Regulatory interactions between daptomycin- and bacitracin-responsive pathways coordinate the cell envelope antibiotic resistance response of Enterococcus faecalis.

Enterococcal infections frequently show high levels of antibiotic resistance, including to cell envelope-acting antibiotics like daptomycin (DAP). While we have a good understanding of the resistance mechanisms, less is known about the control of such resistance genes in enterococci. Previous work unveiled a bacitracin resistance network, comprised of the sensory ABC transporter SapAB, the two-component system (TCS) SapRS and the resistance ABC transporter RapAB. Interestingly, components of this system have recently been implicated in DAP resistance, a role usually regulated by the TCS LiaFSR. To better understand the regulation of DAP resistance and how this relates to mutations observed in DAP-resistant clinical isolates of enterococci, we here explored the interplay between these two regulatory pathways. Our results show that SapR regulates an additional resistance operon, dltXABCD, a known DAP resistance determinant, and show that LiaFSR regulates the expression of sapRS. This regulatory structure places SapRS-target genes under dual control, where expression is directly controlled by SapRS, which itself is up-regulated through LiaFSR. The network structure described here shows how Enterococcus faecalis coordinates its response to cell envelope attack and can explain why clinical DAP resistance often emerges via mutations in regulatory components.

The two-component system CroRS acts as a master regulator of cell envelope homeostasis to confer antimicrobial tolerance in the bacterial pathogen Enterococcus faecalis.

Antimicrobial tolerance is the ability of a microbial population to survive, but not proliferate, during antimicrobial exposure. Significantly, it has been shown to precede the development of bona fide antimicrobial resistance. We have previously identified the two-component system CroRS as a critical regulator of tolerance to antimicrobials like teixobactin in the bacterial pathogen Enterococcus faecalis. To understand the molecular mechanism of this tolerance, we have carried out RNA-seq analyses in the E. faecalis wild-type and isogenic ∆ croRS mutant to determine the teixobactin-induced CroRS regulon. We identified a 132 gene CroRS regulon and demonstrate that CroRS upregulates biosynthesis of all major components of the enterococcal cell envelope in response to teixobactin. This suggests a coordinating role of this regulatory system in maintaining integrity of the multiple layers of the enterococcal envelope during antimicrobial stress, likely contributing to bacterial survival. Using experimental evolution, we observed that truncation of HppS, a key enzyme in the synthesis of the quinone electron carrier demethylmenaquinone, was sufficient to rescue tolerance in the croRS deletion strain. This highlights a key role for isoprenoid biosynthesis in antimicrobial tolerance in E. faecalis. Here, we propose a model of CroRS acting as a master regulator of cell envelope biogenesis and a gate-keeper between isoprenoid biosynthesis and respiration to ensure tolerance against antimicrobial challenge.

Electric Cell-Substrate Sensing for Real-Time Evaluation of Metal-Organic Framework Toxicological Profiles.

Metal-organic frameworks (MOFs) are hybrids formed through the coordination of metal ions and organic linkers in organic solvents. The implementation of MOFs in biomedical and industrial applications has led to concerns regarding their safety. Herein, the profile of a selected MOF, a zeolitic imidazole framework, was evaluated upon exposure to human lung epithelial cells. The platform for evaluation was a real-time technique (i.e., electric cell-substrate impedance sensing [ECIS]). This study identifies and discusses some of the deleterious effects of the selected MOF on the exposed cells. Furthermore, this study demonstrates the benefits of using the real-time method versus other biochemical assays for comprehensive cell evaluations. The study concludes that observed changes in cell behavior could hint at possible toxicity induced upon exposure to MOFs of different physicochemical characteristics and the dosage of those frameworks being used. By understanding changes in cell behavior, one foresees the ability to improve safe-by-design strategies of MOFs to be used for biomedical applications by specifically tailoring their physicochemical characteristics.

Shortwave infrared diffuse optical wearable probe for quantification of water and lipid content in emulsion phantoms using deep learning.

