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Analytical Biochemistry

Lijing Xin, Ivan Tkáč
Localized proton magnetic resonance spectroscopy ((1)H-MRS) is a noninvasive tool for measuring in vivo neurochemical information in animal and human brains. With the increase of magnetic field strength, whereas localized (1)H-MRS benefits from higher sensitivity and spectral dispersion, it is challenged by increased spatial inhomogeneity of the B0 and B1 fields, larger chemical shift displacement error, and shortened T2 relaxation times of metabolites. Advanced localized (1)H-MRS methodologies developed for high magnetic fields have shown promising results and allow the measurement of neurochemical profiles with up to 19 brain metabolites, including less-abundant metabolites, such as glutathione, glycine, γ-aminobutyric acid and ascorbate...
October 20, 2016: Analytical Biochemistry
P Tenreiro, S Rebelo, F Martins, M Santos, E D Coelho, M Almeida, A P Alves de Matos, O A B da Cruz E Silva
Synaptosomes are isolated nerve terminals. They represent an extremely attractive in vitro model system to study synaptic physiology since they preserve morphological and functional characteristics of the synapse. As such they have been used to investigate synaptic dysfunctions associated with neuropathologies like Alzheimer's disease. In the present work two simple methodologies for isolating synaptosomal-enriched fractions were compared for the first time. The starting points of both protocols were rat cortical or hippocampal homogenized tissues that underwent several differential centrifugation steps followed by a final purification of synaptosomal-enriched fractions using either a Percoll gradient or a Sucrose gradient...
October 19, 2016: Analytical Biochemistry
M J Coolbaugh, M J Shakalli Tang, D W Wood
High throughput methods for recombinant protein production using E. coli typically involve the use of affinity tags for simple purification of the protein of interest. One drawback of these techniques is the occasional need for tag removal before study, which can be hard to predict. In this work, we demonstrate two high throughput purification methods for untagged protein targets based on simple and cost-effective self-cleaving intein tags. Two model proteins, E. coli beta-galactosidase (βGal) and superfolder green fluorescent protein (sfGFP), were purified using self-cleaving versions of the conventional chitin-binding domain (CBD) affinity tag and the nonchromatographic elastin-like-polypeptide (ELP) precipitation tag in a 96-well filter plate format...
October 19, 2016: Analytical Biochemistry
Harika Vemula, Yukiko Kitase, Navid J Ayon, Lynda Bonewald, William G Gutheil
Isomeric molecules present a challenge for analytical resolution and quantification, even with MS-based detection. The eight-aminobutyric acid (ABA) isomers are of interest for their various biological activities, particularly γ-aminobutyric acid (GABA) and the d- and l-isomers of β-aminoisobutyric acid (β-AIBA; BAIBA). This study aimed to investigate LC-MS/MS-based resolution of these ABA isomers as their Marfey's (Mar) reagent derivatives. HPLC was able to separate three Mar-ABA isomers l-β-ABA (l-BABA), and l- and d-α-ABA (AABA) completely, with three isomers (GABA, and d/l-BAIBA) in one chromatographic cluster, and two isomers (α-AIBA (AAIBA) and d-BABA) in a second cluster...
October 19, 2016: Analytical Biochemistry
Lin Cheng, BingGuo Wei, Ling Ling He, Ling Mao, Jie Zhang, JinXiang Ceng, DeRong Sun, ChaDan Chen, HanFeng Cui, Nian Hong, Hao Fan
A novel "off-On" electrogenerated chemiluminescence (ECL) biosensor has been developed for the detection of mercury(II) based on molecular recognition technology. The ECL mercury(II) biosensor comprises two main parts: an ECL substrate and an ECL intensity switch. The ECL substrate was made by modifying the complex of Ruthenium(II) tris-(bipyridine)(Ru(bpy)3(2+))/Cyclodextrins-Au nanoparticles(CD-AuNps)/Nafion on the surface of glass carbon electrode (GCE), and the ECL intensity switch is the single hairpin DNA probe designed according to the "molecular recognition" strategy which was functionalized with ferrocene tag at one end and attached to Cyclodextrins (CD) on modified GCE through supramolecular noncovalent interaction...
