Dark Photon Limits from Patchy Dark Screening of the Cosmic Microwave Background.

Dark photons that kinetically mix with the Standard Model photon give rise to new spectral anisotropies (patchy dark screening) in the cosmic microwave background (CMB) due to conversion of photons to dark photons within large-scale structure. We utilize predictions for this patchy dark screening signal to provide the tightest constraints to date on the dark photon kinetic mixing parameter [ϵ≲4.5×10^{-8} (95% confidence level)] over the mass range 10^{-13} eV≲m_{A^{'}}≲10^{-11} eV, almost an order of magnitude stronger than previous limits, by applying state-of-the-art component separation techniques to the cross-correlation of Planck CMB and unWISE galaxy survey data.

Potent activity of polymyxin B is associated with long-lived super-stoichiometric accumulation mediated by weak-affinity binding to lipid A.

Polymyxins are gram-negative antibiotics that target lipid A, the conserved membrane anchor of lipopolysaccharide in the outer membrane. Despite their clinical importance, the molecular mechanisms underpinning polymyxin activity remain unresolved. Here, we use surface plasmon resonance to kinetically interrogate interactions between polymyxins and lipid A and derive a phenomenological model. Our analyses suggest a lipid A-catalyzed, three-state mechanism for polymyxins: transient binding, membrane insertion, and super-stoichiometric cluster accumulation with a long residence time. Accumulation also occurs for brevicidine, another lipid A-targeting antibacterial molecule. Lipid A modifications that impart polymyxin resistance and a non-bactericidal polymyxin derivative exhibit binding that does not evolve into long-lived species. We propose that transient binding to lipid A permeabilizes the outer membrane and cluster accumulation enables the bactericidal activity of polymyxins. These findings could establish a blueprint for discovery of lipid A-targeting antibiotics and provide a generalizable approach to study interactions with the gram-negative outer membrane.

Disulfi de constrained Fabs overcome target size limitation for high-resolution single-particle cryo-EM.

High-resolution structures of proteins are critical to understanding molecular mechanisms of biological processes and in the discovery of therapeutic molecules. Cryo-EM has revolutionized structure determination of large proteins and their complexes1, but a vast majority of proteins that underlie human diseases are small (< 50 kDa) and usually beyond its reach due to low signal-to-noise images and difficulties in particle alignment2. Current strategies to overcome this problem increase the overall size of small protein targets using scaffold proteins that bind to the target, but are limited by inherent flexibility and not being bound to their targets in a rigid manner, resulting in the target being poorly resolved compared to the scaffolds3-11. Here we present an iteratively engineered molecular design for transforming Fabs (antibody fragments), into conformationally rigid scaffolds (Rigid-Fabs) that, when bound to small proteins (~20 kDa), can enable high-resolution structure determination using cryo-EM. This design introduces multiple disulfide bonds at strategic locations, generates a well-folded Fab constrained into a rigid conformation and can be applied to Fabs from various species, isotypes and chimeric Fabs. We present examples of the Rigid Fab design enabling high-resolution (2.3-2.5 Å) structures of small proteins, Ang2 (26 kDa) and KRAS (21 kDa) by cryo-EM. The strategies for designing disulfide constrained Rigid Fabs in our work thus establish a general approach to overcome the target size limitation of single particle cryo-EM.

Acquired Aquagenic Syringeal Keratoderma Following COVID-19 Infection.

Aquagenic syringeal keratoderma (ASK), rare in males, is characterized by the rapid onset of edematous palmar wrinkling with small white papules after brief contact with water or sweat. A 24-year-old atopic male presented with a 2-week subacute history of bilateral palmar edema with whitish-colored papules after exposure to water, 3 months after having had COVID-19 infection treated with a full course of ritonavir-boosted nirmatrelvir (PAXLOVIDTM). He had received 3 COVID-19 vaccines (Pfizer, New York, NY) about 12 months prior. Workup was negative. Initial spontaneous near-resolution 2 months after onset was temporary, with recurrence 1 month later. Treatment with 12% topical aluminum chloride was ineffective. Botulinum toxin injection to both palms led to resolution of symptoms that has been sustained for 7 months. The association between atopy and ASK remains weak. We present a case of new-onset ASK in an adult male 3 months following COVID-19 infection without a history of excessive handwashing. Our patient may have had a predisposition to recurrent ASK due to his history of atopy including atopic dermatitis and food allergy anaphylaxis combined with prior COVID-19 infection. It is possible that ASK is a novel manifestation of post-acute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (PASC) infection or long COVID.

