SlyB encapsulates outer membrane proteins in stress-induced lipid nanodomains.

The outer membrane in Gram-negative bacteria consists of an asymmetric phospholipid-lipopolysaccharide bilayer that is densely packed with outer-membrane ß-barrel proteins (OMPs) and lipoproteins1. The architecture and composition of this bilayer is closely monitored and is essential to cell integrity and survival2-4. Here we find that SlyB, a lipoprotein in the PhoPQ stress regulon, forms stable stress-induced complexes with the outer-membrane proteome. SlyB comprises a 10 kDa periplasmic ß-sandwich domain and a glycine zipper domain that forms a transmembrane α-helical hairpin with discrete phospholipid- and lipopolysaccharide-binding sites. After loss in lipid asymmetry, SlyB oligomerizes into ring-shaped transmembrane complexes that encapsulate ß-barrel proteins into lipid nanodomains of variable size. We find that the formation of SlyB nanodomains is essential during lipopolysaccharide destabilization by antimicrobial peptides or acute cation shortage, conditions that result in a loss of OMPs and compromised outer-membrane barrier function in the absence of a functional SlyB. Our data reveal that SlyB is a compartmentalizing transmembrane guard protein that is involved in cell-envelope proteostasis and integrity, and suggest that SlyB represents a larger family of broadly conserved lipoproteins with 2TM glycine zipper domains with the ability to form lipid nanodomains.

Duration and accuracy of automated stroke CT workflow with AI-supported intracranial large vessel occlusion detection.

The Automation Platform (AP) is a software platform to support the workflow of radiologists and includes a stroke CT package with integrated artificial intelligence (AI) based tools. The aim of this study was to evaluate the diagnostic performance of the AP for the detection of intracranial large vessel occlusions (LVO) on conventional CT angiography (CTA), and the duration of CT processing in a cohort of acute stroke patients. The diagnostic performance for intracranial LVO detection on CTA by the AP was evaluated in a retrospective cohort of 100 acute stroke patients and compared to the diagnostic performance of five radiologists with different levels of experience. The reference standard was set by an independent neuroradiologist, with access to the readings of the different radiologists, clinical data, and follow-up. The data processing time of the AP for ICH detection on non-contrast CT, LVO detection on CTA, and the processing of CTP maps was assessed in a subset 60 patients of the retrospective cohort. This was compared to 13 radiologists, who were prospectively timed for the processing and reading of 21 stroke CTs. The AP showed shorter processing time of CTA (mean 60 versus 395 s) and CTP (mean 196 versus 243-349 s) as compared to radiologists, but showed lower sensitivity for LVO detection (sensitivity 77% of the AP vs mean sensitivity 87% of radiologists). If the AP would have been used as a stand-alone system, 1 ICA occlusion, 2 M1 occlusions and 8 M2 occlusions would have been missed, which would be eligible for mechanical thrombectomy. In conclusion, the AP showed shorter processing time of CTA and CTP as compared with radiologists, which illustrates the potential of the AP to speed-up the diagnostic work-up. However, its performance for LVO detection was lower as compared with radiologists, especially for M2 vessel occlusions.

The small GTPase Sar1, control centre of COPII trafficking.

Sar1 is a small GTPase of the ARF family. Upon exchange of GDP for GTP, Sar1 associates with the endoplasmic reticulum (ER) membrane and recruits COPII components, orchestrating cargo concentration and membrane deformation. Many aspects of the role of Sar1 and regulation of its GTP cycle remain unclear, especially as complexity increases in higher organisms that secrete a wider range of cargoes. This review focusses on the regulation of GTP hydrolysis and its role in coat assembly, as well as the mechanism of Sar1-induced membrane deformation and scission. Finally, we highlight the additional specialisation in higher eukaryotes and the outstanding questions on how Sar1 functions are orchestrated.

No Evidence for Neural Overlap between Unconsciously Processed and Imagined Stimuli.

