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Diverse DNA repair pathways correct ranging types of damage and play central roles in genome editing. In this issue of Cell, two publications leverage a new high-throughput screen that links pathway genes with the outcomes of repair, yielding mechanistic insights into the repair process as well as means to shape editing outcomes.

CRISPR transposons (CASTs) represent unique mobile genetic elements that co-opted CRISPR-Cas immune systems for RNA-guided DNA transposition. However, CAST-encoded CRISPR arrays rarely match the CAST's chromosomal location. A recent publication in Cell helps resolve this paradox by revealing CRISPR-array-independent mechanisms of chromosomal homing unique to different CAST types.

Animals and their commensal bacteria are known to reciprocally influence many traits of their physiology. Specifically, microbes contribute to the maintenance of the immune system homeostasis, improve host digestive processes, and sustain host growth and development. Several studies have reported that such effects result from an intricate network of nutritional, metabolic and immune inputs and partly rely on the capacity of microbes to regulate the host’s transcriptional response. However, these evidences mainly come from comparing the transcriptional response caused by commensal bacteria with that of axenic animals, making it difficult to identify the specific animal genes that are regulated by beneficial microbes. Here, we employ a well-established model of nutritional symbiosis, Drosophila melanogaster associated with Lactiplantibacillus plantarum, to understand the host genetic pathways regulated by beneficial bacteria and leading to improved host growth and development. Using isogenic L. plantarum strains bearing different growth-promoting effects, we show that the microbial benefit to the host relies on the down-regulation of peptidoglycan- recognition proteins. In particular, we report that the lower expression of PGRP-SC1 exerted by growth promoting bacteria is responsible for their higher proliferation and the consequent increased production of beneficial metabolites, which ultimately leads to improved host growth and development. Our study helps elucidate the mechanisms underlying the beneficial effect exerted by commensal bacteria, defining the role of immune effectors and peptidoglycan recognition mechanisms in the relationship between Drosophila and its gut microbes.

The RNA-guided nucleases derived from the CRISPR-Cas systems in bacteria and archaea have found numerous applications in biotechnology, including genome editing, imaging, and gene regulation. However, the discovery of novel Cas nucleases has outpaced their characterization and subsequent exploitation. A key step in characterizing Cas nucleases is determining which protospacer-adjacent motif (PAM) sequences they recognize. Here, we report advances to an in vitro method based on an E. coli cell-free transcription-translation system (TXTL) to rapidly elucidate PAMs recognized by Cas nucleases. The method obviates the need for cloning Cas nucleases or gRNAs, does not require the purification of protein or RNA, and can be performed in less than a day. To advance our previously published method, we incorporated an internal GFP cleavage control to assess the extent of library cleavage as well as Sanger sequencing of the cleaved library to assess PAM depletion prior to next-generation sequencing. We also detail the methods needed to construct all relevant DNA constructs, and how to troubleshoot the assay. We finally demonstrate the technique by determining PAM sequences recognized by the Neisseria meningitidis Cas9, revealing subtle sequence requirements of this highly specific PAM. The overall method offers a rapid means to identify PAMs recognized by diverse CRISPR nucleases, with the potential to greatly accelerate our ability to characterize and harness novel CRISPR nucleases across their many uses.

CRISPR-Cas systems are prokaryotic immune systems whose RNA-guided nucleases have been co-opted for applications ranging from genome editing and gene regulation to in vitro diagnostics and DNA imaging. Here, we review the current efforts toward repurposing CRISPR nucleases as programmable antimicrobials. Antimicrobial activity is achieved by targeted cleavage of multidrug-resistance plasmids or the bacterial chromosome, resulting in antibiotic sensitivity or cell death. As part of the review, we discuss the different types of nucleases available for CRISPR antimicrobials, the use of bacteriophages as delivery vehicles, and opportunities to enhance antimicrobial activity, delivery, and specificity. Through further advances, these programmable DNA-targeting antimicrobials may help quell the spread of antimicrobial resistance and provide a tool for the manipulation of complex microbial communities.

