A prospective study of treatments for adult-onset divergence insufficiency-type esotropia.

Purpose: To describe 10-week and 12-month outcomes following treatment for divergence insufficiency-type esotropia in adults.

Methods: In this prospective observational study, 110 adults with divergence insufficiency-type esotropia, with a distance esodeviation measuring 2 to 30 and at least 25% larger at distance than near, and binocular diplopia present at least "sometimes" at distance, were enrolled at 28 sites when initiating new treatment. Surgery, prism, or divergence exercises/therapy were chosen at the investigator's discretion.

A benchmark of algorithms for the analysis of pooled CRISPR screens.

Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-pooled screens. Here, we provide a review of the commonly used algorithms in the computational analysis of pooled CRISPR screens.

Predicting the Number of Bases to Attain Sufficient Coverage in High-Throughput Sequencing Experiments.

For many types of high-throughput sequencing experiments, success in downstream analysis depends on attaining sufficient coverage for individual positions in the genome. For example, when identifying single-nucleotide variants de novo, the number of reads supporting a particular variant call determines our confidence in that variant call. If sequenced reads are distributed uniformly along the genome, the coverage of a nucleotide position is easily approximated by a Poisson distribution, with rate equal to average sequencing depth.

CRISPR-mediated live imaging of genome editing and transcription.

We report a robust, versatile approach called CRISPR live-cell fluorescent in situ hybridization (LiveFISH) using fluorescent oligonucleotides for genome tracking in a broad range of cell types, including primary cells. An intrinsic stability switch of CRISPR guide RNAs enables LiveFISH to accurately detect chromosomal disorders such as Patau syndrome in prenatal amniotic fluid cells and track multiple loci in human T lymphocytes. In addition, LiveFISH tracks the real-time movement of DNA double-strand breaks induced by CRISPR-Cas9-mediated editing and consequent chromosome translocations.

GEMINI: a variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screens.

Systems for CRISPR-based combinatorial perturbation of two or more genes are emerging as powerful tools for uncovering genetic interactions. However, systematic identification of these relationships is complicated by sample, reagent, and biological variability. We develop a variational Bayes approach (GEMINI) that jointly analyzes all samples and reagents to identify genetic interactions in pairwise knockout screens.

CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming.

Comprehensive identification of factors that can specify neuronal fate could provide valuable insights into lineage specification and reprogramming, but systematic interrogation of transcription factors, and their interactions with each other, has proven technically challenging. We developed a CRISPR activation (CRISPRa) approach to systematically identify regulators of neuronal-fate specification. We activated expression of all endogenous transcription factors and other regulators via a pooled CRISPRa screen in embryonic stem cells, revealing genes including epigenetic regulators such as Ezh2 that can induce neuronal fate.

CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization.

Programmable control of spatial genome organization is a powerful approach for studying how nuclear structure affects gene regulation and cellular function. Here, we develop a versatile CRISPR-genome organization (CRISPR-GO) system that can efficiently control the spatial positioning of genomic loci relative to specific nuclear compartments, including the nuclear periphery, Cajal bodies, and promyelocytic leukemia (PML) bodies. CRISPR-GO is chemically inducible and reversible, enabling interrogation of real-time dynamics of chromatin interactions with nuclear compartments in living cells.

CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens.

Pooled CRISPR screens allow researchers to interrogate genetic causes of complex phenotypes at the genome-wide scale and promise higher specificity and sensitivity compared to competing technologies. Unfortunately, two problems exist, particularly for CRISPRi/a screens: variability in guide efficiency and large rare off-target effects. We present a method, CRISPhieRmix, that resolves these issues by using a hierarchical mixture model with a broad-tailed null distribution.

Unsupervised clustering and epigenetic classification of single cells.

Characterizing epigenetic heterogeneity at the cellular level is a critical problem in the modern genomics era. Assays such as single cell ATAC-seq (scATAC-seq) offer an opportunity to interrogate cellular level epigenetic heterogeneity through patterns of variability in open chromatin. However, these assays exhibit technical variability that complicates clear classification and cell type identification in heterogeneous populations.

ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues.

High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules.

Applications of species accumulation curves in large-scale biological data analysis.

The species accumulation curve, or collector's curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional sampling. Traditional applications have focused on ecological populations but emerging large-scale applications, for example in DNA sequencing, are orders of magnitude larger and present new challenges.

Sexual selection targets cetacean pelvic bones.

Male genitalia evolve rapidly, probably as a result of sexual selection. Whether this pattern extends to the internal infrastructure that influences genital movements remains unknown. Cetaceans (whales and dolphins) offer a unique opportunity to test this hypothesis: since evolving from land-dwelling ancestors, they lost external hind limbs and evolved a highly reduced pelvis that seems to serve no other function except to anchor muscles that maneuver the penis.

Modeling genome coverage in single-cell sequencing.

Motivation: Single-cell DNA sequencing is necessary for examining genetic variation at the cellular level, which remains hidden in bulk sequencing experiments. But because they begin with such small amounts of starting material, the amount of information that is obtained from single-cell sequencing experiment is highly sensitive to the choice of protocol employed and variability in library preparation. In particular, the fraction of the genome represented in single-cell sequencing libraries exhibits extreme variability due to quantitative biases in amplification and loss of genetic material.

Patience is a virtue: an argument for delayed surgical intervention in fulminant Clostridium difficile colitis.

Recently, the incidence and severity of Clostridium difficile infection (CDI) has increased. In cases of fulminant infection, surgery is a viable therapeutic option but associated with high mortality. We sought to examine factors associated with mortality in a large sample of patients with severe CDI that underwent surgery.

Fulminant Clostridium difficile infection: An association with prior appendectomy?

Aim: To examine if fulminant Clostridium difficile infections (CDI) resulting in colectomy was associated with a prior appendectomy and whether any association affected the severity of the disease.

Methods: A retrospective chart review was performed on patients who underwent colectomy for CDI between 2001 and 2011. The appendectomy rate was calculated based on the absence of an appendix on the surgical pathology report.

Resolution of hypertropia with correction of intermittent exotropia.

Purpose: We describe the spontaneous resolution of hypertropia in a subset of patients with preoperative exotropia and hypertropia, who underwent surgery for intermittent exotropia alone.

Design: This was a retrospective case series.

Methods: The charts were reviewed of 17 patients who underwent surgical correction for an intermittent exotropia, who additionally were noted on preoperative exam to have greater than 5 prism dioptres of vertical deviation in primary position.

Predicting the molecular complexity of sequencing libraries.

Predicting the molecular complexity of a genomic sequencing library is a critical but difficult problem in modern sequencing applications. Methods to determine how deeply to sequence to achieve complete coverage or to predict the benefits of additional sequencing are lacking. We introduce an empirical bayesian method to accurately characterize the molecular complexity of a DNA sample for almost any sequencing application on the basis of limited preliminary sequencing.

2-Deoxy-D-glucose reduces epilepsy progression by NRSF-CtBP-dependent metabolic regulation of chromatin structure.

Temporal lobe epilepsy is a common form of drug-resistant epilepsy that sometimes responds to dietary manipulation such as the 'ketogenic diet'. Here we have investigated the effects of the glycolytic inhibitor 2-deoxy-D-glucose (2DG) in the rat kindling model of temporal lobe epilepsy. We show that 2DG potently reduces the progression of kindling and blocks seizure-induced increases in the expression of brain-derived neurotrophic factor and its receptor, TrkB.

Localized domains of G9a-mediated histone methylation are required for silencing of neuronal genes.

Negative regulation of transcription is an important strategy in establishing and maintaining cell-specific gene expression patterns. Many neuronal genes are subject to active transcriptional repression outside the nervous system to establish neuronal specificity. NRSF/REST has been demonstrated to regulate at least 30 genes and contribute to their neuronal targeting by repressing transcription outside the nervous system.