly induced by an adipogenic cocktail containing insulin, dexamethasone (DEX), and 3-isobutyl-1-methylxanthine (IBMX). However, 3T3-L1 cells after freezing and thawing for many times always have a low differentiation efficiency. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00032697183097
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http://dx.doi.org/10.1016/j.ab.2018.12.020DOI Listing
March 2019
2 Reads

Pipeline for the generation of gene knockout mice using dual sgRNA CRISPR/Cas9-mediated gene editing.

Anal Biochem 2019 Mar 26;568:31-40. Epub 2018 Dec 26.

University of Nice Sophia Antipolis, UFR Sciences, Nice, France, Inserm UMR1091, CNRS UMR7277, Nice, France. Electronic address:

Animal models possess undeniable utility for progress on biomedical research projects and developmental and disease studies. Transgenic mouse models recreating specific disease phenotypes associated with β-hemoglobinopathies have been developed previously. However, traditional methods for gene targeting in mouse using embryonic stem cells (ESCs) are laborious and time consuming. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.002DOI Listing
March 2019
2 Reads

SPalmitoylC-PseAAC: A sequence-based model developed via Chou's 5-steps rule and general PseAAC for identifying S-palmitoylation sites in proteins.

Anal Biochem 2019 Mar 26;568:14-23. Epub 2018 Dec 26.

Gordon Life Science Institute, Boston, MA, 02478, USA.

S-Palmitoylation is a uniquely reversible and biologically important post-translational modification as it plays an essential role in a variety of cellular processes including signal transduction, protein-membrane interactions, neuronal development, lipid raft targeting, subcellular localization and apoptosis. Due to its association with the neuronal development, it plays a pivotal role in a variety of neurodegenerative diseases, mainly Alzheimer's, Schizophrenia and Huntington's disease. It is also essential for developmental life cycles and pathogenesis of Toxoplasma gondii and Plasmodium falciparum, known to cause toxoplasmosis and malaria, respectively. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.019DOI Listing
March 2019
2 Reads

Development of a novel l-histidine assay method using histamine dehydrogenase and a stable mutant of histidine decarboxylase.

Anal Biochem 2018 Dec 23;570:13-20. Epub 2018 Dec 23.

Institute for Innovation, Ajinomoto Co., Inc, Kawasaki, Kanagawa, 210-8681, Japan. Electronic address:

l-Histidine analysis is essential in physiological research and clinical applications because l-histidine concentrations in biofluids are associated with various diseases. However, an enzymatic method for l-histidine quantitation has not yet been established. Here, we describe a novel l-histidine quantitation assay using a combination of histidine decarboxylase (HDC) and histamine dehydrogenase (HDH) enzymes. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.017DOI Listing
December 2018
2 Reads

Gold nanoparticles of different shape for bicolor lateral flow test.

Anal Biochem 2019 Mar 22;568:7-13. Epub 2018 Dec 22.

A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospect 33, 119071, Moscow, Russia. Electronic address:

Spherical gold nanoparticles are the most commonly used marker in lateral flow assays. However, the widespread practice of using identical coloration for the test and control zones of test strips can lead to erroneous interpretations of the assay's results. We propose an immunochromatographic test strip with lines of different colors. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.015DOI Listing
March 2019
2 Reads

An LC/MS based method to quantify DNA adduct in tumor and organ tissues.

Anal Biochem 2019 Mar 21;568:1-6. Epub 2018 Dec 21.

Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International, Inc., 35 Landsdowne Street, Cambridge, MA, 02139, USA. Electronic address:

Highly potent DNA damaging agents have become a key class of toxins for antibody-drug conjugate (ADC) based targeted therapy. However, until recently, no quantitative bioanalytical method was available to measure the toxin in the form of DNA adducts. In this work, a novel microwave assisted organic solvent extraction and LC-MS/MS based bioanalytical method was developed to extract and quantify DNA-bound toxin IGN-P1 in tissue samples. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.014DOI Listing
March 2019
3 Reads

UPLC-MS/MS method for the quantification of ertugliflozin and sitagliptin in rat plasma.

Anal Biochem 2019 Feb 20;567:112-116. Epub 2018 Dec 20.

The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, PR China. Electronic address:

In the present study, an ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) approach was designed to concurrently measure the levels of ertugliflozin and sitagliptin in rat plasma with diazepam as the internal standard (IS). Acetonitrile-based protein precipitation was applied for sample preparation, then analytes (ertugliflozin and sitagliptin) were subjected to gradient elution chromatography with a mobile phase composed of acetonitrile (A) and 0.1% formic acid in water (B). Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00032697183109
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http://dx.doi.org/10.1016/j.ab.2018.12.016DOI Listing
February 2019
6 Reads

Glycosaminoglycans in human cerebrospinal fluid determined by LC-MS/MS MRM.

Anal Biochem 2019 Feb 18;567:82-84. Epub 2018 Dec 18.

Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. Electronic address:

Glycosaminoglycans (GAGs) were recovered from human cerebral spinal fluid (CSF) and after their conversion to disaccharides using polysaccharide lyases were analyzed by liquid chromatography tandem mass spectrometry using multiple reaction monitoring. CSF showed ng/mL levels of heparan sulfate, chondroitin sulfates and hyaluronan. The amounts and disaccharide composition of these GAGs differed from those found in human plasma. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6386465PMC
February 2019
1 Read

Fabrication of a low background signal glucose biosensor with 3D network materials as the electrocatalyst.

Anal Biochem 2019 Feb 17;567:63-71. Epub 2018 Dec 17.

Lab of Biochemical Sensing Technology, School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.

Glucose oxidase (GOx) based biosensor is an effective method to determine glucose level. However, the biosensors embedded with high electroactive species suffered from high background signal levels, which leading to relative low sensitivity for glucose sensing. In this work, a novel 3D network materials based glucose biosensor with low background signal was constructed, which demonstrated high sensitivity and selectivity towards glucose assay. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.012DOI Listing
February 2019
2 Reads

Evaluation of metabolite-microbe correlation detection methods.

Anal Biochem 2019 Feb 14;567:106-111. Epub 2018 Dec 14.

Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China. Electronic address:

Different correlation detection methods have been specifically designed for the microbiome data analysis considering the compositional data structure and different sequencing depths. Along with the speedy development of omics studies, there is an increasing interest in discovering the biological associations between microbes and host metabolites. This raises the need of finding proper statistical methods that facilitate the correlation analysis across different omics studies. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.008DOI Listing
February 2019
2 Reads

Proteoglycan-substrate gel zymography for the detection of chondroitin sulfate-degrading enzymes.

Anal Biochem 2019 Mar 14;568:51-52. Epub 2018 Dec 14.

Departments of Bioscience and Laboratory Medicine, Hirosaki University Graduate School of Health Sciences, 66-1 Hon-cho, Hirosaki, Aomori, 036-8564, Japan. Electronic address:

Chondroitin sulfate (CS), a linear polysaccharide, is a major component of the cartilage matrix. Although CS plays various roles in several biological and pathological processes, most details regarding its metabolism are still poorly understood. Some CS-degrading enzymes have been identified in mammals, but their expression patterns and localizations remain unclear. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.010DOI Listing
March 2019
2 Reads

Profiling of 54 plasma glycoproteins by label-free targeted LC-MS/MS.

Anal Biochem 2019 Feb 13;567:72-81. Epub 2018 Dec 13.

Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK. Electronic address:

Glycoproteins play a central role in diverse biological processes and are linked with many serious human diseases. In this paper we present a simple, reproducible and cost-effective analytical workflow that enables the reliable quantification of clinically relevant human plasma glycoproteins using label free microflow LC-MS/MS analysis. Plasma N-glycoproteins were selectively extracted via ConA Sepharose lectin affinity chromatography then separated into two fractions using reversed-phase solid phase extraction. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00032697183103
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http://dx.doi.org/10.1016/j.ab.2018.12.011DOI Listing
February 2019
10 Reads

A novel catalase mimicking nanocomposite of Mn(II)-poly-L-histidine-carboxylated multi walled carbon nanotubes and the application to hydrogen peroxide sensing.

Anal Biochem 2019 Feb 11;567:51-62. Epub 2018 Dec 11.

The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Science, Nankai University, Weijin Road No.94, Tianjin, 300071, China. Electronic address:

In this work, a novel enzyme-mimicking nanocomposite of Mn(II)-poly-L-histidine (PLH) functionalized carboxylated multi walled carbon nanotubes (CMWCNTs) was designed and synthesized. Based on the catalase-like activity of the nanocomposite, a non-enzymatic hydrogen peroxide (HO) biosensor was then established and explored for HO electrochemical detection. The nanocomposite was characterized by Fourier transform infrared spectra, Raman spectroscopy, and transmission electron microscopy. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00032697183076
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http://dx.doi.org/10.1016/j.ab.2018.12.007DOI Listing
February 2019
13 Reads
2.219 Impact Factor

Random subspace-based ensemble modeling for near-infrared spectral diagnosis of colorectal cancer.

Anal Biochem 2019 Feb 11;567:38-44. Epub 2018 Dec 11.

Key Lab of Process Analysis and Control of Sichuan Universities, Yibin University, Yibin, Sichuan, 644000, China. Electronic address:

The feasibility of using near-infrared (NIR) spectroscopy coupled with classifier ensemble for improving the diagnosis of colorectal cancer was explored. A total of 157 NIR spectra from the patients were recorded and partitioned into the training set and the test set. Four algorithms, i. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.009DOI Listing
February 2019
1 Read

Profiling of carboxyl-containing metabolites in smokers and non-smokers by stable isotope labeling combined with LC-MS/MS.

Anal Biochem 2019 Mar 10;569:1-9. Epub 2018 Dec 10.