Machine Learning-Based Predictive Models for 90-Day Readmission of Total Joint Arthroplasty Using Comprehensive Electronic Health Records and Patient-Reported Outcome Measures.

Background: The Centers for Medicare & Medicaid Services currently incentivizes hospitals to reduce postdischarge adverse events such as unplanned hospital readmissions for patients who underwent total joint arthroplasty (TJA). This study aimed to predict 90-day TJA readmissions from our comprehensive electronic health record data and routinely collected patient-reported outcome measures. Methods: We retrospectively queried all TJA-related readmissions in our tertiary care center between 2016 and 2019. A total of 104-episode care characteristics and preoperative patient-reported outcome measures were used to develop several machine learning models for prediction performance evaluation and comparison. For interpretability, a logistic regression model was built to investigate the statistical significance, magnitudes, and directions of associations between risk factors and readmission. Results: Given the significant imbalanced outcome (5.8% of patients were readmitted), our models robustly predicted the outcome, yielding areas under the receiver operating characteristic curves over 0.8, recalls over 0.5, and precisions over 0.5. In addition, the logistic regression model identified risk factors predicting readmission: diabetes, preadmission medication prescriptions (ie, nonsteroidal anti-inflammatory drug, corticosteroid, and narcotic), discharge to a skilled nursing facility, and postdischarge care behaviors within 90 days. Notably, low self-reported confidence to carry out social activities accurately predicted readmission. Conclusions: A machine learning model can help identify patients who are at substantially increased risk of a readmission after TJA. This finding may allow for health-care providers to increase resources targeting these patients. In addition, a poor response to the "social activities" question may be a useful indicator that predicts a significant increased risk of readmission after TJA.

Identifying the origins of countertransference using the Core Conflictual Relationship Theme method: A multiple case study approach.

OBJECTIVE: Measurement of countertransference (CT) has proven challenging throughout the history of studying this construct. We sought to determine the potential value of using a common measure of transference, the Core Conflictual Relationship Theme (CCRT) method, as a means of studying CT. METHOD: The Relationship Anecdote Paradigm and the CCRT method were used to examine CT in two studies. In Study 1, we examined the correspondence between a therapist's wishes with significant people in her life (i.e., her parents and husband) and three long-term patients. In Study 2, we identified the interpersonal wishes of a different therapist and examined 14 of her sessions with 3 patients for evidence of how these wishes and needs were displayed in her clinical work. RESULTS: Analyses revealed that specific wishes in therapists' personal lives could be detected from projective interviews and these wishes were similar, but not necessarily identical, to wishes in therapists' descriptions of, and actual work with, their patients. Evidence of both chronic wishes and patient-specific wishes was revealed. CONCLUSIONS: These findings support the idea that the origins of CT reside in therapists' interpersonal wishes and that the CCRT may be a promising means of identifying CT in research, practice, and supervision.

Do the Words We Choose Matter When Prescribing Medications?

