bluuebunny/crossref_metadata_2025 huggingface dataset:
Asthma: In Plain Language
Authors: Rudd Rima E. , Zobel Emily K. , Fanta Christopher H. , Surkan Pamela , Rodriguez-Louis Jacqueline , Valderrama Yvette , Daltroy Lawren H.
Published: June 2004

The Community Asthma Program was designed to increase awareness of asthma among urban residents and to bring more people into available care. Educational sessions with patients indicated that many adults struggle with the complicated demands of managing a chronic disease. At the same time, however, a good deal of the written materials meant to provide information and assistance instead make inappropriate demands on the average adult reader. The project team members developed a glossary of asthma terms to improve communication between patients and providers and to help patients understand the materials commonly used in neighborhood health centers. We report on the development of the glossary and describe formative research activities, initial dissemination efforts, and an interim evaluation. Health literacy, included in the goals and objectives for Healthy People 2010, can be improved when health materials are written in plain language and designed for the existing skills of the average U.S. adult reader.
Force Field Analysis: A Model for Promoting Adolescents’ Involvement in Their Own Health Care
Authors: MacDuffie Heather , DePoy Elizabeth
Published: June 2004

This article advances a three-step model for engaging adolescents in shaping their own health care supports and services through systems and social change that rely on principles of force field analysis. Consistent with health promotion values and trends for evidence-based practice, force field analysis provides a systematic and multilevel approach to problem assessment, resolution, and social change that is particularly appropriate for adolescents. The article reviews relevant literature, proposes the model, and concludes with a comparative illustration and critical analysis of the use of force field analysis to promote adolescent health.
Involving the Community in HIV Prevention Program Evaluation
Authors: Uhl Gary , Robinson Beatrice , Westover Bonita , Bockting Walter , Cherry-Porter Tonya
Published: June 2004

This article describes the challenges and benefits of involving the community in evaluating an HIV prevention intervention for African American women. The intervention, Women’s Initiative for Sexual Health, was evaluated using a randomized controlled trial. The intervention and the evaluation involved the community in which the intervention was delivered. To solicit criticism and suggestions for the evaluation, the research team conducted a focus group within each of three collaborating community-based organizations. Our goal was to increase the relevance and appropriateness of the evaluation by showing respect for program participants and consequently for cultures other than our own. We recommend that other researchers involve the community in program evaluation.
Stacking the Deck for Success in Interprofessional Collaboration
Authors: Davoli Gerald W. , Fine L-Jay
Published: June 2004

The practice of interprofessional collaboration is increasingly being recognized as an important skill for educators, health professionals, and social service providers. Collaboration involves team building and developing integrated service delivery mechanisms to improve outcomes for recipients of health, education, and social services. The focus on health promotion and illness prevention has led to an increasing demand for health educators to become involved in these collaboratives as members and more often as facilitators. Key concepts associated with early stages of collaborative development are described, with a focus on forming a group identity and weathering the conflicts associated with task and personnel issues. Descriptions and instructions for facilitating activities to move the group successfully through these initial stages are described.
Translating Efficacy Research to Effectiveness Studies in Practice: Lessons From Research to Promote Smoking Cessation in Community Health Centers
Authors: Zapka Jane , Goins Karin Valentine , Pbert Lori , Ockene Judith K.
Published: June 2004

Researchers and their community partners have been challenged by funders and political entities to translate what is learned in research into practice. Such translation is more challenging than it appears, and it is important to systematically make use of opportunities available to learn about facilitators and barriers to the implementation of effectiveness research in real-world settings. This article presents a case study of the process evaluation undertaken as part of Quit Together, a randomized trial of the effectiveness of an intervention to improve smoking cessation and relapse prevention among low-income pregnant and postpartum women who receive care at community health centers (CHCs). The analysis considers areas of program implementation failure that may need critical rethinking. The article demonstrates the importance of process-monitoring methods to examine context factors of collaborative research, outlines lessons learned and the challenges of research carried out in CHCs, and summarizes implications for researchers and for practitioners.
Reflections From the Ivory Tower
Authors: Capwell Ellen M.
Published: June 2004

One health educator reflects on a career shift from public health practitioner to college faculty. The opportunity arose through informal Society for Public Health Education (SOPHE) networking. Similarities between the practitioner and academic roles are noted in relation to politics, mentoring, service on committees, presentations, consultation, and chain of command. Notable differences are discussed in areas of hiring and job security, work rules, teaching versus administration, molding students versus reshaping adults, degree of focus on health content versus program process, amount of bureaucracy and red tape, and degree of freedom to advocate. Recommendations are included for successful transitions. Both roles have unique rewards.
Graft-versus-leukemia activity may overcome therapeutic resistance of chronic lymphocytic leukemia with unmutated immunoglobulin variable heavy-chain gene status: implications of minimal residual disease measurement with quantitative PCR
Authors: Ritgen Matthias , Stilgenbauer Stephan , von Neuhoff Nils , Humpe Andreas , Brüggemann Monika , Pott Christiane , Raff Thorsten , Kröber Alexander , Bunjes Donald , Schlenk Richard , Schmitz Norbert , Döhner Hartmut , Kneba Michael , Dreger Peter
Published: June 2004

