Impacts of florfenicol on the microbiota landscape and resistome as revealed by metagenomic analysis.

BACKGROUND:Drug-resistant fish pathogens can cause significant economic loss to fish farmers. Since 2012, florfenicol has become an approved drug for treating both septicemia and columnaris diseases in freshwater fish. Due to the limited drug options available for aquaculture, the impact of the therapeutical florfenicol treatment on the microbiota landscape as well as the resistome present in the aquaculture farm environment needs to be evaluated. RESULTS:Time-series metagenomic analyses were conducted to the aquatic microbiota present in the tank-based catfish production systems, in which catfish received standard therapeutic 10-day florfenicol treatment following the federal veterinary regulations. Results showed that the florfenicol treatment shifted the structure of the microbiota and reduced the biodiversity of it by acting as a strong stressor. Planctomycetes, Chloroflexi, and 13 other phyla were susceptible to the florfenicol treatment and their abundance was inhibited by the treatment. In contrast, the abundance of several bacteria belonging to the Proteobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia phyla increased. These bacteria with increased abundance either harbor florfenicol-resistant genes (FRGs) or had beneficial mutations. The florfenicol treatment promoted the proliferation of florfenicol-resistant genes. The copy number of phenicol-specific resistance genes as well as multiple classes of antibiotic-resistant genes (ARGs) exhibited strong correlations across different genetic exchange communities (p < 0.05), indicating the horizontal transfer of florfenicol-resistant genes among these bacterial species or genera. Florfenicol treatment also induced mutation-driven resistance. Significant changes in single-nucleotide polymorphism (SNP) allele frequencies were observed in membrane transporters, genes involved in recombination, and in genes with primary functions of a resistance phenotype. CONCLUSIONS:The therapeutical level of florfenicol treatment significantly altered the microbiome and resistome present in catfish tanks. Both intra-population and inter-population horizontal ARG transfer was observed, with the intra-population transfer being more common. The oxazolidinone/phenicol-resistant gene optrA was the most prevalent transferred ARG. In addition to horizontal gene transfer, bacteria could also acquire florfenicol resistance by regulating the innate efflux systems via mutations. The observations made by this study are of great importance for guiding the strategic use of florfenicol, thus preventing the formation, persistence, and spreading of florfenicol-resistant bacteria and resistance genes in aquaculture

Novel PCR-based rapid detection strategies for Escherichia coli O157:H7 and Salmonella in meat products

The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file.Title from PDF of title page (University of Missouri--Columbia, viewed on January 28, 2011).Thesis advisor: Dr. Azlin Mustapha.Vita.Includes bibliographical references.Ph. D. University of Missouri--Columbia 2009.Accurate and fast detection methods for foodborne pathogens from various food samples have always been important goals for scientists from many research areas. DNA-based PCR techniques cannot differentiate between DNA from live and dead cells. Ethidium bromide monoazide (EMA) is a dye that can bind to DNA of dead cells and prevent its amplification by PCR. An EMA staining step prior to real-time PCR allows for the effective inhibition of DNA contamination from dead cells. With an optimized EMA staining step, the detection range was 10₃ to 10₉ CFU/ml for pure cultures, 10₅ to 10₉ CFU/ml for artificially contaminated poult y samples, and 10₈ to 10₄ CFU/g for ground beef samples. After a 12-h enrichment step, EMA combined real-time PCR could detect as low as 10 CFU/ml Salmonella from poultry products, as well as 10 CFU/g E. coli O157:H7 from ground beef. Quantum dots (QDs) are a family of nanosized particles with a 1 to 10 nm in radius. It has long-term stable photostability, high quantum yield, broad absorption spectra, narrow emission spectra and high signal-to-noise ratio. In this study, bead free QD facilitated detection method was used to detect Salmonella and E. coli O157:H7 cells from pure cultures, it can detect as low as 10 CFU/ml cells. When it was applied to artificially contaminated ground beef, it can detect 10₆ CFU/g cells. After enrichment, it can detect as low as 10 CFU/g Salmonella cells from ground beef

Simulation of Pollutant Transport in an Urban Area

The present study is concerned with the feasibility of simulating the release and transport of a ``generic\u27 pollutant within an urban area. The motivation behind this effort lies in the need for accurate and timely predictions of the effects of a pollutant release in a densely populated region, in order to coordinate relief and/or evacuation efforts or design rapid-response scenarios in the event of a possible accident. In order to achieve the above goal, following geometrical, physical, and algorithmic steps have to be taken, generation of a three-dimensional grid, numerical solution of the governing fluid dynamics equations, and numerically solving the transport (reaction/advection/diffusion) equations for a generic pollutant. Some preliminary results will be presented at this time. A sample of representative results will be shown for the generation and transport of a generic pollutant ``plume\u27, using different starting wind conditions and release points. Future efforts in this endeavor will focus on obtaining reasonably accurate simulations of pollutant transport at a reasonable computational price. Specifically, ``reduced\u27 models for the geometry and/or the governing equations will be investigated

Simultaneous quantitation of Escherichia coli O157:H7, salmonella and shigella in ground beef by multiplex real-time PCR and immunomagnetic separation

