The antigenic anatomy of SARS-CoV-2 receptor binding domain.

Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC50 < 0.1 µg/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.

Selective Activation of D3 Dopamine Receptors Ameliorates DOI-Induced Head Twitching Accompanied by Changes in Corticostriatal Processing.

D3 receptors, a key component of the dopamine system, have emerged as a potential target of therapies to improve motor symptoms across neurodegenerative and neuropsychiatric conditions. In the present work, we evaluated the effect of D3 receptor activation on the involuntary head twitches induced by 2,5-dimethoxy-4-iodoamphetamine (DOI) at behavioral and electrophysiological levels. Mice received an intraperitoneal injection of either a full D3 agonist, WC 44 [4-(2-fluoroethyl)-N-[4-[4-(2-methoxyphenyl)piperazin 1-yl]butyl]benzamide] or a partial D3 agonist, WW-III-55 [N-(4-(4-(4-methoxyphenyl)piperazin-1-yl)butyl)-4-(thiophen-3-yl)benzamide] five minutes before the intraperitoneal administration of DOI. Compared to the control group, both D3 agonists delayed the onset of the DOI-induced head-twitch response and reduced the total number and frequency of the head twitches. Moreover, the simultaneous recording of neuronal activity in the motor cortex (M1) and dorsal striatum (DS) indicated that D3 activation led to slight changes in a single unit activity, mainly in DS, and increased its correlated firing in DS or between presumed cortical pyramidal neurons (CPNs) and striatal medium spiny neurons (MSNs). Our results confirm the role of D3 receptor activation in controlling DOI-induced involuntary movements and suggest that this effect involves, at least in part, an increase in correlated corticostriatal activity. A further understanding of the underlying mechanisms may provide a suitable target for treating neuropathologies in which involuntary movements occur.

Modulation of lateral septal and dorsomedial striatal neurons by hippocampal sharp-wave ripples, theta rhythm, and running speed.

Single units were recorded in hippocampus, lateral septum (LS), and dorsomedial striatum (DMS) while freely behaving rats (n = 3) ran trials in a T-maze task and rested in a holding bucket between trials. In LS, 28% (64/226) of recorded neurons were excited and 14% (31/226) were inhibited during sharp wave ripples (SWRs). LS neurons that were excited during SWRs fired preferentially on the downslope of hippocampal theta rhythm and had firing rates that were positively correlated with running speed; LS neurons that were inhibited during SWRs fired preferentially on the upslope of hippocampal theta rhythm and had firing rates that were negatively correlated with running speed. In DMS, only 3.3% (12/366) of recorded neurons were excited and 5.7% (21/366) were inhibited during SWRs. As in LS, DMS neurons that were excited by SWRs tended to have firing rates that were positively modulated by running speed, whereas DMS neurons that were inhibited by SWRs tended to have firing rates that were negatively modulated by running speed. But in contrast with LS, these two DMS subpopulations did not clearly segregate their spikes to different phases of the theta cycle. Based on these results and a review of prior findings, we discuss how concurrent activation of spatial trajectories in hippocampus and motor representations in LS and DMS may contribute to neural computations that support reinforcement learning and value-based decision making.

Lack of mutant huntingtin in cortical efferents improves behavioral inflexibility and corticostriatal dynamics in Huntington's disease mice.

Abnormal communication between cerebral cortex and striatum plays a major role in the motor symptoms of Huntington's disease (HD), a neurodegenerative disorder caused by a mutation of the huntingtin gene (mHTT). Because cortex is the main driver of striatal processing, we recorded local field potential (LFP) activity simultaneously in primary motor cortex (M1) and dorsal striatum (DS) in BACHD mice, a full-length HD gene model, and in a conditional BACHD/Emx-1 Cre (BE) model in which mHTT is suppressed in cortical efferents, while mice freely explored a plus-shaped maze beginning at 20 wk of age. Relative to wild-type (WT) controls, BACHD mice were just as active across >40 wk of testing but became progressively less likely to turn into a perpendicular arm as they approached the choice point of the maze, a sign of HD motor inflexibility. BE mice, in contrast, turned as freely as WT throughout testing. Although BE mice did not exactly match WT in LFP activity, the reduction in alpha (8-13 Hz), beta (13-30 Hz), and low-gamma (30-50 Hz) power that occurred in M1 of turning-impaired BACHD mice was reversed. No reversal occurred in DS. In fact, BE mice showed further reductions in DS theta (4-8 Hz), beta, and low-gamma power relative to the BACHD model. Coherence analysis indicated a dysregulation of corticostriatal information flow in both BACHD and BE mice. Collectively, our results suggest that mHTT in cortical outputs drives the dysregulation of select cortical frequencies that accompany the loss of behavioral flexibility in HD.NEW & NOTEWORTHY BACHD mice, a full-length genetic model of Huntington's disease (HD), express aberrant local field potential (LFP) activity in primary motor cortex (M1) along with decreased probability of turning into a perpendicular arm of a plus-shaped maze, a motor inflexibility phenotype. Suppression of the mutant huntingtin gene in cortical output neurons prevents decline in turning and improves alpha, beta, and low-gamma activity in M1. Our results implicate cortical networks in the search for therapeutic strategies to alleviate HD motor signs.

