Large Multidomain Protein NMR: HIV-1 Reverse Transcriptase Precursor in Solution.

NMR studies of large proteins, over 100 kDa, in solution are technically challenging and, therefore, of considerable interest in the biophysics field. The challenge arises because the molecular tumbling of a protein in solution considerably slows as molecular mass increases, reducing the ability to detect resonances. In fact, the typical 1H-13C or 1H-15N correlation spectrum of a large protein, using a 13C- or 15N-uniformly labeled protein, shows severe line-broadening and signal overlap. Selective isotope labeling of methyl groups is a useful strategy to reduce these issues, however, the reduction in the number of signals that goes hand-in-hand with such a strategy is, in turn, disadvantageous for characterizing the overall features of the protein. When domain motion exists in large proteins, the domain motion differently affects backbone amide signals and methyl groups. Thus, the use of multiple NMR probes, such as 1H, 19F, 13C, and 15N, is ideal to gain overall structural or dynamical information for large proteins. We discuss the utility of observing different NMR nuclei when characterizing a large protein, namely, the 66 kDa multi-domain HIV-1 reverse transcriptase that forms a homodimer in solution. Importantly, we present a biophysical approach, complemented by biochemical assays, to understand not only the homodimer, p66/p66, but also the conformational changes that contribute to its maturation to a heterodimer, p66/p51, upon HIV-1 protease cleavage.

Retroviral RNase H: Structure, mechanism, and inhibition.

All retroviruses encode the enzyme, reverse transcriptase (RT), which is involved in the conversion of the single-stranded viral RNA genome into double-stranded DNA. RT is a multifunctional enzyme and exhibits DNA polymerase and ribonuclease H (RNH) activities, both of which are essential to the reverse-transcription process. Despite the successful development of polymerase-targeting antiviral drugs over the last three decades, no bona fide inhibitor against the RNH activity of HIV-1 RT has progressed to clinical evaluation. In this review article, we describe the retroviral RNH function and inhibition, with primary consideration of the structural aspects of inhibition.

Defining the correctness of a diagnosis: differential judgments and expert knowledge.

Approaches that use a simulated patient case to study and assess diagnostic reasoning usually use the correct diagnosis of the case as a measure of success and as an anchor for other measures. Commonly, the correctness of a diagnosis is determined by the judgment of one or more experts. In this study, the consistency of experts' judgments of the correctness of a diagnosis, and the structure of knowledge supporting their judgments, were explored using a card sorting task. Seven expert pediatricians were asked to sort into piles the diagnoses proposed by 119 individuals who had worked through a simulated patient case of Haemophilus influenzae Type B (HIB) meningitis. The 119 individuals had varying experience levels. The expert pediatricians were asked to sort the proposed diagnoses by similarity of content, and then to order the piles based on correctness, relative to the known correct diagnosis (HIB meningitis). Finally, the experts were asked to judge which piles contained correct or incorrect diagnoses. We found that, contrary to previous studies, experts shared a common conceptual framework of the diagnostic domain being considered and were consistent in how they categorized the diagnoses. However, similar to previous studies, the experts differed greatly in their judgment of which diagnoses were correct. This study has important implications for understanding expert knowledge, for scoring performance on simulated or real patient cases, for providing feedback to learners in the clinical setting, and for establishing criteria that define what is correct in studies of diagnostic error and diagnostic reasoning.

Back to the basic sciences: an innovative approach to teaching senior medical students how best to integrate basic science and clinical medicine.

Abraham Flexner persuaded the medical establishment of his time that teaching the sciences, from basic to clinical, should be a critical component of the medical student curriculum, thus giving rise to the "preclinical curriculum." However, students' retention of basic science material after the preclinical years is generally poor. The authors believe that revisiting the basic sciences in the fourth year can enhance understanding of clinical medicine and further students' understanding of how the two fields integrate. With this in mind, a return to the basic sciences during the fourth year of medical school may be highly beneficial. The purpose of this article is to (1) discuss efforts to integrate basic science into the clinical years of medical student education throughout the United States and Canada, and (2) describe the highly developed fourth-year basic science integration program at the University of Pittsburgh School of Medicine. In their critical review of medical school curricula of 126 U.S. and 17 Canadian medical schools, the authors found that only 19% of U.S. medical schools and 24% of Canadian medical schools require basic science courses or experiences during the clinical years, a minor increase compared with 1985. Curricular methods ranged from simple lectures to integrated case studies with hands-on laboratory experience. The authors hope to advance the national discussion about the need to more fully integrate basic science teaching throughout all four years of the medical student curriculum by placing a curricular innovation in the context of similar efforts by other U.S. and Canadian medical schools.