The aim of this study was to investigate if graft-versus-leukemia (GVL) activity conferred by allogeneic stem cell transplantation (allo-SCT) is effective in chronic lymphocytic leukemia (CLL) with unmutated VH gene status. The kinetics of residual disease (MRD) were measured by quantitative allele-specific immunoglobulin heavy chain (IgH) polymerase chain reaction (PCR) in 9 patients after nonmyeloablative allo-SCT for unmutated CLL. Despite an only modest decrease in the early posttransplantation phase, MRD became undetectable in 7 of 9 patients (78%) from day +100 onwards subsequent to chronic graft-versus-host disease or donor lymphocyte infusions. With a median follow-up of 25 months (range, 14-37 months), these 7 patients remain in continuous clinical and molecular remission. In contrast, PCR negativity was achieved in only 6 of 26 control patients (23%) after autologous SCT for unmutated CLL and it was not durable. Taken together, this study shows for the first time that GVL-mediated immunotherapy might be effective in CLL with unmutated VH.
Exacerbation of autoantibody-mediated thrombocytopenic purpura by infection with mouse viruses
Authors: Musaji Andrei , Cormont Françoise , Thirion Gaëtan , Cambiaso César L. , Coutelier Jean-Paul
Published: June 2004

Antigenic mimicry has been proposed as a major mechanism by which viruses could trigger the development of immune thrombocytopenic purpura (ITP). However, because antigenic mimicry implies epitope similarities between viral and self antigens, it is difficult to understand how widely different viruses can be involved by this sole mechanism in the pathogenesis of ITP. Here, we report that in mice treated with antiplatelet antibodies at a dose insufficient to induce clinical disease by themselves, infection with lactate dehydrogenase-elevating virus (LDV) was followed by severe thrombocytopenia and by the appearance of petechiae similar to those observed in patients with ITP. A similar exacerbation of antiplatelet-mediated thrombocytopenia was induced by mouse hepatitis virus. This enhancement of antiplatelet antibody pathogenicity by LDV was not observed with F(ab′)2 fragments, suggesting that phagocytosis was involved in platelet destruction. Treatment of mice with clodronate-containing liposomes and with total immunoglobulin G (IgG) indicated that platelets were cleared by macrophages. The increase of thrombocytopenia triggered by LDV after administration of antiplatelet antibodies was largely suppressed in animals deficient for γ-interferon receptor. Together, these results suggest that viruses may exacerbate autoantibody-mediated ITP by activating macrophages through γ-interferon production, a mechanism that may account for the pathogenic similarities of multiple infectious agents. (Blood. 2004;104:2102-2106)
Quantitative trait locus on chromosome 8q influences the switch from fetal to adult hemoglobin
Authors: Garner Chad , Silver Nicholas , Best Steve , Menzel Stephan , Martin Charlotte , Spector Tim D. , Thein Swee Lay
Published: June 2004

The switch from fetal to adult hemoglobin is incomplete; the residual fetal hemoglobin in adults is restricted to a subset of erythrocytes called F cells. F-cell levels are influenced by a sequence variant (C → T) at position -158 upstream of the γ-globin gene, termed the XmnI-Gγ polymorphism. How the Gγ-158 C → T variant influences the expression of the Gγ-globin gene is unknown but is likely to involve the interaction of a multiprotein transcription complex. In a recent genome-wide linkage study of a large Asian Indian kindred, a genetic interaction between the XmnI-Gγ site and a locus on chromosome 8q was reported to influence adult F-cell levels. We report the replication of linkage to chromosome 8q in a sample of European twin pairs. This result provides strong evidence that a quantitative trait locus exists on chromosome 8q that influences the developmental switch from fetal to adult hemoglobin. (Blood. 2004;104:2184-2186)
Erythropoietin and hypoxia stimulate erythropoietin receptor and nitric oxide production by endothelial cells
Authors: Beleslin-Cokic Bojana B. , Cokic Vladan P. , Yu Xiaobing , Weksler Babette B. , Schechter Alan N. , Noguchi Constance Tom
Published: June 2004

Erythropoietin (EPO), a hypoxia-inducible cytokine, is required for survival, proliferation, and differentiation of erythroid progenitor cells. EPO can also stimulate proliferation and angiogenesis of endothelial cells that express EPO receptors (EPORs). In this study we investigated the EPO response of vascular endothelial cells at reduced oxygen tension (5% and 2%), in particular the effect of EPO on nitric oxide (NO) release. Endothelial nitric oxide synthase (eNOS) produces NO, which maintains blood pressure homeostasis and blood flow. We find that EPOR is inducible by EPO in primary human endothelial cells of vein (HUVECs) and artery (HUAECs) and cells from a human bone marrow microvascular endothelial line (TrHBMEC) to a much greater extent at low oxygen tension than in room air. We found a corresponding increase in eNOS expression and NO production in response to EPO during hypoxia. Stimulation of NO production was dose dependent on EPO concentration and was maximal at 5 U/mL. NO activates soluble guanosine cyclase to produce cyclic guanosine monophosphate (cGMP), and we observed that EPO induced cGMP activity. These results suggest that low oxygen tension increases endothelial cell capacity to produce NO in response to EPO by induction of both EPOR and eNOS. This effect of EPO on eNOS may be a physiologically relevant mechanism to counterbalance the hypertensive effects of increased hemoglobin-related NO destruction resulting from hypoxia-induced increased red cell mass. (Blood. 2004;104:2073-2080)
Unusual immunophenotype of CD8+ T cells in familial hemophagocytic lymphohistiocytosis
Authors: Karandikar Nitin J. , Kroft Steven H. , Yegappan Subramanian , Rogers Beverly B. , Aquino Victor M. , Lee Kyung-Mi , Kumar Vinay , Guenaga F. Javier , Jaffe Elaine S. , Douek Daniel C. , McKenna Robert W.
Published: June 2004

