Genome-wide identification, characterization and expression analysis of the auxin response factor gene family in Vitis vinifera

Our study has identified and analyzed the VvARF gene family that may be associated with the development of grape berry and other tissues. Auxin response factors (ARFs) are transcription factors that regulate the expression of auxin responsive genes through specific binding to auxin response elements (AuxREs). The ARF genes are represented by a large multigene family in plants. Until now, many ARF families have been characterized based on genome resources. However, there is no specialized research about ARF genes in grapevine (Vitis vinifera). In this study, a comprehensive bioinformatics analysis of the grapevine ARF gene family is presented, including chromosomal locations, phylogenetic relationships, gene structures, conserved domains and expression profiles. Nineteen VvARF genes were identified and categorized into four groups (Classes 1, 2, 3 and 4). Most of VvARF proteins contain B3, AUX_RESP and AUX_IAA domains. The VvARF genes were widely expressed in a range of grape tissues, and fruit had higher transcript levels for most VvARFs detected in the EST sources. Furthermore, analysis of expression profiles indicated some VvARF genes may play important roles in the regulation of grape berry maturation processes. This study which provided basic genomic information for the grapevine ARF gene family will be useful in selecting candidate genes related to tissue development in grapevine and pave the way for further functional verification of these VvARF genes.

Fe-N-C single-atom nanozymes based sensor array for dual signal selective determination of antioxidants

Machine learning algorithms as a powerful tool can efficiently utilize and process large quantities of data generated by high-throughput experiments in various fields. In this work, we used a general ionic salt-assisted synthesis method to prepare oxidase-like Fe-N-C SANs. The possible reason for the excellent enzyme-mimicking activity and affinity of Fe-N-C SANs was further verified by density functional theory calculations. Due to the remarkable oxidase-mimicking activity, the prepared Fe-N-C SANs were used to detect ascorbic acid (AA) with a detection limit of 0.5 μM. Based on the machine learning algorithms, we successfully distinguished six antioxidants (ascorbic acid, glutathione, L-cysteine, dithiothreitol, uric acid, and dopamine) with the same concentration by either one kind of Fe-N-C SANs or three kinds of different Fe-N-C SANs. The usefulness of the Fe-N-C SANs sensor arrays was further validated by the hierarchal cluster analysis, where they also can be correctly identified. More importantly, a SANs-based digital-image colorimetric sensor array has also been successfully constructed and thereby achieved visual and informative colorimetric analysis for practical samples out of the lab. This work not only provides a design synthesis method to prepare SANs but also combines machine learning algorithms with SANs sensors to identify analytes with similar properties, which can further expand to the detection of proteins and cells related to diseases in the future.

A G-quadruplex DNAzyme-based LAMP biosensing platform for a novel colorimetric detection ofListeria monocytogenes

A LAMP-based method for the visual detection ofListeria monocytogeneshas been developed by employing DNAzyme-catalyzed cascade amplification of the colorimetric signal.

Development of an in-situ signal amplified electrochemical assay for detection of Listeria monocytogenes with label-free strategy

Listeria monocytogenes is an important foodborne pathogen, which imposes great burdens on public health. The current methods for detecting L. monocytogene are limited in several ways such as time consuming and lab equipment dependent. In this study, we developed a new electrochemical assay to improve the efficacy. This assay allows us to generate numerous G-quadruplex sequences while loop-mediated isothermal amplification happens. Then, these G-quadruplex sequences form DNAzyme to produce a color change and an electrochemical signal by oxidizing tetramethylbenzidine. This assay could be finished in 2 h, which significantly reduced the detection time. Also, we confirmed the limit of detection of this assay at 6.8 CFU/mL according to 3σ criterion. Our assay shows good sensitivity to detect bacteria range from 52.5 to 5.25 × 10⁴ CFU/mL. This assay's reliability was also confirmed by detecting artificially contaminated pork samples. Thus, we propose this electrochemical assay for rapid and sensitive detection of L. monocytogenes in food.

Species-specific diagnostic marker for rapid identification of Staphylococcus aureus

Staphylococcus aureus is a common bacterial pathogen that has emerged as an increasingly important health concern. Following the recent publication of the genome sequences of 9 S. aureus strains (http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi), a gene of S. aureus that relates signal transduction as a target for rapid detection and identification of the pathogen has been investigated. By sequence analysis of S. aureus signal transduction genes from the complete genome of S. aureus ATCC N315 and their comparison with other DNA sequences using GenBank BLAST searches, we identified a unique gene, vicK. Polymerase chain reaction primers (vicK1 and vicK2) derived from this gene allowed amplification of a 289-bp DNA fragment only from S. aureus and not from other Staphylococcus species and other common bacteria tested. Besides offering an additional target for specific confirmation of S. aureus, further analysis of the signal transduction gene vicK and its related protein product may lead to new insights into the molecular mechanisms of S. aureus maintenance and pathogenicity.

