27,206 results match your criteria Analytical biochemistry[Journal]


Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus.

Anal Biochem 2020 May 30:113781. Epub 2020 May 30.

Department of Biology, Texas Tech University, Lubbock, TX, USA. Electronic address:

MicroRNAs (miRNAs) are 18-24 nucleotide regulatory RNAs. They are involved in the regulation of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Data suggests a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to birds, the closest extant relatives of crocodilians. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113781DOI Listing

Development and Optimization of a Cascade of Screening Assays for Inhibitors of TRF2.

Anal Biochem 2020 May 30:113796. Epub 2020 May 30.

Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, P. R. China. Electronic address:

TRF2 is a telomere associated protein which plays an important role in telomere maintenance. Knockdown of TRF2 can cause chromosomal end to end fusions and induce DNA damage responses. TRF2 exerts its functions partially by recruiting a number of accessory proteins through its TRF homology domain (TRFH), therefore identification of small molecular compounds which can bind to the TRFH domain of TRF2 and block the interactions of TRF2 with its associated proteins is important to elucidate the molecular mechanism of these protein-protein interactions. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113796DOI Listing

Accurate prediction of species-specific 2-hydroxyisobutyrylation sites based on machine learning frameworks.

Anal Biochem 2020 May 27:113793. Epub 2020 May 27.

College of Chemistry, Nanchang University, Nanchang 330031, China; Department of Materials and Chemical Engineering, Pingxiang University, Pingxiang 337055, China. Electronic address:

Lysine 2-hydroxyisobutyrylation (K) is a newly discovered post-translational modification (PTM) across eukaryotes and prokaryotes in recent years, which plays a significant role in diverse cellular functions. Accurate prediction of K sites is a first-crucial step to decipher its molecular mechanism and urgently needed. In this work, based on a large benchmark datasets in multi-species, a novel online species-specific prediction tool, namely KhibPred, was developed to identify K sites. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113793DOI Listing

Mitochondrial DNA methylation misleads global DNA methylation detected by antibody-based methods.

Anal Biochem 2020 May 27:113789. Epub 2020 May 27.

Department of Molecular Biology and Genetics, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey. Electronic address:

Cytosine methylation is the leading epigenetic modification on DNA playing a role in gene regulation. Methylation can occur in cytosines of any nucleic acids in cytosol (as mitochondrial DNA, mtDNA) and in nuclear DNA (ncDNA). mtDNA exists as multiple copies within numerous mitochondria. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113789DOI Listing

A Novel Fluorescent Probe with Extremely Low Background Fluorescence for Sensing Hypochlorite in Zebrafish.

Anal Biochem 2020 May 27:113795. Epub 2020 May 27.

School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013 P. R. China.

Development of an efficient fluorescent probe for sensing hypochlorite in water samples and biological samples is highly demanded. However, the currently reported fluorescent probes for hypochlorite frequently suffered from the problem of high background fluorescence. Herein, based on the combined effect of two different fluorescence quenching groups, we rationally developed a novel fluorescent probe for hypochlorite with extremely low background fluorescence. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113795DOI Listing

Enantioselective determination of econazole in rat plasma and its application to a pharmacokinetic study.

Anal Biochem 2020 May 28:113791. Epub 2020 May 28.

School of Pharmacy, Shenyang Pharmaceutical University, No. 103, Wenhua Road Shenhe District, 110016, Shenyang, Liaoning Province, P. R. China. Electronic address:

Econazole is a widely used chiral antifungal drug. In this paper, an enantioselective liquid chromatography-tandem mass spectrometry (LC-MS/MS) method has been developed and validated for determination of econazole enantiomers in rat plasma for the first time. After addition of the internal standard (IS) clotrimazole, plasma samples were extracted by liquid-liquid extraction with n-hexane:2-propanol (98. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113791DOI Listing

Background-free cell surface glycan analysis using persistent luminescence nanoparticle as an optical probe.

Anal Biochem 2020 May 26:113780. Epub 2020 May 26.

