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Analytical Biochemistry

Mohammad Riaz, Sandeep K Misra, Joshua S Sharp
Protein structural analysis by mass spectrometry has gained significant popularity in recent years, including high-resolution protein topographical mapping by fast photochemical oxidation of proteins (FPOP). The ability to provide protein topographical information at moderate spatial resolution makes FPOP an attractive technology for the protein pharmaceutical discovery and development processes. However, current technology limits the throughput and requires significant manual sample manipulation. Similarly, as FPOP is being used on larger samples, sample flow through the capillary becomes challenging...
September 18, 2018: Analytical Biochemistry
J Alaina Floyd, Christine Siska, Rutilio H Clark, Bruce A Kerwin, Jeremy M Shaver
The chemical unfolding (denaturation) assay can be used to calculate the change in the Gibbs free energy of unfolding, ΔG, and inflection point of unfolding, to collectively inform on molecule stability. Here, we evaluated methods for calculating the ΔG across 23 monoclonal antibody sequence variants. These methods are based on how the measured output (intrinsic fluorescence intensity) is treated, including utilizing (a) a single wavelength, (b) a ratio of two wavelengths, (c) a ratio of a single wavelength to an area, and (d) a scatter correction plus a ratio of a single wavelength to an area...
September 17, 2018: Analytical Biochemistry
Daojin Li, Qi Yuan, Wenliu Yang, Mengke Yang, Shihui Li, Tianyong Tu
Vitamin B12 (VB12) has an important function in human physiology. However, analysis of VB12 at natural levels in foods or biological samples is difficult because of its very low concentration level and the presence of high-abundance components which can interfere with the measuring system. Thus, it is essential to develop efficient and selective enrichment approaches for VB12. Molecularly imprinted polymers (MIPs) have important applications from separation and sensing to catalysis. However, there is no report on the preparation of MIPs for VB12...
September 16, 2018: Analytical Biochemistry
Alireza Alikhani, Milad Gharooni, Hassan Moghtaderi, Fatemeh Farokhmanesh, Hamed Abiri, Mona Salimi, Farnoosh Attari, Mohammad Abdolahad
One of the most interesting fields of research in cancer diagnosis is tracing the relation between extracellular media and cancer progression. Detecting the secreting contents of the cells and translating these molecular identifications into label-free recognizable patterns would open new opportunities in cancer research. Electrochemical responses are in the range of most attractive sensing mechanisms especially in biochemical approaches. Perturbed ionic exchanges as a known biochemical function of cancer cells presented a strong correlation with the pH of the tumor microenvironment...
September 13, 2018: Analytical Biochemistry
Salvatore G De-Simone, Hilton J Nascimento, Isis C Prado, Aniesse S Aguiar, Anibal R Melgarejo, Jorge L Pina, Patricia F Ferreira, David W Provance
The availability of purified antibodies is a prerequisite for many applications and the appropriate choice(s) for antibody-purification is crucial. Numerous methods have been developed for the purification of antibodies from different sources with affinity chromatography-based methods being the most extensively utilized. These methods are based on high specificity, easy reversibility and biological interactions between two molecules (e.g., between receptor and ligand or antibody and antigen). However, no simple techniques have yet been described to characterize and purify subclasses of immunoglobulins (Ig) from some animals of biotechnology importance such as equines, which are frequently used to produce biotherapeutic antibodies...
September 12, 2018: Analytical Biochemistry
Zhe Ju, Shi-Yun Wang
Lipoylation is a highly conserved post-translational modification which has been found to be involved in many biological processes and closely associated with various metabolic diseases. The accurate identification of lipoylation sites is necessary to elucidate the underlying molecular mechanisms of lipoylation. As the traditional experimental methods are time consuming and expensive, it is desired to develop computational methods to predict lipoylation sites. In this study, a novel predictor named LipoPred is proposed to predict lysine lipoylation sites...
September 12, 2018: Analytical Biochemistry
Aleksandra A Zasada, Katarzyna Zacharczuk, Kamila Formińska, Aldona Wiatrzyk, Robert Ziółkowski, Elżbieta Malinowska
The recently developed methods of nucleic acids isothermal amplification are promising tools for point-of-care diagnostics and in the field detection of pathogenic microorganisms. However, application of these methods outside a laboratory faces some challenges such as the rapid and sensitive detection of amplified products and the absence of cross-reactivity with genetically related microorganisms. In the presented study we compared three methods of isothermal DNA amplification loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA) and thermophilic helicase-dependent isothermal DNA amplification (tHDA), for detection of highly dangerous pathogens, such as Bacillus anthracis, Francisella tularensis and Yersinia pestis, and combined them with lateral flow dipsticks for the rapid visualization of amplified products...