Visual representations can be generated via feedforward or feedback processes. The extent to which these processes result in overlapping representations remains unclear. Previous work has shown that imagined stimuli elicit similar representations as perceived stimuli throughout the visual cortex. However, while representations during imagery are indeed only caused by feedback processing, neural processing during perception is an interplay of both feedforward and feedback processing. This means that any representational overlap could be because of overlap in feedback processes. In the current study, we aimed to investigate this issue by characterizing the overlap between feedforward- and feedback-initiated category representations during imagined stimuli, conscious perception, and unconscious processing using fMRI in humans of either sex. While all three conditions elicited stimulus representations in left lateral occipital cortex (LOC), significant similarities were observed only between imagery and conscious perception in this area. Furthermore, connectivity analyses revealed stronger connectivity between frontal areas and left LOC during conscious perception and in imagery compared with unconscious processing. Together, these findings can be explained by the idea that long-range feedback modifies visual representations, thereby reducing representational overlap between purely feedforward- and feedback-initiated stimulus representations measured by fMRI. Neural representations influenced by feedback, either stimulus driven (perception) or purely internally driven (imagery), are, however, relatively similar.

Population codes of prior knowledge learned through environmental regularities.

How the brain makes correct inferences about its environment based on noisy and ambiguous observations is one of the fundamental questions in Neuroscience. Prior knowledge about the probability with which certain events occur in the environment plays an important role in this process. Humans are able to incorporate such prior knowledge in an efficient, Bayes optimal, way in many situations, but it remains an open question how the brain acquires and represents this prior knowledge. The long time spans over which prior knowledge is acquired make it a challenging question to investigate experimentally. In order to guide future experiments with clear empirical predictions, we used a neural network model to learn two commonly used tasks in the experimental literature (i.e. orientation classification and orientation estimation) where the prior probability of observing a certain stimulus is manipulated. We show that a population of neurons learns to correctly represent and incorporate prior knowledge, by only receiving feedback about the accuracy of their inference from trial-to-trial and without any probabilistic feedback. We identify different factors that can influence the neural responses to unexpected or expected stimuli, and find a novel mechanism that changes the activation threshold of neurons, depending on the prior probability of the encoded stimulus. In a task where estimating the exact stimulus value is important, more likely stimuli also led to denser tuning curve distributions and narrower tuning curves, allocating computational resources such that information processing is enhanced for more likely stimuli. These results can explain several different experimental findings, clarify why some contradicting observations concerning the neural responses to expected versus unexpected stimuli have been reported and pose some clear and testable predictions about the neural representation of prior knowledge that can guide future experiments.

ß-Barrels covalently link peptidoglycan and the outer membrane in the α-proteobacterium Brucella abortus.

Gram-negative bacteria are surrounded by a cell envelope that comprises an outer membrane (OM) and an inner membrane that, together, delimit the periplasmic space, which contains the peptidoglycan (PG) sacculus. Covalent anchoring of the OM to the PG is crucial for envelope integrity in Escherichia coli. When the OM is not attached to the PG, the OM forms blebs and detaches from the cell. The Braun lipoprotein Lpp1 covalently attaches OM to the PG but is present in only a small number of γ-proteobacteria; the mechanism of OM-PG attachment in other species is unclear. Here, we report that the OM is attached to PG by covalent cross-links between the N termini of integral OM ß-barrel-shaped proteins (OMPs) and the peptide stems of PG in the α-proteobacteria Brucella abortus and Agrobacterium tumefaciens. Cross-linking is catalysed by L,D-transpeptidases and attached OMPs have a conserved alanyl-aspartyl motif at their N terminus. Mutation of the aspartate in this motif prevents OMP cross-linking and results in OM membrane instability. The alanyl-aspartyl motif is conserved in OMPs from Rhizobiales; it is therefore feasible that OMP-PG cross-links are widespread in α-proteobacteria.

The Bacillus anthracis Cell Envelope: Composition, Physiological Role, and Clinical Relevance.

Anthrax is a highly resilient and deadly disease caused by the spore-forming bacterial pathogen Bacillus anthracis. The bacterium presents a complex and dynamic composition of its cell envelope, which changes in response to developmental and environmental conditions and host-dependent signals. Because of their easy to access extracellular locations, B. anthracis cell envelope components represent interesting targets for the identification and development of novel therapeutic and vaccine strategies. This review will focus on the novel insights regarding the composition, physiological role, and clinical relevance of B. anthracis cell envelope components.

Pneumothorax in patients with prior or current COVID-19 pneumonia.

