27,222 results match your criteria Analytical Biochemistry [Journal]


Development of fluorescence polarization-based competition assay for nicotinamide N-methyltransferase.

Anal Biochem 2020 Jul 2:113833. Epub 2020 Jul 2.

Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana, 47907, United States. Electronic address:

Methylation-mediated pathways play important roles in the progression of various diseases. Thus, targeting methyltransferases has proven to be a promising strategy for developing novel therapies. Nicotinamide N-methyltransferase (NNMT) is a major metabolic enzyme involved in epigenetic regulation through catalysis of methyl transfer from the cofactor S-adenosyl-L-methionine onto nicotinamide and other pyridines. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113833DOI Listing

Identification of ligand-binding residues using protein sequence profile alignment and query-specific support vector machine model.

Anal Biochem 2020 Jul 2:113799. Epub 2020 Jul 2.

College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China.

Information embedded in ligand-binding residues (LBRs) of proteins is important for understanding protein functions. How to accurately identify the potential ligand-binding residues is still a challenging problem, especially only protein sequence is given. In this paper, we establish a new query-specific computational method, named I-LBR, for the identification of LBRs without directly using the information of protein 3D structure. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113799DOI Listing

First study investigating the determination of protamine in seminal plasma from azoospermic donors: Suggestion of new methods to diagnose obstructive azoospermia, and to capture childbearing sperm for testicular sperm extraction (TESE) and insemination sperm injection (ICSI).

Anal Biochem 2020 Jul 2:113792. Epub 2020 Jul 2.

Department of Functional Bioanalysis, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose, Tokyo, 204-8588, Japan.

We analysed seminal plasma of 88 normozoospermic, 40 oligozoospermic and 32 azoospermic donors. During this study, we were the first to record the protamine concentration in the seminal plasma of azoospermic donors. The seminal protamine concentrations were found to be 19. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113792DOI Listing

Dye/Metal Ion-based chemosensing ensemble towards L-histidine and L-lysine determination in water via different optical responses.

Anal Biochem 2020 Jul 2:113811. Epub 2020 Jul 2.

Department of Chemistry, Payame Noor University, 19395-4697, Tehran, Islamic Republic of Iran. Electronic address:

In this study, a novel simple type of label-free, ultra-sensitive, and highly selective UV-Vis absorption and naked-eye detection of histidine (His) and lysine (Lys) using a dye/metal ion ensemble is developed. The outcoming high sensitivity and selectivity for histidine and lysine were attained by changing the metal ions. The indicator is released due to its displacement from the murexide (Mure)/Cu complex by histidine and the change in absorbance may be due to the further complexation of lysine with the additional coordination sites present in the zinc atom of Mure/Zn complex. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113811DOI Listing

Specificity-directed design of a FRET-quenched heptapeptide for assaying thermolysin-like proteases.

Anal Biochem 2020 Jul 2:113826. Epub 2020 Jul 2.

Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada. Electronic address:

Thermolysin (TL) is an industrially important zinc endopeptidase, and the prototype of the M4 family of metallopeptidases. The catalytic function of TL and its relatives is typically assessed using chromogenic or more sensitive fluorescent peptides, with the latter substrates relying on Förster resonance energy transfer (FRET). Here, we demonstrate that a FRET-quenched heptapeptide designed on the basis of the enzyme's substrate specificity (Dabcyl-FKFLGKE-EDANS) is efficiently cleaved by TL and dispase (a TL-like protease) in between the Phe3 and Leu4 residues. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113826DOI Listing

A Fluorescence Quenching-Recovery Sensor Based on RCA for the Specific Analysis of Fusobacterium nucleatum. nucleatum.

Anal Biochem 2020 Jul 2:113808. Epub 2020 Jul 2.

State Key Laboraotry of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, China. Electronic address:

Fusobacterium nucleatum. nucleatum (Fn.n) is associated with colorectal carcinoma. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113808DOI Listing

Ubiquitination of Disease-Causing CFTR Variants in a Microsome-Based Assay.

