Biotransformation of doxycycline by \u3ci\u3eBrevundimonas naejangsanensis\u3c/i\u3e and \u3ci\u3eSphingobacterium mizutaii\u3c/i\u3e strains

The fate of doxycycline (DC), a second generation tetracycline antibiotic, in the environment has drawn increasing attention in recent years due to its wide usage. Little is known about the biodegradability of DC in the environment. The objective of this study was to characterize the biotransformation of DC by pure bacterial strains with respect to reaction kinetics under different environmental conditions and biotransformation products. Two bacterial strains, Brevundimonas naejangsanensis DD1 and Sphingobacterium mizutaii DD2, were isolated from chicken litter and characterized for their biotransformation capability of DC. Results show both strains rely on cometabolism to biotransform DC with tryptone as primary growth substrate. DD2 had higher biotransformation kinetics than DD1. The two strains prefer similar pHs (7 and 8) and temperature (30 °C), however, they exhibited opposite responses to increasing background tryptone concentration. While hydrolysis converted DC to its isomer or epimer, the two bacterial strains converted DC to various biotransformation products through a series of demethylation, dehydration, decarbonylation and deamination. Findings from the study can be used to better predict the fate of DC in the environment

Single-scan, dual-functional interferometer for fast spatiotemporal characterization of few-cycle pulses

Accurate and fast characterization of spatiotemporal information of high-intensity, ultrashort pulses is crucial in the field of strong-field laser science and technology. While conventional self-referenced interferometers were widely used to retrieve the spatial profile of the relative spectral phase of pulses, additional measurements of temporal and spectral information at a particular position of the laser beam were, however, necessary to remove the indeterminacy, which increases the system complexity. Here we report an advanced, dual-functional interferometer that is able to reconstruct the complete spatiotemporal information of ultrashort pulses with a single scan of the interferometer arm. The set-up integrates an interferometric frequency-resolved optical gating (FROG) with a radial shearing Michelson interferometer. Trough scanning one arm of the interferometer, both cross-correlated FROG trace at the central part of the laser beam and delay-dependent interferograms of the entire laser profile are simultaneously obtained, allowing a fast 3-dimensional reconstruction of few-cycle laser pulses

Four-dimensional Cone Beam CT Reconstruction and Enhancement using a Temporal Non-Local Means Method

Four-dimensional Cone Beam Computed Tomography (4D-CBCT) has been developed to provide respiratory phase resolved volumetric imaging in image guided radiation therapy (IGRT). Inadequate number of projections in each phase bin results in low quality 4D-CBCT images with obvious streaking artifacts. In this work, we propose two novel 4D-CBCT algorithms: an iterative reconstruction algorithm and an enhancement algorithm, utilizing a temporal nonlocal means (TNLM) method. We define a TNLM energy term for a given set of 4D-CBCT images. Minimization of this term favors those 4D-CBCT images such that any anatomical features at one spatial point at one phase can be found in a nearby spatial point at neighboring phases. 4D-CBCT reconstruction is achieved by minimizing a total energy containing a data fidelity term and the TNLM energy term. As for the image enhancement, 4D-CBCT images generated by the FDK algorithm are enhanced by minimizing the TNLM function while keeping the enhanced images close to the FDK results. A forward-backward splitting algorithm and a Gauss-Jacobi iteration method are employed to solve the problems. The algorithms are implemented on GPU to achieve a high computational efficiency. The reconstruction algorithm and the enhancement algorithm generate visually similar 4D-CBCT images, both better than the FDK results. Quantitative evaluations indicate that, compared with the FDK results, our reconstruction method improves contrast-to-noise-ratio (CNR) by a factor of 2.56~3.13 and our enhancement method increases the CNR by 2.75~3.33 times. The enhancement method also removes over 80% of the streak artifacts from the FDK results. The total computation time is ~460 sec for the reconstruction algorithm and ~610 sec for the enhancement algorithm on an NVIDIA Tesla C1060 GPU card.Comment: 20 pages, 3 figures, 2 table

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Antibiotics and Resistance Genes in Awash River Basin, Ethiopia

Among contaminants of emerging concern in the environment, a growing attention has been given to antibiotics and antibiotic-resistant genes (ARGs) due to the rise in their usage and potential ecotoxicological and public health effect. However, the occurrence of these contaminants in the environment is little investigated in developing countries particularly in sub-Saharan regions. In this study, the occurrence of three groups of antimicrobials including tetracycline, sulfonamides and fluoroquinolone, and their corresponding ARGs were investigated in the sediments of Awash River Basin, Ethiopia. Out of twelve studied compounds, sulfadiazine and enrofloxacin showed the highest and lowest detection frequency, respectively. Polymerase chain reaction (PCR) analysis revealed that tetA and tetB occurred in all the samples. The relative abundance of the resistant genes was in the following order: tetA > tetB > sul2 > sul1. Redundancy analysis result indicated that some sediment characteristics were found to have influence on the distribution sul1-resistant gene

Microplastic pollution in vegetable farmlands of suburb Wuhan, central China

Microplastic pollution has become an emergency issue in the global environment. However, little is known about the occurrence and distribution of microplastics in agroecological system. In this study, we investigated the pollution of microplastics in vegetable farmlands in suburb of Wuhan, central China. Results showed that the abundance of microplastics ranged from 320 to 12,560 items/kg(dw). Microplastic pollution adjacent to the suburban roads was about 1.8 times as serious as that in the residential areas. Microplastics with size less than 0.2 mm were dominated, reaching 70% in total. The main types of microplastics were fibers and microbeads. Moreover, polyamide (32.5%) and polypropylene (28.8%) were the main types of polymer. This study proclaims the occurrence and characteristics of microplastic pollution in typical farmland soils of suburb land. It may provide significant basis for subsequent research about microplastics contaminant in the terrestrial ecosystem. (C) 2019 Elsevier Ltd. All rights reserved

Defense responses in earthworms (Eisenia fetida) exposed to low-density polyethylene microplastics in soils

The potential threats of microplastics to global health are a new problem. However, little is known about the influence of microplastics on soil organisms. Here, we investigated the effects of low-density polyethylene (LDPE, < 400 mu m) on earthworms (Eisenia fetida) under different concentrations (0.1, 0.25, 0.5, 1.0, 1.5 g/kg dry) with three replicates in artificial soil. Results showed that surface damage of earthworms was observed at the concentration of 1.5 g/kg LDPE after exposure 28 days. The microplastics were ingested in a dose-response manner. Smaller sizes of LDPE microplastics were found in the casts of E. fetida, and approximately 30% of the microplastics egested (size < 100 mu m) were increased compared with initial microplastics in the soil. The catalase activity and malondialdehyde content increased significantly at the concentration of 1.0 g/kg LDPE after exposure 28 days, and acetylcholine esterase was significantly stimulated at concentrations of 1.5 and 1.0 g/kg LDPE on days 21 and 28, respectively. The results of this study demonstrate the potential risk of LDPE microplastics to E. fetida and may provide a reference for the impact of microplastics on terrestrial creatures