Functional expression of diverse post-translational peptide-modifying enzymes in Escherichia coli under uniform expression and purification conditions.

RiPPs (ribosomally-synthesized and post-translationally modified peptides) are a class of pharmaceutically-relevant natural products expressed as precursor peptides before being enzymatically processed into their final functional forms. Bioinformatic methods have illuminated hundreds of thousands of RiPP enzymes in sequence databases and the number of characterized chemical modifications is growing rapidly; however, it remains difficult to functionally express them in a heterologous host. One challenge is peptide stability, which we addressed by designing a RiPP stabilization tag (RST) based on a small ubiquitin-like modifier (SUMO) domain that can be fused to the N- or C-terminus of the precursor peptide and proteolytically removed after modification.

Competitive dCas9 binding as a mechanism for transcriptional control.

Catalytically dead Cas9 (dCas9) is a programmable transcription factor that can be targeted to promoters through the design of small guide RNAs (sgRNAs), where it can function as an activator or repressor. Natural promoters use overlapping binding sites as a mechanism for signal integration, where the binding of one can block, displace, or augment the activity of the other. Here, we implemented this strategy in Escherichia coli using pairs of sgRNAs designed to repress and then derepress transcription through competitive binding.

Selection for constrained peptides that bind to a single target protein.

Peptide secondary metabolites are common in nature and have diverse pharmacologically-relevant functions, from antibiotics to cross-kingdom signaling. Here, we present a method to design large libraries of modified peptides in Escherichia coli and screen them in vivo to identify those that bind to a single target-of-interest. Constrained peptide scaffolds were produced using modified enzymes gleaned from microbial RiPP (ribosomally synthesized and post-translationally modified peptide) pathways and diversified to build large libraries.

Single-cell measurement of plasmid copy number and promoter activity.

Accurate measurements of promoter activities are crucial for predictably building genetic systems. Here we report a method to simultaneously count plasmid DNA, RNA transcripts, and protein expression in single living bacteria. From these data, the activity of a promoter in units of RNAP/s can be inferred.

Transite: A Computational Motif-Based Analysis Platform That Identifies RNA-Binding Proteins Modulating Changes in Gene Expression.

RNA-binding proteins (RBPs) play critical roles in regulating gene expression by modulating splicing, RNA stability, and protein translation. Stimulus-induced alterations in RBP function contribute to global changes in gene expression, but identifying which RBPs are responsible for the observed changes remains an unmet need. Here, we present Transite, a computational approach that systematically infers RBPs influencing gene expression through changes in RNA stability and degradation.

Exploring the utility of assessing early mathematics intervention response via embedded assessment.

The provision of high-quality early mathematics instruction and intervention is critical to ensure that all students are on track for academic success. Given this, identifying and utilizing assessments that can enable the detection of nonresponse to mathematics instruction is a critical aspect of early intervention. To this end, the current study explored the extent to which there were distinct patterns of performance on embedded assessments for intervention participants within the context of a large-scale randomized control trial of the ROOTS intervention.

Principles of synthetic biology: a MOOC for an emerging field.

Synthetic biology requires students and scientists to draw upon knowledge and expertise from many disciplines. While this diversity is one of the field's primary strengths, it also makes it challenging for newcomers to acquire the background knowledge necessary to thrive. To address this gap, we developed a course that provides a structured approach to learning the biological principles and theoretical underpinnings of synthetic biology.

Primary Renal Carcinoid with Bilateral Multiple Clear Cell Papillary Renal Cell Carcinomas.

Clear cell papillary renal cell carcinoma (CCPRCC) is a newly recognized entity in the 2016 WHO classification and usually presents as a small, circumscribed, solitary mass of indolent nature. CCPRCCs could seldom occur in conjunction with other synchronous or metachronous kidney tumors and even less frequently as bilateral masses. To our knowledge, multiple bilateral CCPRCCs have never been described with the existence of a synchronous well-differentiated neuroendocrine tumor of the kidney and hence reported here as a unique case.

Has the new USP assay for heparin affected dosage for patients undergoing cardiopulmonary bypass?

In October 2009, the U.S. Pharmacopoeia (USP) changed the monograph for heparin to bring USP units in line with international units for heparin.

Neurog3 gene dosage regulates allocation of endocrine and exocrine cell fates in the developing mouse pancreas.

The basic helix-loop-helix transcription factor Neurog3 (Neurogenin3 or Ngn3) actively drives endodermal progenitor cells towards endocrine islet cell differentiation during embryogenesis. Here, we manipulate Neurog3 expression levels in endocrine progenitor cells without altering its expression pattern using heterozygosity and a hypomorph. Lowered Neurog3 gene dosage in the developing pancreatic epithelium reduces the overall production of endocrine islet cells without significantly affecting the proportions of various islet cell types that do form.

Cycling of CRYPTOCHROME proteins is not necessary for circadian-clock function in mammalian fibroblasts.

Background: An interlocked transcriptional-translational feedback loop (TTFL) is thought to generate the mammalian circadian clockwork in both the central pacemaker residing in the hypothalamic suprachiasmatic nuclei and in peripheral tissues. The core circadian genes, including Period1 and Period2 (Per1 and Per2), Cryptochrome1 and Cryptochrome2 (Cry1 and Cry2), Bmal1, and Clock are indispensable components of this biological clockwork. The cycling of the PER and CRY clock proteins has been thought to be necessary to keep the mammalian clock ticking.

Myeloid lineage progenitors give rise to vascular endothelium.

Despite an important role in vascular development and repair, the origin of endothelial progenitors remains unknown. Accumulating evidence indicates that cells derived from the hematopoietic system participate in angiogenesis. However, the identity and functional role of these cells remain controversial.

Donor marker infidelity in transgenic hematopoietic stem cells.

Transgenic marking approaches are increasingly used to evaluate the developmental potential of stem cells. However, cell fate mapping studies using different transgenic marking systems have produced conflicting results. These disparate findings may be due in part to the infidelity of donor marker gene expression.

Transplanted human bone marrow contributes to vascular endothelium.

Recent evidence indicates that bone marrow is a source of endothelial progenitor cells that are mobilized into the peripheral blood in response to cytokines or tissue injury. Previously, we showed that functional endothelial cells (ECs) can be clonally derived from phenotypically defined hematopoietic stem cells. To determine the EC potential of human bone marrow and peripheral blood stem cells, blood vessels in sex-mismatched transplant recipients were evaluated.