Institute for Clean Energy and Advanced Materials, School of Materials and Energy, Southwest University, Chongqing, 400715, PR China. Electronic address:

In this work, we report a novel cell surface glycan analysis method based on persistent luminescence nanoparticle (PLNP) ZnGaO: Cr (ZGC) as an optical probe. ZGC was first silanized by (3-Aminopropyl) triethoxysilane (APTES), followed by PEGylation with NHS-P EG-Biotin, which not only introduces biotin, but significantly improves the dispersibility and stability of the nanoparticles. Neutral-avidin was then coupled on ZGC surface through the specific biotin-avidin interaction, producing a ZGC-PEG-avidin nanoprobe. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113780DOI Listing

Study on Polyethylene Glycol Cross-linker in Peptide-conjugated Antibody on Efficiency of Cell Capture and Release.

Anal Biochem 2020 May 26:113790. Epub 2020 May 26.

Department of Bioengineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan. Electronic address:

Cell separation is important in cell therapy and disease diagnosis. Therefore, various cell separation methods have been studied, but cellular damage and the need for pretreatment remain substantial problems. Recently, in the diagnostic field, the detachment and recovery of antibody-captured cells was actively studied to obtain more detailed information on cancer cells. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113790DOI Listing

LPI-CNNCP: Prediction of lncRNA-protein interactions by using convolutional neural network with the copy-padding trick.

Anal Biochem 2020 May 23:113767. Epub 2020 May 23.

Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, 710072, China.

Long noncoding RNAs (lncRNAs) play critical roles in many pathological and biological processes, such as post-transcription, cell differentiation and gene regulation. Increasingly more studies have shown that lncRNAs function through mainly interactions with specific RNA binding proteins (RBPs). However, experimental identification of potential lncRNA-protein interactions is costly and time-consuming. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113767DOI Listing

An efficient method to quantitatively detect competitive adsorption of DNA on single-walled carbon nanotube surfaces.

Anal Biochem 2020 May 22;601:113776. Epub 2020 May 22.

Department of Physics, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo, 162-8601, Japan. Electronic address:

In this study, we quantitatively detected adsorption and desorption of DNA molecules that competed with sodium cholate (SC) molecules on single-walled carbon nanotubes (SWNTs) by fluorescence spectroscopy. In previous studies, competitive adsorption and/or replacement were studied based on techniques such as near-infrared (NIR) absorbance and photoluminescence (PL) spectroscopy of SWNTs. In those studies, adsorption of organic molecules was detected as spectral changes in SWNTs, but not in organic molecules. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113776DOI Listing

A Flow Cytometric Cell-cycle Assay Using Methyl Green.

Anal Biochem 2020 May 22:113782. Epub 2020 May 22.

Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.

Methyl green (MG), a conventional, low-cost histological stain, was used to design a flow cytometric cell-cycle/DNA-ploidy assay. On fluorometry, MG absorbed maximally at 633-nm, showed negligible fluorescence in free-state, but emitted brightly when bound to DNA. Optimal dye and cell concentrations for staining and effects of time and photobleaching on stained cells were determined for a lyse-permeabilize-stain protocol. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113782DOI Listing

Recombinant expression of ecto-nucleotide pyrophosphatase/phosphodiesterase 4 (NPP4) and development of a luminescence-based assay to identify inhibitors.

Anal Biochem 2020 May 20:113774. Epub 2020 May 20.

Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany; PharmaCenter Bonn, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany. Electronic address:

Nucleotide pyrophosphatase/phosphodiesterase 4 (NPP4) is a membrane-bound enzyme that hydrolyzes extracellular diadenosine polyphosphates such as diadenosine triphosphate (ApA) and diadenosine tetraphosphate (ApA) yielding mononucleotides. NPP4 on the surface of endothelial cells was reported to promote platelet aggregation by hydrolyzing ApA to ADP, which activates pro-thrombotic G protein-coupled P2Y and P2Y receptors. Thus, NPP4 inhibitors have potential as novel antithrombotic drugs. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113774DOI Listing

Micro-fabrication by Wax Spraying for Rapid Smartphone-Based Quantification of Bio-Markers.

Anal Biochem 2020 May 20:113777. Epub 2020 May 20.

Sensors and Integrated Biomicrofluidics/Mems Laboratory, School of Mechanical Engineering, Iran University of Science and Technology, 1684613114, Tehran, Iran; Sensors and Integrated Microsystems Laboratory, Mechanical and Mechatronics Engineering Department, University of Waterloo, ON, N2L 3G1, Waterloo, Canada. Electronic address:

A cheap/rapid technique for the fabrication of μPADs is presented for point of care analysis. Hydrophobic channels were formed across the width of the paper by spraying hot pure wax. This biocompatible novel process yielded uniform 300±5 μm hydrophilic microchannels on paper, without the use of the cleanroom, UV lamp, or organic solvents and was completed in a single step without the need for a hotplate. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113777DOI Listing

Subfamily-specific quantification of endogenous mouse L1 retrotransposons by droplet digital PCR.