The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file.Title from title screen of research.pdf file viewed on (February 23, 2007)Includes bibliographical references.Thesis (M.S.) University of Missouri-Columbia 2006.Dissertations, Academic -- University of Missouri--Columbia -- Food science.The objectives of this study were to establish a real-time multiplex polymerase chain reaction (PCR) for simultaneous quantitation of Escherichia coli O157:H7, Salmonella and Shigella that have been implicated in a number of foodborne disease outbreaks. Genomic DNA for the real-time PCR was extracted by the boiling method. Three sets of primers and corresponding TaqMan® probes were designed to target these three pathogens. Multiplex real-time PCR was carried out with TaqMan® Universal PCR Master Mix in an ABI Prism 7700 Sequence Detection System. Final standard curves were calculated by plotting the threshold cycle (Ct) value against log10 CFU/ml by linear regression to analyze the results for each pathogen. With optimized conditions, the quantitative detection ranges of the real-time multiplex PCR for pure cultures were 102 to 109 CFU/ml for E. coli O157:H7, 103 to 109 CFU/ml for Salmonella and 101 to 108 CFU/ml for Shigella. When this established multiplex real-time PCR system was applied to ground beef samples, the lowest detection concentration of three pathogens were increased to 105 CFU/g for E. coli O157:H7, 103 CFU/g for Salmonella and 104 CFU/g for Shigella. Immunomagnetic separation was then used to isolate E. coli O157:H7 and Salmonella from the beef samples. The lowest detection concentrations of three pathogens were reduced to 103 CFU/g. TaqMan® real-time PCR, combined with IMS has the potential to be a faster and more reliable method for rapid quantitation of E. coli O157:H7, Salmonella and Shigella in food, which will take 3 h for the whole process

Qinghai-Tibet Railway, China and the Solutions to Its Major Geotechnical Problems for Construction

The Qinghai-Tibet Railway (QTR) is the highest-elevation one for passenger trains in the world and the first railway to connect central China to Tibet. Construction of this railway starting in 2001 had to contend with major geotechnical challenges, such as permafrost, environmental protection and seismic hazards. Its completion in 2006 is a remarkable feat in the world’s railway construction history and crystallization of wisdom of human beings. In this paper, the planning and preparing history and the construction project of QTR are introduced. The major three thorny problems, permafrost, lack of oxygen and environmental frangibility for the construction and their solutions are presented, which are active methods of riprap roadbeds, heat pipe roadbed and bridges over land for permafrost, health care system for lack of oxygen and environmental protection measures for construction and operation. Seismic safety assessment was carried out for earthquake damage mitigation of the railway. The laboratory test, field test and observation, and it’s operation have shown that design, construction, and measures for earthquake hazards mitigation and environmental protection of the Qinghai-Tibet Railway are completely successful

Applications of gel electrophoresis in quantum dot conjugates' separation and purification

Title from PDF of title page (University of Missouri--Columbia, viewed on Feb 19, 2010).The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file.Thesis advisor: Dr. Xudong Fan and Dr. Azlin Mustapha.M.S. University of Missouri--Columbia 2009.The objectives of this study were to build Quantum dot (QD) crosslinker complexes for antibody conjugation usage, to purify QD crosslinker complexes by gel electrophoresis and to check the biological functionalities of eluted QD crosslinker complexes recovered from gel electrophoresis by cell based microarray. Zero-length crosslinker 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) was chosen to be the first crosslinkers, followed by the conjugation with secondary crosslinker protein A. The purpose of adding secondary crosslinkers was to make uniform QD crosslinker complexes. Due to the high affinity between protein A and the Fc region of antibodies, QD EDC protein A complexes were in uniform structures and all antigen binding sites faced outwardly. Gel electrophoresis is a method used for separating DNA, RNA or proteins in biological studies. In this study, gel electrophoresis was adopted to check the complete conjugation between QDs and protein A. In addition, it was successfully used as a separation method for purifying conjugated QDs. GeBaflex tubes were used to elute the conjugated QDs from the gel, these recovered QD EDC protein A complexes showed their biological functionalities in cell based microarray studies.Includes bibliographical references

From Artifacts to Outcomes: Comparison of HMD VR, Desktop, and Slides Lectures for Food Microbiology Laboratory Instruction

Despite the value of VR (Virtual Reality) for educational purposes, the instructional power of VR in Biology Laboratory education remains under-explored. Laboratory lectures can be challenging due to students' low motivation to learn abstract scientific concepts and low retention rate. Therefore, we designed a VR-based lecture on fermentation and compared its effectiveness with lectures using PowerPoint slides and a desktop application. Grounded in the theory of distributed cognition and motivational theories, our study examined how learning happens in each condition from students' learning outcomes, behaviors, and perceptions. Our result indicates that VR facilitates students' long-term retention to learn by cultivating their longer visual attention and fostering a higher sense of immersion, though students' short-term retention remains the same across all conditions. This study extends current research on VR studies by identifying the characteristics of each teaching artifact and providing design implications for integrating VR technology into higher education

Ferroptosis: new insight into the mechanisms of diabetic nephropathy and retinopathy

Diabetic nephropathy (DN) and diabetic retinopathy (DR) are the most serious and common diabetes-associated complications. DN and DR are all highly prevalent and dangerous global diseases, but the underlying mechanism remains to be elucidated. Ferroptosis, a relatively recently described type of cell death, has been confirmed to be involved in the occurrence and development of various diabetic complications. The disturbance of cellular iron metabolism directly triggers ferroptosis, and abnormal iron metabolism is closely related to diabetes. However, the molecular mechanism underlying the role of ferroptosis in DN and DR is still unclear, and needs further study. In this review article, we summarize and evaluate the mechanism of ferroptosis and its role and progress in DN and DR, it provides new ideas for the diagnosis and treatment of DN and DR