Tracking Conformational Changes in Calmodulin in vitro, in Cell Extract, and in Cells by Electron Paramagnetic Resonance Distance Measurements.

It is an open question whether the conformations of proteins sampled in dilute solutions are the same as in the cellular environment. Here we address this question by double electron-electron resonance (DEER) distance measurements with Gd(III) spin labels to probe the conformations of calmodulin (CaM) in vitro, in cell extract, and in human HeLa cells. Using the CaM mutants N53C/T110C and T34C/T117C labeled with maleimide-DOTA-Gd(III) in the N- and C-terminal domains, we observed broad and varied interdomain distance distributions. The in vitro distance distributions of apo-CaM and holo-CaM in the presence and absence of the IQ target peptide can be described by combinations of closed, open, and collapsed conformations. In cell extract, apo- and holo-CaM bind to target proteins in a similar way as apo- and holo-CaM bind to IQ peptide in vitro. In HeLa cells, however, in the presence or absence of elevated in-cell Ca2+ levels CaM unexpectedly produced more open conformations and very broad distance distributions indicative of many different interactions with in-cell components. These results show-case the importance of in-cell analyses of protein structures.

Viscoelastic polymer flows and elastic turbulence in three-dimensional porous structures.

Viscoelastic polymer solutions flowing through reservoir rocks have been found to improve oil displacement efficiency when the aqueous-phase shear-rate exceeds a critical value. A possible mechanism for this enhanced recovery is elastic turbulence that causes breakup and mobilization of trapped oil ganglia. Here, we apply nuclear magnetic resonance (NMR) pulsed field gradient (PFG) diffusion measurements in a novel way to detect increased motion of disconnected oil ganglia. The data are acquired directly from a three-dimensional (3D) opaque porous structure (sandstone) when viscoelastic fluctuations are expected to be present in the continuous phase. The measured increase in motion of trapped ganglia provides unequivocal evidence of fluctuations in the flowing phase in a fully complex 3D system. This work provides direct evidence of elastic turbulence in a realistic reservoir rock - a measurement that cannot be readily achieved by conventional laboratory methods. We support the NMR data with optical microscopy studies of fluctuating ganglia in simple two-dimensional (2D) microfluidic networks, with consistent apparent rheological behaviour of the aqueous phase, to provide conclusive evidence of elastic turbulence in the 3D structure and hence validate the proposed flow-fluctuation mechanism for enhanced oil recovery.

Insulation Failure of the Linox Defibrillator Lead: A Case Report and Retrospective Review of a Single Center Experience.

Implantable cardioverter defibrillator (ICD) lead insulation failure and conductor externalization have been increasingly reported. The 7.8F silicon-insulated Linox SD and Linox S ICD leads (Biotronik, Berlin, Germany) were released in 2006 and 2007, respectively, with an estimated 85,000 implantations worldwide. A 39-year-old female suffered an out-of-hospital ventricular fibrillation (VF) arrest with successful resuscitation. An ICD was implanted utilizing a single coil active fixation Linox(Smart) S lead (Biotronik, Berlin, Germany). A device-triggered alert approximately 3 years after implantation confirmed nonphysiological high rate sensing leading to VF detection. A chest X-ray showed an abnormality of the ICD lead and fluoroscopic screening confirmed conductor externalization proximal to the defibrillator coil. In view of the combined electrical and fluoroscopic abnormalities, urgent lead extraction and replacement were performed. A review of Linox (Biotronik) and Vigila (Sorin Group, Milan, Italy) lead implantations within our center (n = 98) identified 3 additional patients presenting with premature lead failure, 2 associated with nonphysiological sensed events and one associated with a significant decrease in lead impedance. All leads were subsequently removed and replaced. This case provides a striking example of insulation failure affecting the Linox ICD lead and, we believe, is the first to demonstrate conductor externalization manifesting both electrical and fluoroscopic abnormalities.