Familial hemophagocytic lymphohistiocytosis (FHL) is an inherited, fatal disorder of infancy. We report here a 17-day-old female infant who presented with high fever, hepatosplenomegaly, hypertriglyceridemia, hypofibrinogenemia, thrombocytopenia, and liver failure. Leukocytosis was detected with circulating “atypical” lymphoid cells. Flow cytometric studies revealed expanded subpopulations of CD8+ T cells with unusual immunophenotypic features, including a subset that lacked CD5 expression. A liver biopsy showed hemophagocytic lymphohistiocytosis with exuberant infiltrates of CD8+ T cells that lacked perforin. Mutational studies revealed a 666C→A (H222Q) missense mutation in the perforin gene. T-cell receptor studies on flow-sorted T-cell subpopulations revealed no evidence of monoclonality. Analysis of T-cell receptor excision circle levels indicated long proliferative history in the aberrant CD8+ T-cell subsets. This case provides an instructive example of uncontrolled reactive proliferation of CD8+ T cells in FHL, resulting in atypical morphology and unusual immunophenotypic features that might suggest malignancy in other clinical settings.
Proceedings: The Applications of Bioinformatics in Cancer Detection Workshop
Authors: KAPETANOVIC IZET M. , UMAR ASAD , KHAN JAVED
Published: June 2004

Abstract: The Division of Cancer Prevention of the National Cancer Institute sponsored and organized the Applications of Bioinformatics in Cancer Detection Workshop on August 6‐7, 2002. The goal of the workshop was to evaluate the state of the science of bioinformatics and determine how it may be used to assist early cancer detection, risk identification, risk assessment, and risk reduction. This paper summarizes the proceedings of this conference and points out future directions for research.
Overview of Commonly Used Bioinformatics Methods and Their Applications
Authors: KAPETANOVIC IZET M. , ROSENFELD SIMON , IZMIRLIAN GRANT
Published: June 2004

Abstract:Bioinformatics, in its broad sense, involves application of computer processes to solve biological problems. A wide range of computational tools are needed to effectively and efficiently process large amounts of data being generated as a result of recent technological innovations in biology and medicine. A number of computational tools have been developed or adapted to deal with the experimental riches of complex and multivariate data and transition from data collection to information or knowledge. These include a wide variety of clustering and classification algorithms, includingself‐organized maps(SOM),artificial neural networks(ANN),support vector machines(SVM),fuzzy logic, and even hyphenated techniques asneuro‐fuzzy networks. These bioinformatics tools are being evaluated and applied in various medical areas including early detection, risk assessment, classification, and prognosis of cancer. The goal of these efforts is to develop and identify bioinformatics methods with optimal sensitivity, specificity, and predictive capabilities.
Diagnostic Classification of Cancer Using DNA Microarrays and Artificial Intelligence
Authors: GREER BRADEN T. , KHAN JAVED
Published: June 2004

Abstract: The application of artificial intelligence (AI) to microarray data has been receiving much attention in recent years because of the possibility of automated diagnosis in the near future. Studies have been published predicting tumor type, estrogen receptor status, and prognosis using a variety of AI algorithms. The performance of intelligent computing decisions based on gene expression signatures is in some cases comparable to or better than the current clinical decision schemas. The goal of these tools is not to make clinicians obsolete, but rather to give clinicians one more tool in their armamentarium to accurately diagnose and hence better treat cancer patients. Several such applications are summarized in this chapter, and some of the common pitfalls are noted.
Pathway Databases
Authors: SCHAEFER CARL F.
Published: June 2004

Abstract: Network representations of biological pathways offer a functional view of molecular biology that is different from and complementary to sequence, expression, and structure databases. There is currently available a wide range of digital collections of pathway data, differing in organisms included, functional area covered (e.g., metabolism vs. signaling), detail of modeling, and support for dynamic pathway construction. While it is currently impossible for these databases to communicate with each other, there are several efforts at standardizing a data exchange language for pathway data. Databases that represent pathway data at the level of individual interactions make it possible to combine data from different predefined pathways and to query by network connectivity. Computable representations of pathways provide a basis for various analyses, including detection of broad network patterns, comparison with mRNA or protein abundance, and simulation.
Microarrays and the Gene Expression Profile of a Single Cell
Authors: KAWASAKI ERNEST S.
Published: June 2004

Abstract:With completion of the human genome sequence, it is now possible to study the expression of the entire human gene vcomplement of ∼30,000‐35,000 genes. To accomplish this goal, microarrays have become the leading methodology for the analysis of global gene expression. Improvements in technology have increased the sensitivity of microarrays to the point where it is feasible to study gene expression in a small number of cells andeven at the single cell level. A summary of developments in the area of expression profiling in single cells will be described, and the rationale for these types of studies will be presented. In addition, from a biologist's point of view, some bioinformatic challenges of expression analysis of single cells will be discussed.
Numerical Deconvolution of cDNA Microarray Signal: Simulation Study
Authors: ROSENFELD SIMON , WANG THOMAS , KIM YOUNG , MILNER JOHN
Published: June 2004

