Productivity Research, the U.S. Department of Education, and High-Quality Evidence

America’s leaders have frequently invoked the principle that important policy decisions should be evidence-based. This rhetorical embrace, however, has not always prevailed against the appeal of policy ideas with political resonance or other perceived advantages. The following analysis describes a particularly egregious example of this phenomenon: the approach taken by the U.S. Department of Education in its “Increasing Educational Productivity” project. This example illustrates the harm done when leaders fail to ground policy in high-quality research. The Department of Education has set forth a series of documents explaining how public school districts can stretch their dwindling dollars by becoming more productive and efficient. This brief explains that neither the materials listed nor the recommendations found in those materials are backed by substantive analyses of cost effectiveness or efficiency of public schools, of practices within public schools, of broader policies pertaining to public schools, or of resource allocation strategies. Instead, the sources listed on the website’s resources page are speculative, non-peer-reviewed think tank reports and related documents that generally fail to include or even cite the types of analyses that would need to be conducted before arriving at their conclusions and policy recommendations. These omissions are particularly troubling because high-quality research in this area is available that would provide the sort of policy guidance the Department is ostensibly seeking. This policy brief reviews the Department’s stated policy objectives, provides a brief explanation of the types of analyses that should typically be conducted when attempting to draw conclusions regarding cost-effective strategies, examines the resources listed on the Department’s website, critiques that content, and then offers recommendations for a research agenda that would aid in providing more thoughtful information on improving educational efficiency

Small-molecule biosensors for high-throughput metabolic engineering

Allosteric transcription factors (aTFs) have proven widely applicable for biotechnology and synthetic biology as ligand-specific biosensors enabling real-time monitoring, selection and regulation of cellular metabolism. However, both the biosensor specificity and the correlation between ligand concentration and biosensor output signal, also known as the transfer function, often needs to be optimized before meeting application needs. In this presentation we outline a versatile and high-throughput method to evolve and functionalize prokaryotic aTF ligand specificity and transfer functions in a eukaryote chassis, namely baker’s yeast Saccharomyces cerevisiae. From a single round of directed evolution of the aTF ligand-binding domain coupled with various toggled selection regimes, we robustly select aTF variants evolved for change in ligand specificity, increased dynamic output range, shifts in operational range, and a complete inversion of function from activation to repression. Importantly, by targeting only the ligand-binding domain, the evolved biosensors display DNA-binding affinities similar to parental aTFs and are functional when ported back into a non-native prokaryote chassis. The developed platform technology thus leverages aTF evolvability for the development of new biosensors with user-defined small-molecule specificities and transfer functions. Finally, the presentation will highlight examples on biosensor applications for high-throughput metabolic engineering. Please click Additional Files below to see the full abstract

X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa

The role of seemingly non-enzymatic proteins in complexes interconverting UDP-arabinopyranose and UDP-arabinofuranose (UDP-arabinosemutases; UAMs) in the plant cytosol remains unknown. To shed light on their function, crystallographic and functional studies of the seemingly non-enzymatic UAM2 protein from Oryza sativa (OsUAM2) were undertaken. Here, X-ray diffraction data are reported, as well as analysis of the oligomeric state in the crystal and in solution. OsUAM2 crystallizes readily but forms highly radiation-sensitive crystals with limited diffraction power, requiring careful low-dose vector data acquisition. Using size-exclusion chromatography, it is shown that the protein is monomeric in solution. Finally, limited proteolysis was employed to demonstrate DTT-enhanced proteolytic digestion, indicating the existence of at least one intramolecular disulfide bridge or, alternatively, a requirement for a structural metal ion

Identification of a targetable KRAS-mutant epithelial population in non-small cell lung cancer

Lung cancer is the leading cause of cancer deaths. Tumor heterogeneity, which hampers development of targeted therapies, was herein deconvoluted via single cell RNA sequencingin aggressive human adenocarcinomas (carrying Kras-mutations) and comparable murine model. We identified a tumor-specific, mutant-KRAS-associated subpopulation which is conserved in both human and murine lung cancer. We previously reported a key role for the oncogene BMI-1 in adenocarcinomas. We therefore investigated the effects of in vivo PTC596 treatment, which affects BMI-1 activity, in our murine model. Post-treatment, MRI analysis showed decreased tumor size, while single cell transcriptomics concomitantly detected near complete ablation of the mutant-KRAS-associated subpopulation, signifying the presence of a pharmacologically targetable, tumor-associated subpopulation. Our findings therefore hold promise for the development of a targeted therapy for KRAS-mutant adenocarcinomas

The Justy mutation identifies Gon4-like as a gene that is essential for B lymphopoiesis

A recessive mutation named Justy was found that abolishes B lymphopoiesis but does not impair other major aspects of hematopoiesis. Transplantation experiments showed that homozygosity for Justy prevented hematopoietic progenitors from generating B cells but did not affect the ability of bone marrow stroma to support B lymphopoiesis. In bone marrow from mutant mice, common lymphoid progenitors and pre-pro–B cells appeared normal, but cells at subsequent stages of B lymphopoiesis were dramatically reduced in number. Under culture conditions that promoted B lymphopoiesis, mutant pre-pro–B cells remained alive and began expressing the B cell marker CD19 but failed to proliferate. In contrast, these cells were able to generate myeloid or T/NK precursors. Genetic and molecular analysis demonstrated that Justy is a point mutation within the Gon4-like (Gon4l) gene, which encodes a protein with homology to transcriptional regulators. This mutation was found to disrupt Gon4l pre-mRNA splicing and dramatically reduce expression of wild-type Gon4l RNA and protein. Consistent with a role for Gon4l in transcriptional regulation, the levels of RNA encoding C/EBPα and PU.1 were abnormally high in mutant B cell progenitors. Our findings indicate that the Gon4l protein is required for B lymphopoiesis and may function to regulate gene expression during this process