Novel mechanisms of diversity generation in Acinetobacter baumannii resistance islands driven by Tn7-like elements.

Mobile genetic elements play an important role in the acquisition of antibiotic and biocide resistance, especially through the formation of resistance islands in bacterial chromosomes. We analyzed the contribution of Tn7-like transposons to island formation and diversification in the nosocomial pathogen Acinetobacter baumannii and identified four separate families that recognize different integration sites. One integration site is within the comM gene and coincides with the previously described Tn6022 elements suggested to account for the AbaR resistance island. We established Tn6022 in a heterologous E. coli host and confirmed basic features of transposition into the comM attachment site and the use of a novel transposition protein. By analyzing population features within Tn6022 elements we identified two potential novel transposon-encoded diversification mechanisms with this dynamic genetic island. The activities of these diversification features were confirmed in E. coli. One was a novel natural gain-of-activity allele that could function to broaden transposition targeting. The second was a transposon-encoded hybrid dif-like site that parasitizes the host dimer chromosome resolution system to function with its own tyrosine recombinase. This work establishes a highly active Tn7-like transposon that harnesses novel features allowing the spread and diversification of genetic islands in pathogenic bacteria.

A Tripartite Efflux System Affects Flagellum Stability in Helicobacter pylori.

Helicobacter pylori uses a cluster of polar, sheathed flagella for swimming motility. A search for homologs of H. pylori proteins that were conserved in Helicobacter species that possess flagellar sheaths but were underrepresented in Helicobacter species with unsheathed flagella identified several candidate proteins. Four of the identified proteins are predicted to form part of a tripartite efflux system that includes two transmembrane domains of an ABC transporter (HP1487 and HP1486), a periplasmic membrane fusion protein (HP1488), and a TolC-like outer membrane efflux protein (HP1489). Deleting hp1486/hp1487 and hp1489 homologs in H. pylori B128 resulted in reductions in motility and the number of flagella per cell. Cryo-electron tomography studies of intact motors of the Δhp1489 and Δhp1486/hp1487 mutants revealed many of the cells contained a potential flagellum disassembly product consisting of decorated L and P rings, which has been reported in other bacteria. Aberrant motors lacking specific components, including a cage-like structure that surrounds the motor, were also observed in the Δhp1489 mutant. These findings suggest a role for the H. pylori HP1486-HP1489 tripartite efflux system in flagellum stability. Three independent variants of the Δhp1486/hp1487 mutant with enhanced motility were isolated. All three motile variants had the same frameshift mutation in fliL, suggesting a role for FliL in flagellum disassembly.

Loss of a Cardiolipin Synthase in Helicobacter pylori G27 Blocks Flagellum Assembly.

Helicobacter pylori uses a cluster of polar, sheathed flagella for motility, which it requires for colonization of the gastric epithelium in humans. As part of a study to identify factors that contribute to localization of the flagella to the cell pole, we disrupted a gene encoding a cardiolipin synthase (clsC) in H. pylori strains G27 and B128. Flagellum biosynthesis was abolished in the H. pylori G27 clsC mutant but not in the B128 clsC mutant. Transcriptome sequencing analysis showed that flagellar genes encoding proteins needed early in flagellum assembly were expressed at wild-type levels in the G27 clsC mutant. Examination of the G27 clsC mutant by cryo-electron tomography indicated the mutant assembled nascent flagella that contained the MS ring, C ring, flagellar protein export apparatus, and proximal rod. Motile variants of the G27 clsC mutant were isolated after allelic exchange mutagenesis using genomic DNA from the B128 clsC mutant as the donor. Genome resequencing of seven motile G27 clsC recipients revealed that each isolate contained the flgI (encodes the P-ring protein) allele from B128. Replacing the flgI allele in the G27 clsC mutant with the B128 flgI allele rescued flagellum biosynthesis. We postulate that H. pylori G27 FlgI fails to form the P ring when cardiolipin levels in the cell envelope are low, which blocks flagellum assembly at this point. In contrast, H. pylori B128 FlgI can form the P ring when cardiolipin levels are low and allows for the biosynthesis of mature flagella.IMPORTANCEH. pylori colonizes the epithelial layer of the human stomach, where it can cause a variety of diseases, including chronic gastritis, peptic ulcer disease, and gastric cancer. To colonize the stomach, H. pylori must penetrate the viscous mucous layer lining the stomach, which it accomplishes using its flagella. The significance of our research is identifying factors that affect the biosynthesis and assembly of the H. pylori flagellum, which will contribute to our understanding of motility in H. pylori, as well as other bacterial pathogens that use their flagella for host colonization.

Closed-loop modulation of remote hippocampal representations with neurofeedback.