Anal Biochem 2020 May 19:113779. Epub 2020 May 19.

Department of Pharmaceutical Sciences, South Dakota State University, Brookings, South Dakota, 57007, United States. Electronic address:

Long interspersed element type 1 (LINE-1; L1) mobilizes during early embryogenesis, neurogenesis, and germ cell development, accounting for 25% of disease-causing heritable insertions and 98% of somatic insertions in cancer. To better understand the regulation and impact of L1 mobilization in the genome, reliable methods for measuring L1 copy number variation (CNV) are needed. Here we present a comprehensive analysis of a droplet digital PCR (ddPCR) based method for quantifying endogenous mouse L1. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113779DOI Listing

GC-FID-based quantification of the sum of the three forms of vitamin B from animal liver.

Anal Biochem 2020 May 18;601:113778. Epub 2020 May 18.

Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Savoyenstraße 1, A-1160, Vienna, Austria. Electronic address:

Vitamin B (nicotinic acid, nicotinamide) is an essential water-soluble vitamin and cellular energy metabolism depends on the vitamin B-derived cofactors. Inaccessible covalently-linked nicotinic acid in food such as maize can cause vitamin B deficiency in animals since maize is also deficient in tryptophan, the precursor of nicotinic acid. A sensitive and reproducible GC-FID-based method for the quantification of the sum of the three forms of vitamin B from animal liver was developed. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113778DOI Listing

Differential expressions of L1-chimeric transcripts in normal and matched-cancer tissues.

Anal Biochem 2020 Jul 8;600:113769. Epub 2020 May 8.

Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea; NGS Clinical Laboratory, Dankook University Hospital, Cheonan, 31116, Republic of Korea; Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea. Electronic address:

L1s are a cis-regulatory elements and contain bidirectional internal promoters within the 5' untranslated region (UTR). L1s provide bidirectional promoters that generate alternative transcripts and affect differential expressions in the human genome. In particular, L1 antisense promoters (L1ASPs) could produce aberrant transcripts in cancer tissues compared to normal tissues. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113769DOI Listing

Benchtop holdup assay for quantitative affinity-based analysis of sequence determinants of protein-motif interactions.

Anal Biochem 2020 May 16:113772. Epub 2020 May 16.

(Équipe LLabellisée Ligue, 2015) Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS UMR 7104, Université; de Strasbourg, Illkirch, France. Electronic address:

Many protein-protein interactions are mediated by short linear peptide motifs binding to cognate proteins or protein domains. Such interactions often display affinities in the mid-micromolar range, that are challenging to quantify accurately, especially when the motifs harbor single-point mutations. Here, we present a manual benchtop assay for determining affinities of weak interactions between a purified protein and a peptide array representing mutants of a target motif. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113772DOI Listing

Feasibility of an automated coagulation factor XIIIa test using its isopeptidase activity.

Anal Biochem 2020 Jul 15;600:113757. Epub 2020 May 15.

Technoclone Herstellung von Diagnostika und Arzneimitteln GmbH, Brunner Str. 67, 1230, Vienna, Austria. Electronic address:

Plasma transglutaminase FXIII provides mechanical and biochemical stability to blood clots. Congenital or acquired deficiency may be associated with bleeding diathesis and requires therefore careful monitoring. The precise automated measurement of a large number of plasma samples can provide new insights regarding the clinical relevance of certain FXIII levels. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113757DOI Listing

Improvement of immunodetection of the transcription factor C/EBP homologous protein by western blot.

Anal Biochem 2020 May 13;601:113775. Epub 2020 May 13.

Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249, Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Plateforme CYROI, 2, Rue Maxime Rivière, 97490, Sainte-Clotilde, Ile de La Réunion, France. Electronic address:

Accumulation of misfolded proteins within the endoplasmic reticulum (ER) induces an unfolded protein response (UPR) that either restores homeostasis or triggers apoptosis in case of adaptation failure. The three activated branches of UPR lead to IRE1-, PERK- and ATF6- dependent transcriptional induction of the gene encoding the transcription factor C/EBP homologous protein (CHOP) which plays an important role in apoptosis induction. In conventional immunoblotting conditions, detection of CHOP is a difficult task. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113775DOI Listing

Reverse transcriptase kinetics for one-step RT-PCR.

