scholarly journals Correction: Mobility shift-based electrophoresis coupled with fluorescent detection enables real-time enzyme analysis of carbohydrate sulfatase activity

2021 ◽  
Vol 478 (13) ◽  
pp. 2537-2538
Author(s):  
Dominic P. Byrne ◽  
James A. London ◽  
Patrick A. Eyers ◽  
Edwin A. Yates ◽  
Alan Cartmell
2020 ◽  
Author(s):  
Dominic P Byrne ◽  
James A London ◽  
Patrick A Eyers ◽  
Edwin A Yates ◽  
Alan Cartmell

AbstractSulfated carbohydrate metabolism is a fundamental process, which occurs in all domains of life. Carbohydrate sulfatases are enzymes that remove sulfate groups from carbohydrates and are essential to the depolymerisation of complex polysaccharides. Despite their biological importance, carbohydrate sulfatases are poorly studied and challenges remain in accurately assessing the activity, specificity and kinetic parameters. Most notably, separation of desulfated products from sulfated substrates is currently a time-consuming process. In this paper, we describe the development of rapid capillary electrophoresis coupled to substrate fluorescence detection as a high-throughput and facile means of analysing carbohydrate sulfatase activity. The approach has utility for the determination of both kinetic and inhibition parameters and is based on existing microfluidic technology coupled to a new synthetic fluorescent 6S-GlcNAc carbohydrate substrate. Furthermore, we compare this technique in terms of both time and resources, to high performance anion exchange chromatography and NMR-based methods, which are the two current ‘gold standards’ for enzymatic carbohydrate sulfation analysis. Our study clearly demonstrates the advantages of mobility shift assays for the quantification of near real-time carbohydrate desulfation by purified sulfatases, and could support the search for small molecule inhibitors of these disease-associated enzymes.One sentence summarySulfatases remove sulfate groups from biomolecules; in this study we report a rapid and robust capillary electrophoresis assay for the quantification of carbohydrate desulfation.


2021 ◽  
Vol 478 (4) ◽  
pp. 735-748
Author(s):  
Dominic P. Byrne ◽  
James A. London ◽  
Patrick A. Eyers ◽  
Edwin A. Yates ◽  
Alan Cartmell

Sulfated carbohydrate metabolism is a fundamental process, which occurs in all domains of life. Carbohydrate sulfatases are enzymes that remove sulfate groups from carbohydrates and are essential to the depolymerisation of complex polysaccharides. Despite their biological importance, carbohydrate sulfatases are poorly studied and challenges remain in accurately assessing the enzymatic activity, specificity and kinetic parameters. Most notably, the separation of desulfated products from sulfated substrates is currently a time-consuming process. In this paper, we describe the development of rapid capillary electrophoresis coupled to substrate fluorescence detection as a high-throughput and facile means of analysing carbohydrate sulfatase activity. The approach has utility for the determination of both kinetic and inhibition parameters and is based on existing microfluidic technology coupled to a new synthetic fluorescent 6S-GlcNAc carbohydrate substrate. Furthermore, we compare this technique, in terms of both time and resources, to high-performance anion exchange chromatography and NMR-based methods, which are the two current ‘gold standards’ for enzymatic carbohydrate sulfation analysis. Our study clearly demonstrates the advantages of mobility shift assays for the quantification of near real-time carbohydrate desulfation by purified sulfatases, and will support the search for small molecule inhibitors of these disease-associated enzymes.


2000 ◽  
Vol 88 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Cassie A Roberts ◽  
Ralf G Dietzgen ◽  
Lisa A Heelan ◽  
Donald J Maclean

2017 ◽  
Vol 22 (4) ◽  
pp. 418-424
Author(s):  
Thomas Lanyon-Hogg ◽  
Neki V. Patel ◽  
Markus Ritzefeld ◽  
Katherine J. Boxall ◽  
Rosemary Burke ◽  
...  

The Hedgehog pathway is a key developmental signaling pathway but is also implicated in many types of cancer. The extracellular signaling protein Sonic hedgehog (Shh) requires dual lipidation for functional signaling, whereby N-terminal palmitoylation is performed by the enzyme Hedgehog acyltransferase (Hhat). Hhat is an attractive target for small-molecule inhibition to arrest Hedgehog signaling, and methods for assaying Hhat activity are central to understanding its function. However, all existing assays to quantify lipidation of peptides suffer limitations, such as safety hazards, high costs, extensive manual handling, restriction to stopped-assay measurements, or indirect assessment of lipidation. To address these limitations, we developed a microfluidic mobility shift assay (MSA) to analyze Shh palmitoylation. MSA allowed separation of fluorescently labeled Shh amine-substrate and palmitoylated Shh amide-product peptides based on differences in charge and hydrodynamic radius, coupled with online fluorescence intensity measurements for quantification. The MSA format was employed to study Hhat-catalyzed reactions, investigate Hhat kinetics, and determine small-molecule inhibitor IC50 values. Both real-time and stopped assays were performed, with the latter achieved via addition of excess unlabeled Shh peptide. The MSA format therefore allows direct and real-time fluorescence-based measurement of acylation and represents a powerful alternative technique in the study of N-lipidation.