Model study of enhanced oil recovery by flooding with aqueous surfactant solution and comparison with theory.

With the aim of elucidating the details of enhanced oil recovery by surfactant solution flooding, we have determined the detailed behavior of model systems consisting of a packed column of calcium carbonate particles as the porous rock, n-decane as the trapped oil, and aqueous solutions of the anionic surfactant sodium bis(2-ethylhexyl) sulfosuccinate (AOT). The AOT concentration was varied from zero to above the critical aggregation concentration (cac). The salt content of the aqueous solutions was varied to give systems of widely different, post-cac oil-water interfacial tensions. The systems were characterized in detail by measuring the permeability behavior of the packed columns, the adsorption isotherms of AOT from the water to the oil-water interface and to the water-calcium carbonate interface, and oil-water-calcium carbonate contact angles. Measurements of the percent oil recovery by pumping surfactant solutions into calcium carbonate-packed columns initially filled with oil were analyzed in terms of the characterization results. We show that the measured contact angles as a function of AOT concentration are in reasonable agreement with those calculated from values of the surface energy of the calcium carbonate-air surface plus the measured adsorption isotherms. Surfactant adsorption onto the calcium carbonate-water interface causes depletion of its aqueous-phase concentration, and we derive equations which enable the concentration of nonadsorbed surfactant within the packed column to be estimated from measured parameters. The percent oil recovery as a function of the surfactant concentration is determined solely by the oil-water-calcium carbonate contact angle for nonadsorbed surfactant concentrations less than the cac. For surfactant concentrations greater than the cac, additional oil removal occurs by a combination of solubilization and emulsification plus oil mobilization due to the low oil-water interfacial tension and a pumping pressure increase.

Flow of concentrated viscoelastic polymer solutions in porous media: effect of M(W) and concentration on elastic turbulence onset in various geometries.

Viscoelastic polymer solutions exhibit a variety of flow instabilities and in particular, in mixed shear and extensional flow, elastic turbulence. Coincident with the transition to turbulence is additional dissipation that, in porous flow, may be characterised as an increased apparent viscosity. We report elastic turbulence and apparent thickening in the flow of polymer solutions both in rock samples and in microfluidic analogues and we correlate the onset of thickening and turbulence with rheological measurements. Contrary to expectations, the characteristic relaxation time associated with the transition to turbulence is found to be independent of polymer concentration over the range studied (10c* ≲c≲ 100c*). Furthermore, this characteristic time scales with the square of molecular weight. Thus the characteristic time associated with the transition to turbulence is not the linear-viscoelastic timescale usually measured but rather scales as a dilute Rouse time despite being an entangled system.

Mechanism of anomalously increased oil displacement with aqueous viscoelastic polymer solutions.

Single-phase flows of viscoelastic polymer solutions in both microfluidic devices and rock cores exhibit apparent flow thickening. We demonstrate that this thickening occurs above a critical Deborah number corresponding to the onset of spatio-temporal fluctuations. These fluctuations are observed to occur over a broad range of spatial and temporal scales consistent with elastic turbulence. The fluctuations provide a previously unreported mechanism for enhancing the displacement of a second, capillary trapped, immiscible phase.

Views from GP and Psychiatric trainees about getting experience in each other's specialty during training: A way to develop a shared culture?

The need to deliver holistic medical care that addresses both physical and mental health requirements has never been more important. The UK medical training system has been designed to provide all medical graduates with a broad experience of different medical specialities and psychiatry prior to entering specialist training. Furthermore there is a distinct crossover between Psychiatric and General Practice training, with programmes providing trainees with the opportunity to work alongside each other in the care of mental health patients. The video presentation will explain the UK medical training system in more detail, before going on to explore how the organisation of training may foster a shared culture among different specialities and how it could form a model for improving parity of esteem of medical and physical health care. In addition it will discuss the strengths and weaknesses of this system from a trainee perspective and will conclude with comments from eminent Psychiatrists whom have special interests in medical training and developingparity of mental and physical health care.

A service-based approach to cryoEM facility processing pipelines at eBIC.

Electron cryo-microscopy image-processing workflows are typically composed of elements that may, broadly speaking, be categorized as high-throughput workloads which transition to high-performance workloads as preprocessed data are aggregated. The high-throughput elements are of particular importance in the context of live processing, where an optimal response is highly coupled to the temporal profile of the data collection. In other words, each movie should be processed as quickly as possible at the earliest opportunity. The high level of disconnected parallelization in the high-throughput problem directly allows a completely scalable solution across a distributed computer system, with the only technical obstacle being an efficient and reliable implementation. The cloud computing frameworks primarily developed for the deployment of high-availability web applications provide an environment with a number of appealing features for such high-throughput processing tasks. Here, an implementation of an early-stage processing pipeline for electron cryotomography experiments using a service-based architecture deployed on a Kubernetes cluster is discussed in order to demonstrate the benefits of this approach and how it may be extended to scenarios of considerably increased complexity.