Visual detection of Listeria monocytogenes using unmodified gold nanoparticles based on a novel marker

Listeria monocytogenes(L. monocytogenes) causes listeriosis in people and animals.

Development of DNAzyme-based PCR signal cascade amplification for visual detection of Listeria monocytogenes in food

Listeria monocytogenes is an important foodborne pathogen, and it can cause severe diseases. Rapid detection of L. monocytogenes is crucial to control this pathogen. A simple and robust strategy based on the cascade of PCR and G-quadruplex DNAzyme catalyzed reaction was used to detect L. monocytogenes. In the presence of hemin and the aptamer formed during PCR, the catalytic horseradish peroxidase-mimicking G-quadruplex DNAzymes allow the colorimetric responses of target DNA from L. monocytogenes. This assay can detect genomic DNA of L. monocytogenes specifically with as low as 50 pg/reaction with the naked eye. Through 20 pork samples assay, visual detection assay had the same results as conventional detection methods, and had a good performance. This is a powerful demonstration of the ability of G-quadruplex DNAzyme to be used for PCR-based assay with significant advantages of high sensitivity, low cost and simple manipulation over existing approaches and offers the opportunity for application in pathogen detection.

Visual diagnostic of Helicobacter pylori based on a cascade amplification of PCR and G-quadruplex DNAzyme as a color label

Helicobacter pylori is a spiral-shaped, Gram-negative, microaerophilic and fastidious bacterium. It is the main cause of chronic gastritis as well as gastric and duodenal ulcers. The diagnosis of H. pylori infection is significant for the selection of therapy and for the follow up of eradication success. A simple and robust strategy based on the cascade of PCR and DNAzyme catalyzed reaction was utilized to detect H. pylori. The design of the primer pair would enable PCR to synthesize aptamer of DNAzyme at the 3' end of PCR products. G-quadruplex DNAzyme as a color label can exhibit peroxidase-like activity to amplify the specific signal and demonstrate a colorimetric signal to indicate the diagnostic result. This assay can detect genomic DNA of H. pylori specifically with as low as 100 pg/reaction by the naked eye. This is a powerful demonstration of G-quadruplex DNAzyme to be used for PCR-based assay with significant advantages of high sensitivity, low cost and simple manipulation over existing approaches and offers the potential opportunity for clinical application.

Visual detection of Maize chlorotic mottle virus using unmodified gold nanoparticles

Visual detection of Maize chlorotic mottle virus was investigated using unmodified gold nanoparticles (AuNPs).

A signal cascade amplification strategy based on RT-PCR triggering of a G-quadruplex DNAzyme for a novel electrochemical detection of viable Cronobacter sakazakii

Cronobacter sakazakii is an important opportunistic food-borne pathogen, and it can cause severe diseases with main symptoms including neonatal meningitis, necrotizing enterocolitis, and sepsis. For the achievement of practical and convenient detection of viable C. sakazakii, a simple and robust strategy based on the cascade signal amplification of RT-PCR triggered G-quadruplex DNAzyme catalyzed reaction was firstly used to develop an effective and sensitive DNAzyme electrochemical assay. Without viable C. sakazakii in the samples there are no RT-PCR and DNAzyme products, which can cause a weak electrochemical response. Once viable C. sakazakii exists in the samples, an obvious enhancement of the electrochemical response can be achieved after the target signal is amplified by RT-PCR and the resulting DNAzyme, which catalyze the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) by H2O2 with the assistance of the cofactor hemin. Our novel assay can be performed in a range of 2.4 × 107 CFU mL-1 to 3.84 × 104 CFU mL-1 (R2 = 0.9863), with a detection limit of 5.01 × 102 CFU mL-1. Through the assay of 15 real samples, electrochemical detection assay provided the same results as conventional detection methods. Therefore, detection of viable C. sakazakii based on G-quadruplex DNAzyme electrochemical assay with RT-PCR demonstrates the significant advantages of high sensitivity, low cost and simple manipulation over existing approaches and offers an opportunity for potential application in pathogen detection.