Anal Biochem 2020 May 13;601:113768. Epub 2020 May 13.

Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, 84132, USA. Electronic address:

Understanding reverse transcriptase (RT) activity is critical for designing fast one-step RT-PCRs. We report a stopped-flow assay that monitors SYBR Green I fluorescence to investigate RT activity in PCR conditions. We studied the influence of PCR conditions on RT activity and assessed the accuracy of cDNA synthesis predictions for one-step RT-PCR. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113768DOI Listing

Resuspending Samples in Analytical Ultracentrifugation.

Anal Biochem 2020 May 11:113771. Epub 2020 May 11.

Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Bethesda, Maryland, 20892, U.S.A. Electronic address:

In analytical ultracentrifugation it is often very useful to resuspend samples in situ after sedimentation experiments for further investigation. This can be achieved by manually subjecting the entire sample cell assembly to gentle motion that causes the air bubble in the sample compartment to repeatedly move through the solution and thereby cause convection. Here we describe a cell mixing device that can accomplish the same through axial rotation and slow rocking motion. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113771DOI Listing

Impact of transposable elements on genome size variation between two closely related crustacean species.

Anal Biochem 2020 Jul 8;600:113770. Epub 2020 May 8.

Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France. Electronic address:

Identifying and quantifying genome size variation among species and understanding the underlying causes is a long-standing objective in evolutionary biology. Here, we investigated the basis of genome size variation between two closely related species of terrestrial isopods: Armadillidium vulgare and Armadillidium nasatum. The two species diverged 25 million years ago and the A. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113770DOI Listing

LC/MS/MS-based Quantitation of Pig and Human S100A1 Protein in Cardiac Tissues: Application to Gene Therapy.

Anal Biochem 2020 May 7:113766. Epub 2020 May 7.

Pharmaceutical Candidate Optimization. Electronic address:

The S100A1 protein is a target of interest for the treatment of heart failure as it has been previously reported to be depleted in failing cardiomyocytes. A gene therapy approach leading to increased expression levels of the protein directly in the heart could potentially lead to restoration of contractile function and improve overall cell survival. S100A1 is a relatively small soluble protein that is extremely well conserved across species with only a single amino acid difference between the sequences in human and pig, a commonly used pre-clinical model for evaluation of efficacy, biodistribution and safety for cardiac-directed gene therapy approaches. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113766DOI Listing

Synergetic performance of isothermal amplification techniques and lateral flow approach for nucleic acid diagnostics.

Anal Biochem 2020 Jul 5;600:113762. Epub 2020 May 5.

School of Food Science and Engineering, Foshan University, Foshan, 528231, China. Electronic address:

The advancement in developing sensitive, rapid, and specific sensing tools is crucial in diagnostics and biotechnological applications. Although various isothermal amplification approaches exist for the detection and identification of nucleic acids, post-amplicon analysis is still based on traditional methods such as gel electrophoresis, colorimetry, turbidity, which could be non-specific and inconvenient. Thus, this review will first elaborate various isothermal amplification techniques (principle, merits, and demerits) and their potentials when combined with lateral flow approach for point-of-care nucleic acid diagnostics. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113762DOI Listing

Atypical cells parameter in an automated urine analyzer: Does it have a future?

Authors:
Ozgur Aydin

Anal Biochem 2020 Jul 4;600:113763. Epub 2020 May 4.

Biochemistry Laboratory, Kepez Public Hospital, Antalya, Turkey. Electronic address:

Sysmex UN-Series automated urine analyzer has recently introduced "atypical cells" parameter. These cells are supposed to be epithelial cells with features of suspicion for a neoplastic proliferation. Atypical cells parameter in urinalysis should be considered to be as useful as the blast parameter in hematology. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113763DOI Listing

Multichannel bacterial discrimination based on recognition and disintegration disparity of short antimicrobial peptides.

Anal Biochem 2020 Jul 30;600:113764. Epub 2020 Apr 30.

Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; University of the Chinese Academy of Sciences, Beijing, 100039, China.

