Countering cooperative effects in protease inhibitors using constrained b-strand-mimicking templates in focused combinatorial libraries

A major problem in de novo design of enzyme inhibitors is the unpredictability of the induced fit, with the shape of both ligand and enzyme changing cooperatively and unpredictably in response to subtle structural changes within a ligand. We have investigated the possibility of dampening the induced fit by using a constrained template as a replacement for adjoining segments of a ligand. The template preorganizes the ligand structure, thereby organizing the local enzyme environment. To test this approach, we used templates consisting of constrained cyclic tripeptides, formed through side chain to main chain linkages, as structural mimics of the protease-bound extended beta-strand conformation of three adjoining amino acid residues at the N- or C-terminal sides of the scissile bond of substrates. The macrocyclic templates were derivatized to a range of 30 structurally diverse molecules via focused combinatorial variation of nonpeptidic appendages incorporating a hydroxyethylamine transition-state isostere. Most compounds in the library were potent inhibitors of the test protease (HIV-1 protease). Comparison of crystal structures for five protease-inhibitor complexes containing an N-terminal macrocycle and three protease-inhibitor complexes containing a C-terminal macrocycle establishes that the macrocycles fix their surrounding enzyme environment, thereby permitting independent variation of acyclic inhibitor components with only local disturbances to the protease. In this way, the location in the protease of various acyclic fragments on either side of the macrocyclic template can be accurately predicted. This type of templating strategy minimizes the problem of induced fit, reducing unpredictable cooperative effects in one inhibitor region caused by changes to adjacent enzyme-inhibitor interactions. This idea might be exploited in template-based approaches to inhibitors of other proteases, where a beta-strand mimetic is also required for recognition, and also other protein-binding ligands where different templates may be more appropriate.

Gene expression profiles in murine hematopoietic stem cells revisited: Analysis of cDNA libraries reveals high levels of translational and metabolic activities

Gene expression studies from hematopoietic stem cell (HSC) populations purified to variable degrees have defined a set of sternness genes. Unexpectedly, results also hinted toward a HSC chromatin poised in a wide-open state. With the aim of providing a robust tool for further studies into the molecular biology of HSCs, the studies herein describe the construction and comparative molecular analysis of A-phage cDNA libraries from highly purified HSCs that retained their long-term repopulating activities (long-term HSCs [LT-HSCs]) and from short-term repopulating HSCs that were largely depleted of these activities. Microarray analysis of the libraries confirmed the previous results but also revealed an unforeseen preferential expression of translation- and metabolism-associated genes in the LT-HSCs. Therefore, these data indicate that HSCs are quiescent only in regard of proliferative activities but are in a state of readiness to provide the metabolic and translational activities required after induction of proliferation and exit from the HSC pool.

Motivating Medical Students To Learn Basic Science Concepts Using Chronic Myeloid Leukemia As An Integration Theme.

To report on the use of chronic myeloid leukemia as a theme of basic clinical integration for first year medical students to motivate and enable in-depth understanding of the basic sciences of the future physician. During the past thirteen years we have reviewed and updated the curriculum of the medical school of the Universidade Estadual de Campinas. The main objective of the new curriculum is to teach the students how to learn to learn. Since then, a case of chronic myeloid leukemia has been introduced to first year medical students and discussed in horizontal integration with all themes taught during a molecular and cell biology course. Cell structure and components, protein, chromosomes, gene organization, proliferation, cell cycle, apoptosis, signaling and so on are all themes approached during this course. At the end of every topic approached, the students prepare in advance the corresponding topic of clinical cases chosen randomly during the class, which are then presented by them. During the final class, a paper regarding mutations in the abl gene that cause resistance to tyrosine kinase inhibitors is discussed. After each class, three tests are solved in an interactive evaluation. The course has been successful since its beginning, 13 years ago. Great motivation of those who participated in the course was observed. There were less than 20% absences in the classes. At least three (and as many as nine) students every year were interested in starting research training in the field of hematology. At the end of each class, an interactive evaluation was performed and more than 70% of the answers were correct in each evaluation. Moreover, for the final evaluation, the students summarized, in a written report, the molecular and therapeutic basis of chronic myeloid leukemia, with scores ranging from 0 to 10. Considering all 13 years, a median of 78% of the class scored above 5 (min 74%-max 85%), and a median of 67% scored above 7. Chronic myeloid leukemia is an excellent example of a disease that can be used for clinical basic integration as this disorder involves well known protein, cytogenetic and cell function abnormalities, has well-defined diagnostic strategies and a target oriented therapy.