Unconscious Communications by the Body in Catatonia-A Jungian Perspective.

Outside of specific motor conditions, bodily movements are rarely considered in contemporary psychiatry. Stereotypies and mannerisms in clinical cases of catatonia are seen as having no deeper meaning in contemporary psychiatry. Perhaps we are missing something that could be important for us and our patients. The psychiatrist and analyst Carl Jung suggested there was an unconscious communication, and therefore a meaning in psychotic symptoms, including the movements in catatonia. The unconscious is rarely considered in psychotic presentations, yet psychosis is a prevalent condition in clinical settings. In this article Jung's ideas are presented along with case examples that invite the reader to consider them in their own future practice.

Molecular architecture and conservation of an immature human endogenous retrovirus.

The human endogenous retrovirus K (HERV-K) is the most recently acquired endogenous retrovirus in the human genome and is activated and expressed in many cancers and amyotrophic lateral sclerosis. We present the immature HERV-K capsid structure at 3.2 Å resolution determined from native virus-like particles using cryo-electron tomography and subtomogram averaging. The structure shows a hexamer unit oligomerized through a 6-helix bundle, which is stabilized by a small molecule analogous to IP6 in immature HIV-1 capsid. The HERV-K immature lattice is assembled via highly conserved dimer and trimer interfaces, as detailed through all-atom molecular dynamics simulations and supported by mutational studies. A large conformational change mediated by the linker between the N-terminal and the C-terminal domains of CA occurs during HERV-K maturation. Comparison between HERV-K and other retroviral immature capsid structures reveals a highly conserved mechanism for the assembly and maturation of retroviruses across genera and evolutionary time.

Molecular architecture and conservation of an immature human endogenous retrovirus.

A significant part of the human genome consists of endogenous retroviruses sequences. Human endogenous retrovirus K (HERV-K) is the most recently acquired endogenous retrovirus, is activated and expressed in many cancers and amyotrophic lateral sclerosis and possibly contributes to the aging process. To understand the molecular architecture of endogenous retroviruses, we determined the structure of immature HERV-K from native virus-like particles (VLPs) using cryo-electron tomography and subtomogram averaging (cryoET STA). The HERV-K VLPs show a greater distance between the viral membrane and immature capsid lattice, correlating with the presence of additional peptides, SP1 and p15, between the capsid (CA) and matrix (MA) proteins compared to the other retroviruses. The resulting cryoET STA map of the immature HERV-K capsid at 3.2 Å resolution shows a hexamer unit oligomerized through a 6-helix bundle which is further stabilized by a small molecule in the same way as the IP6 in immature HIV-1 capsid. The HERV-K immature CA hexamer assembles into the immature lattice via highly conserved dimmer and trimer interfaces, whose interactions were further detailed through all-atom molecular dynamics simulations and supported by mutational studies. A large conformational change mediated by the flexible linker between the N-terminal and the C-terminal domains of CA occurs between the immature and the mature HERV-K capsid protein, analogous to HIV-1. Comparison between HERV-K and other retroviral immature capsid structures reveals a highly conserved mechanism for the assembly and maturation of retroviruses across genera and evolutionary time.

Characterization of the rotavirus assembly pathway in situ using cryoelectron tomography.

Rotavirus assembly is a complex process that involves the stepwise acquisition of protein layers in distinct intracellular locations to form the fully assembled particle. Understanding and visualization of the assembly process has been hampered by the inaccessibility of unstable intermediates. We characterize the assembly pathway of group A rotaviruses observed in situ within cryo-preserved infected cells through the use of cryoelectron tomography of cellular lamellae. Our findings demonstrate that the viral polymerase VP1 recruits viral genomes during particle assembly, as revealed by infecting with a conditionally lethal mutant. Additionally, pharmacological inhibition to arrest the transiently enveloped stage uncovered a unique conformation of the VP4 spike. Subtomogram averaging provided atomic models of four intermediate states, including a pre-packaging single-layered intermediate, the double-layered particle, the transiently enveloped double-layered particle, and the fully assembled triple-layered virus particle. In summary, these complementary approaches enable us to elucidate the discrete steps involved in forming an intracellular rotavirus particle.

