In this study, the short-term effect of roxithromycin(ROX) on the abundance and diversity of ammonia-oxidizing archaea(AOA) and ammonia-oxidizing bacteria(AOB) based on gene in activated sludge were investigated by high-throughput sequencing and quantitative real-time PCR(qPCR). High-throughput sequencing overcomes the drawbacks of low sequencing depth, significant randomness and great bias of traditional Sanger sequencing. This approach can provide enough sequencing depth to comprehensively investigate the sensitive and insensitive ammonia-oxidizing microorganisms under ROX selective pressure. Lab-scale reactors were operated under ten different ROX levels. The results indicated that the environmental(0.3-30 μg·L) and medium(300 μg·Land 3000 μg·L) levels of ROX did not affect ammonia oxidation, while the higher concentration(5000-12000 μg·L) of ROX showed a significant negative effect on ammonia oxidation. The environmental and medium levels of ROX stimulated the growth of AOA, however, the higher level of ROX decreased the abundance of AOA. In addition, different levels of ROX(except 0.3 μg·L) caused the decrease of the abundance of AOB, which suggested that AOA was less sensitive than AOB under ROX selective pressure. The results of high-throughput sequencing showed that ROX selective pressure caused the decrease of the numbers of OTUs for AOA and increase of that for AOB. The insensitive AOA, accounting for 57.70%-97.81% of the total sequences, were Nitrososphaera gargensis and Nitrosoarchaeum koreensis. The insensitive AOB were and , accounting for 0.76%-5.10% of the total sequences. These results also indicated that AOA was insensitive to ROX, but AOB was sensitive to ROX. RDA analyses showed that AOA . Nitrososphaera gargensis, . Nitrosoarchaeum koreensis and AOB were positively correlated with ROX concentrations.
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http://dx.doi.org/10.13227/j.hjkx.201612262 | DOI Listing |
Mol Diagn Ther
January 2025
Istituto Europeo di Oncologia, IRCCS, Via Adamello 16, 20139, Milan, Italy.
Background: Predicting response to targeted cancer therapies increasingly relies on both simple and complex genetic biomarkers. Comprehensive genomic profiling using high-throughput assays must be evaluated for reproducibility and accuracy compared with existing methods.
Methods: This study is a multicenter evaluation of the Oncomine™ Comprehensive Assay Plus (OCA Plus) Pan-Cancer Research Panel for comprehensive genomic profiling of solid tumors.
Nucleic Acids Res
January 2025
Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania.
The expansion of single-cell analytical techniques has empowered the exploration of diverse biological questions at the individual cells. Droplet-based single-cell RNA sequencing (scRNA-seq) methods have been particularly widely used due to their high-throughput capabilities and small reaction volumes. While commercial systems have contributed to the widespread adoption of droplet-based scRNA-seq, their relatively high cost limits the ability to profile large numbers of cells and samples.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang 330000, China.
Monkeypox (MPOX) is a zoonotic viral disease caused by the Monkeypox virus (MPXV), which has become the most significant public health threat within the genus since the eradication of the Variola virus (VARV). Despite the extensive attention MPXV has garnered, little is known about its clinical manifestations in humans. In this study, a high-throughput RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach was employed to investigate the transcriptional and metabolic responses of HEK293T cells to the MPXV A5L protein.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
Department of System Biology, Institute of Cytology and Genetics, Novosibirsk 630090, Russia.
Transcription factors (TFs) are the main regulators of eukaryotic gene expression. The cooperative binding of at least two TFs to genomic DNA is a major mechanism of transcription regulation. Massive analysis of the co-occurrence of overrepresented pairs of motifs for different target TFs studied in ChIP-seq experiments can clarify the mechanisms of TF cooperation.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China.
With the rapid advancement of high-throughput sequencing technologies, whole genome sequencing (WGS) has emerged as a crucial tool for studying genetic variation and population structure. Utilizing population genomics tools to analyze resequencing data allows for the effective integration of selection signals with population history, precise estimation of effective population size, historical population trends, and structural insights, along with the identification of specific genetic loci and variations. This paper reviews current whole genome sequencing technologies, detailing primary research methods, relevant software, and their advantages and limitations within population genomics.
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