Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness.

Pluripotent stem cells have remarkable self-renewal capacity: the ability to proliferate indefinitely while maintaining the pluripotent identity essential for their ability to differentiate into almost any cell type in the body. To investigate the interplay between these two aspects of self-renewal, we perform four parallel genome-scale CRISPR-Cas9 loss-of-function screens interrogating stem cell fitness in hPSCs and the dissolution of primed pluripotent identity during early differentiation. These screens distinguish genes with distinct roles in pluripotency regulation, including mitochondrial and metabolism regulators crucial for stem cell fitness, and chromatin regulators that control pluripotent identity during early differentiation.

CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant.

Functional enhancer annotation is critical for understanding tissue-specific transcriptional regulation and prioritizing disease-associated non-coding variants. However, unbiased enhancer discovery in disease-relevant contexts remains challenging. To identify enhancers pertinent to diabetes, we conducted a CRISPR interference (CRISPRi) screen in the human pluripotent stem cell (hPSC) pancreatic differentiation system.

CRISPR Screening Uncovers a Long-Range Enhancer for in Pancreatic Differentiation and Links a Diabetes Risk Variant.

Functional enhancer annotation is a valuable first step for understanding tissue-specific transcriptional regulation and prioritizing disease-associated non-coding variants for investigation. However, unbiased enhancer discovery in physiologically relevant contexts remains a major challenge. To discover regulatory elements pertinent to diabetes, we conducted a CRISPR interference screen in the human pluripotent stem cell (hPSC) pancreatic differentiation system.

Correction to "Carbodiimide Ring-Opening Metathesis Polymerization".

[This corrects the article DOI: 10.1021/acscentsci.3c00032.

Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells.

Unlabelled: The mechanisms underlying the ability of embryonic stem cells (ESCs) to rapidly activate lineage-specific genes during differentiation remain largely unknown. Through multiple CRISPR-activation screens, we discovered human ESCs have pre-established transcriptionally competent chromatin regions (CCRs) that support lineage-specific gene expression at levels comparable to differentiated cells. CCRs reside in the same topological domains as their target genes.

Carbodiimide Ring-Opening Metathesis Polymerization.

Controlled incorporation of nitrogen into macromolecular skeletons is a long-standing challenge whose resolution would enable the preparation of soft materials with the scalability of man-made plastics and functionality of Nature's proteins. Nylons and polyurethanes notwithstanding, nitrogen-rich polymer backbones remain scarce, and their synthesis typically lacks precision. Here we report a strategy that begins to address this limitation founded on a mechanistic discovery: ring-opening metathesis polymerization (ROMP) of carbodiimides followed by carbodiimide derivatization.

Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness.

Pluripotent stem cells are defined by their self-renewal capacity, which is the ability of the stem cells to proliferate indefinitely while maintaining the pluripotent identity essential for their ability to differentiate into any somatic cell lineage. However, understanding the mechanisms that control stem cell fitness versus the pluripotent cell identity is challenging. To investigate the interplay between these two aspects of pluripotency, we performed four parallel genome-scale CRISPR-Cas9 loss-of-function screens interrogating stem cell fitness in hPSC self-renewal conditions, and the dissolution of the primed pluripotency identity during early differentiation.

Genetic Engineering of Immune Evasive Stem Cell-Derived Islets.

Genome editing has the potential to revolutionize many investigative and therapeutic strategies in biology and medicine. In the field of regenerative medicine, one of the leading applications of genome engineering technology is the generation of immune evasive pluripotent stem cell-derived somatic cells for transplantation. In particular, as more functional and therapeutically relevant human pluripotent stem cell-derived islets (SCDI) are produced in many labs and studied in clinical trials, there is keen interest in studying the immunogenicity of these cells and modulating allogeneic and autoimmune immune responses for therapeutic benefit.

Efficient Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Exhaled Breath.

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is transmitted through airborne particles in exhaled breath, causing severe respiratory disease, coronavirus disease-2019 (COVID-19), in some patients. Samples for SARS-CoV-2 testing are typically collected by nasopharyngeal swab, with the virus detected by PCR; however, patients can test positive for 3 months after infection. Without the capacity to assay SARS-CoV-2 in breath, it is not possible to understand the risk for transmission from infected individuals.

Evaluating Closures of Fresh Fruit and Vegetable Vendors During the COVID-19 Pandemic: Methodology and Preliminary Results Using Omnidirectional Street View Imagery.

Background: The COVID-19 pandemic has significantly disrupted the food retail environment. However, its impact on fresh fruit and vegetable vendors remains unclear; these are often smaller, more community centered, and may lack the financial infrastructure to withstand supply and demand changes induced by such crises.

Objective: This study documents the methodology used to assess fresh fruit and vegetable vendor closures in New York City (NYC) following the start of the COVID-19 pandemic by using Google Street View, the new Apple Look Around database, and in-person checks.

Developmental vascular anomaly associated hemi facial spasms and botox injections therapy.

Hemifacial spasm (HFS) is characterized by involuntary synchronous contractions or spasms of one side of the face, usually beginning around the eye. They are typically brief, irregular clonic movements but are occasionally tonic. We present a case of a 41-year-old female who presented to the neurology clinic with complaints of recurrent right facial spasms.

A More Efficient Method for Synthetic Textile Fiber Analysis Using Polarized Light Microscopy.

The efficiency of conventional polarized light microscopy (PLM) methods for analyzing synthetic fiber evidence analyses is improved. Historically, using PLM for fiber identification relied on measuring refractive index. This prior PLM technology is reliable, but it is not efficient.