Mentors, students, and the undergraduate medical course: a virtuous circle

BACKGROUND: Mentoring Programs have been developed in several medical schools, but few studies have investigated the mentors'perspective. PURPOSES: To explore mentors'perceptions regarding their experience. METHODS: Mentors at a medical school were invited to participate in an in-depth interview including questions on satisfaction, difficulties, and perception of changes resulting from the program. RESULTS: Mentors' satisfaction and difficulties are strongly associated with students'involvement in the activity. Mentors believe changes observed in students were more related to life issues; for some mentors, there is no recognition or awareness of the program. However, most of the mentors acknowledged important changes in relation to themselves: as teachers, faculty members, and individuals. CONCLUSION: Attendance is crucial for both the mentoring relationship and strengthening of the program. Students involved in the activity motivate mentors in teaching and curriculum development, thereby creating a virtuous circle and benefiting undergraduate medical education as a whole.

Drug consumption among medical students in São Paulo, Brazil: influences of gender and academic year

OBJECTIVE: To analyze alcohol, tobacco and other drug use among medical students. METHOD: Over a five-year period (1996-2001), we evaluated 457 students at the Universidade de São Paulo School of Medicine, located in São Paulo, Brazil. The students participated by filling out an anonymous questionnaire on drug use (lifetime, previous 12 months and previous 30 days). The influence that gender and academic year have on drug use was also analyzed. RESULTS: During the study period, there was an increase in the use of illicit drugs, especially inhalants and amphetamines, among the medical students evaluated. Drug use (except that of marijuana and inhalants) was comparable between the genders, and academic year was an important influencing factor. DISCUSSION: Increased inhalant use was observed among the medical students, especially among males and students in the early undergraduate years. This is suggestive of a specific behavioral pattern among medical students. Our findings corroborate those of previous studies. CONCLUSION: Inhalant use is on the rise among medical students at the Universidade de São Paulo School of Medicine. Because of the negative health effects of illicit drug use, further studies are needed in order to deepen the understanding of this phenomenon and to facilitate the development of preventive measures.

Transcriptional profiling reveals the expression of novel genes in response to various stimuli in the human dermatophyte Trichophyton rubrum

Background: Cutaneous mycoses are common human infections among healthy and immunocompromised hosts, and the anthropophilic fungus Trichophyton rubrum is the most prevalent microorganism isolated from such clinical cases worldwide. The aim of this study was to determine the transcriptional profile of T. rubrum exposed to various stimuli in order to obtain insights into the responses of this pathogen to different environmental challenges. Therefore, we generated an expressed sequence tag (EST) collection by constructing one cDNA library and nine suppression subtractive hybridization libraries. Results: The 1388 unigenes identified in this study were functionally classified based on the Munich Information Center for Protein Sequences (MIPS) categories. The identified proteins were involved in transcriptional regulation, cellular defense and stress, protein degradation, signaling, transport, and secretion, among other functions. Analysis of these unigenes revealed 575 T. rubrum sequences that had not been previously deposited in public databases. Conclusion: In this study, we identified novel T. rubrum genes that will be useful for ORF prediction in genome sequencing and facilitating functional genome analysis. Annotation of these expressed genes revealed metabolic adaptations of T. rubrum to carbon sources, ambient pH shifts, and various antifungal drugs used in medical practice. Furthermore, challenging T. rubrum with cytotoxic drugs and ambient pH shifts extended our understanding of the molecular events possibly involved in the infectious process and resistance to antifungal drugs.

