Science.gov

Sample records for alternative gene programs

  1. A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis

    PubMed Central

    Pimentel, Harold; Parra, Marilyn; Gee, Sherry; Ghanem, Dana; An, Xiuli; Li, Jie; Mohandas, Narla; Pachter, Lior; Conboy, John G.

    2014-01-01

    Alternative pre-messenger RNA splicing remodels the human transcriptome in a spatiotemporal manner during normal development and differentiation. Here we explored the landscape of transcript diversity in the erythroid lineage by RNA-seq analysis of five highly purified populations of morphologically distinct human erythroblasts, representing the last four cell divisions before enucleation. In this unique differentiation system, we found evidence of an extensive and dynamic alternative splicing program encompassing genes with many diverse functions. Alternative splicing was particularly enriched in genes controlling cell cycle, organelle organization, chromatin function and RNA processing. Many alternative exons exhibited differentiation-associated switches in splicing efficiency, mostly in late-stage polychromatophilic and orthochromatophilic erythroblasts, in concert with extensive cellular remodeling that precedes enucleation. A subset of alternative splicing switches introduces premature translation termination codons into selected transcripts in a differentiation stage-specific manner, supporting the hypothesis that alternative splicing-coupled nonsense-mediated decay contributes to regulation of erythroid-expressed genes as a novel part of the overall differentiation program. We conclude that a highly dynamic alternative splicing program in terminally differentiating erythroblasts plays a major role in regulating gene expression to ensure synthesis of appropriate proteome at each stage as the cells remodel in preparation for production of mature red cells. PMID:24442673

  2. Alternative Work Programs

    ERIC Educational Resources Information Center

    Kuehn, Kerri L.

    2004-01-01

    Employers are feeling the strain of needing to offer alternative work arrangements to retain and recruit employees. Due to a change in demographics, dual-career couples and increased technology; people are demanding a transformation in the workplace environment. Two alternatives, which are being offered by employers, are flextime and…

  3. Integrating alternative splicing detection into gene prediction

    PubMed Central

    Foissac, Sylvain; Schiex, Thomas

    2005-01-01

    Background Alternative splicing (AS) is now considered as a major actor in transcriptome/proteome diversity and it cannot be neglected in the annotation process of a new genome. Despite considerable progresses in term of accuracy in computational gene prediction, the ability to reliably predict AS variants when there is local experimental evidence of it remains an open challenge for gene finders. Results We have used a new integrative approach that allows to incorporate AS detection into ab initio gene prediction. This method relies on the analysis of genomically aligned transcript sequences (ESTs and/or cDNAs), and has been implemented in the dynamic programming algorithm of the graph-based gene finder EuGÈNE. Given a genomic sequence and a set of aligned transcripts, this new version identifies the set of transcripts carrying evidence of alternative splicing events, and provides, in addition to the classical optimal gene prediction, alternative optimal predictions (among those which are consistent with the AS events detected). This allows for multiple annotations of a single gene in a way such that each predicted variant is supported by a transcript evidence (but not necessarily with a full-length coverage). Conclusions This automatic combination of experimental data analysis and ab initio gene finding offers an ideal integration of alternatively spliced gene prediction inside a single annotation pipeline. PMID:15705189

  4. GATEWAYS: Degree program alternatives

    SciTech Connect

    Strong, K.R.; Thayer, M.M.

    1991-11-01

    Los Alamos National Laboratory is using non-traditional solutions to assist employees in attaining degrees required for essential Laboratory operations. Varieties of distance learning technologies have been implemented to meet some degree needs. While distance learning is not always a perfect solution, it enables the Laboratory to provide education that would otherwise not be practical for full-time employees. The Laboratory has also formed partnerships with local colleges to design programs to fill particular needs. Meeting the challenge of providing cost-effective, viable degree programs in an isolated location requires both patience and innovation.