Abstract: A computational model for simulation of the cDNA microarray experiments has been created. The simulation allows one to foresee the statistical properties of replicated experiments without actually performing them. We introduce a new concept, the so‐called bio‐weight, which allows for reconciliation between conflicting meanings of biological and statistical significance in microarray experiments. It is shown that, for a small sample size, the bio‐weight is a more powerful criterion of the presence of a signal in microarray data as compared to the standard approach based on t test. Joint simulation of microarray and quantitative PCR data shows that the genes recovered by using the bio‐weight have better chances to be confirmed by PCR than those obtained by the t test technique. We also employ extreme value considerations to derive plausible cutoff levels for hypothesis testing.
Automated Interpretation of Protein Subcellular Location Patterns: Implications for Early Cancer Detection and Assessment
Authors: MURPHY ROBERT F.
Published: June 2004

Abstract:Fluorescence microscopy is a powerful tool for analyzing the subcellular distributions of proteins, but that power has not been fully utilized because most analysis of those distributions has been done by visual examination. This limitation can be overcome using automated pattern recognition methods widely used in other fields. This article summarizes work demonstrating that automated systems can recognize the patterns of major organelles in both two‐ and three‐dimensional images of cultured cells, and that these systems can distinguish similar patterns better than visual examination. The basis for these systems are sets of Subcellular Location Features that capture the essence of subcellular patterns without being sensitive to the extensive variation that occurs in the size, shape, and orientation of cells in microscope images. These features can also be used to make sensitive, statistical comparisons of the distribution of a protein between two conditions, such as in the presence and absence of a drug. The possible use of automated pattern analysis methods for improving detection of abnormal cells in cancerous or precancerous tissues is also discussed.
Data‐Driven Computer Simulation of Human Cancer Cell
Authors: CHRISTOPHER R , DHIMAN A , FOX J , GENDELMAN R , HABERITCHER T , KAGLE D , SPIZZ G , KHALIL I G. , HILL C
Published: June 2004

Abstract: Using the Diagrammatic Cell Language™, Gene Network Sciences (GNS) has created a network model of interconnected signal transduction pathways and gene expression networks that control human cell proliferation and apoptosis. It includes receptor activation and mitogenic signaling, initiation of cell cycle, and passage of checkpoints and apoptosis. Time‐course experiments measuring mRNA abundance and protein activity are conducted on Caco‐2 and HCT 116 colon cell lines. These data were used to constrain unknown regulatory interactions and kinetic parameters via sensitivity analysis and parameter optimization methods contained in the DigitalCell™ computer simulation platform. FACS, RNA knockdown, cell growth, and apoptosis data are also used to constrain the model and to identify unknown pathways, and cross talk between known pathways will also be discussed. Using the cell simulation, GNS tested the efficacy of various drug targets and performed validation experiments to test computer simulation predictions. The simulation is a powerful tool that can in principle incorporate patient‐specific data on the DNA, RNA, and protein levels for assessing efficacy of therapeutics in specific patient populations and can greatly impact success of a given therapeutic strategy.
Application of the Random Forest Classification Algorithm to a SELDI‐TOF Proteomics Study in the Setting of a Cancer Prevention Trial
Authors: IZMIRLIAN GRANT
Published: June 2004

Abstract:A thorough discussion of the random forest (RF) algorithm as it relates to a SELDI‐TOF proteomics study is presented, with special emphasis on its application for cancer prevention: specifically, what makes it an efficient, yet reliable classifier, and what makes it optimal among the many available approaches. The main body of the paper treats the particulars of how to successfully apply the RF algorithm in a proteomics profiling study to construct a classifier and discover peak intensities most likely responsible for the separation between the classes.
Improved Small Volume Lung Cancer Detection with Computer‐Aided Detection: Database Characteristics and Imaging of Response to Breast Cancer Risk Reduction Strategies
Authors: FREEDMAN MATTHEW
Published: June 2004

Abstract: Computer‐aided detection (CAD) and diagnosis (CADx) of in vivo imaging studies are important tools based on bioinformatics. Currently, there are two diseases for which the United States Food and Drug Administration (FDA) has given premarket approval (PMA): the detection of signs consistent with lung cancer on chest radiographs and breast cancer on mammograms. There are systems for other diseases and other types of images under development; however, this process depends on the availability of an accurate database. The author helped in the development of the databases for such systems and management of the clinical trial that resulted in the FDA‐PMA of the system that detects findings consistent with lung cancer. The characteristics of the database used will be described. Further, a woman's risk of developing breast cancer differs from those of other women. Risk can be high, average, or low. There are now pharmaceuticals that decrease the risk that women, as a group, will develop breast cancer and it has been suggested that dietary changes could have similar effects. The pharmaceutical agents, though, have some associated side effects, and it is clinically important to determine whether these agents have decreased an individual woman's risk of breast cancer. In vivo imaging biomarkers of risk and successful risk reduction are therefore sought, but the information on possible in vivo imaging biomarkers is less mature than activities in CAD. Bioinformatics will be an important contributor to this in vivo imaging biomarker development.
InfoEvolve™
Authors: VAIDYANATHAN GANESH
Published: June 2004

