gene detection
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Lab on a Chip ◽  
2022 ◽  
Author(s):  
Chongyang Liang ◽  
weihan sun ◽  
wei guo ◽  
zhiyi liu ◽  
Sennan Qiao ◽  
...  

Traditional methods for single-nucleotide variants based on the amplification and the fluorescent signals require expensive reagents and cumbersome instruments, and they are time-consuming for each trial. Here, a porous anodised...


2021 ◽  
Author(s):  
Marketa Nykrynova ◽  
Vojtech Barton ◽  
Roman Jakubicek ◽  
Matej Bezdicek ◽  
Martina Lengerova ◽  
...  

Recently, nanopore sequencing has come to the fore as library preparation is rapid and simple, sequencing can be done almost anywhere, and longer reads are obtained than with next-generation sequencing. The main bottleneck still lies in data postprocessing which consists of basecalling, genome assembly, and localizing significant sequences, which is time consuming and computationally demanding, thus prolonging delivery of crucial results for clinical practice. Here, we present a neural network-based method capable of detecting and classifying specific genomic regions already in raw nanopore signals - squiggles. Therefore, the basecalling process can be omitted entirely as the raw signals of significant genes, or intergenic regions can be directly analysed, or if the nucleotide sequences are required, the identified squiggles can be basecalled, preferably to others. The proposed neural network could be included directly in the sequencing run, allowing real-time squiggle processing.


Author(s):  
Hanna S.I Kawulur ◽  
Hotma Martogi Lorensi Hutapea ◽  
Ivon Ayomi ◽  
Melda Suebu ◽  
Mardi Raharjo Pardi

Malaria is still a health problem in Indonesia, particularly in Eastern part of Indonesia. The use of LLIN insecticide bed nets is one of the efforts to reduce the malaria morbidity rate by protecting human from malaria vector bites. The Anopheles flavirostris, Anopheles barbirostris, and Anopheles subpictus mosquitoes are three of the species reported as malaria vectors in West-Southeast Maluku Regency. The aim of this research was to detect the kdr gene in An. flavirostris, An. barbirostris, and An.subpictus mosquitoes collected from Alusi Kelaan village, West-Southeast Maluku Regency. The research was conducted at the Papua Biomedical Research and Development Center, in June 2016. A total of six An. flavirostris, 42 An. barbirostris, and 24 An. subpictus were pooled separately for genomic DNA extraction. The sample used was the An. flavirostris, An. barbirostris, and An. subpictus that survived after the impregnated paper test. The kdr gene detection was carried out using quantitative PCR (qPCR) focused on points V1010 and L1014. The results showed that there were no kdr mutant strains in the An. flavirostris, An. barbirostris, and An. subpictus. These results indicated that the sensitivity of pyrethroid insecticides contained in LLIN mosquito nets to An. flavirostris, An. barbirostris, and An. subpictus mosquitoes was not decreased in West Southeast Maluku Regency.


Antibiotics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1445
Author(s):  
Yueh-Ling Chen ◽  
Eugene Yu-Chuan Kang ◽  
Lung-Kun Yeh ◽  
David H. K. Ma ◽  
Hsin-Yuan Tan ◽  
...  

This study analyzed the clinical features and molecular characteristics of methicillin-susceptible Staphylococcus aureus (MSSA) ocular infections in Taiwan and compared them between community-associated (CA) and health-care-associated (HA) infections. We collected S. aureus ocular isolates from patients at Chang Gung Memorial Hospital between 2010 and 2017. The infections were classified as CA or HA using epidemiological criteria, and the isolates were molecularly characterized using pulsed-field gel electrophoresis, multilocus sequence typing, and Panton-Valentine leukocidin (PVL) gene detection. Antibiotic susceptibility was evaluated using disk diffusion and an E test. A total of 104 MSSA ocular isolates were identified; 46 (44.2%) were CA-MSSA and 58 (55.8%) were HA-MSSA. Compared with HA-MSSA strains, CA-MSSA strains caused a significantly higher rate of keratitis, but a lower rate of conjunctivitis. We identified 14 pulsotypes. ST 7/pulsotype BA was frequently identified in both CA-MSSA (28.3%) and HA-MSSA (37.9%) cases. PVL genes were identified in seven isolates (6.7%). Both CA-MSSA and HA-MSSA isolates were highly susceptible to vancomycin, teicoplanin, tigecycline, sulfamethoxazole–trimethoprim, and fluoroquinolones. The most common ocular manifestations were keratitis and conjunctivitis for CA-MSSA and HA-MSSA, respectively. The MSSA ocular isolates had diverse molecular characteristics; no specific genotype differentiated CA-MSSA from HA-MSSA. Both strains exhibited similar antibiotic susceptibility.


2021 ◽  
Author(s):  
jiawei Zou ◽  
miaochen Wang ◽  
zhen Zhang ◽  
zheqi Liu ◽  
xiaobin Zhang ◽  
...  

Differential expression (DE) gene detection in single-cell RNA-seq (scRNA-seq) data is a key step to understand the biological question investigated. We find that DE methods together with gene filtering have profound impact on DE gene identification, and different datasets will benefit from personalized DE gene detection strategies. Existing tools don't take gene filtering into consideration, and couldn't evaluate DE performance on real datasets without prior knowledge of true results. Based on two new metrics, we propose scCODE (single cell Consensus Optimization of Differentially Expressed gene detection), an R package to automatically optimize DE gene detection for each experimental scRNA-seq dataset.


Author(s):  
Sharon Miller ◽  
Terence Lee ◽  
Adam Merritt ◽  
Todd Pryce ◽  
Avram Levy ◽  
...  

This paper reports the identification of single-point mutations in the N gene of SARS-CoV-2 associated with a gene target failure by the Cepheid Xpert commercial system. In order to determine the mutation(s) responsible for the N gene detection failures, the genomic products from the Cepheid Xpert system were sequenced and compared to whole genomes of SARS-CoV-2 from clinical cases.


2021 ◽  
Author(s):  
Sooyeol Kim ◽  
Lauren Kennedy ◽  
Marlene Wolfe ◽  
Craig Criddle ◽  
Dorothea Duong ◽  
...  

Wastewater-based epidemiology has gained attention throughout the world for detection of SARS-CoV-2 RNA in wastewater to supplement clinical testing. Methods have been developed using both the liquid and the solid fraction of wastewater, with some studies reporting higher concentrations in solids. To investigate this relationship further, we collaborated with six other laboratories to conduct a study across five publicly owned treatment works (POTWs) where both primary solids and raw wastewater influent samples were collected and quantified for SARS-CoV-2 RNA. Solids and influent samples were processed by participating laboratories using their respective methods and retrospectively paired based on date of collection. SARS-CoV-2 RNA concentrations by mass (gene copies per gram) were higher in solids than in influent by approximately three orders of magnitude. Concentrations in matched solids and influent were positively and significantly correlated at all five POTWs. RNA concentrations in both solids and influent were correlated to COVID-19 incidence rates in the sewershed and thus representative of disease burden; the solids methods appeared to produce a comparable relationship between SARS-CoV-2 RNA concentration measurements and incidence rates across all POTWs. Solids and influent methods showed comparable sensitivity, N gene detection frequency, and calculated empirical incidence rate lower limits. Analysis of solids has the advantage of using less sample volume to achieve similar sensitivity to influent methods.


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