Anal Biochem 2020 Jul 1:113829. Epub 2020 Jul 1.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA. Electronic address:

Soluble secreted proteins and membrane proteins are subjected to protein quality control pathways during their synthesis in the endoplasmic reticulum (ER) and delivery to other destinations. Foremost among these quality control pathways is the selection of misfolded proteins for ER-associated degradation (ERAD). A growing number of diseases, including Cystic Fibrosis, are linked to the ERAD pathway. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113829DOI Listing

Rapid detection of the Streptococcus mutans cnm gene by loop-mediated isothermal amplification.

Anal Biochem 2020 Jun 24:113812. Epub 2020 Jun 24.

Center of Oral Clinical Examination, Hiroshima University Hospital, Hiroshima, Japan; Department of Periodontal Medicine, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan.

This study investigated a method using loop-mediated isothermal amplification (LAMP) for the rapid detection of cnm-positive Streptococcus mutans (S. mutans) associated with cerebral microhemorrhage. LAMP amplified the cnm gene plasmid vector, but not human or microbial genomic DNA. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315161PMC

Advantages of formate dehydrogenase reaction for efficient NAD quantification in biological samples.

Anal Biochem 2020 Jun 18;603:113797. Epub 2020 Jun 18.

Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234, Moscow, Russia; A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234, Moscow, Russia; Department of Biochemistry, Sechenov University, 119991, Moscow, Russia. Electronic address:

The medical significance of NAD-dependent metabolic regulation acquires increasing attention, demanding rapid and clinically feasible quantification of NAD in complex biological samples. Here we describe the usage of formate dehydrogenase for a straightforward and highly specific fluorometric assay of NAD in tissue extracts, not requiring chromatographic separation of nucleotides. The assay employs the irreversible reaction of formate oxidation coupled to NAD reduction, catalyzed by the enzyme which has high affinity and specificity to NAD, and is stable under a variety of conditions. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113797DOI Listing

Analysis and Uncertainty Quantification of DNA Fluorescence Melt Data: Applications of Affine Transformations.

Anal Biochem 2020 Jun 8:113773. Epub 2020 Jun 8.

National Institute of Standards and Technology.

Fluorescence-based measurements are a standard tool for characterizing the thermodynamic properties of DNA systems. Nonetheless, experimental melt data obtained from polymerase chain-reaction (PCR) machines (for example) often leads to signals that vary significantly between datasets. In many cases, this lack of reproducibility has led to difficulties in analyzing results and computing reasonable uncertainty estimates. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113773DOI Listing

Unified Dimensionless Transformation in Enzyme Kinetics: Application to Mathematical Analyses of Ten Biochemical Reaction Systems.

Authors:
Tsuneo

Anal Biochem 2020 Jun 8:113794. Epub 2020 Jun 8.

Graduate School of Biological and Agricultural Sciences, Nagoya University, Furoh-cho, Chikusa Ward, Nagoya, 464-8601, Japan. Electronic address:

A novel general principle was proposed to transform enzyme kinetic equations into unified dimensionless forms. The principle consists of six steps. The principle was applied to ten complex biochemical reaction systems and their characteristics were mathematically analyzed. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113794DOI Listing

Label-free liquid crystal-based biosensor for detection of dopamine using DNA aptamer as recognition probe.

Anal Biochem 2020 Jun 8:113807. Epub 2020 Jun 8.

Department of Chemistry, Gachon University, Seongnam-daero 1342, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea. Electronic address:

We present a label-free liquid crystal-based biosensor for the detection of dopamine (DA) in aqueous solutions using dopamine-binding aptamers (DBA) as recognition elements. In this system, the dimethyloctadecyl [3-(trimethoxysilyl) propyl] ammonium chloride (DMOAP) self-assembled monolayers immobilized on glass slides support the long alkyl chains that keep the liquid crystal (LC) molecules in a homeotropic orientation. Glutaraldehyde (GA) is used as a cross-linker to immobilize DBA onto the surface of glass slides. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113807DOI Listing

Determination of free fatty acids in plasma by gas chromatography.

