Deaminase-mediated chromatin accessibility profiling with single-allele resolution.

Binding of transcription factors (TFs) at gene regulatory elements controls cellular epigenetic state and gene expression. Current genome-wide chromatin profiling approaches have inherently limited resolution, complicating assessment of TF occupancy and co-occupancy, especially at individual alleles. In this work, we introduce Accessible Chromatin by Cytosine Editing Site Sequencing with ATAC-seq (ACCESS-ATAC), which harnesses a double-stranded DNA cytosine deaminase (Ddd) enzyme to stencil TF binding locations within accessible chromatin regions.

FUSE: Improving the estimation and imputation of variant impacts in functional screening.

Deep mutational scanning enables high-throughput functional assessment of genetic variants. While phenotypic measurements from screening assays generally align with clinical outcomes, experimental noise may affect the accuracy of individual variant estimates. We developed the FUSE (functional substitution estimation) pipeline, which leverages measurements collectively within screening assays to improve the estimation of variant impacts.

Global neurotrauma: A systematic review and summary of the current state of registries around the world.

Neurotrauma registries (NTR) collect data on traumatic brain injuries (TBI) to advance knowledge, shape policies, and improve outcomes. This study reviews global NTRs from High-Income (HICs) and Low- and Middle-Income countries (LMICs). A systematic review was conducted using PubMed, Google Scholar, Embase, and Web of Science following PRISMA guidelines to identify relevant NTRs.

Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification.

CRISPR base editing screens enable analysis of disease-associated variants at scale; however, variable efficiency and precision confounds the assessment of variant-induced phenotypes. Here, we provide an integrated experimental and computational pipeline that improves estimation of variant effects in base editing screens. We use a reporter construct to measure guide RNA (gRNA) editing outcomes alongside their phenotypic consequences and introduce base editor screen analysis with activity normalization (BEAN), a Bayesian network that uses per-guide editing outcomes provided by the reporter and target site chromatin accessibility to estimate variant impacts.

Epigenetic profiling reveals key genes and cis-regulatory networks specific to human parathyroids.

In all terrestrial vertebrates, the parathyroid glands are critical regulators of calcium homeostasis and the sole source of parathyroid hormone (PTH). Hyperparathyroidism and hypoparathyroidism are clinically important disorders affecting multiple organs. However, our knowledge regarding regulatory mechanisms governing the parathyroids has remained limited.

Catheter ablation for supraventricular tachycardia and health resource utilization and expenditures: A propensity-matched cohort study.

Background: Few data are available regarding temporal patterns of health resource utilization (HRU) and expenditures among patients undergoing catheter ablation for paroxysmal supraventricular tachycardia (PSVT). This study aimed to describe expenditures and HRU in patients with PSVT who underwent catheter ablation compared to a matched cohort of patients on medical therapy alone.

Methods: Using a large US administrative database, we identified adult patients (age 18 to 65 years) with a new PSVT diagnosis between 2008 and 2016.

Cross-sectional data accurately model longitudinal growth in the craniofacial skeleton.

Dense, longitudinal sampling represents the ideal for studying biological growth. However, longitudinal samples are not typically possible, due to limits of time, prohibitive cost, or health concerns of repeat radiologic imaging. In contrast, cross-sectional samples have few such drawbacks, but it is not known how well estimates of growth milestones can be obtained from cross-sectional samples.

Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification.

CRISPR base editing screens are powerful tools for studying disease-associated variants at scale. However, the efficiency and precision of base editing perturbations vary, confounding the assessment of variant-induced phenotypic effects. Here, we provide an integrated pipeline that improves the estimation of variant impact in base editing screens.

Systematic elucidation of genetic mechanisms underlying cholesterol uptake.

Genetic variation contributes greatly to LDL cholesterol (LDL-C) levels and coronary artery disease risk. By combining analysis of rare coding variants from the UK Biobank and genome-scale CRISPR-Cas9 knockout and activation screening, we substantially improve the identification of genes whose disruption alters serum LDL-C levels. We identify 21 genes in which rare coding variants significantly alter LDL-C levels at least partially through altered LDL-C uptake.

A molecular glue approach to control the half-life of CRISPR-based technologies.

Cas9 is a programmable nuclease that has furnished transformative technologies, including base editors and transcription modulators (e.g., CRISPRi/a), but several applications of these technologies, including therapeutics, mandatorily require precision control of their half-life.

Systematic elucidation of genetic mechanisms underlying cholesterol uptake.

Genetic variation contributes greatly to LDL cholesterol (LDL-C) levels and coronary artery disease risk. By combining analysis of rare coding variants from the UK Biobank and genome-scale CRISPR-Cas9 knockout and activation screening, we have substantially improved the identification of genes whose disruption alters serum LDL-C levels. We identify 21 genes in which rare coding variants significantly alter LDL-C levels at least partially through altered LDL-C uptake.

Joint estimation and imputation of variant functional effects using high throughput assay data.

Deep mutational scanning assays enable the functional assessment of variants in high throughput. Phenotypic measurements from these assays are broadly concordant with clinical outcomes but are prone to noise at the individual variant level. We develop a framework to exploit related measurements within and across experimental assays to jointly estimate variant impact.

Peptide fusion improves prime editing efficiency.

Prime editing enables search-and-replace genome editing but is limited by low editing efficiency. We present a high-throughput approach, the Peptide Self-Editing sequencing assay (PepSEq), to measure how fusion of 12,000 85-amino acid peptides influences prime editing efficiency. We show that peptide fusion can enhance prime editing, prime-enhancing peptides combine productively, and a top dual peptide-prime editor increases prime editing significantly in multiple cell lines across dozens of target sites.