Humans can remember specific events without acting on them and can influence which memories are retrieved based on internal goals. However, current animal models of memory typically present sensory cues to trigger retrieval and assess retrieval based on action 1-5 . As a result, it is difficult to determine whether measured patterns of neural activity relate to the cue(s), the retrieved memory, or the behavior. We therefore asked whether we could develop a paradigm to isolate retrieval-related neural activity in animals without retrieval cues or the requirement of a behavioral report. To do this, we focused on hippocampal "place cells." These cells primarily emit spiking patterns that represent the animal's current location (local representations), but they can also generate representations of previously visited locations distant from the animal's current location (remote representations) 6-13 . It is not known whether animals can deliberately engage specific remote representations, and if so, whether this engagement would occur during specific brain states. So, we used a closed-loop neurofeedback system to reward expression of remote representations that corresponded to uncued, experimenter-selected locations, and found that rats could increase the prevalence of these specific remote representations over time; thus, demonstrating memory retrieval modulated by internal goals in an animal model. These representations occurred predominately during periods of immobility but outside of hippocampal sharp-wave ripple (SWR) 13-15 events. This paradigm enables future direct studies of memory retrieval mechanisms in the healthy brain and in models of neurological disorders.

Spyglass: a framework for reproducible and shareable neuroscience research.

Scientific progress depends on reliable and reproducible results. Progress can also be accelerated when data are shared and re-analyzed to address new questions. Current approaches to storing and analyzing neural data typically involve bespoke formats and software that make replication, as well as the subsequent reuse of data, difficult if not impossible. To address these challenges, we created Spyglass, an open-source software framework that enables reproducible analyses and sharing of data and both intermediate and final results within and across labs. Spyglass uses the Neurodata Without Borders (NWB) standard and includes pipelines for several core analyses in neuroscience, including spectral filtering, spike sorting, pose tracking, and neural decoding. It can be easily extended to apply both existing and newly developed pipelines to datasets from multiple sources. We demonstrate these features in the context of a cross-laboratory replication by applying advanced state space decoding algorithms to publicly available data. New users can try out Spyglass on a Jupyter Hub hosted by HHMI and 2i2c: https://spyglass.hhmi.2i2c.cloud/.

GhostiPy: An Efficient Signal Processing and Spectral Analysis Toolbox for Large Data.

Recent technological advances have enabled neural recordings consisting of hundreds to thousands of channels. As the pace of these developments continues to grow rapidly, it is imperative to have fast, flexible tools supporting the analysis of neural data gathered by such large-scale modalities. Here we introduce GhostiPy (general hub of spectral techniques in Python), a Python open source software toolbox implementing various signal processing and spectral analyses including optimal digital filters and time-frequency transforms. GhostiPy prioritizes performance and efficiency by using parallelized, blocked algorithms. As a result, it is able to outperform commercial software in both time and space complexity for high-channel count data and can handle out-of-core computation in a user-friendly manner. Overall, our software suite reduces frequently encountered bottlenecks in the experimental pipeline, and we believe this toolset will enhance both the portability and scalability of neural data analysis.

Combined Epithelial, Stromal, and Anterior Chamber Ingrowth After Penetrating Keratoplasty.

PURPOSE: To present a case of primary graft failure after penetrating keratoplasty found to have epithelial ingrowth into the host stroma on histopathologic analysis. METHODS: This is a single observational case report. RESULTS: We herein describe the clinical course of a case of primary graft failure after penetrating keratoplasty. The corneal button was sent for histopathologic analysis. Analysis of the patient's failed corneal button revealed circumferential epithelial full-thickness wound invasion and stromal epithelial invasion into corneal stroma. CONCLUSIONS: Based on histopathologic analysis and this patient's presentation, the stromal ingrowth followed recipient epithelial invasion of the wound and stromal invasion through clefts in the donor corneal edges. Cases of primary graft failure should be assessed for histopathologic evidence of epithelial stromal ingrowth, despite its rarity. To our knowledge, epithelial ingrowth into the corneal donor stroma after penetrating keratoplasty has not been previously reported.

Phylogenetic Distribution, Ultrastructure, and Function of Bacterial Flagellar Sheaths.

A number of Gram-negative bacteria have a membrane surrounding their flagella, referred to as the flagellar sheath, which is continuous with the outer membrane. The flagellar sheath was initially described in Vibrio metschnikovii in the early 1950s as an extension of the outer cell wall layer that completely surrounded the flagellar filament. Subsequent studies identified other bacteria that possess flagellar sheaths, most of which are restricted to a few genera of the phylum Proteobacteria. Biochemical analysis of the flagellar sheaths from a few bacterial species revealed the presence of lipopolysaccharide, phospholipids, and outer membrane proteins in the sheath. Some proteins localize preferentially to the flagellar sheath, indicating mechanisms exist for protein partitioning to the sheath. Recent cryo-electron tomography studies have yielded high resolution images of the flagellar sheath and other structures closely associated with the sheath, which has generated insights and new hypotheses for how the flagellar sheath is synthesized. Various functions have been proposed for the flagellar sheath, including preventing disassociation of the flagellin subunits in the presence of gastric acid, avoiding activation of the host innate immune response by flagellin, activating the host immune response, adherence to host cells, and protecting the bacterium from bacteriophages.

