Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressure.

The evolution of circulating viruses is shaped by their need to evade antibody response, which mainly targets the viral spike. Because of the high density of spikes on the viral surface, not all antigenic sites are targeted equally by antibodies. We offer here a geometry-based approach to predict and rank the probability of surface residues of SARS spike (S protein) and influenza H1N1 spike (hemagglutinin) to acquire antibody-escaping mutations utilizing in-silico models of viral structure.

C5 Palsy Following Cervical Spine Decompression.

Background: Cervical spinal surgery is considered safe and effective. One of the few specific complications of this procedure is C5 nerve root palsy. Expressed primarily by deltoid muscle and biceps brachii weakness, it is rare and has been related to nerve root traction or to ischemic spinal cord damage.

Learning from HIV-1 to predict the immunogenicity of T cell epitopes in SARS-CoV-2.

We describe a physics-based learning model for predicting the immunogenicity of cytotoxic T lymphocyte (CTL) epitopes derived from diverse pathogens including SARS-CoV-2. The model was trained and optimized on the relative immunodominance of CTL epitopes in human immunodeficiency virus infection. Its accuracy was tested against experimental data from patients with COVID-19.

Damage-induced chromatome dynamics link Ubiquitin ligase and proteasome recruitment to histone loss and efficient DNA repair.

Eukaryotic cells package their genomes around histone octamers. In response to DNA damage, checkpoint activation in yeast induces core histone degradation resulting in 20%-40% reduction in nucleosome occupancy. To gain insight into this process, we developed a new approach to analyze the chromatin-associated proteome comprehensively before and after damage.

Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressure.

The evolution of circulating viruses is shaped by their need to evade antibody response, which mainly targets the glycoprotein (spike). However, not all antigenic sites are targeted equally by antibodies, leading to complex immunodominance patterns. We used 3D computational models to estimate antibody pressure on the seasonal influenza H1N1 and SARS spikes.

Defining and Manipulating B Cell Immunodominance Hierarchies to Elicit Broadly Neutralizing Antibody Responses against Influenza Virus.

The antibody repertoire possesses near-limitless diversity, enabling the adaptive immune system to accommodate essentially any antigen. However, this diversity explores the antigenic space unequally, allowing some pathogens like influenza virus to impose complex immunodominance hierarchies that distract antibody responses away from key sites of virus vulnerability. We developed a computational model of affinity maturation to map the patterns of immunodominance that evolve upon immunization with natural and engineered displays of hemagglutinin (HA), the influenza vaccine antigen.

DNA Damage-Induced Nucleosome Depletion Enhances Homology Search Independently of Local Break Movement.

To determine whether double-strand break (DSB) mobility enhances the physical search for an ectopic template during homology-directed repair (HDR), we tested the effects of factors that control chromatin dynamics, including cohesin loading and kinetochore anchoring. The former but not the latter is altered in response to DSBs. Loss of the nonhistone high-mobility group protein Nhp6 reduces histone occupancy and increases chromatin movement, decompaction, and ectopic HDR.

Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields.

Nucleosomes package genomic DNA into chromatin. By regulating DNA access for transcription, replication, DNA repair, and epigenetic modification, chromatin forms the nexus of most nuclear processes. In addition, dynamic organization of chromatin underlies both regulation of gene expression and evolution of chromosomes into individualized sister objects, which can segregate cleanly to different daughter cells at anaphase.

Guided nuclear exploration increases CTCF target search efficiency.

The enormous size of mammalian genomes means that for a DNA-binding protein the number of nonspecific, off-target sites vastly exceeds the number of specific, cognate sites. How mammalian DNA-binding proteins overcome this challenge to efficiently locate their target sites is not known. Here, through live-cell single-molecule tracking, we show that CCCTC-binding factor, CTCF, is repeatedly trapped in small zones that likely correspond to CTCF clusters, in a manner that is largely dependent on an internal RNA-binding region (RBR).

The association between pregnancies complicated with isolated polyhydramnios or oligohydramnios and offspring long-term gastrointestinal morbidity.

Objective: Infants born to mothers with pregnancies complicated by polyhydramnios or oligohydramnios are at an increased risk for significant adverse perinatal outcome. We sought to assess whether in utero exposure to amniotic fluid abnormalities increases the risk of long-term gastrointestinal (GI) morbidity in the offspring.

Methods: In a population-based cohort study, the incidence of GI-related hospitalizations was compared between singletons exposed and unexposed to oligohydramnios or polyhydramnios.

The Role of 18F-Fluorodeoxyglucose Positron-Emission Tomography/Computed Tomography in the Diagnosis of Postoperative Hardware-Related Spinal Infections.

Background: Implant-related spinal infections are a surgical complication associated with high morbidity. Due to infection, hardware removal may be necessary, which could lead to pseudarthrosis and the loss of stability and alignment.

