Project description:Is single-cell genomics a useful technique to address evolutionary questions? Insights from three Monosiga brevicollis single-cell amplified genomes
Project description:This study describes the combined sequencing of the genomes and transcriptomes of single blastomeres from mouse 8-cell stage embryos.
Project description:Incomplete antibiotic removal in pharmaceutical wastewater treatment plants (PWWTPs) could lead to the development and spread of antibiotic-resistant bacteria (ARBs) and genes (ARGs) in the environment, posing a growing public health threat. In this study, two multiantibiotic-resistant bacteria, Ochrobactrum intermedium (N1) and Stenotrophomonas acidaminiphila (N2), were isolated from the sludge of a PWWTP in Guangzhou, China. The N1 strain was highly resistant to ampicillin, cefazolin, chloramphenicol, tetracycline, and norfloxacin, while the N2 strain exhibited high resistance to ampicillin, chloramphenicol, and cefazolin. Whole-genome sequencing revealed that N1 and N2 had genome sizes of 0.52 Mb and 0.37 Mb, respectively, and harbored 33 and 24 ARGs, respectively. The main resistance mechanism in the identified ARGs included efflux pumps, enzymatic degradation, and target bypass, with the N1 strain possessing more multidrug-resistant efflux pumps than the N2 strain (22 vs 12). This also accounts for the broader resistance spectrum of N1 than of N2 in antimicrobial susceptibility tests. Additionally, both genomes contain numerous mobile genetic elements (89 and 21 genes, respectively) and virulence factors (276 and 250 factors, respectively), suggesting their potential for horizontal transfer and pathogenicity. Overall, this research provides insights into the potential risks posed by ARBs in pharmaceutical wastewater and emphasizes the need for further studies on their impact and mitigation strategies.
Project description:Wastewater has been extensively studied along the years. However, these studies have been focused on the analysis of small molecules. There are no studies about the proteins present in wastewater and let alone an established method to study them. We propose a method for the study of the proteins in wastewater overcoming their low concentration and the interference of other molecules. Moreover, we differentiate between the proteins that are soluble and the ones in the particulate. This method is based on concentration, lysis and clean-up steps. The samples were analyzed afterward using liquid chromatography coupled to high-resolution mass spectrometry (HR-LC/MS) and the data searched with Proteome Discoverer. Thus, this complete method has allowed us to characterize the proteomic composition of different wastewater samples with a low volume.
Project description:This study (McConnell, et al. Science 2012) used both SNP array and sequencing data to examine copy number variation in neuronal genomes. Encolsed here are the SNP Array data from the 42 fibroblasts, 19 human induced pluripotent stem cell (hiPSC)-derived neural progenitor cells (NPCs), and 40 hiPSC-derived neurons that were reported in the manuscript. Copy number analysis was performed on .CEL files using Partek Genomics Suite with a custom single cell reference file.