Deorphanization of the human leukocyte tyrosine kinase (LTK) receptor by a signaling screen of the extracellular proteome.

There are many transmembrane receptor-like proteins whose ligands have not been identified. A strategy for finding ligands when little is known about their tissue source is to screen each extracellular protein individually expressed in an array format by using a sensitive functional readout. Taking this approach, we have screened a large collection (3,191 proteins) of extracellular proteins for their ability to activate signaling of an orphan receptor, leukocyte tyrosine kinase (LTK). Only two related secreted factors, FAM150A and FAM150B (family with sequence similarity 150 member A and member B), stimulated LTK phosphorylation. FAM150A binds LTK extracellular domain with high affinity (K(D) = 28 pM). FAM150A stimulates LTK phosphorylation in a ligand-dependent manner. This strategy provides an efficient approach for identifying functional ligands for other orphan receptors.

Microscopic superfluidity in 4He clusters stirred by a rotating impurity molecule.

The effective moment of inertia of a CO impurity molecule in 4HeN and p-(H2)N solvent clusters initially increases with N but then commences a nonclassical decrease at N=4 (4He) or N=6 (p-H2). This suggests molecule-solvent decoupling and a transition to microscopic superfluidity. However, the quantum decoupling mechanism has not been elucidated. To understand the decoupling mechanism, a one-dimensional model is introduced in which the 4He atoms are confined to a ring. This model captures the physics and shows that decoupling happens primarily because of bosonic solvent-solvent repulsion. Quantum Monte Carlo and basis set calculations suggest that the system can be modeled as a stirred Tonks-Girardeau gas. This allows the N-particle time-dependent Schrödinger equation to be solved directly. Computations of the integrated particle current reveal a threshold for stirring and current generation, indicative of superfluidity.

Diabetes: Screening, Diagnosis, and Prevention of Type 2 Diabetes.

From 2013-2016, 34.5% of US adults had prediabetes. The U.S. Preventive Services Task Force (USPSTF) recommends screening all adults ages 40 to 70 years with overweight or obesity for abnormal blood glucose, and screening for gestational diabetes in pregnant women after 24 weeks. The American Diabetes Association (ADA) recommends screening all patients older than 45 years for prediabetes and diabetes, and screening earlier for patients with risk factors. Screening in younger patients is based on risk factors. The diagnostic criteria for prediabetes and diabetes require two abnormal test results from the same sample or from two separate samples, in the absence of unequivocal hyperglycemia or symptomatic hyperglycemia. Physical activity and healthy eating patterns continue to be the cornerstones of diabetes prevention. Although no drugs are approved by the Food and Drug Administration (FDA) for diabetes prevention, strong evidence supports the use of metformin in adults with prediabetes. In children, metformin use for the prevention of diabetes requires more study. Rates of progression from prediabetes to type 2 diabetes range from 5.8% to 18.3% per year, depending on the population studied.

Diabetes: Type 1 Diabetes.

Type 1 diabetes is defined as a state of hyperglycemia due to insulin deficiency caused by autoimmune pancreatic beta-cell destruction. The risk among individuals in the general population has been estimated at 0.5%. A family history of diabetes and a personal history of conditions associated with type 1 diabetes (ie, autoimmune diseases) increase the risk. Currently, the American Diabetes Association (ADA) recommends screening asymptomatic patients for type 1 diabetes autoimmune markers in the context of clinical research trials. All patients with diabetes should be referred to a diabetes self-management education program and for medical nutrition therapy. Medical nutrition therapy has been shown to lower the A1c by up to 1.9% in patients with type 1 diabetes. The mainstay of management is a regimen of multiple daily injections of insulin or continuous subcutaneous insulin delivered via an insulin pump. For most patients, a regimen consisting of 50% of the total daily dose prescribed as basal insulin and 50% prescribed as bolus insulin is used. Currently, pramlintide is the only Food Drug Administration (FDA)-approved adjunct to insulin therapy for patients with type 1 diabetes. Patients with type 1 diabetes should be screened regularly for hypertension and other associated conditions and complications.