Significance: The shortwave infrared (SWIR, ∼900 to 2000 nm) holds promise for label-free measurements of water and lipid content in thick tissue, owed to the chromophore-specific absorption features and low scattering in this range. In vivo water and lipid estimations have potential applications including the monitoring of hydration, volume status, edema, body composition, weight loss, and cancer. To the best of our knowledge, there are currently no point-of-care or wearable devices available that exploit the SWIR wavelength range, limiting clinical and at-home translation of this technology. Aim: To design and fabricate a diffuse optical wearable SWIR probe for water and lipid quantification in tissue. Approach: Simulations were first performed to confirm the theoretical advantage of SWIR wavelengths over near infrared (NIR). The probe was then fabricated, consisting of light emitting diodes at three wavelengths (980, 1200, 1300 nm) and four source-detector (S-D) separations (7, 10, 13, 16 mm). In vitro validation was then performed on emulsion phantoms containing varying concentrations of water, lipid, and deuterium oxide (D2O). A deep neural network was developed as the inverse model for quantity estimation. Results: Simulations indicated that SWIR wavelengths could reduce theoretical water and lipid extraction errors from ∼6% to ∼1% when compared to NIR wavelengths. The SWIR probe had good signal-to-noise ratio (>32 dB up to 10 mm S-D) and low drift (<1.1% up to 10 mm S-D). Quantification error in emulsion phantoms was 2.1±1.1% for water and -1.2±1.5% for lipid. Water estimation during a D2O dilution experiment had an error of 3.1±3.7%. Conclusions: This diffuse optical SWIR probe was able to quantify water and lipid contents in vitro with good accuracy, opening the door to human investigations.

Look twice: A generalist computational model predicts return fixations across tasks and species.

Primates constantly explore their surroundings via saccadic eye movements that bring different parts of an image into high resolution. In addition to exploring new regions in the visual field, primates also make frequent return fixations, revisiting previously foveated locations. We systematically studied a total of 44,328 return fixations out of 217,440 fixations. Return fixations were ubiquitous across different behavioral tasks, in monkeys and humans, both when subjects viewed static images and when subjects performed natural behaviors. Return fixations locations were consistent across subjects, tended to occur within short temporal offsets, and typically followed a 180-degree turn in saccadic direction. To understand the origin of return fixations, we propose a proof-of-principle, biologically-inspired and image-computable neural network model. The model combines five key modules: an image feature extractor, bottom-up saliency cues, task-relevant visual features, finite inhibition-of-return, and saccade size constraints. Even though there are no free parameters that are fine-tuned for each specific task, species, or condition, the model produces fixation sequences resembling the universal properties of return fixations. These results provide initial steps towards a mechanistic understanding of the trade-off between rapid foveal recognition and the need to scrutinize previous fixation locations.

Visual prototypes in the ventral stream are attuned to complexity and gaze behavior.

Early theories of efficient coding suggested the visual system could compress the world by learning to represent features where information was concentrated, such as contours. This view was validated by the discovery that neurons in posterior visual cortex respond to edges and curvature. Still, it remains unclear what other information-rich features are encoded by neurons in more anterior cortical regions (e.g., inferotemporal cortex). Here, we use a generative deep neural network to synthesize images guided by neuronal responses from across the visuocortical hierarchy, using floating microelectrode arrays in areas V1, V4 and inferotemporal cortex of two macaque monkeys. We hypothesize these images ("prototypes") represent such predicted information-rich features. Prototypes vary across areas, show moderate complexity, and resemble salient visual attributes and semantic content of natural images, as indicated by the animals' gaze behavior. This suggests the code for object recognition represents compressed features of behavioral relevance, an underexplored aspect of efficient coding.

Thin Films of Metal-Organic Framework Interfaces Obtained by Laser Evaporation.