September 11, 2018: Analytical Biochemistry
Gabriel Tassi Mousquer, Lila Partichelli Maciel, Ana Carolina Pompeu Saraiva, Elis Regina Dalla Costa, Maria Lucia Rosa Rossetti
No abstract text is available yet for this article.
September 11, 2018: Analytical Biochemistry
Wei Chen, Hui Ding, Xu Zhou, Hao Lin, Kuo-Chen Chou
As a prevalent post-transcriptional modification, N6 -methyladenosine (m6 A) plays key roles in a series of biological processes. Although experimental technologies have been developed and applied to identify m6 A sites, they are still cost-ineffective for transcriptome-wide detections of m6 A. As good complements to the experimental techniques, some computational methods have been proposed to identify m6 A sites. However, their performance remains unsatisfactory. In this study, we firstly proposed an Euclidean distance based method was proposed to construct a high quality benchmark dataset...
September 7, 2018: Analytical Biochemistry
Wanli Yan, Lide Gu, Shu Liu, Wei Ren, Mingsheng Lyu, Shujun Wang
A novel screening method for protein aptamer selection was developed in this study. Aptamers with high affinity and specificity to the surface recombinant antigen of Helicobacter pylori (HP-Ag) and to tumor markers carcinoembryonic antigen (CEA), cancer antigen 125 (CA125) and cancer antigen 19-9(CA19-9) were screened using trypsin enhanced screening method. Briefly, the target proteins above were immobilized onto 96-well polystyrene plates and incubated with a single-stranded DNA (ssDNA) library for aptamer selection...
September 6, 2018: Analytical Biochemistry
Dillon Friday, Paul Freidhoff, Tilman Baumstark, Michael F Bruist
Enrichment of specific RNAs is important for RNA analysis. MnCl2 has been used previously to enrich viroid RNA fractions from total RNA from infected plants. We have expanded this method to show that MnCl2 can enrich single-stranded as well as structured RNAs of 450 nt and below from a total RNA preparation. We have applied this method to map the transcription start sites of a PSTVd transcript from total RNA from yeast under conditions where the RNA was previously undetectable.
September 5, 2018: Analytical Biochemistry
Regina Cencic, Jerry Pelletier
All cellular cytoplasmic mRNAs are capped at their 5' ends with an m7 GpppN group. Several proteins that mediate cap function have been identified by cap affinity purification, enabling their characterization in a number of biological processes. Among these, eukaryotic initiation factor (eIF) 4E is the best characterized and plays a critical role in regulating ribosome recruitment to mRNAs during translation initiation. Cap affinity chromatography is often used to identify eIF4E-interacting proteins, which could play critical roles in molding the eIF4E-interactome and impacting on eIF4E-directed translation...
September 4, 2018: Analytical Biochemistry
Xiao-Ling Tang, Hui Suo, Ren-Chao Zheng, Yu-Guo Zheng
Tyrosine phenol-lyase (TPL) naturally catalyzes the reversible β-elimination of l-tyrosine to phenol, pyruvate and ammonium. With its reverse reaction (synthetic activity), l-tyrosine and its derivatives could be synthesized with high atom economy, which are widely used in pharmaceutical industries. In this study, a high-throughput screening method for synthetic activity of TPL was developed. One of the substrate, sodium pyruvate was found to react with salicylaldehyde under alkali condition, forming a yellow color compound...
August 31, 2018: Analytical Biochemistry
Jinseob Rim, Chang-Hyun Jang
In this study, a simple, rapid, and label-free sensor was developed for detecting the enzymatic activity of catalase (CAT) with liquid crystals (LCs) confined in microcapillaries. Inside a microcapillary functionalized with n-octyltrichlorosilane, aldehyde-doped LCs anchored radially so that a pattern of straight lines was observed under a polarized optical microscope (POM). However, once hydrogen peroxide (HP) oxidized the aldehyde into carboxylic acid, which has surface activity, the orientation of the LCs at the interface changed, resulting in a distinct pattern change, from straight to crossed...