Abstract:InfoEvolve™ is a unified suite of data mining and empirical modeling tools capable of discovering low‐bias and low‐variance solutions to complex processes. The method is based on a common set of principles involving information theory and genetic algorithms. InfoEvolve™ can also discover multiple strategies embedded in complex data sets for achieving a desired target or goal. This latter aspect may prove to be very useful in drug design. The paper analyzes the following: InfoEvolve™ from a theoretical standpoint; a conceptual overview of InfoEvolve™ with a short description of the modeling method; the method using the example of homogeneous identification of DNA from an analysis of its melting curve behavior; and key learnings and additional applications of the technology for both drug design and genome analysis.
The Steroidogenic Acute Regulatory Protein Is Expressed in Steroidogenic Cells of the Day-Old Brain
Authors: King Steven R. , Ginsberg Stephen D. , Ishii Tomohiro , Smith Roy G. , Parker Keith L. , Lamb Dolores J.
Published: June 2004

Although recent research has focused on the fundamental role(s) of steroids synthesized de novo in the brain on development, the mechanism by which production of these neurosteroids is regulated remains unclear. Steroid production in peripheral tissues is acutely regulated by the steroidogenic acute regulatory (StAR) protein, which mediates the rate-limiting step in steroid biosynthesis: the intramitochondrial delivery of cholesterol to cytochrome P450scc for conversion to steroid. We recently demonstrated that StAR is present in discrete cell types in the adult brain, suggesting that neurosteroid production is mediated by StAR. Nevertheless, little is known regarding the presence of StAR in the developing brain. In the present study, the presence of StAR and for the first time, its homolog, the putative cholesterol transport protein metastatic lymph node 64 (MLN64), were defined in the neonatal mouse brain using immunocytochemical techniques. Both StAR and MLN64 were found to be present in the brain with staining patterns characteristic to each protein, indicating the authenticity of StAR and MLN64 immunoreactivity. Furthermore, we found MLN64 to be expressed in the adult brain as well, apparently at higher levels than StAR. Importantly, StAR protein is present in cells that also express P450scc. These data suggest that, as with the adult, neurosteroid production during development occurs through a StAR-mediated pathway.
Site of Action of Acute Alcohol Administration in Stimulating the Rat Hypothalamic-Pituitary-Adrenal Axis: Comparison between the Effect of Systemic and Intracerebroventricular Injection of this Drug on Pituitary and Hypothalamic Responses
Authors: Lee Soon , Selvage Daniel , Hansen Keith , Rivier Catherine
Published: June 2004

The peripheral injection of alcohol stimulates the activity of the hypothalamic-pituitary-adrenal (HPA) axis, but the ready penetration of this drug in most bodily compartments has made it difficult to identify its specific sites of action. Here we determined whether alcohol can directly influence the corticotropes. We first determined whether alcohol acted within the brain to stimulate neurons in the paraventricular nucleus (PVN) of the hypothalamus, which synthesizes corticotropin-releasing factor (CRF) and vasopressin (VP). To test this hypothesis, we injected alcohol intracerebroventricularly (icv; 5 μl of 200-proof; 86 μmol) and compared these results with those obtained after its ip administration (3.0 g/kg). Although not causing neuronal damage and not leading to detectable levels of the drug in the general circulation, icv alcohol significantly up-regulated PVN CRF heteronuclear RNA levels and increased plasma ACTH levels, a change comparable to the one observed in the ip model. To determine whether alcohol stimulated the corticotropes independently of CRF and/or VP, we injected the drug ip or icv and measured changes in anterior pituitary proopiomelanocortin (POMC) transcripts and ACTH release in the presence or absence of endogenous CRF and/or VP. Intracerebroventricular and ip alcohol significantly increased POMC primary transcript levels, measured by ribonuclease protection assay, over a time-course that corresponded to ACTH release. Both the POMC and the ACTH responses were completely abolished by removal of CRF and VP. Collectively, these results indicate that alcohol-induced activation of the corticotropes does not represent a direct influence of the drug on the pituitary but requires CRF and VP.
Effects of Medroxyprogesterone and Estradiol on the Recovery of Spermatogenesis in Irradiated Rats
Authors: Shetty Gunapala , Weng Connie C. Y. , Bolden-Tiller Olga U. , Huhtaniemi Ilpo , Handelsman David J. , Meistrich Marvin L.
Published: June 2004