Summary Jin et al. (2020) engineered new variants of CRISPR base editors that make precise genomic edits in rice protoplasts while minimizing untargeted mutagenesis.

New drugs are desperately needed to combat methicillin-resistant Staphylococcus aureus (MRSA) infections. Here, we report screening commercial kinase inhibitors for antibacterial activity and found the anticancer drug sorafenib as major hit that effec-tively kills MRSA strains. Varying the key structural features led to the identification of a potent analogue, PK150, that showed antibacterial activity against several pathogenic strains at submicromolar concentrations. Furthermore, this antibiotic eliminated challenging persisters as well as established biofilms. PK150 holds promising therapeutic potential as it did not induce in vitro resistance, and shows oral bioavailability and in vivo efficacy. Analysis of the mode of action using chemical proteomics revealed several targets, which included interference with menaquinone biosynthesis by inhibiting demethylmenaquinone methyltrans-ferase and the stimulation of protein secretion by altering the activity of signal peptidase IB. Reduced endogenous menaquinone levels along with enhanced levels of extracellular proteins of PK150-treated bacteria support this target hypothesis. The associ-ated antibiotic effects, especially the lack of resistance development, probably stem from the compound’s polypharmacology.

Clustered regularly interspaced short palindromic repeat (CRISPR) loci and their flanking CRISPR-associated (cas) genes make up RNA-guided, adaptive immune systems in prokaryotes whose effector proteins have become powerful tools for basic research and biotechnology. While the Cas effector proteins are remarkably diverse, they commonly rely on protospacer-adjacent motifs (PAMs) as the first step in target recognition. PAM sequences are known to vary considerably between systems and have proven to be difficult to predict, spurring the need for new tools to rapidly identify and communicate these sequences. Recent advances have also shown that Cas proteins can be engineered to alter PAM recognition, opening new opportunities to develop CRISPR-based tools with enhanced targeting capabilities. In this review, we discuss the properties of the CRISPR PAM and the emerging tools for determining, visualizing, and engineering PAM recognition. We also propose a standard means of orienting the PAM to simplify how its location and sequence are communicated.

The timely recognition of shock secondary to hemorrhage from severe facial trauma or as a complication of complex oral and maxillofacial surgery presents formidable challenges. Specific hemostatic disorders are induced by hemorrhage and several extreme homeostatic imbalances may appear during or after resuscitation. Damage control resuscitation has evolved from massive transfusion to a more complex therapeutic paradigm that includes hemodynamic resuscitation, hemostatic resuscitation, and homeostatic resuscitation. Definitive control of bleeding is the principal objective of any comprehensive resuscitation scheme for hemorrhagic shock.

CRISPR-Cas adaptive immune systems in prokaryotes boast a diversity of protein families and mechanisms of action, where most systems rely on protospacer-adjacent motifs (PAMs) for DNA target recognition. Here, we developed an in vivo, positive, and tunable screen termed PAM-SCANR (PAM screen achieved by NOT-gate repression) to elucidate functional PAMs as well as an interactive visualization scheme termed the PAM wheel to convey individual PAM sequences and their activities. PAM-SCANR and the PAM wheel identified known functional PAMs while revealing complex sequence-activity landscapes for the Bacillus halodurans I-C (Cascade), Escherichia coli I-E (Cascade), Streptococcus thermophilus II-A CRISPR1 (Cas9), and Francisella novicida V-A (Cpf1) systems. The PAM wheel was also readily applicable to existing high-throughput screens and garnered insights into SpyCas9 and SauCas9 PAM diversity. These tools offer powerful means of elucidating and visualizing functional PAMs toward accelerating our ability to understand and exploit the multitude of CRISPR-Cas systems in nature.