The renal adverse effects of cancer immunotherapy.

Over the past decade, the development and clinical use of immunotherapy agents has increased exponentially. As clinical experience builds with these agents so too does our understanding of the associated adverse effects. In particular, the effects of immunotherapy on the kidneys, individual nephrons, and kidney function remain less well described than the adverse effects on barrier organ systems such as the gastrointestinal tract and skin. However, phase IV post-marketing surveillance and clinical case studies together with basic research has begun to reveal mechanisms by which immunotherapy mediates renal adverse effects. This work may lead to improvements in treatment guidelines and therapy. These advances are particularly important as post-cancer survival increases leaving patients to cope with the consequences of not only the cancer, but the short- and long-term adverse effects of treatment. Here we discuss the major renal adverse effects encountered with individual immunotherapeutic agents, putative mechanisms, their current management, and how cancer survivorship programs can help patients who have been treated with immunotherapy.

A Pilot Screen of a Novel Peptide Hormone Library Identified Candidate GPR83 Ligands.

The identification of novel peptide hormones by functional screening is challenging because posttranslational processing is frequently required to generate biologically active hormones from inactive precursors. We developed an approach for functional screening of novel potential hormones by expressing them in endocrine host cells competent for posttranslational processing. Candidate preprohormones were selected by bioinformatics analysis, and stable endocrine host cell lines were engineered to express the preprohormones. The production of mature hormones was demonstrated by including the preprohormones insulin and glucagon, which require the regulated secretory pathway for production of the active forms. As proof of concept, we screened a set of G-protein-coupled receptors (GPCRs) and identified protein FAM237A as a specific activator of GPR83, a GPCR implicated in central nervous system and regulatory T-cell function. We identified the active form of FAM237A as a C-terminally cleaved, amidated 9 kDa secreted protein. The related protein FAM237B, which is 64% homologous to FAM237A, demonstrated similar posttranslational modification and activation of GPR83, albeit with reduced potency. These results demonstrate that our approach is capable of identifying and characterizing novel hormones that require processing for activity.

Integration of Microbiology, Pharmacology, Immunology, and Infectious Disease Using Active Teaching and Self-Directed Learning.

In an era of decreasing basic science curriculum at medical schools, we sought to re-imagine how to optimally deliver three core basic science disciplines (microbiology, pharmacology, and immunology) together with infectious disease in a 5-week course. This course, developed as part of a new 1-year pre-clinical basic science curriculum at the recently established Dell Medical School (DMS) at the University of Texas at Austin, featured a fully integrated curriculum in which the majority of the sessions were team-taught. This course, in line with the goals and missions of DMS, presented material using primarily self-directed and active learning approaches. Here, we describe the format and content of the course. We present our strategy and rationale for selecting these particular learning modalities and topics for pre-class and in-class coverage, using educational and cognitive psychology literature as a guide. We also discuss how, based on feedback from both student evaluations and performance data, the course evolved over the first two iterations.

Introduction to Mindfulness: Evidence-Based Medicine Lecture and Active Session.