Tracing a Path for Memory in the Hippocampus.

The hippocampal activity supporting trace fear conditioning has long been mysterious, but a leading hypothesis posits "time-cell"-like sequential patterns. In this issue of Neuron, Ahmed et al. (2020) present new data suggesting that, at least during the first session of learning, a subset of neurons coalesce to selectively encode the task but without expressing reliable sequences.

Evaluating the effect of intravitreal triamcinolone-moxifloxacin during cataract surgery on central macular edema in patients with preexisting diabetic retinopathy.

PURPOSE: To evaluate the effect of intravitreal triamcinolone acetonide-moxifloxacin at the time of cataract surgery on central macular edema in patients with preexisting diabetic retinopathy. SETTING: Loma Linda University Eye Institute, California, USA. DESIGN: Retrospective observational clinical study. METHODS: Retrospective chart review included 75 eyes of 64 patients who had cataract surgery between February 2015 and October 2018 performed by 2 surgeons. Intravitreal injection of triamcinolone-moxifloxacin (15 mg/1 mg/mL, 0.2 mL injection with 3.0 mg triamcinolone acetonide and 0.2 mg moxifloxacin) was given at the time of surgery. Visual acuity and central macular thickness (CMT) with optical coherence tomography were recorded at preoperative and postoperative visits. RESULTS: Mean visual acuity (logarithm of the minimum angle of resolution) at 4 to 6 weeks, 6 to 12 weeks, and 12 weeks or more postoperatively was 0.32, 0.35, and 0.43, respectively. Baseline mean CMT of 75 eyes was 294 µm (SD = 72). Mean CMT 4 to 6 weeks postoperatively for 46 eyes decreased from 299 µm (78) to 297 µm (79), with a mean decrease of 2 µm (50) (P = .97). Mean CMT 6 to 12 weeks postoperatively for 34 eyes increased from 317 µm (88) to 344 µm (111), with a mean increase of 26 µm (98) (P = .021). Mean CMT 12 weeks or more for 60 eyes increased from 295 µm (72) to 328 µm (108), with a mean increase of 33 µm (85) (P = .0023). CONCLUSIONS: Triamcinolone acetonide-moxifloxacin maintained stability of postoperative CMT in patients undergoing cataract surgery with preexisting diabetic retinopathy in the short term, with the greatest effect at 4 to 6 weeks postoperatively.

Brimonidine Can Prevent In Vitro Hydroquinone Damage on Retinal Pigment Epithelium Cells and Retinal Müller Cells.

PURPOSE: Brimonidine is a selective alpha-2 adrenergic agonist used to reduce intraocular pressure and it has been shown to have some neuroprotective effects. Hydroquinone (HQ) is a toxicant present in cigarette smoke, and other sources. In this study, we investigated the cyto-protective effects in vitro of Brimonidine on human retinal pigment epithelium cells (ARPE-19) and human retinal Müller cells (MIO-M1) that had been treated with HQ. METHODS: Cells were pretreated for 6 h with different doses of Brimonidine tartrate 0.1% (1/2×, 1×, 5×, 10×), followed by a 24-h exposure to 100 µM of HQ, while the Brimonidine was still present. Assays were used to measure cell viability, mitochondrial membrane potential (ΔΨm), reactive oxygen species (ROS) production, and lactate dehydrogenase (LDH) release. RESULTS: Brimonidine increased the cell viability at all concentrations studied in both cell lines studied. ΔΨm also improved at all Brimonidine doses in ARPE-19 cells and in the 5× and 10× dosages MIO-M1 cells. The ROS levels decreased at 1×, 5×, and 10× doses of Brimonidine in ARPE-19 but only at 10× on MIO-M1 cells. The 10×-Brimonidine ARPE-19 cells had decreased LDH release, but no LDH changes were observed on MIO-M1 cells. CONCLUSION: HQ-induced toxicity is mediated through mitochondrial damaging, oxidative stress-related and necrosis-related pathways; Brimonidine significantly prevented the mitochondrial damaging and oxidative stress-related effects but had little effect on blocking the necrosis component of HQ-toxicity. Brimonidine protective effects differ between the different retinal cell types and high concentrations of Brimonidine (10×) have minimal damaging effects on human retinal cells.