ChAdOx1 COVID vaccines express RBD open prefusion SARS-CoV-2 spikes on the cell surface.

Vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been proven to be an effective means of decreasing COVID-19 mortality, hospitalization rates, and transmission. One of the vaccines deployed worldwide is ChAdOx1 nCoV-19, which uses an adenovirus vector to drive the expression of the original SARS-CoV-2 spike on the surface of transduced cells. Using cryo-electron tomography and subtomogram averaging, we determined the native structures of the vaccine product expressed on cell surfaces in situ. We show that ChAdOx1-vectored vaccines expressing the Beta SARS-CoV-2 variant produce abundant native prefusion spikes predominantly in one-RBD-up conformation. Furthermore, the ChAdOx1-vectored HexaPro-stabilized spike yields higher cell surface expression, enhanced RBD exposure, and reduced shedding of S1 compared to the wild type. We demonstrate in situ structure determination as a powerful means for studying antigen design options in future vaccine development against emerging novel SARS-CoV-2 variants and broadly against other infectious viruses.

Jung and Working with Acute Psychosis.

Carl Jung is one of the founders of depth psychology. What is less known is his career as a psychiatrist before the creation of his analytical psychology. Jung made significant contributions to the understanding of psychotic illness. However, Jung's contributions go largely unrecognized. This is a loss for the psychiatrist who wants to incorporate psychodynamic ways of working into their daily practice. In this short essay, I describe an overview of Jung's suggestions on treating acute psychosis. A comment follows on use in contemporary practice based on personal accounts and relevant literature.

A Case Study Using a Behavioural Contract in Alcohol Dependence within a Crisis Home Treatment Team.

In this case study, we present a novel approach to care within a Home Treatment Team, using a behavioural contract. This is a signed, written agreement that targets specific behaviours for change. The concept draws on social learning theory in that it requires social interaction and a relationship to work. In psychiatric settings, the behavioural contract often finds use in Democratic Therapeutic Communities but rarely in crisis or acute services. In this case study, we attempted to use a behavioural contract within our Home Treatment Team to help a patient address his alcohol dependence and its subsequent effect on his daily living activities. The behavioural contract provided an alternative way to manage a crisis episode. We hope that other crisis service staff reading this case study may use a behavioural contract in their work to a similar beneficial effect.

Electrocatalytic water oxidation from a mixed linker MOF based on NU-1000 with an integrated ruthenium-based metallo-linker.

A novel tetratopic metallo-linker, [Ru(tda)(py(PhCOOH)2)2], 1, (tda = 2,2':6',2''-terpyridine-6,6''-dicarboxylate; py(PhCOOH)2 = (4,4'-(pyridine-3,5-diyl)dibenzoic acid), that is structurally based on one of the most active molecular water oxidation catalysts has been prepared and fully characterized, including single crystal X-ray diffraction. 1 bears geometric similarities to H4TBAPy (H4TBAPy = 4,4',4'',4'''-(pyrene-1,3,6,8-tetrayl)tetrabenzoic acid), i.e. the native linker in NU-1000, which offers the possibility to synthesize NU-1000-Ru mixed linker MOFs solvothermally. Mixed linker MOF formation was demonstrated by powder X-ray diffraction (PXRD) and scanning electron microscopy (SEM), and Ru linker incorporation confirmed by FT-IR, energy-dispersive X-ray (EDX) spectroscopy and inductively coupled plasma optical emission spectroscopy (ICP-OES). It was found that the Ru contents in the final mixed linker MOFs correlate with the amount of Ru linker present during solvothermal synthesis, albeit not in a linear fashion. The cyclic voltammograms (CV) of the mixed linker MOFs are largely dominated by TBAPy-based oxidations with features attributed to 1. Interestingly, Ru linkers near the crystal surface are oxidized directly by interfacial hole transfer form the electrode, while those in the crystal interior can be oxidized indirectly from oxidized TBAPy linkers at more anodic potential. Upon repeated scanning, the CVs show the appearance of new waves that arise from irreversible TBAPy oxidation, as well as from the activation of the Ru-based water oxidation catalyst. Of the materials prepared, the one with the highest Ru content, NU-1000-Ruhigh, was shown to catalyze the electrochemical oxidation of water to dioxygen. The Faradaic efficiency (FE) of the construct is 37%, due to water oxidation being accompanied by oxidative transformations of the TBAPy linkers. Despite the low FE, NU-1000-Ruhigh is still among the best MOF-based water oxidation catalysts, operating by a unique co-linker mediated hole-transport mechanism to supply oxidizing equivalents also to catalysts in the crystal interior.