Staphylococcus aureus is an important human pathogen, but studies of the organism have suffered from the lack of a robust tool set for its genetic and genomic manipulation. Here we report the development of a system for the facile and high-throughput genomic engineering of S. aureus using single-stranded DNA (ssDNA) oligonucleotide recombineering coupled with clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-mediated counterselection. We identify recombinase EF2132, derived from Enterococcus faecalis, as being capable of integrating single-stranded DNA oligonucleotides into the S. aureus genome. We found that EF2132 can readily mediate recombineering across multiple characterized strains (3 of 3 tested) and primary clinical isolates (6 of 6 tested), typically yielding thousands of recombinants per transformation. Surprisingly, we also found that some S. aureus strains are naturally recombinogenic at measurable frequencies when oligonucleotides are introduced by electroporation, even without exogenous recombinase expression. We construct a temperature-sensitive, two-vector system which enables conditional recombineering and CRISPR/Cas9-mediated counterselection in S. aureus without permanently introducing exogenous genetic material or unintended genetic lesions. We demonstrate the ability of this system to efficiently and precisely engineer point mutations and large single-gene deletions in the S. aureus genome and to yield highly enriched populations of engineered recombinants even in the absence of an externally selectable phenotype. By virtue of utilizing inexpensive, commercially synthesized synthetic DNA oligonucleotides as substrates for recombineering and counterselection, this system provides a scalable, versatile, precise, inexpensive, and generally useful tool for producing isogenic strains in S. aureus which will enable the high-throughput functional assessment of genome variation and gene function across multiple strain backgrounds.

An increasing number of reports have revealed that long non-coding RNAs are important players in tumorigenesis. Here we showed that long non-coding RNA LINC00461 is highly expressed in glioma tissues compared to non-neoplastic brain tissues. The knockdown of LINC00461 suppressed cyclinD1/A/E expression which led to G0/G1 cell cycle arrest and inhibited cell proliferation in glioma cells. LINC00461 suppression also inhibited glioma cell migration and invasion. The function of LINC00461 in glioma cells is partially mediated by MAPK/ERK and PI3K/AKT signaling pathways as down-regulation of LINC00461 expression suppressed ERK1/2 and AKT activities. Moreover, LINC00461 knockdown decreased expression levels of microRNA miR-9 and flanking genes MEF2C and TMEM161B. Taken together, our results demonstrate that LINC00461 is important for glioma progression affecting cell proliferation, migration and invasion via MAPK/ERK, PI3K/AKT, and possibly other signaling pathways.

Objective. Repair and regeneration of peripheral nerve defect by engineered conduits have greatly advanced in the past decades while still facing great challenges. Approach. In this work, we fabricated a new highly oriented poly(L-lactic acid) (PLLA)/soy protein isolate (SPI) nanofibrous conduit (HO-PSNC) for nerve regeneration. Main results. Firstly, we observed that SPI could efficiently modify PLLA for the electrospinning of PLLA/SPI nanofibers with enhanced physical and biological properties. Incorporation of SPI decreased the fiber diameter and ductility of PLLA/SPI nanofibrous films (PSNFs), improved the tensile strength and surface wettability of PSNFs and increased the in vivo degradability of the PSNFs. When the hybrid ratio of SPI was 20 and 40%, PSNFs could efficiently promote neural cell extension and differentiation in vitro. Based on these data, 20% SPI (PSNF-20) was chosen for further investigation. Next, PSNF-20 with different fiber orientations (random/low orientation, medium, and high orientation, respectively) were developed and used for evaluating neural cell behaviors on the materials. Results revealed that the PSNF-20 with highly oriented nanofibers (HO-PSNF-20) or mediumly oriented nanofibers (MO-PSNF-20) showed a better performance in directing cell extension and enhancing neurite outgrowth. Finally, the highly oriented nanofibers conduits (HO-PSNC-20) were used to bridge sciatic nerve defect in rats with highly oriented PLLA and autografts as controls. HO-PSNC-20 exhibited a significant promotion in nerve regeneration and functional reconstruction comparing to highly oriented PLLA as proven by the evaluations of walking track, electrophysiology, toluidine blue nerve staining, transmission electron microscopy, neural factors staining and qPCR, and gastrocnemius histology. Significance. In conclusion, nerve conduit fabricated from aligned electrospinning of SPI-modified PLLA nanofibers is promising for peripheral nerve regeneration.

Inhaled aztreonam is increasingly used for chronic Pseudomonas aeruginosa suppression in patients with cystic fibrosis (CF), but the potential for that organism to evolve aztreonam resistance remains incompletely explored. Here, we performed genomic analysis of clonally related pre- and posttreatment CF clinical isolate pairs to identify genes that are under positive selection during aztreonam therapy in vivo. We identified 16 frequently mutated genes associated with aztreonam resistance, the most prevalent being ftsI and ampC, and 13 of which increased aztreonam resistance when introduced as single gene transposon mutants. Several previously implicated aztreonam resistance genes were found to be under positive selection in clinical isolates even in the absence of inhaled aztreonam exposure, indicating that other selective pressures in the cystic fibrosis airway can promote aztreonam resistance. Given its potential to confer plasmid-mediated resistance, we further characterized mutant ampC alleles and performed artificial evolution of ampC for maximal activity against aztreonam. We found that naturally occurring ampC mutants conferred variably increased resistance to aztreonam (2- to 64-fold) and other β-lactam agents but that its maximal evolutionary capacity for hydrolyzing aztreonam was considerably higher (512- to 1,024-fold increases) and was achieved while maintaining or increasing resistance to other drugs. These studies implicate novel chromosomal aztreonam resistance determinants while highlighting that different mutations are favored during selection in vivo and in vitro, show that ampC has a high maximal potential to hydrolyze aztreonam, and provide an approach to disambiguate mutations promoting specific resistance phenotypes from those more generally increasing bacterial fitness in vivo.

The first name of the third author was misspelled. The name should appear as shown above.