As the number of COVID-19 cases emerge, new complications associated with the disease are recognized. We present three cases of spontaneous pneumothorax in patients with COVID-19. They show that a pneumothorax can occur during different phases of disease, in patients without a pulmonary disease history and is not necessarily associated to positive pressure ventilation or severity of COVID-19. Although the exact causative mechanisms remain unknown, this observation might imply that extensive alveolar destruction due to COVID-19 may lead to bulla formation resulting in subsequent pneumothorax.

A dual-constriction biological nanopore resolves homonucleotide sequences with high fidelity.

Single-molecule long-read DNA sequencing with biological nanopores is fast and high-throughput but suffers reduced accuracy in homonucleotide stretches. We now combine the CsgG nanopore with the 35-residue N-terminal region of its extracellular interaction partner CsgF to produce a dual-constriction pore with improved signal and base-calling accuracy for homopolymer regions. The electron cryo-microscopy structure of CsgG in complex with full-length CsgF shows that the 33 N-terminal residues of CsgF bind inside the ß-barrel of the pore, forming a defined second constriction. In complexes of CsgG bound to a 35-residue CsgF constriction peptide, the second constriction is separated from the primary constriction by ~25 Å. We find that both constrictions contribute to electrical signal modulation during single-stranded DNA translocation. DNA sequencing using a prototype CsgG-CsgF protein pore with two constrictions improved single-read accuracy by 25 to 70% in homopolymers up to 9 nucleotides long.

Evidence for confounding eye movements under attempted fixation and active viewing in cognitive neuroscience.

Eye movements can have serious confounding effects in cognitive neuroscience experiments. Therefore, participants are commonly asked to fixate. Regardless, participants will make so-called fixational eye movements under attempted fixation, which are thought to be necessary to prevent perceptual fading. Neural changes related to these eye movements could potentially explain previously reported neural decoding and neuroimaging results under attempted fixation. In previous work, under attempted fixation and passive viewing, we found no evidence for systematic eye movements. Here, however, we show that participants' eye movements are systematic under attempted fixation when active viewing is demanded by the task. Since eye movements directly affect early visual cortex activity, commonly used for neural decoding, our findings imply alternative explanations for previously reported results in neural decoding.

Structure of S-layer protein Sap reveals a mechanism for therapeutic intervention in anthrax.

Anthrax is an ancient and deadly disease caused by the spore-forming bacterial pathogen Bacillus anthracis. At present, anthrax mostly affects wildlife and livestock, although it remains a concern for human public health-primarily for people who handle contaminated animal products and as a bioterrorism threat due to the high resilience of spores, a high fatality rate of cases and the lack of a civilian vaccination programme1,2. The cell surface of B. anthracis is covered by a protective paracrystalline monolayer-known as surface layer or S-layer-that is composed of the S-layer proteins Sap or EA1. Here, we generate nanobodies to inhibit the self-assembly of Sap, determine the structure of the Sap S-layer assembly domain (SapAD) and show that the disintegration of the S-layer attenuates the growth of B. anthracis and the pathology of anthrax in vivo. SapAD comprises six ß-sandwich domains that fold and support the formation of S-layers independently of calcium. Sap-inhibitory nanobodies prevented the assembly of Sap and depolymerized existing Sap S-layers in vitro. In vivo, nanobody-mediated disruption of the Sap S-layer resulted in severe morphological defects and attenuated bacterial growth. Subcutaneous delivery of Sap inhibitory nanobodies cleared B. anthracis infection and prevented lethality in a mouse model of anthrax disease. These findings highlight disruption of S-layer integrity as a mechanism that has therapeutic potential in S-layer-carrying pathogens.

Eye movements explain decodability during perception and cued attention in MEG.

Eye movements are an integral part of human perception, but can induce artifacts in many magneto-encephalography (MEG) and electroencephalography (EEG) studies. For this reason, investigators try to minimize eye movements and remove these artifacts from their data using different techniques. When these artifacts are not purely random, but consistent regarding certain stimuli or conditions, the possibility arises that eye movements are actually inducing effects in the MEG signal. It remains unclear how much of an influence eye movements can have on observed effects in MEG, since most MEG studies lack a control analysis to verify whether an effect found in the MEG signal is induced by eye movements. Here, we find that we can decode stimulus location from eye movements in two different stages of a working memory match-to-sample task that encompass different areas of research typically done with MEG. This means that the observed MEG effect might be (partly) due to eye movements instead of any true neural correlate. We suggest how to check for eye movement effects in the data and make suggestions on how to minimize eye movement artifacts from occurring in the first place.