INTRODUCTION: There is a growing body of evidence regarding the effectiveness of mindfulness practices and the benefits for the resilience of patients and medical professionals. Thus, there is a need to educate medical students in this technique and its benefits, but there are no readily available resources that emphasize the current evidence. We developed an introductory session for the mindfulness technique as an evidenced-based medicine lecture combined with an active mindfulness exercise. METHODS: This session consisted of a PowerPoint lecture overview of mindfulness, a topic unknown to most students, with an emphasis on evidence-based facts, as well as an active practical mindfulness exercise. The effectiveness of the lecture was assessed using a survey instrument, which was designed to assess the learners' knowledge and interest in learning and using mindfulness (before and after the session) and their interest in integrating mindfulness into the medical school curriculum. The survey contained six multiple-choice questions. Participation was voluntary and anonymous, with the use of Turning Point technology (an audience response system). RESULTS: The session was administered to and evaluated by first- and second-year medical students with no prior instruction in mindfulness. The session was held by a physician who uses mindfulness in the clinic. After the session, 90% of students were interested in learning more about mindfulness, and the majority were interested in having mindfulness integrated into the medical curriculum. DISCUSSION: The results suggest the session can be effectively used as is in other medical teaching institutions to introduce students to mindfulness and to assess students' perception of knowledge in the area and their interest in both having more comprehensive training on the subject and practicing mindfulness in medical care.

Controlling feature selection in random forests of decision trees using a genetic algorithm: classification of class I MHC peptides.

Feature selection is an important challenge in many classification problems, especially if the number of features greatly exceeds the number of examples available. We have developed a procedure--GenForest--which controls feature selection in random forests of decision trees by using a genetic algorithm. This approach was tested through our entry into the Comparative Evaluation of Prediction Algorithms 2006 (CoEPrA) competition (accessible online at: http://www.coepra.org). CoEPrA was a modeling competition organized to provide an objective testing for various classification and regression algorithms via the process of blind prediction. In the competition GenForest ranked 10/23, 5/16 and 9/16 on CoEPrA classification problems 1, 3 and 4, respectively, which involved the classification of type I MHC nonapeptides i.e. peptides containing nine amino acids. These problems each involved the classification of different sets of nonapeptides. Associated with each amino acid was a set of 643 features for a total of 5787 features per peptide. The method, its application to the CoEPrA datasets, and its performance in the competition are described.

Discovery of a cytokine and its receptor by functional screening of the extracellular proteome.

To understand the system of secreted proteins and receptors involved in cell-cell signaling, we produced a comprehensive set of recombinant secreted proteins and the extracellular domains of transmembrane proteins, which constitute most of the protein components of the extracellular space. Each protein was tested in a suite of assays that measured metabolic, growth, or transcriptional responses in diverse cell types. The pattern of responses across assays was analyzed for the degree of functional selectivity of each protein. One of the highly selective proteins was a previously undescribed ligand, designated interleukin-34 (IL-34), which stimulates monocyte viability but does not affect responses in a wide spectrum of other assays. In a separate functional screen, we used a collection of extracellular domains of transmembrane proteins to discover the receptor for IL-34, which was a known cytokine receptor, colony-stimulating factor 1 (also called macrophage colony-stimulating factor) receptor. This systematic approach is thus useful for discovering new ligands and receptors and assessing the functional selectivity of extracellular regulatory proteins.

E. coli selection of human genes encoding secreted and membrane proteins based on cDNA fusions to a leaderless beta-lactamase reporter.

Although several signal peptide-trapping methods have been devised and used to detect signal sequences, none have relied on using E.coli to identify eukaryotic proteins with signal peptides. Here, we describe a system for selecting human secreted and membrane proteins in E. coli followed by the direct validation of secretion in human cells. The method is based on cDNA fusions to a leaderless beta-lactamase reporter gene to isolate clones encoding signal peptides of human genes. We found that beta-lactamase fusion proteins carrying a eukaryotic signal peptide at its N-terminus were able to direct their export into the periplasm in E. coli to confer survival upon challenge with carbenicillin. When libraries constructed from 5' end-enriched cDNAs fused to beta-lactamase were screened in E.coli, approximately 0.5%-1% of the cDNAs are selected, and over half of the surviving clones were found to encode for secreted fusion proteins when tested in human cells. These clones were sequenced and shown to represent human genes encoding signal peptides of secreted and membrane proteins. We conclude that this is an efficient and effective strategy to easily enrich cDNA libraries for the identification of novel genes likely to encode secreted enzymes, growth factors, and receptors.