Summary We present a protocol to rapidly test DNA binding and cleavage activity by CRISPR nucleases using cell-free transcription-translation (TXTL). Nuclease activity is assessed by adding DNA encoding a nuclease, a guide RNA, and a targeted reporter to a TXTL reaction and by measuring the fluorescence for several h. The reactions, performed in a few microliters, allow for parallel testing of many nucleases and guide RNAs. The protocol includes representative results for (d)Cas9 from Streptococcus pyogenes targeting a GFP reporter gene. For complete information on the generation and use of this protocol, please refer to the paper by Marshall et al. (2018) .

Synthetic biology employs traditional engineering concepts in the construction of cells and organisms. One of the most fundamental concepts is feedback, where the activity of a system is influenced by its output. Feedback can imbue the system with a range of desirable properties such as reducing the rise time or exhibiting an ultrasensitive response. Feedback is also commonly found in nature, further supporting the incorporation of feedback into synthetic biological systems. In this review, we discuss the common attributes of negative and positive feedback loops in gene regulatory networks, whether alone or in combination, and describe recent applications of feedback in metabolic engineering, population control, and the development of advanced biosensors. The examples principally come from synthetic systems in the bacterium Escherichia coli and in the budding yeast Saccharomyces cerevisiae , the two major workhorses of synthetic biology. Through this review, we argue that biological feedback represents a powerful yet underutilized tool that can advance the construction of biological systems.

The ability to fabricate flexible filtration membranes that can selectively separate particles of different sizes is of considerable interest. In this article, we describe a facile, reproducible and simple one-step method to produce pores in polydimethylsiloxane (PDMS) membranes. We embedded micron-sized NaHCO 3 particles in 50 μm thick PDMS films. After curing, the membranes were immersed in concentrated HCl acid. Pores were generated in the membrane by the evolution of CO 2 gas from the reaction of NaHCO 3 and HCl. High resolution scanning electron microscope images clearly reveal the presence of openings on the surface and the cross-section of the membranes. Fluorescence and back-scattered electron imaging of porous PDMS membrane with embedded gold nanoparticles and comparison with non-porous PDMS membranes provided unambiguous evidence of pores in the membrane. Transport studies of molecular fluoresceinate ions, ions (sodium and chloride) and 240 nm polystyrene nanoparticles through these membranes demonstrate passable pores and existence of channels within the body of the membrane. Mechanically stretching the porous PDMS membrane and comparing the flow rates of fluoresceinate ions and the polystyrene beads through the stretched and unstretched membranes allowed a direct proof of the modulation of transport rate in the membranes. We show that stretching the membranes by 10% increases the flow rate of fluorescein molecules by 2.8 times and by a factor of approximately ∼40% for the polystyrene nanoparticles.

This manuscript provides a critical and comprehensive review of research on race socialization within Black families. Race socialization is defined as specific verbal and non-verbal messages transmitted to younger generations for the development of values, attitudes, behaviors, and beliefs regarding the meaning and significance of race and racial stratification, intergroup and intragroup interactions, and personal and group identity. Reviewed are published articles that address either analytical or theoretical approaches to understanding Black families’ race socialization practices. First, theoretical perspectives of the race socialization process are reviewed. Second, this review defines race socialization in Black families. It then describes modes of message transmittal. Next, it focuses on three domains of research on race socialization: (a) prevalence, (b) content, and (c) race socialization as a predictor of child and adult outcomes. It concludes by outlining important challenges and issues in the literature to encourage the development of future research.