Properties such as large surface area, high pore volume, high chemical and thermal stability, and structural flexibility render zeolitic imidazolate frameworks (ZIFs) well-suited materials for gas separation, chemical sensors, and optical and electrical devices. For such applications, film processing is a prerequisite. Herein, matrix-assisted pulsed laser evaporation (MAPLE) was successfully used as a single-step deposition process to fabricate ZIF-8 films. By correlating laser fluency and controlling the specific transfer of lab-synthesized ZIF-8, films with user-controlled physical and chemical properties were obtained. Films' characteristics were evaluated by scanning electron microscopy (SEM), energy-dispersive X-ray (EDX) spectroscopy, X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, and X-ray photoelectron spectroscopy (XPS). The analysis showed that frameworks of ZIF-8 can be deposited successfully and controllably to yield polycrystalline films. The deposited films maintained the integrity of the individual ZIF-8 framework, while undergoing minor crystalline and surface chemistry changes. No significant changes in particle size were observed. Our study demonstrated control over both the MAPLE deposition conditions and the outcome, as well as the suitability of the listed deposition method to create composite architectures that could potentially be used in applications ranging from selective membranes to gas sensors.

Toxicity screening of two prevalent metal organic frameworks for therapeutic use in human lung epithelial cells.

INTRODUCTION: The flexibility and tunability of metal organic frameworks (MOFs), crystalline porous materials composed of a network of metal ions coordinated by organic ligands, confer their variety of applications as drug delivery systems or as sensing and imaging agents. However, such properties also add to the difficulty in ensuring their safe implementation when interaction with biological systems is considered. METHODS: In the current study, we used real-time sensorial strategies and cellular-based approaches to allow for fast and effective screening of two MOFs of prevalent use, namely, MIL-160 representative of a hydrophilic and ZIF-8 representative of a hydrophobic framework. The two MOFs were synthesized "in house" and exposed to human bronchial epithelial (BEAS-2B) cells, a pertinent toxicological screening model. RESULTS: Analysis allowed evaluation and differentiation of particle-induced cellular effects as well identification of different degrees and routes of toxicity, all in a high-throughput manner. Our results show the importance of performing screening toxicity assessments before introducing MOFs to biomedical applications. DISCUSSION: Our proposed screening assays could be extended to a wider variety of cell lines to allow for identification of any deleterious effects of MOFs, with the range of toxic mechanisms to be differentiated based on cell viability, morphology and cell-substrate interactions, respectively. CONCLUSION: Our analysis highlights the importance of considering the physicochemical properties of MOFs when recommending a MOF-based therapeutic option or MOFs implementation in biomedical applications.

Tourette syndrome research highlights from 2018.

This is the fifth yearly article in the Tourette Syndrome Research Highlights series, summarizing research from 2018 relevant to Tourette syndrome and other tic disorders. The authors briefly summarize reports they consider most important or interesting. The  highlights from 2019 article is being drafted on the Authorea online authoring platform, and readers are encouraged to add references or give feedback on our selections using the comments feature on that page. After the calendar year ends, the article is submitted as the annual update for the  Tics collection on F1000Research.

Impact of pore size, interconnections, and dynamic conductivity on the electrochemistry of vanadium pentoxide in well defined porous structures.

Considering the tortuous, random porous nanostructures existing in many battery electrodes, it is essential to understand electronic and ionic behaviors in such a confined nanoscale porous geometry in which electron and ion transports can change dynamically. Here, we have carefully designed three dimensional (3D) interconnected porous electrode structures and performed experiments to probe how the ion and electron transport is impacted within these controlled geometries. By using anodized aluminum oxide as a template, we were able to fabricate both 1D array electrodes and 3D electrodes with varying numbers of interconnections, utilizing vanadium oxide (V2O5) as the active material. We demonstrate that the inherent properties of the electrode material in combination with the structural properties of the electrodes can both positively and negatively impact electrochemical characteristics. Most notably, electrodes with seven interconnecting layers in their structure had 19.7% less capacity at 25C than electrodes with zero interconnecting layers, demonstrating the negative effect of interconnections combined with poor electronic conductivity of V2O5 upon lithiation beyond one Li insertion. These results indicate that a careful consideration of the material and structural properties is needed for the design of high performance battery systems.