Objectives: To evaluate the accuracy and diagnostic value of 18F-fluorodeoxyglucose positron-emission tomography/computed tomography (18F-FDG PET/CT) in the workup of patients with suspected implant-related infections of the spine and to assess the clinical impact of PET/CT results on the management of these infections.

Advances Using Single-Particle Trajectories to Reconstruct Chromatin Organization and Dynamics.

Chromatin organization remains complex and far from understood. In this article, we review recent statistical methods of extracting biophysical parameters from in vivo single-particle trajectories of loci to reconstruct chromatin reorganization in response to cellular stress such as DNA damage. We look at methods for analyzing both single locus and multiple loci tracked simultaneously and explain how to quantify and describe chromatin motion using a combination of extractable parameters.

The low spike density of HIV may have evolved because of the effects of T helper cell depletion on affinity maturation.

The spikes on virus surfaces bind receptors on host cells to propagate infection. High spike densities (SDs) can promote infection, but spikes are also targets of antibody-mediated immune responses. Thus, diverse evolutionary pressures can influence virus SDs.

Identifying Tyrosine Kinase Inhibitor Nonadherence in Chronic Myeloid Leukemia: Subanalysis of TAKE-IT Pilot Study.

Background: There are inconsistencies in reports on correlates for nonadherence (NA) to tyrosine kinase inhibitors (TKIs) in chronic myeloid leukemia (CML). The diagnostic accuracy of subjective adherence measures using electronic monitoring (EM) as the reference standard is yet to be determined. This study aimed to evaluate correlates of TKI NA using EM and test the diagnostic accuracy of subjective adherence measures.

Effect of Adherence-enhancing Interventions on Adherence to Tyrosine Kinase Inhibitor Treatment in Chronic Myeloid Leukemia (TAKE-IT): A Quasi-experimental Pre-Post Intervention Multicenter Pilot Study.

Background: Nonadherence to tyrosine kinase inhibitors (TKIs) in chronic myeloid leukemia (CML) has been associated with inferior outcomes. Scarce evidence exists on the effectiveness of adherence-enhancing interventions. The present pilot study evaluated the feasibility and effectiveness of an intervention to improve TKI adherence in adult CML patients.

Encounter times of chromatin loci influenced by polymer decondensation.

The time for a DNA sequence to find its homologous counterpart depends on a long random search inside the cell nucleus. Using polymer models, we compute here the mean first encounter time (MFET) between two sites located on two different polymer chains and confined locally by potential wells. We find that reducing tethering forces acting on the polymers results in local decondensation, and numerical simulations of the polymer model show that these changes are associated with a reduction of the MFET by several orders of magnitude.

The Discrepancy between Subjective and Objective Measures of Convergence Insufficiency in Whiplash-Associated Disorder versus Control Participants.

Purpose: Motor vehicle accidents (MVAs) are a pandemic associated with human suffering and a burden to national economies. Whiplash-associated disorders (WADs) after MVAs are associated commonly with disability claims, many of which are related to vision. Convergence insufficiency (CI) leads to visual disability associated with symptoms of ocular discomfort.

A Population Dynamics Model for Clonal Diversity in a Germinal Center.

Germinal centers (GCs) are micro-domains where B cells mature to develop high affinity antibodies. Inside a GC, B cells compete for antigen and T cell help, and the successful ones continue to evolve. New experimental results suggest that, under identical conditions, a wide spectrum of clonal diversity is observed in different GCs, and high affinity B cells are not always the ones selected.

Radiographic Risk Factors For Interprosthetic Femur Fractures.

Purpose: Total hip arthroplasty (THA) and total knee arthroplasty (TKA) are among the most common orthopaedic procedures performed in the United States annually. As the number of patients undergoing these procedures increases so too does the incidence of periprosthetic femur fractures. A number of these periprosthetic fractures occur between two ipsilateral implants, so-called interprosthetic fractures.

Visualization of Chromatin Decompaction and Break Site Extrusion as Predicted by Statistical Polymer Modeling of Single-Locus Trajectories.

Chromatin moves with subdiffusive and spatially constrained dynamics within the cell nucleus. Here, we use single-locus tracking by time-lapse fluorescence microscopy to uncover information regarding the forces that influence chromatin movement following the induction of a persistent DNA double-strand break (DSB). Using improved time-lapse imaging regimens, we monitor trajectories of tagged DNA loci at a high temporal resolution, which allows us to extract biophysical parameters through robust statistical analysis.

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates.

Nucleosomes are essential for proper chromatin organization and the maintenance of genome integrity. Histones are post-translationally modified and often evicted at sites of DNA breaks, facilitating the recruitment of repair factors. Whether such chromatin changes are localized or genome-wide is debated.