Conformations and inversion pathways leading to racemization of all the tautomers of gossypol, gossypolone, anhydrogossypol, and a diethylamine Schiff's base of gossypol were investigated with MM3(2000). All forms have hindered rotation because of clashes between the methyl carbon atom and oxygen-containing moieties ortho to the bond linking the two naphthalene rings. Inversion energies generally agree with available experimental data. Gossypol preferentially inverts in its dihemiacetal tautomeric form through the cis pathway (where similar groups clash). Gossypolone inverts more easily than gossypol, and preferentially through the trans pathway (where dissimilar groups clash) when one of its outer rings has an enol-keto group and the other has an aldehyde group. Anhydrogossypol racemizes through the cis pathway. The bridge bond and the ortho exo-cyclic bonds in all the structures bend from planarity, and the inner naphthalene rings pucker to accommodate the inversion. For gossypol, the transition is achieved through greater bending of the exo-cyclic bonds (up to 12°) and less distortion of the inner benzyl rings ( q ≤0.34 A), (up to 12.7°) . For gossypolone the transition occurs with greater distortion of the inner benzyl rings ( q ≤0.63 A) and less out-of-plane bending (up to 8.4°). By isolating individual clashes, their contribution to the overall barrier can be analyzed, as shown for the dialdehyde tautomer of gossypol.

Summary CRISPR-Cas systems offer versatile technologies for genome engineering, yet their implementation has been outpaced by ongoing discoveries of new Cas nucleases and anti-CRISPR proteins. Here, we present the use of E. coli cell-free transcription-translation (TXTL) systems to vastly improve the speed and scalability of CRISPR characterization and validation. TXTL can express active CRISPR machinery from added plasmids and linear DNA, and TXTL can output quantitative dynamics of DNA cleavage and gene repression—all without protein purification or live cells. We used TXTL to measure the dynamics of DNA cleavage and gene repression for single- and multi-effector CRISPR nucleases, predict gene repression strength in E. coli , determine the specificities of 24 diverse anti-CRISPR proteins, and develop a fast and scalable screen for protospacer-adjacent motifs that was successfully applied to five uncharacterized Cpf1 nucleases. These examples underscore how TXTL can facilitate the characterization and application of CRISPR technologies across their many uses.

The morphology of the organ of Corti has a radial asymmetry and also changes longitudinally from base to apex. Cellular localization of transcripts within the inner ear has relied primarily on the use of sectioned tissue with in situ hybridization. However, radial and longitudinal gradients of expression are not readily recognized using sectioned tissue owing to problems in visualization of signals with varying intensities. Herein, we describe the use of whole mount in situ hybridization for identification of cochlear longitudinal and radial expression gradients in the neurosensory epithelium, hair cells. Not only can these hair cell gradients be shown in adult tissues, but also the developmental up-regulation and down-regulation of genes and their associated spatio-temporal expression patterns can be demonstrated.

Thoracic aortic anomalies are rare and may be associated with pathologic vascular conditions necessitating intervention. We present a case of a patient with a left aortic arch, right descending thoracic aorta, and a Kommerell's diverticulum giving rise to an aberrant right subclavian artery. The Kommerell's diverticulum was successfully managed with a right carotid to subclavian artery bypass and thoracic endograft exclusion.

Ovarian cancer is the number one cause of death due to gynecological malignancies, and the fifth leading cause of death in cancer in women. While surgical debulking and chemotherapy cause an initial remission in disease, approximately 75% of patients will relapse. The relapse is characterized by chemotherapy refractory disease. Currently there are no definitive second line treatments for patients who fail standard of care. Patients with ovarian cancer have a 5-year survival rate of 25–30%, making it one of the most aggressive malignancies. We have designed a new cell therapy by using the patient’s innate immune system (monocytes primed with Interferon Alpha and Gamma) to kill metastatic lesions of the peritoneal cavity. Monocytes isolated from patients with therapy resistant ovarian cancer and stimulated with interferons alpha and gamma are potent killers of tumor cell lines in vitro. We have also found that patient monocytes are more cytotoxic than age match healthy controls. We have shown that the major mechanism of monocyte-mediated killing is the up regulation of TRAIL on monocytes. Ovarian cancer cell death is mediated in a Caspase-8 dependent manner. Furthermore, we have shown that the non-classical (CD14loCD16+) subset of monocytes is more cytotoxic than the classical (CD14 + CD16−) subset. Finally, we have shown that this therapy is effective in a mouse model of ovarian cancer. Based upon these results we are preparing an investigational new drug (IND) with the FDA to test this therapy in human subjects.