BACKGROUND: Caregivers are often apprehensive about treating childhood atopic dermatitis (AD) with topical corticosteroids but may find comfort if treatments are presented in a patient-centered manner. OBJECTIVE: We assessed caregivers' willingness to treat AD with either a "topical steroid," "topical medication," or "treatment, similar to the all-natural signals produced by the adrenal glands in the body." METHODS: A survey randomized 874 caregivers of children with AD to receive a "topical steroid," "topical medication," or "treatment, similar to the all-natural signals produced by the adrenal glands in the body." A scenario-only dataset received these descriptions, while a descriptive heading dataset and expanded scale dataset also received headings of "Topical Steroid Use," "Topical Medication Use," and "All-Natural Treatment Use," respectively. Responses were recorded on a 6-point Likert scale or 0-100 slider scale. Whole and dichotomized responses were evaluated using 2-tailed, independent sample t-tests. RESULTS: For the descriptive heading and expanded scale datasets, those presented with a "topical medication" reported greater willingness to treat than those presented with a "topical steroid" and "all-natural treatment" in the descriptive heading dataset (P<0.05). For the dichotomized scenario-only dataset, those presented with a "treatment, similar to the all-natural signals produced by the adrenal glands in the body," reported greater willingness than those presented with a "topical medication" (P<0.05). CONCLUSION: Initially presenting caregivers with a "topical medication" rather than a "topical steroid" may improve willingness to treat AD for some caregivers. However, tailoring the discussion to best fit caregivers’ understanding of treatment may be the most beneficial approach. J Drugs Dermatol. 2023;22(12):1216-1219. doi:10.36849/JDD.5746.

Inhibiting membrane rupture with NINJ1 antibodies limits tissue injury.

Plasma membrane rupture (PMR) in dying cells undergoing pyroptosis or apoptosis requires the cell-surface protein NINJ11. PMR releases pro-inflammatory cytoplasmic molecules, collectively called damage-associated molecular patterns (DAMPs), that activate immune cells. Therefore, inhibiting NINJ1 and PMR may limit the inflammation that is associated with excessive cell death. Here we describe an anti-NINJ1 monoclonal antibody that specifically targets mouse NINJ1 and blocks oligomerization of NINJ1, preventing PMR. Electron microscopy studies showed that this antibody prevents NINJ1 from forming oligomeric filaments. In mice, inhibition of NINJ1 or Ninj1 deficiency ameliorated hepatocellular PMR induced with TNF plus D-galactosamine, concanavalin A, Jo2 anti-Fas agonist antibody or ischaemia-reperfusion injury. Accordingly, serum levels of lactate dehydrogenase, the liver enzymes alanine aminotransaminase and aspartate aminotransferase, and the DAMPs interleukin 18 and HMGB1 were reduced. Moreover, in the liver ischaemia-reperfusion injury model, there was an attendant reduction in neutrophil infiltration. These data indicate that NINJ1 mediates PMR and inflammation in diseases driven by aberrant hepatocellular death.

Core defense hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems.

Bacteria use a diverse arsenal of anti-phage immune systems, including CRISPR-Cas and restriction enzymes. Recent advances in anti-phage system discovery and annotation tools have unearthed many unique systems, often encoded in horizontally transferred defense islands, which can be horizontally transferred. Here, we developed Hidden Markov Models (HMMs) for defense systems and queried microbial genomes on the NCBI database. Out of the 30 species with >200 completely sequenced genomes, our analysis found Pseudomonas aeruginosa exhibits the greatest diversity of anti-phage systems, as measured by Shannon entropy. Using network analysis to identify the common neighbors of anti-phage systems, we identified two core defense hotspot loci (cDHS1 and cDHS2). cDHS1 is up to 224 kb (median: 26 kb) with varied arrangements of more than 30 distinct immune systems across isolates, while cDHS2 has 24 distinct systems (median: 6 kb). Both cDHS regions are occupied in a majority of P. aeruginosa isolates. Most cDHS genes are of unknown function potentially representing new anti-phage systems, which we validated by identifying a novel anti-phage system (Shango) commonly encoded in cDHS1. Identifying core genes flanking immune islands could simplify immune system discovery and may represent popular landing spots for diverse MGEs carrying anti-phage systems.

Targeted degradation via direct 26S proteasome recruitment.