October 18, 2016: Analytical Biochemistry
Hiroshi Imamura, Shinya Honda
Calibration-free concentration analysis (CFCA) based on surface plasmon resonance uses the diffusion coefficient of an analyte to determine the concentration of that analyte in a bulk solution. In general, CFCA is avoided when investigating analytes prone to self-association, as the heterogeneous diffusion coefficient results in a loss of precision. The derivation for self-association of the analyte was presented here. By using the diffusion coefficient for the monomeric state, CFCA provides the lowest possible concentration even though the analyte is self-associated...
October 16, 2016: Analytical Biochemistry
Partha Pratim Bose, Prakash Kumar
In high-throughput biotechnology and structural biology, molecular cloning is an essential prerequisite for attaining high yields of recombinant protein. However, a rapid, cost-effective, easy clone screening protocol is still required to identify colonies with desired insert along with a cross check method to certify the expression of the desired protein as the end product. We report an easy, fast, sensitive and cheap visual clone screening and protein expression cross check protocol employing gold nanoparticle based plasmonic detection phenomenon...
October 15, 2016: Analytical Biochemistry
Zhihui Xu, Xueyan Shi, Huijun Jiang, Yiyan Song, Liying Zhang, Fangyuan Wang, Shuhu Du, Jin Chen
We developed a method to regenerate arrayed gold microelectrodes equipped for a commercial label-free cell analyzer. The regeneration process includes efficient treatment of the gold surface with trypsin (0.25%, v/v) digestion, rinsing with ethanol and deionized water and spinning steps. The proposed method ensured complete regeneration and repeated usage of gold microchips up to 4 times for the real-time electric impedance measurement of anti-cancer drug cytotoxicity.
October 13, 2016: Analytical Biochemistry
I Velázquez-López, E León-Cruz, J P Pardo, A Sosa-Peinado, M González-Andrade
Eight new fluorescent biosensors of human calmodulin (hCaM) using Alexa Fluor(®) 350, 488, 532, and 555 dyes were constructed. These biosensors are thermodynamically stable, functional, and highly sensitive to ligands of the CaM. They resolve the problem of CaM ligands with similar spectroscopic properties to the intrinsic and extrinsic fluorophores of other biosensors previously reported. Additionally, they can be used in studies of protein-protein interaction through Förster resonance energy transfer (FRET)...
October 12, 2016: Analytical Biochemistry
Chase A Klingaman, Matthew J Wagner, Justin R Brown, John B Klecker, Ethan H Pauley, Colin J Noldner, Jared R Mays
Glucosinolates are plant secondary metabolites abundant in Brassica vegetables that are substrates for the enzyme myrosinase, a thioglucoside hydrolase. Enzyme-mediated hydrolysis of glucosinolates forms several organic products, including isothiocyanates (ITCs) that have been explored for their beneficial effects in humans. Myrosinase has been shown to be tolerant of non-natural glucosinolates, such as 2,2-diphenylethyl glucosinolate, and can facilitate their conversion to non-natural ITCs, some of which are leads for drug development...
October 11, 2016: Analytical Biochemistry
Jutta Speda, Mikaela A Johansson, Uno Carlsson, Martin Karlsson
Enzyme discovery in individual strains of microorganisms is compromised by the limitations of pure culturing. In principle, metaproteomics allows for fractionation and study of different parts of the protein complement but has hitherto mainly been used to identify intracellular proteins. However, the extracellular environment is also expected to comprise a wealth of information regarding important proteins. An absolute requirement for metaproteomic studies of protein expression, and irrespective of downstream methods for analysis, is that sample preparation methods provide clean, concentrated and representative samples of the protein complement...
October 11, 2016: Analytical Biochemistry
Carolyn M Shirey, Jordan L Scott, Robert V Stahelin
To reduce costs of lipid-binding assays, allow for multiple lipids to be screened for protein binding simultaneously, and to make lipid binding more user friendly, lipids have been dotted onto membranes to investigate lipid-protein interactions. These assays are similar to a western blot where the membrane is blocked, incubated with a protein of interest and detected using antibodies. Although the assay is inexpensive and straightforward, problems with promiscuous or poor binding, as well as insufficient blocking occur frequently...
October 11, 2016: Analytical Biochemistry
Zenon Starčuk, Jana Starčuková
Current possibilities and limitations of the simulation of in vivo magnetic resonance spectroscopic signals are demonstrated from the point of view of a simulation software user as well as its programmer. A brief review of the quantum-mechanical background addresses the specific needs of simulation implementation and in vivo MR spectroscopy in general. Practical application examples demonstrate how flexible simulation software, such as NMRScopeB, can be utilized not only for the preparation of metabolite basis signals for quantification of metabolite concentrations, but also in pulse sequence development, assessment of artifacts and analyzing mechanism leading to unexpected signal phenomena...
