The Annotation of Zebrafish Enhancer Trap Lines Generated with PB Transposon.

An enhancer trap (ET) mediated by a transposon is an effective method for functional gene research. Here, an ET system based on a PB transposon that carries a mini Krt4 promoter (the keratin4 minimal promoter from zebrafish) and the green fluorescent protein gene (GFP) has been used to produce zebrafish ET lines. One enhancer trap line with eye-specific expression GFP named EYE was used to identify the trapped enhancers and genes. Firstly, GFP showed a temporal and spatial expression pattern with whole-embryo expression at 6, 12, and 24 hpf stages and eye-specific expression from 2 to 7 dpf. Then, the genome insertion sites were detected by splinkerette PCR (spPCR). The Krt4-GFP was inserted into the fourth intron of the gene itgav (integrin, alpha V) in chromosome 9 of the zebrafish genome, with the GFP direction the same as that of the itgav gene. By the alignment of homologous gene sequences in different species, three predicted endogenous enhancers were obtained. The trapped endogenous gene itgav, whose overexpression is related to hepatocellular carcinoma, showed a similar expression pattern as GFP detected by in situ hybridization, which suggested that GFP and itgav were possibly regulated by the same enhancers. In short, the zebrafish enhancer trap lines generated by the PB transposon-mediated enhancer trap technology in this study were valuable resources as visual markers to study the regulators and genes. This work provides an efficient method to identify and isolate tissue-specific enhancer sequences.

Early human albumin administration is associated with reduced mortality in septic shock patients with acute respiratory distress syndrome: A retrospective study from the MIMIC-III database.

Background: Sepsis-induced acute respiratory distress syndrome (ARDS) was associated with higher mortality. It is unclear whether albumin supplementation early in the course of ARDS can affect the prognostic outcomes of septic shock (SS) patients with ARDS. Methods: The MIMIC-III database was employed to identify SS patients with ARDS. The effect of early application (<24 h after ICU admission) of human albumin on 28-day mortality in SS patients with ARDS was explored. The propensity score matching was used to minimize the bias between the non-albumin and early albumin treatment groups. Results: The analysis for all eligible patients who received human albumin showed significantly lower 28-hospital mortality rates than the non-albumin group (37% versus 47%, p = 0.018). After propensity matching, the difference between the two groups also significantly (34.8% versus 48.1%, p = 0.031). Moreover, we found that the relationship between albumin use and reduced 28-day mortality was inconsistent across SOFA score subgroups (Pinteraction = 0.004, non-adjustment for multiple testing). Conclusion: Early human albumin administration in SS patients with ARDS was independently associated with a reduction of 28-day mortality. Furthermore, the benefit of human albumin treatment appeared to be more pronounced in patients with a SOFA score of ≤ 10.

Phylogenetic Relationships among TnpB-Containing Mobile Elements in Six Bacterial Species.

Some families of mobile elements in bacterial genomes encode not only a transposase but also an accessory TnpB gene. This gene has been shown to encode an RNA-guided DNA endonuclease, co-evolving with Y1 transposase and serine recombinase in mobile elements IS605 and IS607. In this paper, we reveal the evolutionary relationships among TnpB-containing mobile elements (TCMEs) in well-assembled genomes of six bacterial species: Bacillus cereus, Clostridioides difficile, Deinococcus radiodurans, Escherichia coli, Helicobacter pylori and Salmonella enterica. In total, 9996 TCMEs were identified in 4594 genomes. They belonged to 39 different insertion sequences (ISs). Based on their genetic structures and sequence identities, the 39 TCMEs were classified into three main groups and six subgroups. According to our phylogenetic analysis, TnpBs include two main branches (TnpB-A and TnpB-B) and two minor branches (TnpB-C and TnpB-D). The key TnpB motifs and the associated Y1 and serine recombinases were highly conserved across species, even though their overall sequence identities were low. Substantial variation was observed for the rate of invasion across bacterial species and strains. Over 80% of the genomes of B. cereus, C. difficile, D. radiodurans and E. coli contained TCMEs; however, only 64% of the genomes of H. pylori and 44% of S. enterica genomes contained TCMEs. IS605 showed the largest rate of invasion in these species, while IS607 and IS1341 had a relatively narrow distribution. Co-invasions of IS605, IS607 and IS1341 elements were observed in various genomes. The largest average copy number was observed for IS605b elements in C. difficile. The average copy numbers of most other TCMEs were smaller than four. Our findings have important implications for understanding the co-evolution of TnpB-containing mobile elements and their biological roles in host genome evolution.

PiggyBac Transposon Mining in the Small Genomes of Animals.

TEs, including DNA transposons, are major contributors of genome expansions, and have played a very significant role in shaping the evolution of animal genomes, due to their capacity to jump from one genomic position to the other. In this study, we investigated the evolution landscapes of PB transposons, including their distribution, diversity, activity and structure organization in 79 species of small (compact) genomes of animals comprising both vertebrate and invertebrates. Overall, 212 PB transposon types were detected from almost half (37) of the total number of the small genome species (79) investigated. The detected PB transposon types, which were unevenly distributed in various genera and phyla, have been classified into seven distinct clades or families with good bootstrap support (>80%). The PB transposon types that were identified have a length ranging from 1.23 kb to 9.51 kb. They encode transposases of approximately ≥500 amino acids in length, and possess terminal inverted repeats (TIRs) ranging from 4 bp to 24 bp. Though some of the transposon types have long TIRs (528 bp), they still maintain the consistent and reliable 4 bp target site duplication (TSD) of TTAA. However, PiggyBac-2_Cvir transposon originating from the Crassostrea virginica species exhibits a unique TSD of TATG. The TIRs of the transposons in all the seven families display high divergence, with a highly conserved 5' end motif. The core transposase domains (DDD) were better conserved among the seven different families compared to the other protein domains, which were less prevalent in the vertebrate genome. The divergent evolution dynamics analysis also indicated that the majority of the PB transposon types identified in this study are either relatively young or old, with some being active. Additionally, numerous invasions of PB transposons were found in the genomes of both vertebrate and invertebrate animals. The data reveals that the PB superfamily is widely distributed in these species. PB transposons exhibit high diversity and activity in the small genomes of animals, and might play a crucial role in shaping the evolution of these small genomes of animals.

Dielectric barrier discharge coupled with Fe2+, Mn2+ and Cu2+ scrubbing for toluene removal.

By-product ozone emission is one of the challenges for applying dielectric barrier discharge (DBD) technology for volatile organic compounds (VOCs) removal. In this study, a DBD reactor followed by a wet scrubber (WS) containing a solution of metal ions (Fe2+/Mn2+/Cu2+) was used to reuse ozone for further oxidation of typical VOC toluene. Compared with the degradation effect of the DBD reactor alone, DBD coupled WS/iron system not only improved the toluene removal efficiency but also significantly reduced the ozone emission. The ozone removal efficiency reached as high as 98% in the DBD coupled WS/Fe2+ system. Electron paramagnetic resonance (EPR) tests showed that ozone was converted into radicals such as hydroxyl radicals in Fe2+ and Cu2+ solution, which further oxidized toluene in WS/iron. Quenching experiments showed that the contribution for toluene degradation by radicals was up to 75% and 62% in Fe2+ and Mn2+ reactor, respectively. This study demonstrates that the DBD coupled WS system has the potential to be an environmentally friendly technology for gaseous VOCs removal.