August 31, 2018: Analytical Biochemistry
Zou Bin, Chu Yanhong, Xia Jiaojiao, Yao Jing
Monocrotophos (Ops) has been widely used as pesticide in crop production but simultaneously could accumulate in the nature and seriously impact food safety and human health. It is necessary to develop a high sensitivity biosensor for accurate and fast detection of OPs. In this study, multi-walled carbon nanotubes (MWCNTs) were selected as acetylcholinesterase (AChE) carrier and their surface was modified by introducing different functional groups (-SH, -NH2 , -Cl, -OH), hydrophobic alkyl groups (-CH3 , -(CH2 )2 CH3 , -(CH2 )7 CH3 , -(CH2 )15 CH3 ) and ionic liquids (-IL1 , -IL2 )...
August 31, 2018: Analytical Biochemistry
Jaimie Dufresne, Angelique Florentinus-Mefailoski, Pei-Hong Zhu, Peter Bowden, John G Marshall
A Rabbit myosin standard, like that used to create the empirical statistical model, was randomly and independently sampled by liquid chromatography micro electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) with a linear quadrupole ion trap. The rabbit myosin protein standard appeared pure by SDS-PAGE and CBBR staining but showed many other proteins by silver staining. The LC-MS intensity from myosin and IgG samples were above the 99% safe limit of detection and quantification computed from 36 blank LC-ESI-MS/MS runs...
August 29, 2018: Analytical Biochemistry
C Ben Ali Hassine, H Barhoumi
The electrochemical modification of a glassy carbon electrode using reduced poly-4 nitroaniline (P-4NA) and it's applicability for determination of metallic ions was performed in this study. The electrode modification was performed by cyclic voltammetry in the potential range between 0.9 V and 1.4 V vs Ag/Ag+ (in 10 mM AgNO3 ) at the scan rate of 100 mV/s by 50 cycles in non-aqueous media. The reduction of nitro groups on the P-4NA modified glassy carbon electrode surface was performed in the potential range between -0...
August 29, 2018: Analytical Biochemistry
Yuanyuan Wang, Xu Sun, Jianxiong Zeng, Minggang Deng, Nan Li, Qiutong Chen, Hua Zhu, Fenyong Liu, Xiwen Xing
Terminal deoxynucleotidyl transferase (TdT) is a unique template-free polymerase that randomly adds multiple deoxyribonucleoside triphosphates (dNTPs) to the 3'-OH terminus of ssDNA. This characteristic makes TdT a versatile enzymatic tool in many fields. Moreover, aberrant TdT expression is a well-recognized biomarker of several leukemic diseases and is related to carcinogenesis. In this study, we developed a facile, rapid, label-free, and convenient assay for TdT detection. TdT-generated poly A tails formed a fluorescent enhancement complex in the presence of coralyne...
August 26, 2018: Analytical Biochemistry
Kaito Kobayashi, Hiroki Aramasa, Hiroyuki Nakai, Masahiro Nakajima, Hayao Taguchi
A colorimetric determination method measuring the reducing ends of sugars is usually used for quantitative evaluation of polysaccharide-degrading activity of endo-type enzymes. However, no appropriate colorimetric method has been established for enzymatic assay of β-1,2-glucanases, which produce β-1,2-glucooligosaccharides from β-1,2-glucans. The Anthon-MBTH method has been potentially the most adaptable for color development of β-1,2-glucooligosaccharides among various known colorimetric methods for detecting the reducing power of oligosaccharides, since the difference between sophorose and other β-1,2-glucooligosaccharides in absorbance is relatively small...
August 25, 2018: Analytical Biochemistry
Joel Tellinghuisen
Isothermal titration calorimetry data recorded on a MicroCal/Malvern VP-ITC instrument for water-water blanks and for dilution of aqueous solutions of BaCl2 and Ba(NO3)2 are analyzed using Origin software, the freeware NITPIC program, and in-house algorithms, to compare precisions for estimating the heat per injection q. The data cover temperatures 6-47 °C, injection volumes 4-40 μL, and average heats 0-200 μcal. For water-water blanks, where baseline noise limits precision, NITPIC and the in-house algorithm achieve precisions of 0...
August 24, 2018: Analytical Biochemistry
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