Development of compact transcriptional effectors using high-throughput measurements in diverse contexts.

Transcriptional effectors are protein domains known to activate or repress gene expression; however, a systematic understanding of which effector domains regulate transcription across genomic, cell type and DNA-binding domain (DBD) contexts is lacking. Here we develop dCas9-mediated high-throughput recruitment (HT-recruit), a pooled screening method for quantifying effector function at endogenous target genes and test effector function for a library containing 5,092 nuclear protein Pfam domains across varied contexts. We also map context dependencies of effectors drawn from unannotated protein regions using a larger library tiling chromatin regulators and transcription factors.

In vivo perturb-seq of cancer and microenvironment cells dissects oncologic drivers and radiotherapy responses in glioblastoma.

Background: Genetic perturbation screens with single-cell readouts have enabled rich phenotyping of gene function and regulatory networks. These approaches have been challenging in vivo, especially in adult disease models such as cancer, which include mixtures of malignant and microenvironment cells. Glioblastoma (GBM) is a fatal cancer, and methods of systematically interrogating gene function and therapeutic targets in vivo, especially in combination with standard of care treatment such as radiotherapy, are lacking.

Pathways for macrophage uptake of cell-free circular RNAs.

Circular RNAs (circRNAs) are stable RNAs present in cell-free RNA, which may comprise cellular debris and pathogen genomes. Here, we investigate the phenomenon and mechanism of cellular uptake and intracellular fate of exogenous circRNAs. Human myeloid cells and B cells selectively internalize extracellular circRNAs.

A Genome-Wide CRISPR Screen Identifies Sortilin as the Receptor Responsible for Galectin-1 Lysosomal Trafficking.

Galectins are a family of mammalian glycan-binding proteins that have been implicated as regulators of myriad cellular processes including cell migration, apoptosis, and immune modulation. Several members of this family, such as galectin-1, exhibit both cell-surface and intracellular functions. Interestingly, galectin-1 can be found in the endomembrane system, nucleus, or cytosol, as well as on the cell surface.

Elucidating the cellular determinants of targeted membrane protein degradation by lysosome-targeting chimeras.

Targeted protein degradation can provide advantages over inhibition approaches in the development of therapeutic strategies. Lysosome-targeting chimeras (LYTACs) harness receptors, such as the cation-independent mannose 6-phosphate receptor (CI-M6PR), to direct extracellular proteins to lysosomes. In this work, we used a genome-wide CRISPR knockout approach to identify modulators of LYTAC-mediated membrane protein degradation in human cells.

Direct mapping of ligandable tyrosines and lysines in cells with chiral sulfonyl fluoride probes.

Advances in chemoproteomic technology have revealed covalent interactions between small molecules and protein nucleophiles, primarily cysteine, on a proteome-wide scale. Most chemoproteomic screening approaches are indirect, relying on competition between electrophilic fragments and a minimalist electrophilic probe with inherently limited proteome coverage. Here we develop a chemoproteomic platform for direct electrophile-site identification based on enantiomeric pairs of clickable arylsulfonyl fluoride probes.

The peroxisomal exportomer directly inhibits phosphoactivation of the pexophagy receptor Atg36 to suppress pexophagy in yeast.

Autophagy receptor (or adaptor) proteins facilitate lysosomal destruction of various organelles in response to cellular stress, including nutrient deprivation. To what extent membrane-resident autophagy receptors also respond to organelle-restricted cues to induce selective autophagy remains poorly understood. We find that latent activation of the yeast pexophagy receptor Atg36 by the casein kinase Hrr25 in rich media is repressed by the ATPase activity of Pex1/6, the catalytic subunits of the exportomer AAA+ transmembrane complex enabling protein import into peroxisomes.

Inter-cellular CRISPR screens reveal regulators of cancer cell phagocytosis.

Monoclonal antibody therapies targeting tumour antigens drive cancer cell elimination in large part by triggering macrophage phagocytosis of cancer cells. However, cancer cells evade phagocytosis using mechanisms that are incompletely understood. Here we develop a platform for unbiased identification of factors that impede antibody-dependent cellular phagocytosis (ADCP) using complementary genome-wide CRISPR knockout and overexpression screens in both cancer cells and macrophages.

Efficacy of sealants and bonding materials during fixed orthodontic treatment to prevent enamel demineralization: a systematic review and meta-analysis.

To analyse clinical studies investigating coating agents such as sealants and other bonding materials to prevent the initiation or inhibit the progress of white spot lesions (WSL) during orthodontic treatment with fixed appliances. Electronic databases (Pubmed, CENTRAL, EMBASE) were screened for studies. No language restrictions were applied.

A genome-wide atlas of co-essential modules assigns function to uncharacterized genes.

A central question in the post-genomic era is how genes interact to form biological pathways. Measurements of gene dependency across hundreds of cell lines have been used to cluster genes into 'co-essential' pathways, but this approach has been limited by ubiquitous false positives. In the present study, we develop a statistical method that enables robust identification of gene co-essentiality and yields a genome-wide set of functional modules.

CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities.

Cancer genomics studies have identified thousands of putative cancer driver genes. Development of high-throughput and accurate models to define the functions of these genes is a major challenge. Here we devised a scalable cancer-spheroid model and performed genome-wide CRISPR screens in 2D monolayers and 3D lung-cancer spheroids.

Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens.