Fecal calprotectin concentrations in cancer patients with Clostridium difficile infection.

Fecal calprotectin (fCPT) has been used as a surrogate marker for assessment of intestinal inflammation. We explore the utility of fCPT values as a diagnostic aid in cancer patients with suspected Clostridium difficile infection (CDI). A total of 232 stool specimens submitted for GeneXpert C.

Identification and Characterization of Clostridium difficile Sequence Type 37 Genotype by Matrix-Assisted Laser Desorption IonizationTime of Flight Mass Spectrometry.

multilocus sequence type 37 (ST37), which mainly corresponds to ribotype 017, has been a dominant genotype circulating in China. In this study, we report the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to analyze and characterize 204 clinical isolates, including 49 ST37 and 155 non-ST37 isolates collected in China and other countries. The distributions of two major protein peaks ( 3,242 and 3,286) were significantly different between ST37 and non-ST37 prototype strains and clinical isolates.

Detection of HPV related oropharyngeal cancer in oral rinse specimens.

Background: The majority of patients diagnosed with oropharyngeal squamous cell cancer (OPSCC) are due to HPV infection. At present, there are no reliable tests for screening HPV in patients with OPSCC. The objective of this study was to assess the Cobas® HPV Test on oral rinse specimens as an early, non-invasive tool for HPV-related OPSCC.

Parallel Validation of Three Molecular Devices for Simultaneous Detection and Identification of Influenza A and B and Respiratory Syncytial Viruses.

Rapid identification of respiratory pathogens, such as influenza virus A (FluA), influenza virus B (FluB), and respiratory syncytial virus (RSV), reduces unnecessary antimicrobial use and enhances infection control practice. We performed a comparative evaluation of three molecular methods: (i) the Aries Flu A/B & RSV, (ii) the Xpert Xpress Flu/RSV, and (iii) the Cobas Flu A/B & RSV assays. The clinical performances of the three methods were evaluated using 200 remnant nasopharyngeal swab (NPS) specimens against a combined reference standard.

Epigenetic Reprogramming Strategies to Reverse Global Loss of 5-Hydroxymethylcytosine, a Prognostic Factor for Poor Survival in High-grade Serous Ovarian Cancer.

A major challenge in platinum-based cancer therapy is the clinical management of chemoresistant tumors, which have a largely unknown pathogenesis at the level of epigenetic regulation. We evaluated the potential of using global loss of 5-hydroxymethylcytosine (5-hmC) levels as a novel diagnostic and prognostic epigenetic marker to better assess platinum-based chemotherapy response and clinical outcome in high-grade serous tumors (HGSOC), the most common and deadliest subtype of ovarian cancer. Furthermore, we identified a targetable pathway to reverse these epigenetic changes, both genetically and pharmacologically.

Rapid Molecular Detection and Differentiation of Influenza Viruses A and B.

Influenza is a contagious respiratory illness caused by influenza viruses A and B in humans and causes a significant amount of morbidity and mortality every year. The Influenza A and B assay was the first CLIA-waived molecular rapid flu test available. The Influenza A and B test works by employing isothermal amplification with influenza-specific primers followed by target detection with molecular beacon probes.

Laboratory Diagnosis of Central Nervous System Infection.

Central nervous system (CNS) infections are potentially life threatening if not diagnosed and treated early. The initial clinical presentations of many CNS infections are non-specific, making a definitive etiologic diagnosis challenging. Nucleic acid in vitro amplification-based molecular methods are increasingly being applied for routine microbial detection.

Transcriptome response to nitrosative stress in Rhodobacter sphaeroides 2.4.1.

The facultative photosynthetic bacterium Rhodobacter sphaeroides 2.4.1 has a nitric oxide-response transcriptional regulator, NnrR, and nitric oxide reductase (NOR), although it is incapable of denitrification.

Revealing linear aggregates of light harvesting antenna proteins in photosynthetic membranes.

How light energy is harvested in a natural photosynthetic membrane through energy transfer is closely related to the stoichiometry and arrangement of light harvesting antenna proteins in the membrane. The specific photosynthetic architecture facilitates a rapid and efficient energy transfer among the light harvesting proteins (LH2 and LH1) and to the reaction center. Here we report the identification of linear aggregates of light harvesting proteins, LH2, in the photosynthetic membranes under ambient conditions by using atomic force microscopy (AFM) imaging and spectroscopic analysis.

Regulation of gene expression by PrrA in Rhodobacter sphaeroides 2.4.1: role of polyamines and DNA topology.

In the present study, we show in vitro binding of PrrA, a global regulator in Rhodobacter sphaeroides 2.4.1, to the PrrA site 2, within the RSP3361 locus.

Half-Site DNA sequence and spacing length contributions to PrrA binding to PrrA site 2 of RSP3361 in Rhodobacter sphaeroides 2.4.1.

The consensus DNA binding sequence for PrrA, a global regulator in Rhodobacter sphaeroides 2.4.1, is poorly defined.

The use of chromatin immunoprecipitation to define PpsR binding activity in Rhodobacter sphaeroides 2.4.1.

The expression of genes involved in photosystem development in Rhodobacter sphaeroides is dependent upon three major regulatory networks: FnrL, the PrrBA (RegBA) two-component system, and the transcriptional repressor/antirepressor PpsR/AppA. Of the three regulators, PpsR appears to have the narrowest range of physiological effects, which are limited to effects on the structural and pigment biosynthetic activities involved in photosynthetic membrane function. Although a PrrA(-) mutant is unable to grow under photosynthetic conditions, when a ppsR mutation was present, photosynthetic growth occurred.