Structural, Morphological, Optical and Electrical Characterization of Gahnite Ferroan Nano Composite Derived from Fly Ash Silica and ZnO Mixture.

The synthesis of a high value-added product, gahnite ferroan nano composite, from a mixture of fly ash silica and ZnO is a low-cost and non-expensive technique. The XRD pattern clearly reveals the synthesized product from fly ash after leaching is a product of high-purity gahnite ferroan composite. The grains are mostly cubical in shape.

Craniofacial growth and morphology among intersecting clinical categories.

Differential patterns of craniofacial growth are important sources of variation that can result in skeletal malocclusion. Understanding the timing of growth milestones and morphological change associated with adult skeletal malocclusions is critical for developing individualized orthodontic growth modification strategies. To identify patterns in the timing and geometry of growth, we used Bayesian modeling of cephalometrics and geometric morphometric analyses with a dense, longitudinal sample consisting of 15,407 cephalograms from 1,913 individuals between 2 and 31 years of age.

Early non-neutralizing, afucosylated antibody responses are associated with COVID-19 severity.

A damaging inflammatory response is implicated in the pathogenesis of severe coronavirus disease 2019 (COVID-19), but mechanisms contributing to this response are unclear. In two prospective cohorts, early non-neutralizing, afucosylated immunoglobulin G (IgG) antibodies specific to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were associated with progression from mild to more severe COVID-19. To study the biology of afucosylated IgG immune complexes, we developed an in vivo model that revealed that human IgG-Fc-gamma receptor (FcγR) interactions could regulate inflammation in the lung.

Genetic influences on dentognathic morphology in the Jirel population of Nepal.

Patterns of genetic variation and covariation impact the evolution of the craniofacial complex and contribute to clinically significant malocclusions in modern human populations. Previous quantitative genetic studies have estimated the heritabilities and genetic correlations of skeletal and dental traits in humans and nonhuman primates, but none have estimated these quantitative genetic parameters across the dentognathic complex. A large and powerful pedigree from the Jirel population of Nepal was leveraged to estimate heritabilities and genetic correlations in 62 maxillary and mandibular arch dimensions, incisor and canine lengths, and post-canine tooth crown areas (N ≥ 739).

Vitamin D kinetics in nonpregnant and pregnant women after a single oral dose of trideuterated vitamin D.

The plasma pool of the hormone 1,25-dihydroxyvitamin D (1,25(OH)D) is increased throughout most of human pregnancy. Mechanisms behind this adaptation are unclear, in part due to limited data on vitamin D kinetics during pregnancy. Stable isotopes make it possible to study vitamin D kinetics in vulnerable study populations like pregnant women.

Tibial Bone Quality in Former Bariatric Surgery Patients with Osteoarthritis.

Unlabelled: Downstream effects of bariatric weight-loss surgery have been associated with bone resorption, potentially jeopardizing total knee arthroplasty (TKA) implant fixation/ingrowth.

Purpose: This case-control study sought to determine if TKA patients with history of bariatric surgery exhibit altered microanatomy of subchondral bone quality in the tibial plateau compared to controls.

Materials And Methods: With IRB approval, 41 bone samples were evaluated from 12 former bariatric surgery patients and 10 sex-, age-, weight-, height-, and BMI-matched controls.

Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency.

Mutational outcomes following CRISPR-Cas9-nuclease cutting in mammalian cells have recently been shown to be predictable and, in certain cases, skewed toward single genotypes. However, the ability to control these outcomes remains limited, especially for 1-bp insertions, a common and therapeutically relevant class of repair outcomes. Here, through a small molecule screen, we identify the ATM kinase inhibitor KU-60019 as a compound capable of reproducibly increasing the fraction of 1-bp insertions relative to other Cas9 repair outcomes.

Geometric morphometric analysis of growth patterns among facial types.

Introduction: Extreme patterns of vertical facial divergence are of great importance to clinicians because of their association with dental malocclusion and functional problems of the orofacial complex. Understanding the growth patterns associated with vertical facial divergence is critical for clinicians to provide optimal treatment. This study evaluates and compares growth patterns from childhood to adulthood among 3 classifications of vertical facial divergence using longitudinal, lateral cephalograms from the Craniofacial Growth Consortium Study.

Structurally and functionally distinct early antibody responses predict COVID-19 disease trajectory and mRNA vaccine response.

Unlabelled: A damaging inflammatory response is strongly implicated in the pathogenesis of severe COVID-19 but mechanisms contributing to this response are unclear. In two prospective cohorts, early non-neutralizing, afucosylated, anti-SARS-CoV-2 IgG predicted progression from mild, to more severe COVID-19. In contrast to the antibody structures that predicted disease progression, antibodies that were elicited by mRNA SARS-CoV-2 vaccines were low in Fc afucosylation and enriched in sialylation, both modifications that reduce the inflammatory potential of IgG.

Estimating Craniofacial Growth Cessation: Comparison of Asymptote- and Rate-Based Methods.

Objective: To identify differences between asymptote- and rate-based methods for estimating age and size at growth cessation in linear craniofacial measurements.

Design: This is a retrospective, longitudinal study. Five linear measurements were collected from lateral cephalograms as part of the Craniofacial Growth Consortium Study (CGCS).

Using CRISPR to understand and manipulate gene regulation.

Understanding how genes are expressed in the correct cell types and at the correct level is a key goal of developmental biology research. Gene regulation has traditionally been approached largely through observational methods, whereas perturbational approaches have lacked precision. CRISPR-Cas9 has begun to transform the study of gene regulation, allowing for precise manipulation of genomic sequences, epigenetic functionalization and gene expression.