A time-resolved fluorescent microsphere-lateral flow immunoassay strip assay with image visual analysis for quantitative detection of Helicobacter pylori in saliva

Helicobacter pylori (H. pylori) is a kind of microaerobic and food-borne pathogen. More than 4.4 billion individuals have been infected by H. pylori and H. pylori was listed as Group I carcinogen by WHO in 1994. Considering the high infection rate of H. pylori and the limited medical resources, self-testing is helpful for diagnosis and timely treatment. Although the amount of H. pylori in human saliva is low, the sampling of saliva is simple and convenient compared with stomach, blood and stool samples. Therefore, H. pylori in human saliva can be an indicator for self-testing, and a sensitive and easy-to-use assay is necessary. In this study, we developed a time-resolved fluorescent microsphere-lateral flow immunoassay (TRFM-LFIA) strip assay with image visual analysis for detection of H. pylori in saliva. The detection of the TRFM-LFIA strip was easy to use and had a low dependency on equipment. With optimized preparation and detection parameters, the whole detection process could be finished in 8 min and the LOD by naked eyes was 102 CFU/mL. For quantitative analysis by image visual analysis, the LOD was as low as 1.05 CFU/mL in the linear range of 101-105 CFU/mL. Besides, the TRFM-LFIA strip also had good stability, reliability, repeatability and accuracy. All these advantages indicated that the TRFM-LFIA strips developed in this study had a good potential for self-testing for H. pylori infection.

Amplified visual detection of microRNA-378 through a T4 DNA ligase-mediated circular template specific to target and target-triggering rolling circle amplification

MicroRNA-378 (miRNA-378) is widely regarded as a novel noninvasive serum biomarker for early detection of gastric cancer.

Diagnostic techniques for COVID-19: A mini-review

COVID-19, a new respiratory infectious disease, was first reported at the end of 2019, in Wuhan, China. Now, COVID-19 is still causing major loss of human life and economic productivity in almost all countries around the world. Early detection, early isolation, and early diagnosis of COVID-19 patients and asymptomatic carriers are essential to blocking the spread of the pandemic. This paper briefly reviewed COVID-19 diagnostic assays for clinical application, including nucleic acid tests, immunological methods, and Computed Tomography (CT) imaging. Nucleic acid tests (NAT) target the virus genome and indicates the existence of the SARS-CoV-2 virus. Currently, real-time quantitative PCR (qPCR) is the most widely used NAT and, basically, is the most used diagnostic assay for COVID-19. Besides qPCR, many novel rapid and sensitive NAT assays were also developed. Serological testing (detection of serum antibodies specific to SARS-CoV-2), which belongs to the immunological methods, is also used in the diagnosis of COVID-19. The positive results of serological testing indicate the presence of antibodies specific to SARS-CoV-2 resulting from being infected with the virus. Viral antigen detection assays are also important immunological methods used mainly for rapid virus detection. However, only a few of these assays had been reported. CT imaging is still an important auxiliary diagnosis tool for COVID-19 patients, especially for symptomatic patients in the early stage, whose viral load is low and different to be identified by NAT. These diagnostic techniques are all good in some way and applying a combination of them will greatly improve the accuracy of COVID-19 diagnostics.

Colorimetric detection of Maize chlorotic mottle virus by reverse transcription loop-mediated isothermal amplification (RT-LAMP) with hydroxynapthol blue dye

Maize chlorotic mottle virus causes corn lethal necrosis disease, and can be transmitted via infected maize seeds. A colorimetric assay for the detection of Maize chlorotic mottle virus was developed which utilises RT-LAMP and hydroxynapthol blue dye (HNB).

Impact of Germinated Brown Rice and Brown Rice on Metabolism, Inflammation, and Gut Microbiome in High Fat Diet-Induced Insulin Resistant Mice

The constituents of germinated brown rice (GBR), brown rice (BRR), and white rice (WHR) and their impact on metabolism, inflammation, and gut microbiota in high fat (HF) diet-fed mice were examined. The contents of total fiber and γ-aminobutyric acid in BRR and GBR were higher than that in WHR (p < 0.05). Male C57 BL/6J mice received HF diet+26 g% of WHR, BRR, or GBR for 12 weeks. BRR and GBR comparably reduced HF diet-induced increases in fasting plasma glucose, lipids, insulin resistance, and inflammatory markers compared to WHR (p < 0.01). The abundance of fecal Bacteroidetes in mice fed HF+GBR or HF+BRR was higher than in HF+WHR-fed mice (p < 0.05). The abundance of fecal Lactobacillus gasseri in GBR-fed mice was greater than that in WHR- or BRR-fed mice (p < 0.05). The results indicated that GBR or BRR attenuated hyperglycemia, insulin resistance, and inflammation in mice. HF+GBR, but not HF+BRR, increased a probiotic bacteria in the gut.