China National Tobacco Quality Supervision and Test Center, Zhengzhou, 450001, China. Electronic address:

Profiling of carboxyl-containing metabolites in smokers and non-smokers provides insight into the smoking-related biological events and causal relationships between exposure and adverse events. However, more comprehensive analysis of carboxyl-containing metabolites in bio-matrices with high sensitivity and accuracy is challenging. In this work, stable isotope labeling in combination with liquid chromatography-tandem mass spectrometry was used for untargeted profiling and relative quantification of carboxyl-containing metabolites in plasma of smokers and non-smokers. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.006DOI Listing
March 2019
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Development of high throughput screening methods for inhibitors of ClpC1P1P2 from Mycobacteria tuberculosis.

Anal Biochem 2019 Feb 10;567:30-37. Epub 2018 Dec 10.

Department Cell Biology, Harvard Medical School, USA.

Tuberculosis affects about 100 million people worldwide and causes nearly 2 million deaths annually. It has been estimated that one third of all humans is infected with latent Mycobacterium tuberculosis (Mtb). Moreover, Mtb has become increasingly resistant to available antibiotics. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.004DOI Listing
February 2019
2 Reads

Corticosterone determination in bronchoalveolar lavage fluid and its relationship to free and total plasma corticosterone.

Anal Biochem 2019 Feb 5;567:27-29. Epub 2018 Dec 5.

Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada. Electronic address:

Endogenous glucocorticoids modulate airway and lung inflammation in various respiratory diseases and after exposure to airborne contaminants. Although bronchoalveolar lavage fluid (BALF) is commonly used to evaluate the inflammatory and immune response in the lungs, limited information is available on determination of endogenous glucocorticoid levels in BALF. Here we describe a simple method to determine corticosterone in BALF, and evaluate the relationship between BALF and plasma corticosterone. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.005DOI Listing
February 2019
1 Read

Direct detection of cysteine peptidases for MALDI-TOF MS analysis using fluorogenic substrates.

Anal Biochem 2019 Feb 5;567:45-50. Epub 2018 Dec 5.

Department of Chemistry, Moscow State University, Moscow, 119991, Russia.

A method is described for the direct detection of unstable cysteine peptidase activity in polyacrylamide gels after native electrophoresis using new selective fluorogenic peptide substrates, pyroglutamyl-phenylalanyl-alanyl-4-amino-7-methylcoumaride (Glp-Phe-Ala-AMC) and pyroglutamyl-phenylalanyl-alanyl-4-amino-7-trifluoromethyl-coumaride (Glp-Phe-Ala-AFC). The detection limit of the model enzyme papain was 17 pmol (0.29 μg) for Glp-Phe-Ala-AMC and 43 pmol (0. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.001DOI Listing
February 2019
3 Reads

Solid phase synthesis and spectroscopic characterization of the active and inactive forms of bacteriophage S pinholin protein.

Anal Biochem 2019 Feb 4;567:14-20. Epub 2018 Dec 4.

Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA. Electronic address:

The mechanism for the lysis pathway of double-stranded DNA bacteriophages involves a small hole-forming class of membrane proteins, the holins. This study focuses on a poorly characterized class of holins, the pinholin, of which the S protein of phage ϕ21 is the prototype. Here we report the first in vitro synthesis of the wildtype form of the S pinholin, S68, and negative-dominant mutant form, SIRS, both prepared using solid phase peptide synthesis and studied using biophysical techniques. Read More

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http://dx.doi.org/10.1016/j.ab.2018.12.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6328262PMC
February 2019
1 Read

Calibration and characterization of intracellular Asante Potassium Green probes, APG-2 and APG-4.

Anal Biochem 2019 Feb 30;567:8-13. Epub 2018 Nov 30.

Department of Biological Sciences, Kent State University, Kent, OH, USA. Electronic address:

The response of fluorescent ion probes to ions is affected by intracellular environment. To properly calibrate them, intracellular and extracellular concentrations of the measured ion must be made equal. In the first, computational, part of this work, we show, using the example of potassium, that the two requirements for ion equilibration are complete dissipation of membrane potential and high membrane permeability for both potassium and sodium. Read More

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http://dx.doi.org/10.1016/j.ab.2018.11.024DOI Listing
February 2019
2 Reads

Characterization and quantification of succinimide using peptide mapping under low-pH conditions and hydrophobic interaction chromatography.

Anal Biochem 2019 Feb 29;566:151-159. Epub 2018 Nov 29.

Department of Analytical Sciences, MedImmune, Gaithersburg, MD, USA. Electronic address:

Characterization of asparagine deamidation and aspartic acid isomerization is an important aspect of biotherapeutic protein analysis due to the potential negative effect of these modifications on drug efficacy and stability. Succinimide has long been known to be an intermediate product of asparagine deamidation and aspartic acid isomerization, but despite the key role of succinimide in these reactions, its analysis remains challenging due to its instability. We have developed a paradigm in which two interlinked analytical methods are used to develop an optimized approach to analyze succinimide. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00032697183105
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http://dx.doi.org/10.1016/j.ab.2018.11.021DOI Listing
February 2019
5 Reads