Neuroimaging Findings on Amodal Completion: A Review.

Amodal completion is the phenomenon of perceiving completed objects even though physically they are partially occluded. In this review, we provide an extensive overview of the results obtained from a variety of neuroimaging studies on the neural correlates of amodal completion. We discuss whether low-level and high-level cortical areas are implicated in amodal completion; provide an overview of how amodal completion unfolds over time while dissociating feedforward, recurrent, and feedback processes; and discuss how amodal completion is represented at the neuronal level. The involvement of low-level visual areas such as V1 and V2 is not yet clear, while several high-level structures such as the lateral occipital complex and fusiform face area seem invariant to occlusion of objects and faces, respectively, and several motor areas seem to code for object permanence. The variety of results on the timing of amodal completion hints to a mixture of feedforward, recurrent, and feedback processes. We discuss whether the invisible parts of the occluded object are represented as if they were visible, contrary to a high-level representation. While plenty of questions on amodal completion remain, this review presents an overview of the neuroimaging findings reported to date, summarizes several insights from computational models, and connects research of other perceptual completion processes such as modal completion. In all, it is suggested that amodal completion is the solution to deal with various types of incomplete retinal information, and highly depends on stimulus complexity and saliency, and therefore also give rise to a variety of observed neural patterns.

Shared Neural Mechanisms of Visual Perception and Imagery.

For decades, the extent to which visual imagery relies on the same neural mechanisms as visual perception has been a topic of debate. Here, we review recent neuroimaging studies comparing these two forms of visual experience. Their results suggest that there is a large overlap in neural processing during perception and imagery: neural representations of imagined and perceived stimuli are similar in the visual, parietal, and frontal cortex. Furthermore, perception and imagery seem to rely on similar top-down connectivity. The most prominent difference is the absence of bottom-up processing during imagery. These findings fit well with the idea that imagery and perception rely on similar emulation or prediction processes.

Measurement method for objective cyclist behavior parameters.

Objective: The objective of this research is to study the feasibility of measuring behavioral indicators that reflect effects of infrastructure and interaction with other road users.Methods: An observation study was performed using 6 cameras above a separated cycle path next to a road which included a crossing with both cyclists and cars. A learning method based on Single Shot MultiBox Detector was applied to automatically detect the cyclists, and cyclist tracks were determined. Next, kinematic parameters were calculated from the cyclists' tracks. Amongst others, the cyclists' intensity, speed, position on the cycle path, and the distance to each other were analyzed for a busy period as well as for a quiet period of the day.Results: With the measurement method developed in this study it is possible to analyze the cyclists' intensity, the space they use at the cycle path, their average velocity, waiting times, the space and velocity amongst each other, and red light negation. However, collisions were not seen in the dataset analyzed, and the data is not sufficiently accurate to analyze sudden braking actions.Conclusion: It can be concluded that the developed measurement method provides insight of the cyclists' behavior in such a way that it can already be used for obtaining information to make changes to the infrastructure that will improve the comfort and safety of cyclists. The method could be further developed for doing qualitative comfort and safety analyses, and for doing analyses of the interaction between various types of road participants.

The Role of Functional Amyloids in Bacterial Virulence.

Amyloid fibrils are best known as a product of human and animal protein misfolding disorders, where amyloid formation is associated with cytotoxicity and disease. It is now evident that for some proteins, the amyloid state constitutes the native structure and serves a functional role. These functional amyloids are proving widespread in bacteria and fungi, fulfilling diverse functions as structural components in biofilms or spore coats, as toxins and surface-active fibers, as epigenetic material, peptide reservoirs or adhesins mediating binding to and internalization into host cells. In this review, we will focus on the role of functional amyloids in bacterial pathogenesis. The role of functional amyloids as virulence factor is diverse but mostly indirect. Nevertheless, functional amyloid pathways deserve consideration for the acute and long-term effects of the infectious disease process and may form valid antimicrobial targets.

Mouse Keratinocytes Without Keratin Intermediate Filaments Demonstrate Substrate Stiffness Dependent Behaviors.