Oral Health Promotion Through an Online Training Program for Medical Students

The objective of this study was to compare the impact on knowledge and counseling skills of face-to-face and Internet-based oral health training programs on medical students. Participants consisted of 148 (82 percent) of the 180 invited students attending their fifth academic year at the Faculty of Medicine, University of Sao Paulo, Brasil, in 2007. The interventions took place during a three-month training period in the clinical Center for Health Promotion, which comprised part of a clerkship in Internal Medicine. The students were divided into four groups: 1) Control Group (Control), with basic intervention; 2) Brochure Group (Br), with basic intervention plus complete brochure with oral health themes; 3) Cybertutor Group (Cy), with basic intervention plus access to an Internet-based training program about oral health themes; and 4) Cybertutor + Contact Group (Cy+C), the same as Cy plus brief proactive contact with a tutor. The impact of these interventions on student knowledge was measured with pre- and post assessments, and student skills in asking and counseling about oral health were assessed with an objective structured clinical examination (OSCE). Multivariate logistic regression models were applied to identify the odds ratios of scoring above Control's medians on the final assessment and the OSCE. In the results, Cy+C performed significantly better than Control on both the final assessment (OR 9.4; 95% CI 2.7-32.8) and the OSCE (OR 5.6; 95% CI 1.9-16.3) and outperformed all the other groups. The Cy+C group showed the most significant increase in knowledge and the best skills in asking and counseling about oral health.

The characteristics of depressive symptoms in medical students during medical education and training: a cross-sectional study

Background: Medical education and training can contribute to the development of depressive symptoms that might lead to possible academic and professional consequences. We aimed to investigate the characteristics of depressive symptoms among 481 medical students (79.8% of the total who matriculated). Methods: The Beck Depression Inventory (BDI) and cluster analyses were used in order to better describe the characteristics of depressive symptoms. Medical education and training in Brazil is divided into basic (1(st) and 2(nd) years), intermediate (3(rd) and 4(th) years), and internship (5(th) and 6(th) years) periods. The study organized each item from the BDI into the following three clusters: affective, cognitive, and somatic. Statistical analyses were performed using analysis of variance (ANOVA) with post-hoc Tukey corrected for multiple comparisons. Results: There were 184 (38.2%) students with depressive symptoms (BDI > 9). The internship period resulted in the highest BDI scores in comparison to both the basic (p < .001) and intermediate (p < .001) periods. Affective, cognitive, and somatic clusters were significantly higher in the internship period. An exploratory analysis of possible risk factors showed that females (p = .020) not having a parent who practiced medicine (p = .016), and the internship period (p = .001) were factors for the development of depressive symptoms. Conclusion: There is a high prevalence towards depressive symptoms among medical students, particularly females, in the internship level, mainly involving the somatic and affective clusters, and not having a parent who practiced medicine. The active assessment of these students in evaluating their depressive symptoms is important in order to prevent the development of co-morbidities and suicide risk.

Genetic Background of Patients from a University Medical Center in Manhattan: Implications for Personalized Medicine

Background: The rapid progress currently being made in genomic science has created interest in potential clinical applications; however, formal translational research has been limited thus far. Studies of population genetics have demonstrated substantial variation in allele frequencies and haplotype structure at loci of medical relevance and the genetic background of patient cohorts may often be complex. Methods and Findings: To describe the heterogeneity in an unselected clinical sample we used the Affymetrix 6.0 gene array chip to genotype self-identified European Americans (N = 326), African Americans (N = 324) and Hispanics (N = 327) from the medical practice of Mount Sinai Medical Center in Manhattan, NY. Additional data from US minority groups and Brazil were used for external comparison. Substantial variation in ancestral origin was observed for both African Americans and Hispanics; data from the latter group overlapped with both Mexican Americans and Brazilians in the external data sets. A pooled analysis of the African Americans and Hispanics from NY demonstrated a broad continuum of ancestral origin making classification by race/ethnicity uninformative. Selected loci harboring variants associated with medical traits and drug response confirmed substantial within-and between-group heterogeneity. Conclusion: As a consequence of these complementary levels of heterogeneity group labels offered no guidance at the individual level. These findings demonstrate the complexity involved in clinical translation of the results from genome-wide association studies and suggest that in the genomic era conventional racial/ethnic labels are of little value.

Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts

Background: Alternative splicing (AS) is a central mechanism in the generation of genomic complexity and is a major contributor to transcriptome and proteome diversity. Alterations of the splicing process can lead to deregulation of crucial cellular processes and have been associated with a large spectrum of human diseases. Cancer-associated transcripts are potential molecular markers and may contribute to the development of more accurate diagnostic and prognostic methods and also serve as therapeutic targets. Alternative splicing-enriched cDNA libraries have been used to explore the variability generated by alternative splicing. In this study, by combining the use of trapping heteroduplexes and RNA amplification, we developed a powerful approach that enables transcriptome-wide exploration of the AS repertoire for identifying AS variants associated with breast tumor cells modulated by ERBB2 (HER-2/neu) oncogene expression. Results: The human breast cell line (C5.2) and a pool of 5 ERBB2 over-expressing breast tumor samples were used independently for the construction of two AS-enriched libraries. In total, 2,048 partial cDNA sequences were obtained, revealing 214 alternative splicing sequence-enriched tags (ASSETs). A subset with 79 multiple exon ASSETs was compared to public databases and reported 138 different AS events. A high success rate of RT-PCR validation (94.5%) was obtained, and 2 novel AS events were identified. The influence of ERBB2-mediated expression on AS regulation was evaluated by capillary electrophoresis and probe-ligation approaches in two mammary cell lines (Hb4a and C5.2) expressing different levels of ERBB2. The relative expression balance between AS variants from 3 genes was differentially modulated by ERBB2 in this model system. Conclusions: In this study, we presented a method for exploring AS from any RNA source in a transcriptome-wide format, which can be directly easily adapted to next generation sequencers. We identified AS transcripts that were differently modulated by ERBB2-mediated expression and that can be tested as molecular markers for breast cancer. Such a methodology will be useful for completely deciphering the cancer cell transcriptome diversity resulting from AS and for finding more precise molecular markers.

Use of Medical Subject Headings (MeSH) in Portuguese for categorizing web-based healthcare content

Introduction: Internet users are increasingly using the worldwide web to search for information relating to their health. This situation makes it necessary to create specialized tools capable of supporting users in their searches. Objective: To apply and compare strategies that were developed to investigate the use of the Portuguese version of Medical Subject Headings (MeSH) for constructing an automated classifier for Brazilian Portuguese-language web-based content within or outside of the field of healthcare, focusing on the lay public. Methods: 3658 Brazilian web pages were used to train the classifier and 606 Brazilian web pages were used to validate it. The strategies proposed were constructed using content-based vector methods for text classification, such that Naive Bayes was used for the task of classifying vector patterns with characteristics obtained through the proposed strategies. Results: A strategy named InDeCS was developed specifically to adapt MeSH for the problem that was put forward. This approach achieved better accuracy for this pattern classification task (0.94 sensitivity, specificity and area under the ROC curve). Conclusions: Because of the significant results achieved by InDeCS, this tool has been successfully applied to the Brazilian healthcare search portal known as Busca Saude. Furthermore, it could be shown that MeSH presents important results when used for the task of classifying web-based content focusing on the lay public. It was also possible to show from this study that MeSH was able to map out mutable non-deterministic characteristics of the web. (c) 2010 Elsevier Inc. All rights reserved.

Building a Open Source Framework for Virtual Medical Training

This paper presents a framework to build medical training applications by using virtual reality and a tool that helps the class instantiation of this framework. The main purpose is to make easier the building of virtual reality applications in the medical training area, considering systems to simulate biopsy exams and make available deformation, collision detection, and stereoscopy functionalities. The instantiation of the classes allows quick implementation of the tools for such a purpose, thus reducing errors and offering low cost due to the use of open source tools. Using the instantiation tool, the process of building applications is fast and easy. Therefore, computer programmers can obtain an initial application and adapt it to their needs. This tool allows the user to include, delete, and edit parameters in the functionalities chosen as well as storing these parameters for future use. In order to verify the efficiency of the framework, some case studies are presented.