Parasitology ◽  
2008 ◽  
Vol 135 (5) ◽  
pp. 575-583 ◽  
Author(s):  
L. MOERTEL ◽  
G. N. GOBERT ◽  
D. P. McMANUS

SUMMARYSchistosomes are complex parasitic helminths with discrete life-cycle stages, adapted for survival in their mammalian and snail hosts and the external aquatic environment. Recently, we described the fabrication and use of a microarray to investigate gender-specific transcription inSchistosoma japonicum. To address transcriptional differences, 8 gender-associated gene transcripts identified previously by the microarray analysis were selected for further study. First, differential transcription patterns were investigated in 4 developmental stages using real-time PCR. Subsequently, we undertook functional analysis of a subset of 4 transcripts encoding metabolic enzymes, so as to correlate gender-associated transcript levels with enzyme activity in protein extracts from adult worms. The 8 characterized molecules serve as a basis for further investigation of differential gene expression during the schistosome life-cycle and for studying the sexual dimorphism of adult worms. Continual refinement and annotation of the microarray used in the current study should support future work on these aspects.


Author(s):  
A. O. Sementsova ◽  
A. N. Shikov ◽  
V. A. Ternovoy ◽  
A. V. Vinokurova ◽  
N. E. Kostina ◽  
...  

Presented are the data on the development and approbation of the method of Marburg, Ebola, and Lassa viruses identification based on real-time multiplex PCR with hybridization-fluorescent detection. This method is meant for the differential diagnostics of hemorrhagic fevers caused by these viruses. Displayed are the results of determination of multiplex PCR analytical sensitivity and specific activity.


Nematology ◽  
2019 ◽  
Vol 21 (3) ◽  
pp. 243-251 ◽  
Author(s):  
Sergei A. Subbotin

Summary Rapid diagnosis tools for detection of root-knot nematodes play an important role in the disease control and eradication programme. Recombinase polymerase amplification (RPA) assays were developed targeting the IGS rRNA gene of the pacara earpod tree root-knot nematode, Meloidogyne enterolobii. The RPA assays using TwistAmp® Basic and TwistAmp® exo kits allowed detection of M. enterolobii from gall tissues and crude nematode extracts of all stages of target species without a DNA extraction step. The results of real-time RPA assays using a real-time fluorescent detection of a series of crude nematode extracts showed reliable detection with sensitivity of 1/10 of a second-stage juvenile in a RPA reaction tube after 15-20 min. The RPA assay provides affordable, simple, fast and sensitive detection of M. enterolobii.


Author(s):  
K. A. Nikiforov ◽  
E. G. Oglodin ◽  
L. M. Kukleva ◽  
G. A. Eroshenko ◽  
V. G. Germanchuk ◽  
...  

Aim. Develop a method of differentiation of Y.pestis strains of different subspecies based on PCR with hybridization-fluorescent detection in real-time. Materials and methods. DNA target search for differentiation of subspecies of plague causative agent was carried out by Mauve 2.3.1, Mega 5.0 and BLAST algorithm based on comparison offull-genome sequences of Y.pestis strains. Primers and TaqMan probes were calculated for the DNA targets found, conditions of PCR with hybridization-fluorescent detection - optimized. Results. DNA targets carrying marker mutations for the caucasus, altai, gissar, ulegei subspecies, strains from Talass alpine plague reservoir were detected. The effectiveness of the DNA targets found and the developed approach of subspecies differentiation is confirmed on 101 Y.pestis strains of different subspecies, isolated from natural foci of Russia, near and far abroad. Conclusion. The developed approach based on PCR with real-time detection allows for a rapid and effective differentiation of Y.pestis strains of various subspecies.


2021 ◽  
Author(s):  
Pan Li ◽  
Hongjuan Ge ◽  
Lei Zhang ◽  
Jing Shu ◽  
Zhuojing Sun ◽  
...  