Anal Biochem 2020 Jun 6;603:113810. Epub 2020 Jun 6.

Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Kyoto, 606-8522, Japan.

A method was developed for determination of free fatty acids (FFAs) in plasma by gas chromatography. Plasma was extracted with 3 vol of methanol. Most cholesterol esters and triacylglycerols did not dissolve in the aqueous methanol. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113810DOI Listing

The linker region of LINEs modulates DNA cleavage and DNA polymerization.

Anal Biochem 2020 Jun 6;603:113809. Epub 2020 Jun 6.

Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA. Electronic address:

Long interspersed elements (LINEs) replicate by target primed reverse transcription (TPRT). Insertion involves two half reactions. Each half reaction involves DNA cleavage followed by DNA synthesis. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113809DOI Listing

Colorimetric biosensing of nopaline synthase terminator using FeO@Au and hemin-functionalized reduced graphene oxide.

Anal Biochem 2020 Aug 4;602:113798. Epub 2020 Jun 4.

Technology Center of Hefei Customs, Hefei, 230032, China.

In this paper, we present a simple and label-free colorimetric biosensor for detection of the nopaline synthase (NOS) terminator in genetically modified (GM) plants. The "signal on" colorimetric biosensor was developed using a nanocomposite consisted of gold nanoparticles doped magnetic FeO nanoparticles (FeO@Au NP), capture probe DNA (cDNA), and hemin-functionalized reduced graphene oxide nanosheets (H-GN). The nanocomposite was successfully prepared by means of Au-S bonds and the strong π interactions between cDNA and H-GN. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113798DOI Listing

Mapping of polyglutamylation in tubulins using nanoLC-ESI-MS/MS.

Anal Biochem 2020 Jun 2:113761. Epub 2020 Jun 2.

New England Biolabs, Ipswich, MA, 01938, USA. Electronic address:

Tubulin polyglutamylation is a polymeric modification that extends from the carboxyl-terminus of tubulins. Molecular description of amino acids and their branching polyglutamyls is a hallmark of tubulin in microtubules. There are different chemical approaches for detecting these polymeric structures, mostly reported prior to development of nESI peptide analysis. Read More

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http://dx.doi.org/10.1016/j.ab.2020.113761DOI Listing

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

Anal Biochem 2020 Aug 30;602:113781. Epub 2020 May 30.

Department of Biological Sciences, 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
August 2020
2.219 Impact Factor

Development and optimization of a cascade of screening assays for inhibitors of TRF2.

Anal Biochem 2020 Aug 30;602:113796. 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, PR 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 Aug 28;602:113793. Epub 2020 May 28.

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 Jul 27;601:113789. 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 Aug 28;602:113795. Epub 2020 May 28.

School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013 PR 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 Aug 29;602:113791. Epub 2020 May 29.

School of Pharmacy, Shenyang Pharmaceutical University, No. 103, Wenhua Road Shenhe District, 110016, Shenyang, Liaoning Province, PR 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 Jul 26;601:113780. 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 Aug 26;602:113790. 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 Jul 23;601:113767. 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 Jul 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 Jul 22;601:113782. 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
July 2020
2.219 Impact Factor

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

Anal Biochem 2020 May 20;603:113774. 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;603:113777. 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 Jul 20;601:113779. Epub 2020 May 20.

Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 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 Jul 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 07 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 07 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 Jul 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 Jul 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;604:113771. 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, MD, 20892, USA. 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 07 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 Aug 8;602:113766. Epub 2020 May 8.

Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, NJ, United States. 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 07 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 07 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 07 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 07 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 07 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 07 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 06 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 07 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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7302536PMC

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 07 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