Phagocytosis is required for a broad range of physiological functions, from pathogen defense to tissue homeostasis, but the mechanisms required for phagocytosis of diverse substrates remain incompletely understood. Here, we developed a rapid magnet-based phenotypic screening strategy, and performed eight genome-wide CRISPR screens in human cells to identify genes regulating phagocytosis of distinct substrates. After validating select hits in focused miniscreens, orthogonal assays and primary human macrophages, we show that (1) the previously uncharacterized gene NHLRC2 is a central player in phagocytosis, regulating RhoA-Rac1 signaling cascades that control actin polymerization and filopodia formation, (2) very-long-chain fatty acids are essential for efficient phagocytosis of certain substrates and (3) the previously uncharacterized Alzheimer's disease-associated gene TM2D3 can preferentially influence uptake of amyloid-β aggregates.

Does orthodontic treatment have a permanent effect on tooth color? : A systematic review and meta-analysis.

Objectives: Aim of this systematic review was to assess the effect of orthodontic treatment with fixed appliances on the tooth color of patients.

Methods: Nine databases were searched up to May 2017 for clinical cohort studies on the effect of fixed appliance treatment on tooth color. After elimination of duplicate studies, data extraction, and risk of bias assessment according to the Cochrane guidelines, random effects meta-analyses of mean differences (MD) or means and their 95% confidence intervals (CIs) were performed, followed by GRADE (Grading of Recommendations Assessment, Development and Evaluation) assessment of the quality of evidence.

The AAA protein Msp1 mediates clearance of excess tail-anchored proteins from the peroxisomal membrane.

Msp1 is a conserved AAA ATPase in budding yeast localized to mitochondria where it prevents accumulation of mistargeted tail-anchored (TA) proteins, including the peroxisomal TA protein Pex15. Msp1 also resides on peroxisomes but it remains unknown how native TA proteins on mitochondria and peroxisomes evade Msp1 surveillance. We used live-cell quantitative cell microscopy tools and drug-inducible gene expression to dissect Msp1 function.

A pathway of targeted autophagy is induced by DNA damage in budding yeast.

Autophagy plays a central role in the DNA damage response (DDR) by controlling the levels of various DNA repair and checkpoint proteins; however, how the DDR communicates with the autophagy pathway remains unknown. Using budding yeast, we demonstrate that global genotoxic damage or even a single unrepaired double-strand break (DSB) initiates a previously undescribed and selective pathway of autophagy that we term genotoxin-induced targeted autophagy (GTA). GTA requires the action primarily of Mec1/ATR and Rad53/CHEK2 checkpoint kinases, in part via transcriptional up-regulation of central autophagy proteins.

Tolerance to Ethanol or Nicotine Results in Increased Ethanol Self-Administration and Long-Term Depression in the Dorsolateral Striatum.

Ethanol (EtOH) and nicotine are the most widely coabused drugs. Tolerance to EtOH intoxication, including motor impairment, results in greater EtOH consumption and may result in a greater likelihood of addiction. Previous studies suggest that cross-tolerance between EtOH and nicotine may contribute to the abuse potential of these drugs.

A molecular switch for selective autophagosome formation.

Selective macroautophagy (hereafter autophagy) can eliminate large cytotoxic structures that are designated for degradation by autophagy receptors. In our recent paper, we showed that a key function of target-bound autophagy receptors is to activate the autophagy kinase, Atg1, via interactions with the scaffold protein Atg11. Our work thus reveals a mechanism by which target recognition coordinates the earliest steps in autophagosome biogenesis.

Receptor-Bound Targets of Selective Autophagy Use a Scaffold Protein to Activate the Atg1 Kinase.

Selective autophagy eliminates protein aggregates, damaged organelles, and other targets that otherwise accumulate and cause disease. Autophagy receptors mediate selectivity by connecting targets to the autophagosome membrane. It has remained unknown whether receptors perform additional functions.

[Ultrasonographic findings in a cow with extraskeletal chondroblastic osteosarcoma of the neck region].

This case report describes the clinical, ultrasonographic and pathological findings in a five-year-old Swiss Braunvieh cow with extraskeletal chondroblastic osteosarcoma of the neck region. The cow was referred because of a firm, non-painful swelling, approximately 25 cm in diameter, which was situated mainly on the lower left side of the neck but extended to the right. Ultrasonographic examination of the mass revealed a chambered structure containing echoic material that was separated by hyperechoic septa.

Mapping loci associated with tail color and sex determination in the short-lived fish Nothobranchius furzeri.

The African fish Nothobranchius furzeri is the shortest-lived vertebrate species that can reproduce in captivity, with a median life span of 9-11 weeks for the shortest-lived strain. Natural populations of N. furzeri display differences in life span, aging biomarkers, behavior, and color, which make N.

Studies on the supply of immunoglobulin G to newborn camel calves (Camelus dromedarius).

A major problem in camel productivity is the high mortality rate of camel calves in the first 3 months. The causes for mortality are mainly poor management practice and infectious diseases. The purpose of this research, carried out on a ranch in Kenya, was to determine the immunoglobulin G (IgG) concentration in camel colostrum as well as the extent of the calves' passive immunization by maternal antibodies.

[The supply of newborn camel foals (Camelus dromedarius) with immunoglobulin G].

A major problem in camel breeding in East Africa is the high mortality rate of young camel calves. The purpose of this research was to examine the quality of camel colostrum and extent of the calves passive immunization by maternal antibodies. In 31 camel birth on a ranch in Kenya, IgG concentrations in the colostrum and in the serum of the calf during the first three days of life were measured.