Developmental downregulation of P2X3 receptors in motoneurons of the compact formation of the nucleus ambiguus.

Motoneurons of the compact division of the nucleus ambiguus (cNA) are the final output neurons of the swallowing pattern generator. Thus, their normal function is critical to neonatal survival. To explore the role of purinergic signaling in modulating the excitability of these motoneurons during development, immunohistochemical and whole-cell recording techniques were used to characterize expression patterns of ionotropic P2X receptors and the effects of ATP on cNA motoneurons. Medullary slices containing the cNA were prepared from neonatal (P0-4) and juvenile (P15-21) rats. In neonatal cNA motoneurons, local application of 1 mM ATP produced a large (-133 +/- 17 pA; n = 78), desensitizing, inward current that was mimicked by 1 mM alpha,beta meATP and 2meSATP, and inhibited by the P2 antagonist, PPADS (5 microM), and the P2X3 antagonist, A-317481 (0.1-1 mM). In juvenile cNA motoneurons, 1 mM ATP produced negligible currents, while 10 mM ATP produced small (-59 +/- 14 pA; n = 42), primarily non-desensitizing currents. Immunohistochemistry demonstrated that in the neonate, the expression of P2X3 was robust, P2X2 and P2X5 moderate, P2X4 and P2X6 weak, and P2X1 absent. In the juvenile cNA, only low levels of P2X5 and P2X6 labeling were detected. These data indicate that P2X receptors in cNA motoneurons are profoundly downregulated during the first two postnatal weeks, and suggest a role for the purinoceptor system, particularly P2X3 receptors, in the control of esophageal motor networks during early postnatal periods.

Expression of Phox2 transcription factors and induction of the dopaminergic phenotype in primary sensory neurons.

Cell-type-specific transcription factors may regulate phenotypic diversity by conferring selective responsiveness to relatively nonspecific environmental cues. To test this hypothesis, we examined whether the homeodomain transcription factors Phox2a/2b play a role in activity-dependent expression of the dopaminergic phenotype using petrosal ganglion (PG) sensory neurons as a model. The timing of Phox2a/2b expression is precisely correlated with the ability of PG neurons to express the dopamine-synthesizing enzyme, tyrosine hydroxylase (TH), in response to depolarizing stimuli. Phox2a/2b expression is highest at embryonic day 16.5, when virtually all PG neurons exhibit activity-dependent TH induction, and subsequently falls in parallel with the loss of activity-dependent TH induction. Expression is maintained, however, in all dopaminergic neurons. Physiologic stimulation of PG neurons in vivo induces TH expression exclusively in Phox2a/2b(+) cells. Our data suggest that constitutive expression of Phox2a/2b defines the potential of neurons to become dopaminergic in response to membrane depolarization during a critical window of phenotypic plasticity.

Cranial sensory neuron development in the absence of brain-derived neurotrophic factor in BDNF/Bax double null mice.

To investigate the role of brain-derived neurotrophic factor (BDNF) in differentiation of cranial sensory neurons in vivo, we analyzed development of nodose (NG), petrosal (PG), and vestibular (VG) ganglion cells in genetically engineered mice carrying null mutations in the genes encoding BDNF and the proapoptotic Bcl-2 homolog Bax. In bax(-/-) mutants, ganglion cell numbers were increased significantly compared to wild-type animals, indicating that naturally occurring cell death in these ganglia is regulated by Bax signaling. Analysis of bdnf(-/-)bax(-/-) mutants revealed that, although the Bax null mutation completely rescued cell loss in the absence of BDNF, it did not rescue the lethality of the BDNF null phenotype. Moreover, despite rescue of BDNF-dependent neurons by the bax null mutation, sensory target innervation was abnormal in double null mutants. Vagal sensory innervation to baroreceptor regions of the cardiac outflow tract was completely absent, and the density of vestibular sensory innervation to the cristae organs was markedly decreased, compared to wild-type controls. Moreover, vestibular afferents failed to selectively innervate their hair cell targets within the cristae organs in the double mutants. These innervation failures occurred despite successful navigation of sensory fibers to the peripheral field, demonstrating that BDNF is required locally for afferent ingrowth into target tissues. In addition, the bax null mutation failed to rescue expression of the dopaminergic phenotype in a subset of NG and PG neurons. These data demonstrate that BDNF signaling is required not only to support survival of cranial sensory neurons, but also to regulate local growth of afferent fibers into target tissues and, in some cells, transmitter phenotypic expression is required.