INTRODUCTION: Traditionally thought to serve active vs. passive mechanical functions, respectively, a growing body of evidence suggests that actin microfilament and keratin intermediate filament (IF) networks, together with their associated cell-cell and cell-matrix anchoring junctions, may have a large degree of functional interdependence. Therefore, we hypothesized that the loss of keratin IFs in a knockout mouse keratinocyte model would affect the kinematics of colony formation, i.e., the spatiotemporal process by which individual cells join to form colonies and eventually a nascent epithelial sheet. METHODS: Time-lapse imaging and deformation tracking microscopy was used to observe colony formation for both wild type (WT) and keratin-deficient knockout (KO) mouse keratinocytes over 24 h. Cells were cultured under high calcium conditions on collagen-coated substrates with nominal stiffnesses of ~ 1.2 kPa (soft) and 24 kPa (stiff). Immunofluorescent staining of actin and selected adhesion proteins was also performed. RESULTS: The absence of keratin IFs markedly affected cell morphology, spread area, and cytoskeleton and adhesion protein organization on both soft and stiff substrates. Strikingly, an absence of keratin IFs also significantly reduced the ability of mouse keratinocytes to mechanically deform the soft substrate. Furthermore, KO cells formed colonies more efficiently on stiff vs. soft substrates, a behavior opposite to that observed for WT keratinocytes. CONCLUSIONS: Collectively, these data are strongly supportive of the idea that an interdependence between actin microfilaments and keratin IFs does exist, while further suggesting that keratin IFs may represent an important and under-recognized component of keratinocyte mechanosensation and the force generation apparatus.

Bioelectrochemical nitrogen removal as a polishing mechanism for domestic wastewater treated effluents.

Addition of an external carbon source is usually necessary to guarantee a sufficiently high C/N ratio and enable denitrification in wastewater treatment plants (WWTPs). Alternatively, denitrification processes using autotrophic microorganisms have been proposed i.e., with the use of H2 as electron donor or with the use of cathodic denitrification in bioelectrochemical systems (BES), in which electrons are transferred directly to a denitrifying biofilm. The aim of this work was to investigate and demonstrate the feasibility of applying an easy-to-operate BES as a polishing mechanism for treated secondary clarified effluent from a municipal WWTP, containing low levels of organic matter, buffer capacity and low concentrations of remaining nitrate. In the proposed system, nitrogen removal rates (0.018-0.121 Kg N m-3 d-1) increased with the nitrogen loading rates, suggesting that biofilm kinetics were not rate limiting. The lowest energy consumption for denitrification was 12.7 kWh Kg N-1, equivalent to 0.021 kWh m-3 and could be further reduced by 14% by adding recirculation circuits within both the anode and cathode.

Vividness of Visual Imagery Depends on the Neural Overlap with Perception in Visual Areas.

Research into the neural correlates of individual differences in imagery vividness point to an important role of the early visual cortex. However, there is also great fluctuation of vividness within individuals, such that only looking at differences between people necessarily obscures the picture. In this study, we show that variation in moment-to-moment experienced vividness of visual imagery, within human subjects, depends on the activity of a large network of brain areas, including frontal, parietal, and visual areas. Furthermore, using a novel multivariate analysis technique, we show that the neural overlap between imagery and perception in the entire visual system correlates with experienced imagery vividness. This shows that the neural basis of imagery vividness is much more complicated than studies of individual differences seemed to suggest. SIGNIFICANCE STATEMENT: Visual imagery is the ability to visualize objects that are not in our direct line of sight: something that is important for memory, spatial reasoning, and many other tasks. It is known that the better people are at visual imagery, the better they can perform these tasks. However, the neural correlates of moment-to-moment variation in visual imagery remain unclear. In this study, we show that the more the neural response during imagery is similar to the neural response during perception, the more vivid or perception-like the imagery experience is.

Mnemonic convergence in the human hippocampus.

The ability to form associations between a multitude of events is the hallmark of episodic memory. Computational models have espoused the importance of the hippocampus as convergence zone, binding different aspects of an episode into a coherent representation, by integrating information from multiple brain regions. However, evidence for this long-held hypothesis is limited, since previous work has largely focused on representational and network properties of the hippocampus in isolation. Here we identify the hippocampus as mnemonic convergence zone, using a combination of multivariate pattern and graph-theoretical network analyses of functional magnetic resonance imaging data from humans performing an associative memory task. We observe overlap of conjunctive coding and hub-like network attributes in the hippocampus. These results provide evidence for mnemonic convergence in the hippocampus, underlying the integration of distributed information into episodic memory representations.