Suppression of intratesticular testosterone (ITT) levels is required for spermatogenic recovery in rats after irradiation, but maintenance of peripheral testosterone (T) levels is important for many male functions. Considering the preservation of peripheral T while suppressing ITT, we tested the effects of a combination of a progestin, medroxyprogesterone acetate (MPA), plus T on spermatogenic recovery after irradiation, and compared its effects to those of T alone or T combined with estradiol (E2). Rats were given testicular irradiation (6 Gy) and treated during wk 3–7 after irradiation with MPA + T, or the individual steroids with or without GnRH antagonist (GnRH-ant), or GnRH-ant alone, or T + E2. Whereas GnRH-ant alone stimulated differentiation in 55% of tubules 13 wk after irradiation compared with 0% in irradiated-only rats, the addition of MPA reduced the percentage of tubules showing differentiation to 18%. However, T or MPA alone or the combination of the two induced germ cell differentiation in only 2–4% of tubules. In contrast, E2 stimulated differentiation in 88% of tubules, and T combined with E2 still resulted in differentiation in 30% of tubules. Although both MPA and E2 suppressed ITT levels to approximately 2% of control (2 ng/g testis), MPA was a less effective stimulator of spermatogenic recovery than E2 or GnRH-ant alone. MPA’s function as a weak androgen was likely responsible for inhibiting spermatogenic recovery, as was the case for all other tested androgens. Thus, for clinical protection or restoration of spermatogenesis after radiation or chemotherapy by suppressing T production, MPA, at least in the doses used in the present study, is suboptimal. The combination of an estrogen with T appears to be most effective for stimulating such recovery.
Estrogen Directly Induces Expression of Retinoic Acid Biosynthetic Enzymes, Compartmentalized between the Epithelium and Underlying Stromal Cells in Rat Uterus
Authors: Li Xiao-Hong , Kakkad Bharati , Ong David E.
Published: June 2004

Estrogen (E2) has been shown to induce the biosynthesis of retinoic acid (RA) in rat uterus. Here we examined whether E2 could directly induce the enzymes involved in this process by using the ovariectomized rat. A retinol dehydrogenase that we have previously described, eRolDH, and the retinal dehydrogenase, RalDH II, were found to have markedly increased uterine mRNA levels within 4 h of E2 administration, independent of the prior administration of puromycin. eRolDH and RalDH II and their mRNAs were also increased in uteri of rats during estrus. This indicated that RA biosynthesis in rat uterus is directly controlled by E2 and provides a direct link between the action of a steroid hormone and retinoid action. We also examined the cell-specific localization of RalDH II by immunohistochemistry. The enzyme was observed in the stromal compartment, particularly in cells close to the uterine lumenal epithelium. eRolDH was observed only in the lining epithelial cells. Taken together with the previous observations of cellular retinol-binding protein and cellular retinoic acid-binding protein, type two also being expressed in the lumenal epithelium, we propose that RA production is compartmentalized, with retinol oxidation occurring in the lumenal epithelium and subsequent oxidation of retinal to RA occurring in the underlying stromal cells.
Prospero-Related Homeobox (Prox1) Is a Corepressor of Human Liver Receptor Homolog-1 and Suppresses the Transcription of the Cholesterol 7-α-Hydroxylase Gene
Authors: Qin Jun , Gao Da-ming , Jiang Quan-Feng , Zhou Qing , Kong Yu-Ying , Wang Yuan , Xie You-Hua
Published: June 2004

Cholesterol 7-α-hydroxylase (CYP7A1) catalyzes a rate-limiting step in bile acid synthesis in liver, and its gene transcription is under complex regulation by multiple nuclear receptors in response to bile acids, cholesterol derivatives, and hormones. The liver receptor homolog-1 (LRH-1), a member of the fushi tarazu factor 1 subfamily of nuclear receptors, has emerged as an essential regulator for the expression of cyp7a1. In this report, we demonstrate Prox1, a prospero-related homeobox transcription factor, identified through a yeast two-hybrid screening, can directly interact with human LRH-1 (hLRH-1) and suppresses hLRH-1-mediated transcriptional activation of human cyp7a1 gene. Biochemical analysis demonstrates that Prox1 interacts with both the ligand binding domain (LBD) and the DNA binding domain (DBD) of hLRH-1. An LRKLL motif in Prox1 is important for the interaction with the LBD but not the DBD of hLRH-1. In hLRH-1 LBD, helices 2 and 10 are essential for Prox1 recruitment. The suppression by Prox1 on the transcriptional activity of hLRH-1 can be mediated through its interaction with the LBD or the DBD of hLRH-1. Gel shift assays reveal that Prox1 impairs the binding of hLRH-1 to the promoter of human cyp7a1 gene.
Long-term evolution of the S788 fungal nuclear small subunit rRNA group I introns
Authors: HAUGEN PEIK , RUNGE HENRY JOSEPH , BHATTACHARYA DEBASHISH
Published: June 2004

More than 1000 group I introns have been identified in fungal rDNA. Little is known, however, of the splicing and secondary structure evolution of these ribozymes. Here, we use a combination of comparative and biochemical methods to address the evolution and splicing of a vertically inherited group I intron found at position 788 in the fungal small subunit (S) rRNA. The ancestral state of the S788 intron contains a highly conserved core and an extended P5 domain typical of IC1 introns. In contrast, the more derived introns have lost most of P5, and have an accelerated divergence rate within the core region with three functionally important substitutions that unambiguously separate them from the ancestral pool. Of 14 S788 group I introns that were tested for splicing, five, all of the ancestral type, were able to self-splice and produced intron RNA circles in vitro. The more derived S788 introns did not self-splice, and potentially rely on fungal-specific factors to facilitate splicing. In summary, we demonstrate one possible fate of vertically inherited group I introns, the loss of secondary structure elements, lessened selective constraints in the intron core, and ultimately, dependence on host-mediated splicing.
Identification and analysis of the minimal promoter activity of a novel noncoding nuclear RNA gene, AncR-1, from the honeybee (Apis mellifera L.)
Authors: SAWATA MIYUKI , TAKEUCHI HIDEAKI , KUBO TAKEO
Published: June 2004