Engineered destruction of target proteins by recruitment to the cell's degradation machinery has emerged as a promising strategy in drug discovery. The majority of molecules that facilitate targeted degradation do so via a select number of ubiquitin ligases, restricting this therapeutic approach to tissue types that express the requisite ligase. Here, we describe a new strategy of targeted protein degradation through direct substrate recruitment to the 26S proteasome. The proteolytic complex is essential and abundantly expressed in all cells; however, proteasomal ligands remain scarce. We identify potent peptidic macrocycles that bind directly to the 26S proteasome subunit PSMD2, with a 2.5-Å-resolution cryo-electron microscopy complex structure revealing a binding site near the 26S pore. Conjugation of this macrocycle to a potent BRD4 ligand enabled generation of chimeric molecules that effectively degrade BRD4 in cells, thus demonstrating that degradation via direct proteasomal recruitment is a viable strategy for targeted protein degradation.

Erratum: New Semiclassical Picture of Vacuum Decay [Phys. Rev. Lett. 123, 031601 (2019)].

This corrects the article DOI: 10.1103/PhysRevLett.123.031601.

The imperfect storm: An uncommon presentation of Chagas disease.

Electrical storm is defined as three or more sustained episodes of ventricular tachycardia, ventricular fibrillation, or appropriate cardioverter-defibrillator shocks during a 24-h period. These patients are notoriously difficult to manage. We present a case secondary to Chagas disease that was responsive to lidocaine. Although an uncommon presentation, given the large-scale population movement from South America, Chagas has an increased incidence and is an important diagnostic consideration in patients with new onset heart failure, arrhythmia, or electrical storm.

The Peel-Blot Technique: A Cryo-EM Sample Preparation Method to Separate Single Layers from Multi-Layered or Concentrated Biological Samples.

The peel-blot cryo-EM grid preparation technique is a significantly modified back-injection method with the objective of achieving a reduction in layers of multi-layered samples. This removal of layers prior to plunge freezing can aid in reducing sample thickness to a level suitable for cryo-EM data collection, improving sample flatness, and facilitating image processing. The peel-blot technique allows for the separation of multilamellar membranes into single layers, of layered 2D crystals into individual crystals, and of stacked, sheet-like structures of soluble proteins to likewise be separated into single layers. The high sample thickness of these types of samples frequently poses insurmountable problems for cryo-EM data collection and cryo-EM image processing, especially when the microscope stage must be tilted for data collection. Furthermore, grids of high concentrations of any of these samples can be prepared for efficient data collection since sample concentration prior to grid preparation can be increased and the peel-blot technique adjusted to result in a dense distribution of single-layered specimen.

Concurrent Atopic Dermatitis and Psoriasis Vulgaris: Implications for Targeted Biologic Therapy.

Psoriasis vulgaris, a helper T cell TH1/TH17-mediated inflammatory dermatosis, may be effectively treated with biologic medications such as secukinumab, an IL-17A inhibitor. However, suppression of the TH1-mediated axis may result in the paradoxical appearance of TH2-mediated inflammatory skin conditions, such as atopic dermatitis (AD). Dupilumab, a biologic medication that inhibits IL-4/IL-13-cytokines involved in TH2-mediated inflammation-has demonstrated efficacy in treating AD but may result in phenotypic switching to psoriasis. We describe a patient with psoriasis that was well controlled on secukinumab who developed severe AD that improved with dupilumab. After several months of effective treatment with dupilumab, he subsequently developed re-emergence of psoriatic lesions. This case highlights how pharmacologic interventions targeted at specific immunologic pathways, such as the TH1/TH2 axis, may have unintended consequences.

Structural basis for SHOC2 modulation of RAS signalling.