SummaryFlavonoids are a class of polyphenol compounds that are widespread in plants. They play an important role in plant growth and development. In this study, we found a mutant strain of M. baccata with yellow leaves (YL). Transcriptome sequencing revealed that it exhibited significant changes in the flavonoid metabolism pathway, which screening revealed was associated with a glycosyltransferase gene, MD09G1064900 (MdGT1). Analysis of its spatiotemporal expression showed that MdGT1 was mainly expressed in the stem and leaves, it means that MdGT1 may have a functional role in these parts. Real-time PCR and HPLC showed that MdGT1 was significantly upregulated by anthocyanin and exhibited strong anthocyaninase activity in vitro, respectively. An MdGT1 plant expression vector was constructed and overexpressed in apple fruit callus, resulting in a significant decrease of anthocyanin. Phenotypic observation also revealed that the MdGT1-overexpressing lines exhibited worse growth than the wild type after NaCl treatment, while they grew better upon the addition of exogenous anthocyanins. Moreover, real-time PCR and physiological data showed that MdGT1 is involved in salt stress and closely related to antioxidant pathways. Electrophoretic mobility shift assays (EMSA) and yeast one-hybrid experiments also proved that the transcription factor MdMYB88 is an upstream regulatory factor of MdGT1. The sequencing results revealed an amino acid insertion in an MdMYB88 HTH domain (between 77-131 amino acids) in the YL mutant strain. In conclusion, we identified a new apple glycosyltransferase gene, MdGT1, which may affect the color of apple leaves by glycosylating anthocyanins, and be regulated by the upstream transcription factor MdMYB88.Significance statementThe glycosyltransferases and their physiological significance in apple are largely unknown. Here we revealed that the MdMYB88-regulated apple glycosyltransferase gene MdGT1 plays a crucial role in the color of apple leaves and enhances plant tolerance to salt by antioxidant pathways via anthocyanin metabolism.


2010 ◽  
Vol 22 (1) ◽  
pp. 282
Author(s):  
P. V. Silva ◽  
S. E. F. Guimarães ◽  
J. D. Guimarães ◽  
P. S. Lopes ◽  
L. S. Amorim

During each estrous cycle, more than 99% of the ovarian follicles undergo a degenerative process known as atresia. The p53 is an antiproliferative transcription factor that enhances the transcription rate of important genes in the apoptotic pathway. The aim of the current study was to investigate the pattern of p53 mRNA expression during estrous cycle in the pig ovary by real-time PCR technique. Sixteen prepubertal gilts (Landrace × Large White × Pietrain) were obtained from the pig farm at the Universidade Federal de Viçosa (Viçosa, MG, Brazil). The estrous cycle was synchronized with P.G. 600® (Intervet/Schering-Plough Animal Health, Millsboro, DE, USA; 400 IU eCG and 200 IU hCG). The onset of estrus was checked twice a day using a mature boar. The gilts, n = 4 per group, were slaughtered on Days 0, 6, 12, and 18 of estrous cycle. Granulosa cells from follicles were collected by vacuum aspiration and washed in PBS by centrifugation at 5.000 × g for 6 min, and the RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA). The ovarian cortex was stored in RNAlater (Ambion, Austin, TX, USA) and frozen at -80°C. Its RNA was extracted from 30 mg using the same Kit. For each animal in each stage, a pool of equivalent amounts of RNA from granulosa cells and ovary cortex was reverse transcribed with SuperScript III/RNaseOUT Enzyme Mix (Invitrogen Life Technologies, Carlsbad, CA, USA) to evaluate gene expression for the ovary as a whole. Quantitative real-time PCR was performed using SYBR green fluorescent detection system on ABI Prism 7300 Sequence Detection Systems (Applied Biosystems, Foster City, CA, USA). The primers were designed from swine sequences available at GenBank. The linearity of amplification for p53 mRNA was similar to the endogenous control gene, glyceraldehyde-3-phosphate dehydrogenase. Reactions were performed using 200 nM primer and 100 ng of the cDNA per reaction for both genes. The thermal cycling conditions consisted of 40 cycles of 30 s of melting at 95°C followed by 30 s of annealing and extension at 60°C. After amplification, a melting curve analysis was performed to validate the absence of non-specific products. Gene expression data were presented using the 2ACt method (Livak and Schimittgen 2001). The results of gene expression were analyzed using linear regression after transformation ln(2ACt + 1) as the dependent variable and days of estrous cycle as independent variables using the general linear model procedure (SAS Institute, Inc., Cary, NC, USA). The mRNA expression was not affected by days of estrous cycle (P = 0.86). In rats, the expression of p53 mRNA in granulosa cells has been already described. Despite the fact that no difference has been found during the estrous cycle in this study, the expression of this messenger in the pig ovary seems to be undescribed until now. In the future, for a better understanding of p53 regulation in the pig, gene expression analysis in different follicle sizes and physiological status will be presented by our group to examine the expression patterns of this gene, as well as other related ones, included in this apoptotic pathway.


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