In this paper, we present a facile and rapid multichannel approach for the simultaneous detection and discrimination of multiple bacterial species. The proposed assay employed four short antimicrobial peptides (SAMPs) for recognition due to their disparity in antibacterial activity against different bacterial strains, and utilized fluorescence measurements to explicate the bacterial recognition and disintegration disparity of the SAMPs. Then, linear discriminant analysis (LDA) was used to effectively discriminate and classify the observed characteristic fluorescence patterns of SAMPs towards target bacteria, exhibiting excellent bacterial discrimination and classification accuracy. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113764DOI Listing

An immuno-dot blot assay for screening histidine kinase inhibitors.

Anal Biochem 2020 Jul 30;600:113765. Epub 2020 Apr 30.

Department of Functional Molecular Science, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.

Two-component signal transduction systems (TCSs), consisting of a histidine kinase (HK) and its cognate response regulator, are ubiquitous among bacteria and are associated with the virulence of pathogens. TCSs are potential targets for alternative antibiotics and antivirulence agents. It is, thus, very important to determine HK activity in bacterial TCSs. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113765DOI Listing

Selective chemiluminescent TURN-ON quantitative bioassay and imaging of intracellular hydrogen peroxide in human living cells.

Anal Biochem 2020 Jul 28;600:113760. Epub 2020 Apr 28.

Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum - University of Bologna, Via Selmi 2, 40126, Bologna, Italy; Interdepartmental Centre for Renewable Sources, Environment, Sea and Energy (CIRI FRAME), Alma Mater Studiorum - University of Bologna, Via Sant'Alberto 163, 48123, Ravenna, Italy; Biostructures and Biosystems National Institute (INBB), Viale Delle Medaglie D'Oro 305, 00136, Rome, Italy; Interdepartmental Centre of Industrial Agrifood Research (CIRI Agrifood), Alma Mater Studiorum - University of Bologna, Piazza Goidanich 60, 47521, Cesena, FC, Italy.

Hydrogen peroxide is an unavoidable by-product of cell metabolism, but when it is not properly managed by the body it can lead to several pathologies (e.g., premature aging, cardiovascular and neurodegenerative diseases, cancer). Read More

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http://dx.doi.org/10.1016/j.ab.2020.113760DOI Listing

Radical-based photoinactivation of fatty acid photodecarboxylases.

Anal Biochem 2020 Jul 26;600:113749. Epub 2020 Apr 26.

The Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom; EPSRC/BBSRC Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, United Kingdom. Electronic address:

Fatty acid photodecarboxylases (FAP) are a recently discovered family of FAD-containing, light-activated enzymes, which convert fatty acids to n-alkanes/alkenes with potential applications in the manufacture of fine and speciality chemicals and fuels. Poor catalytic stability of FAPs is however a major limitation. Here, we describe a methodology to purify catalytically stable and homogeneous samples of recombinant Chlorella variabilis NC64A FAP (CvFAP) from Escherichia coli. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113749DOI Listing

Overexpression and characterization of TnCel12B, a hyperthermophilic GH12 endo-1,4-β-glucanase cloned from Thermotoga naphthophila RKU-10.

Anal Biochem 2020 Jun 24;599:113741. Epub 2020 Apr 24.

Institute of Industrial Biotechnology, GC University, Lahore, 54000, Pakistan. Electronic address:

A putative cellulolytic gene (825 bp) from Thermotoga naphthophila RKU-10 was overexpressed as an active soluble endo-1,4-β-glucanase (TnCel12B), belongs to glycoside hydrolase family 12 (GH12), in a mesophilic expression host. Heterologous expression and engineered bacterial cell mass was improved through specific strategies (induction and cultivation). Hence, intracellular activity of TnCel12B was enhanced in ZYBM9 modified medium (pH 7. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113741DOI Listing

Identification of new biomarkers of pyridoxine-dependent epilepsy by GC/MS-based urine metabolomics.

Anal Biochem 2020 Apr 24:113739. Epub 2020 Apr 24.

Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, 10595, USA.

α-Aminoadipic semialdehyde and its cyclic form (Δ-piperideine-6-carboxylate) accumulate in patients with α-aminoadipic semialdehyde dehydrogenase (AASADH; antiquitin; ALDH7A1) deficiency. Δ-Piperideine-6-carboxylate reacts with pyridoxal 5'-phosphate (PLP) to form a Knoevenagel condensation product, resulting in pyridoxine-dependent epilepsy. Despite dramatic clinical improvement following pyridoxine supplementation, many patients still suffer some degree of intellectual disability due to delayed diagnosis. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113739DOI Listing

Characteristic fragment ions associated with dansyl cadaverine and biotin cadaverine adducts on glutamine.