The RAS-RAF pathway is one of the most commonly dysregulated in human cancers1-3. Despite decades of study, understanding of the molecular mechanisms underlying dimerization and activation4 of the kinase RAF remains limited. Recent structures of inactive RAF monomer5 and active RAF dimer5-8 bound to 14-3-39,10 have revealed the mechanisms by which 14-3-3 stabilizes both RAF conformations via specific phosphoserine residues. Prior to RAF dimerization, the protein phosphatase 1 catalytic subunit (PP1C) must dephosphorylate the N-terminal phosphoserine (NTpS) of RAF11 to relieve inhibition by 14-3-3, although PP1C in isolation lacks intrinsic substrate selectivity. SHOC2 is as an essential scaffolding protein that engages both PP1C and RAS to dephosphorylate RAF NTpS11-13, but the structure of SHOC2 and the architecture of the presumptive SHOC2-PP1C-RAS complex remain unknown. Here we present a cryo-electron microscopy structure of the SHOC2-PP1C-MRAS complex to an overall resolution of 3 Å, revealing a tripartite molecular architecture in which a crescent-shaped SHOC2 acts as a cradle and brings together PP1C and MRAS. Our work demonstrates the GTP dependence of multiple RAS isoforms for complex formation, delineates the RAS-isoform preference for complex assembly, and uncovers how the SHOC2 scaffold and RAS collectively drive specificity of PP1C for RAF NTpS. Our data indicate that disease-relevant mutations affect complex assembly, reveal the simultaneous requirement of two RAS molecules for RAF activation, and establish rational avenues for discovery of new classes of inhibitors to target this pathway.

Lack of Cas13a inhibition by anti-CRISPR proteins from Leptotrichia prophages.

CRISPR systems are prokaryotic adaptive immune systems that use RNA-guided Cas nucleases to recognize and destroy foreign genetic elements. To overcome CRISPR immunity, bacteriophages have evolved diverse families of anti-CRISPR proteins (Acrs). Recently, Lin et al. (2020) described the discovery and characterization of 7 Acr families (AcrVIA1-7) that inhibit type VI-A CRISPR systems. We detail several inconsistencies that question the results reported in the Lin et al. (2020) study. These include inaccurate bioinformatics analyses and bacterial strains that are impossible to construct. Published strains were provided by the authors, but MS2 bacteriophage plaque assays did not support the published results. We also independently tested the Acr sequences described in the original report, in E. coli and mammalian cells, but did not observe anti-Cas13a activity. Taken together, our data and analyses prompt us to question the claim that AcrVIA1-7 reported in Lin et al. are type VI anti-CRISPR proteins.

Structural basis for HCMV Pentamer receptor recognition and antibody neutralization.

Human cytomegalovirus (HCMV) represents the viral leading cause of congenital birth defects and uses the gH/gL/UL128-130-131A complex (Pentamer) to enter different cell types, including epithelial and endothelial cells. Upon infection, Pentamer elicits the most potent neutralizing response against HCMV, representing a key vaccine candidate. Despite its relevance, the structural basis for Pentamer receptor recognition and antibody neutralization is largely unknown. Here, we determine the structures of Pentamer bound to neuropilin 2 (NRP2) and a set of potent neutralizing antibodies against HCMV. Moreover, we identify thrombomodulin (THBD) as a functional HCMV receptor and determine the structures of the Pentamer-THBD complex. Unexpectedly, both NRP2 and THBD also promote dimerization of Pentamer. Our results provide a framework for understanding HCMV receptor engagement, cell entry, antibody neutralization, and outline strategies for antiviral therapies against HCMV.

IMPDH1 retinal variants control filament architecture to tune allosteric regulation.

Inosine-5'-monophosphate dehydrogenase (IMPDH), a key regulatory enzyme in purine nucleotide biosynthesis, dynamically assembles filaments in response to changes in metabolic demand. Humans have two isoforms: IMPDH2 filaments reduce sensitivity to feedback inhibition, while IMPDH1 assembly remains uncharacterized. IMPDH1 plays a unique role in retinal metabolism, and point mutants cause blindness. Here, in a series of cryogenic-electron microscopy structures we show that human IMPDH1 assembles polymorphic filaments with different assembly interfaces in extended and compressed states. Retina-specific splice variants introduce structural elements that reduce sensitivity to GTP inhibition, including stabilization of the extended filament form. Finally, we show that IMPDH1 disease mutations fall into two classes: one disrupts GTP regulation and the other has no effect on GTP regulation or filament assembly. These findings provide a foundation for understanding the role of IMPDH1 in retinal function and disease and demonstrate the diverse mechanisms by which metabolic enzyme filaments are allosterically regulated.