Previously, we identified a gene for a noncoding nuclear RNA, termed Ks-1, that is expressed preferentially in a restricted set of neurons in the honeybee brain. In the present study, we identified another novel gene, termed AncR-1, whose transcripts were localized to nuclei in the whole cortex region of the honeybee brain, as a candidate novel noncoding nuclear RNA gene. RNA fluorescent in situ hybridization revealed that AncR-1 and Ks-1 transcripts were located in a distinct portion of a single neural nucleus, suggesting that they have distinct functions in brain neurons. cDNA cloning revealed that the AncR-1 transcripts were up to 7 kb in size, had mRNA-like structures, and were alternatively spliced. The reporter assay using Drosophila SL-2 cells demonstrated that a TATA box-like sequence located −30 bp upstream of the 5′ end of AncR-1 cDNA had promoter activity. None of the alternatively spliced AncR-1 cDNA variants contained significant open reading frames, strongly suggesting that AncR-1 transcripts function as novel noncoding nuclear RNAs. Furthermore, in situ hybridization revealed that AncR-1 was expressed not only in the brain but also in the sex organs in the queen and drones and in the hypopharyngeal glands and oenocytes of the worker bees, suggesting that AncR-1 is involved in diverse organ functions. Some of the AncR-1 transcripts enriched in the nuclei of the hypopharyngeal glands were polyadenylated, indicating the presence of mRNA-like AncR-1 transcripts in the nuclei.
A novel function for Sam68: Enhancement of HIV-1 RNA 3′ end processing
Authors: MCLAREN MEREDITH , ASAI KENGO , COCHRANE ALAN
Published: June 2004

Both cis elements and host cell proteins can significantly affect HIV-1 RNA processing and viral gene expression. Previously, we determined that the exon splicing silencer (ESS3) within the terminal exon of HIV-1 not only reduces use of the adjacent 3′ splice site but also prevents Rev-induced export of the unspliced viral RNA to the cytoplasm. In this report, we demonstrate that loss of unspliced viral RNA export is correlated with the inhibition of 3′ end processing by the ESS3. Furthermore, we find that the host factor Sam68, a stimulator of HIV-1 protein expression, is able to reverse the block to viral RNA export mediated by the ESS3. The reversal is associated with a stimulation of 3′ end processing of the unspliced viral RNA. Our findings identify a novel activity for the ESS3 and Sam68 in regulating HIV-1 RNA polyadenylation. Furthermore, the observations provide an explanation for how Sam68, an exclusively nuclear protein, modulates cytoplasmic utilization of the affected RNAs. Our finding that Sam68 is also able to enhance 3′ end processing of a heterologous RNA raises the possibility that it may play a similar role in regulating host gene expression.
A horizontally acquired group II intron in the chloroplastpsbAgene of a psychrophilicChlamydomonas: In vitro self-splicing and genetic evidence for maturase activity
Authors: ODOM OBED W. , SHENKENBERG DAVID L. , GARCIA JOSHUA A. , HERRIN DAVID L.
Published: June 2004

The majority of known group II introns are from chloroplast genomes, yet the first self-splicing group II intron from a chloroplast gene was reported only recently, from thepsbAgene of the euglenoid,Euglena myxocylindracea. Herein, we describe a large (2.6-kb) group II intron from thepsbAgene (psbA1) of a psychrophilicChlamydomonas sp.from Antarctica that self-splices accurately in vitro. Remarkably, this intron, which also encodes an ORF with putative reverse transcriptase, maturase, and endonuclease domains, is in the same location, and is related to theE. myxocylindraceaintron, as well as to group IIB2 introns from cyanobacteria. In vitro self-splicing ofChs.psbA1occurred via a lariat, and required Mg2+(>12 mM) and NH4+. Self-splicing was improved by deleting most of the ORF and by using pre-RNAs directly from transcription reactions, suggestive of a role for folding during transcription. Self-splicing ofChs.psbA1pre-RNAs showed temperature optima of ~44°C, but with a broad shoulder on the low side of the peak; splicing was nearly absent at 50°C, indicative of thermolability. Splicing of wild-typeChs.psbA1also occurred inEscherichia coli, but not when the ORF was disrupted by mutations, providing genetic evidence that it has maturase activity. This work provides the first description of a ribozyme from a psychrophilic organism. It also appears to provide a second instance of interkingdom horizontal transfer of this group IIB2 intron (or a close relative) from cyanobacteria to chloroplasts.
Interference probing of rRNA with snoRNPs: A novel approach for functional mapping of RNA in vivo
Authors: LIU BEN , FOURNIER MAURILLE J.
Published: June 2004

Synthesis of eukaryotic ribosomal RNAs (rRNAs) includes methylation of scores of nucleotides at the 2′-O-ribose position (Nm) by small nucleolar RNP complexes (snoRNPs). Sequence specificity is provided by the snoRNA component through base-pairing of a guide sequence with rRNA. Here, we report that methylation snoRNPs can be targeted to many new sites in yeast rRNA, by providing the snoRNA with a novel guide sequence, and that in some cases growth and translation activity are strongly impaired. Novel snoRNAs can be expressed individually or by a unique library strategy that yields guide sequences specific for a large target region. Interference effects were observed for sites in both the small and large subunits, including the reaction center region. Targeting guide RNAs to nucleotides flanking the sensitive sites caused little or no defect, indicating that methylation is responsible for the interference rather than a simple antisense effect or misguided chaperone function. To our knowledge, this is the only approach that has been used to mutagenize the backbone of rRNA in vivo.
Cross-linking experiments reveal the presence of novel structural features between a hepatitis delta virus ribozyme and its substrate
Authors: OUELLET JONATHAN , PERREAULT JEAN-PIERRE
Published: June 2004