Anal Biochem 2020 Jul 23;600:113718. Epub 2020 Apr 23.

University of Nebraska Medical Center, Omaha, NE, 68198, USA. Electronic address:

Glutamine residues susceptible to transglutaminase-catalyzed crosslinking can be identified by incorporation of dansyl cadaverine or biotin cadaverine. Bacterial transglutaminase and human transglutaminase 2 were used to modify residues in beta-casein with dansyl cadaverine. Bacterial transglutaminase was used to modify residues in human butyrylcholinesterase with biotin cadaverine. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113718DOI Listing

Inhibitors of blood coagulation factor XIIIa.

Anal Biochem 2020 Apr 23:113708. Epub 2020 Apr 23.

Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany. Electronic address:

The blood coagulation factor XIII (FXIII) plays an essential role in the stabilization of fibrin clots. This factor, belonging to the class of transglutaminases, catalyzes the final step of secondary hemostasis, i.e. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113708DOI Listing

Protein-peptide based assay for the characterization of human blood coagulation factor XIII-A isopeptidase activity.

Anal Biochem 2020 Jul 23;600:113699. Epub 2020 Apr 23.

Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, Hungary. Electronic address:

Blood coagulation factor XIII-A (FXIII-A), a member of the transglutaminase enzyme family, is best known for its fibrin clot stabilizing function during blood coagulation. It possesses amine incorporating and protein crosslinking transamidase activities, but it is also able to cleave the previously formed isopeptide bond by its isopeptidase activity. Our aim was to develop a protein-based assay for better characterization of FXIII-A isopeptidase activity. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113699DOI Listing

PolyTag: A peptide tag that affords scaffold-less covalent protein assembly catalyzed by microbial transglutaminase.

Anal Biochem 2020 Jul 23;600:113700. Epub 2020 Apr 23.

Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan; Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan. Electronic address:

Assembling proteins in close vicinity to each other provides an opportunity to gain unique function because collaborative and even synergistic functionalities can be expected in an assembled form. There have been a variety of strategies to synthesize functional protein assemblies but site-specific covalent assembly of monomeric protein units without impairing their intrinsic function remains challenging. Herein we report a powerful strategy to design protein assemblies by using microbial transglutaminase (MTG). Read More

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http://dx.doi.org/10.1016/j.ab.2020.113700DOI Listing

Synthesis and mass spectra of rearrangement bio-signature metabolites of anaerobic alkane degradation via fumarate addition.

Anal Biochem 2020 Jul 22;600:113746. Epub 2020 Apr 22.

State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China; Engineering Research Center of Microbial Enhanced Oil Recovery, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China. Electronic address:

Metabolite profiling in anaerobic alkane biodegradation plays an important role in revealing activation mechanisms. Apart from alkylsuccinates, which are considered to be the usual biomarkers via fumarate addition, the downstream metabolites of C-skeleton rearrangement can also be regarded as biomarkers. However, it is difficult to detect intermediate metabolites in both environmental samples and enrichment cultures, resulting in lacking direct evidence to prove the occurrence of fumarate addition pathway. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113746DOI Listing
July 2020
2.219 Impact Factor

Generation of mouse iPS cells using an inducible expression of transgenes via the cumate gene-switch.

Anal Biochem 2020 Jun 22;599:113748. Epub 2020 Apr 22.

Graduate School of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidoh-batanishi, Shimoshinjho Nakano, Akita 010-0195, Japan. Electronic address:

We applied an inducible gene expression system that utilizes the p-cmt operon, the cumate gene-switch, to generate mouse induced pluripotent stem (iPS) cells. Mouse embryonic fibroblast (MEF) E6E7-MEF cells were transfected with a single cumate gene-switch vector enabling concomitant expression of Oct4, Sox2, c-Myc, Klf4, and Gfp. Then, the cells were cultured with cumate, a monoterpene. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113748DOI Listing

iTTCA-Hybrid: Improved and robust identification of tumor T cell antigens by utilizing hybrid feature representation.

Anal Biochem 2020 Jun 22;599:113747. Epub 2020 Apr 22.

Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand. Electronic address:

In spite of the repertoire of existing cancer therapies, the ongoing recurrence and new cases of cancer poses a challenging health concern that prompts for novel and effective treatment. Cancer immunotherapy represents a promising venue for treatment by harnessing the body's immune system to combat cancer. Therefore, the identification of tumor T cell antigen represents an exciting area to explore. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113747DOI Listing

Refining our methodologies for assessing quadruplex DNA ligands; selectivity or an illusion of selectivity?

Anal Biochem 2020 Apr 20:113744. Epub 2020 Apr 20.

Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran. Electronic address:

Regulation of transcription and replication by the tetrad patterns of DNA has drawn the attention of many scientists. In this note, we discuss some disparaged parameters in the study of G-quadruplex structures (G4-tetrads). Besides, the implication of "destabilization as a side-effect" by these ligands on quadruplexes is explained. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113744DOI Listing

Quantitative analysis of protein in thermosensitive hydroxypropyl chitin for biomedical applications.

Anal Biochem 2020 Jun 20;599:113745. Epub 2020 Apr 20.

Key Laboratory of Biomedical Polymers of the Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, PR China. Electronic address:

Accurate determination of residual protein content in hydroxypropyl chitin (HPCH), a temperature-sensitive chitin derivative developed recently, is of great importance for biomedical applications. Coomassie brilliant blue (Bradford) method, Lowry method and Bicinchoninic acid (BCA) method were investigated to estimate the content of residual protein in HPCH. It was found that both Bradford and Lowry methods are not suitable for the protein assay in the HPCH sample. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113745DOI Listing

A new ELISA assay demonstrates sex differences in the concentration of serum polysialic acid.

Anal Biochem 2020 Jul 21;600:113743. Epub 2020 Apr 21.

Department of Chemistry, University of Toronto, Toronto, ON, M5S3H4, Canada; Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G2T2, Canada; Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G2T2, Canada; Women and Children's Health Research Institute, Edmonton, AB, T6G2T2, Canada. Electronic address:

Male and female immune systems are strikingly different and yet little is known about sex differences in immune glycans, though glycans play central roles in regulating the immune response. Polysialic acid (polySia) occurs on the majority of leukocytes and is a potent immunomodulatory glycan which enables cell migration and serves as an immune checkpoint. Due to widespread influence of polySia on the immune system, we aimed to characterize its levels in serum, its presence on specific proteins, and differences in the amounts of polySia in male and female serum. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113743DOI Listing

A standardized method for incorporation of drugs into food for use with Drosophila melanogaster.

Anal Biochem 2020 Jun 19;599:113740. Epub 2020 Apr 19.

Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, 99201, United States. Electronic address:

With any in vivo model, diet plays an important role, even in an organism as simple as the fruit fly - Drosophila melanogaster. Flies serve as good surrogates to study human diseases as approximately 77% of human disease genes are orthologous in the fly. Though breeding and caring for fruit flies is simple, the use of this organism in drug discovery is wide-ranging, especially in the administration of drugs to flies, via their food. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7255952PMC

Mathematical approaches in estimating aptamer-target binding affinity.

Anal Biochem 2020 Jul 18;600:113742. Epub 2020 Apr 18.

Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia; Department of Mechanical Engineering, Columbia University, New York, NY, 10027, United States. Electronic address:

The performance of aptamers as versatile tools in numerous analytical applications is critically dependent on their high target binding specificity and selectivity. However, only the technical or methodological aspects of measuring aptamer-target binding affinities are focused, ignoring the equally important mathematical components that play pivotal roles in affinity measurements. In this study, we aim to provide a comprehensive review regarding the utilization of different mathematical models and equations, along with a detailed description of the computational steps involved in mathematically deriving the binding affinity of aptamers against their specific target molecules. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113742DOI Listing

The preparation of endotoxin-free genetically engineered murine B1 antisense RNA.

Anal Biochem 2020 Jun 17;599:113737. Epub 2020 Apr 17.

Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, 050017, Hebei Province, China. Electronic address:

One of the major limitations in the production of genetically engineered RNA from Escherichia coli (E. coli) is contamination by endotoxin. Here we report the first method that is capable of removing endotoxin from genetically engineered RNA. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113737DOI Listing

A new tool for quantification of membrane protein partitioning between different cell membranes.

Anal Biochem 2020 Jun 16;599:113734. Epub 2020 Apr 16.

Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia. Electronic address:

The aqueous two-phase partition system (ATPS) is a method widely used to separate and purify plant and animal membranes carrying bound proteins. However, a common problem of this separation is a mutual contamination of obtained phases. Such contamination adversely affects the accuracy of values of the protein of interest partition between particular membranes when determined by direct measurement. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113734DOI Listing

Label-free horizontal EMSA for analysis of protein-RNA interactions.

Anal Biochem 2020 Jun 15;599:113736. Epub 2020 Apr 15.

Department of Chemistry, Hunter College of the City University of New York, 695 Park Ave, New York, NY, 10065, USA; Graduate Center of the City University of New York, 365 5th Ave, New York, NY, 10016, USA. Electronic address:

We describe a method to analyze the affinity and specificity of interactions between proteins and RNA using horizontal PAGE under non-denaturing conditions. The method permits tracking of migration of anionic and cationic biomolecules and complexes toward anode and cathode, respectively, therefore enabling quantification of bound and free biomolecules of different charges and affinity of their intermolecular interactions. The gel is stained with a fluorescent intercalating dye (SYBR®Gold or ethidium bromide) for visualization of nucleic acids followed by Coomassie® Brilliant Blue R-250 for visualizations of proteins; the dissociation constant is determined separately from the intensity of unshifted and shifted bands visualized by each dye. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113736DOI Listing

Development of an ELISA for detection of mitragynine and its metabolites in human urine.

Anal Biochem 2020 Jun 14;599:113733. Epub 2020 Apr 14.

Institute for Research in Molecular Medicine (INFORMM), Main Campus, Universiti Sains Malaysia, 11800, Penang, Malaysia.

An enzyme-linked immunosorbent assay for detection of mitragynine, other closely related Kratom alkaloids and metabolites was developed using polyclonal antibodies. Mitragynine was conjugated to a carrier protein, cationized-bovine serum albumin using Mannich reaction. The synthesized antigen was injected into rabbits to elicit specific polyclonal antibodies against mitragynine. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113733DOI Listing

Elevated homocarnosine and GABA in subject on isoniazid as assessed through 1H MRS at 7T.

Anal Biochem 2020 Jun 14;599:113738. Epub 2020 Apr 14.

Biomedical Engineering, Columbia University Fu Foundation School of Engineering and Applied Science, New York, NY, USA; Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT, USA; Department of Neurology, Yale University, New Haven, CT, USA; Department of Radiology, Columbia University College of Physicians and Surgeons, New York, NY, USA.

Typical magnetic resonance spectroscopy J-editing methods designed to quantify GABA suffer from contamination of both overlapping macromolecules and homocarnosine signal, introducing potential confounds. The aim of this study was to develop a novel method to assess accurately both the relative concentrations of homocarnosine as well as GABA free from overlapping creatine, homocarnosine and macromolecule signal. A novel method which utilized the combination of echo time STEAM and MEGA-sLASER magnetic resonance spectroscopy experiments at 7T were used to quantify the concentration of GABA and homocarnsoine independently, which are typically quantified in tandem. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113738DOI Listing

Development and validation of an LC-MS/MS method for the quantification of flavonoid glucuronides (wogonoside, baicalin, and apigenin-glucuronide) in the bile and blood samples: Application to a portal vein infusion study.

Anal Biochem 2020 Apr 13;601:113723. Epub 2020 Apr 13.

Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, 4849 Calhoun Road, Room 7047, 77204, USA. Electronic address:

Glucuronidation is one of the major metabolic pathways for flavonoids. However, quantification of flavonoid glucuronides in biological samples, especially in the bile, is sometimes challenging due to signal suppression by bile acids. The purpose of this study is to establish a robust LC-MS/MS method for directly measuring flavonoid glucuronides in bile and blood. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113723DOI Listing
April 2020
2.219 Impact Factor

Molecular orientation and specificity in the identification of biomolecules via surface enhanced Raman spectroscopy.

Anal Biochem 2020 Jun 13;599:113709. Epub 2020 Apr 13.

Department of Materials Science and Engineering, University of California, Los Angeles, CA, 90095, United States; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, 90095, United States. Electronic address:

The orientation dependence of the Raman spectral features of individual protein/biomolecules is studied using surface-enhanced Raman spectroscopy (SERS). Large variation in spectral features mainly in term of peak intensity is observed from small proteins/peptides. We aim to address the question of whether the spectral features of SERS are uniquely determined by the type of protein/molecules or are influenced prominently by factors more than the identity of the molecules such as orientation of molecules relative to the substrate surface. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113709DOI Listing