October 8, 2016: Analytical Biochemistry
Peter Kesa, Mangesh Bhide, Veronika Lysakova, Andrey Musatov
A rapid separation of the ten nuclearly-encoded subunits of mitochondrial cytochrome c oxidase, and ten out of the eleven subunits of cytochrome bc1, was achieved using a short, 50 mm C18-reversed-phase column. The short column decreased the elution time 4-7 fold while maintaining the same resolution quality. Elution was similar to a previously published protocol, i.e., a water/acetonitrile elution gradient containing trifluoroacetic acid. Isolated subunits were identified by MALDI-TOF. The rapidity of the described method makes it extremely useful for determining the subunit composition of isolated mitochondrial complexes...
October 6, 2016: Analytical Biochemistry
Afsaneh Salahvarzi, Mohamad Mahani, Masoud Torkzadeh-Mahani, Reza Alizadeh
An immunoassay method based on the peak shift of the localized surface plasmon resonance (LSPR) absorption maxima has been developed for the determination of the thyroid stimulating hormone (TSH) in human blood serum. The anti-TSH antibody was adsorbed on the synthesized gold nanoparticles by electrostatic forces. The efficiency of the nanobiosensor was improved by optimizing the factors affecting the probe construction such as the pH and the antibody to gold nanoparticles ratio. Dynamic light scattering was applied for the characterization of the constructed probe...
October 4, 2016: Analytical Biochemistry
Eiko Seki, Natsuko Matsuda, Shigeyuki Yokoyama, Takanori Kigawa
No abstract text is available yet for this article.
October 3, 2016: Analytical Biochemistry
Mor Mishkovsky, Arnaud Comment
The advent of dissolution dynamic nuclear polarization (DNP) led to the emergence of a new kind of magnetic resonance (MR) measurements providing the opportunity to probe metabolism in vivo in real time. It has been shown that, following the injection of hyperpolarized substrates prepared using dissolution DNP, specific metabolic bioprobes that can be used to differentiate between healthy and pathological tissue in preclinical and clinical studies can be readily detected by MR thanks to the tremendous signal enhancement...
September 22, 2016: Analytical Biochemistry
Jenson Qi, Wensheng Lang, Margery A Connelly, Fuyong Du, Yin Liang, Gary W Caldwell, Tonya Martin, Michael K Hansen, Gee-Hong Kuo, Michael D Gaul, Alessandro Pocai, Seunghun Lee
Monoacylglycerol acyltransferase 2 (MGAT2) catalyzes the synthesis of diacylglycerol (DAG) from free fatty acids (FFA) and sn-monoacylglycerol (MG), the two major hydrolysis products of dietary fat. To demonstrate MGAT2-mediated cellular activity of triglyceride (TG) synthesis, we utilized 1-oleoyl-glycerol-d5 as a substrate to trace MGAT2-driven 1-oleoyl-glycerol-d5 incorporation into TG in HEK293 cells stably expressing human MGAT2. The oleoyl-glycerol-d5 incorporated major TG species were then quantified by liquid chromatography electrospray ionization tandem mass spectrometry (LC/ESI/MS/MS) in a 96-well format...
September 22, 2016: Analytical Biochemistry
Sarah E Hancock, Berwyck L J Poad, Amani Batarseh, Sarah K Abbott, Todd W Mitchell
As the field of lipidomics grows and its application becomes wide and varied it is important that we don't forget its foundation, i.e. the identification and measurement of molecular lipids. Advances in liquid chromatography and the emergence of ion mobility as a useful tool in lipid analysis are allowing greater separation of lipid isomers than ever before. At the same time, novel ion activation techniques, such as ozone-induced dissociation, are pushing lipid structural characterization by mass spectrometry to new levels...
September 17, 2016: Analytical Biochemistry
Giulio Gambarota
Magnetic resonance spectroscopy (MRS) is a well established modality for investigating tissue metabolism in vivo. In recent years, many efforts by the scientific community have been directed towards the improvement of metabolite detection and quantitation. Quantum mechanics simulations allow for investigations of the MR signal behaviour of metabolites; thus, they provide an essential tool in the optimization of metabolite detection. In this review, we will examine quantum mechanics simulations based on the density matrix formalism...
September 2, 2016: Analytical Biochemistry
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