The kinetic pathway of a trans-acting delta ribozyme includes an essential structural rearrangement involving the P1 stem, a stem that is formed between the substrate and the ribozyme. We performed cross-linking experiments to determine the substrate position within the catalytic center of an antigenomic, trans-acting, delta ribozyme. Substrates that included a 4-thiouridine either in position −1, +4, or +8 (i.e., adjacent to the cleavage site, or located either in the middle of or at the 3′-end of the P1 stem, respectively) were synthesized and shown to be efficiently cleaved. Examination of the cross-linking conditions, the use of various mutated ribozymes, as well as the probing and characterization of the resulting ribozyme–substrate complexes, revealed several new features of the molecular mechanism: (1) the close proximity of several bases between nucleotides of the substrate and ribozyme; (2) the active ribozyme–substrate complex folds in a manner that docks the middle of the P1 stem on the P3 stem, while concomitantly the scissile phosphate is in close proximity to the catalytic cytosine; and, (3) some complexes appear to be compatible with being active intermediates along the folding pathway, while others seem to correspond to misfolded structures. To provide a model representation of these data, a three-dimensional structure of the delta ribozyme was developped using several RNA bioinformatic software packages.
Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold
Authors: HOANG CHARMAINE , FERRÉ-D’AMARÉ ADRIAN R.
Published: June 2004

The pseudouridine (Ψ) synthases Pus7p and TruD define a family of RNA-modifying enzymes with no sequence similarity to previously characterized Ψ synthases. The 2.2 Å resolution structure of Escherichia coli TruD reveals a U-shaped molecule with a catalytic domain that superimposes closely on that of other Ψ synthases. A domain that appears to be unique to TruD/Pus7p family enzymes hinges over the catalytic domain, possibly serving to clasp the substrate RNAs. The active site comprises residues that are conserved in other Ψ synthases, although at least one comes from a structurally distinct part of the protein. Remarkably, the connectivity of the structural elements of the TruD catalytic domain is a circular permutation of that of its paralogs. Because the sequence of the permuted segment, a β-strand that bisects the catalytic domain, is conserved among orthologs from bacteria, archaea and eukarya, the permutation likely happened early in evolution.
The Euplotes telomerase subunit p43 stimulates enzymatic activity and processivity in vitro
Authors: AIGNER STEFAN , CECH THOMAS R.
Published: June 2004

Telomerase is a reverse transcriptase that synthesizes telomeric DNA repeats at the ends of eukaryotic chromosomes. Although it is minimally composed of a conserved catalytic protein subunit (TERT) and an RNA component, additional accessory factors present in the holoenzyme play crucial roles in the biogenesis and function of the enzyme complex. Telomerase from the ciliate Tetrahymena can be reconstituted in active form in vitro. Using this system, we show that p43, a telomerase-specific La-motif protein from the ciliate Euplotes, stimulates activity and increases repeat addition processivity of telomerase. Activity enhancement by p43 requires its incorporation into a TERT•RNA•p43 ternary complex but is independent of other dissociable protein factors functioning in telomerase complex assembly. Stimulation is enhanced at elevated temperatures, supporting a role for p43 in structural stabilization of a critical region of the RNA subunit. To our knowledge, this represents the first demonstration that an authentic telomerase accessory protein can directly affect the enzymatic activity of the core enzyme in vitro.
Expression of Unique and Developmental Myosin Heavy Chain Isoforms in Adult Human Digastric Muscle
Authors: Wang Jun , Han Yingshi , Su Hungxi , Mu Liancai
Published: June 2004

Digastric muscle (DGM) is a powerful jaw-opening muscle that participates in chewing, swallowing, breathing, and speech. For better understanding of its contractile properties, five pairs of adult human DGMs were obtained from autopsies and processed with immunocytochemistry and/or immunoblotting. Monoclonal antibodies against α-cardiac, slow tonic, neonatal, and embryonic myosin heavy chain (MHC) isoforms were employed to determine whether the DGM fibers contain these MHC isoforms, which have previously been demonstrated in restricted specialized craniocervical skeletal muscles but have not been reported in normal adult human trunk and limb muscles. The results showed expression of all these MHC isoforms in adult human DGMs. About half of the fibers reacted positively to the antibody specific for the α-cardiac MHC isoform in DGMs, and the number of these fibers decreased with age. Slow tonic MHC isoform containing fibers accounted for 19% of the total fiber population. Both the α-cardiac and slow tonic MHC isoforms were found to coexist mainly with the slow twitch MHC isoform in a fiber. A few DGM fibers expressed the embryonic or neonatal MHC isoform. The findings suggest that human DGM fibers may be specialized to facilitate performance of complex motor behaviors in the upper airway and digestive tract. (J Histochem Cytochem 52:851–859, 2004)