  5. Academic Programs in Alternative Education: An Overview

    ERIC Educational Resources Information Center

    Ruzzi, Betsy Brown; Kraemer, Jacqueline

    2006-01-01

    This paper, second in a series of papers on alternative education, examines the academic programming in alternative education programs by reviewing the literature specifically focused on the academic programs in alternative education and summarizing a survey of fifteen alternative education programs. It suggests options for further research on…

  6. An alternative splicing program promotes adipose tissue thermogenesis.

    PubMed

    Vernia, Santiago; Edwards, Yvonne Jk; Han, Myoung Sook; Cavanagh-Kyros, Julie; Barrett, Tamera; Kim, Jason K; Davis, Roger J

    2016-01-01

    Alternative pre-mRNA splicing expands the complexity of the transcriptome and controls isoform-specific gene expression. Whether alternative splicing contributes to metabolic regulation is largely unknown. Here we investigated the contribution of alternative splicing to the development of diet-induced obesity. We found that obesity-induced changes in adipocyte gene expression include alternative pre-mRNA splicing. Bioinformatics analysis associated part of this alternative splicing program with sequence specific NOVA splicing factors. This conclusion was confirmed by studies of mice with NOVA deficiency in adipocytes. Phenotypic analysis of the NOVA-deficient mice demonstrated increased adipose tissue thermogenesis and improved glycemia. We show that NOVA proteins mediate a splicing program that suppresses adipose tissue thermogenesis. Together, these data provide quantitative analysis of gene expression at exon-level resolution in obesity and identify a novel mechanism that contributes to the regulation of adipose tissue function and the maintenance of normal glycemia. PMID:27635635

  7. Alternative Teacher Certification: A Program Theory Analysis

    ERIC Educational Resources Information Center

    Scribner, Jay Paredes; Heinen, Ethan

    2009-01-01

    "Alternative teacher certification program" (ATCP) is widely used as a term for a variety of programs designed to train and credential teachers in expedited fashion. In practice, however, ATCPs consist of a loose confederation of programs and practices ranging from "emergency certification to very sophisticated and well-designed programs that…

  8. ALTERNATIVE OXIDASE: From Gene to Function.

    PubMed

    Vanlerberghe, Greg C.; McIntosh, Lee

    1997-06-01

    Plants, some fungi, and protists contain a cyanide-resistant, alternative mitochondrial respiratory pathway. This pathway branches at the ubiquinone pool and consists of an alternative oxidase encoded by the nuclear gene Aox1. Alternative pathway respiration is only linked to proton translocation at Complex 1 (NADH dehydrogenase). Alternative oxidase expression is influenced by stress stimuli-cold, oxidative stress, pathogen attack-and by factors constricting electron flow through the cytochrome pathway of respiration. Control is exerted at the levels of gene expression and in response to the availability of carbon and reducing potential. Posttranslational control involves reversible covalent modification of the alternative oxidase and activation by specific carbon metabolites. This dynamic system of coarse and fine control may function to balance upstream respiratory carbon metabolism and downstream electron transport when these coupled processes become imbalanced as a result of changes in the supply of, or demand for, carbon, reducing power, and ATP.

  9. ["Matreshka" Genes with Alternative Reading Frames].

    PubMed

    Sheshukova, E V; Shindyapina, A V; Komarova, T V; Dorokhov, Yu L

    2016-02-01

    Although a relatively small part of the human genome contains protein encoding genes, the latest data on the discovery of alternative open reading frames (ORFs) in conventional mRNAs has highlighted the expanded coding potential of these genes. Until recently, it was believed that each mRNA transcript encodes a single protein. Recent proteogenomics data indicate the existence of exceptions to this rule, which greatly changes the usual meaning of the term "gene". The topology of a gene with overlapping ORFs resembles a Russian "matreshka" toy. There are two levels of "matreshka" genetic systems. First, the chromosomal level, when the "nested" gene is located within introns and exons of the main chromosomal gene, both in the sense and antisense orientation relative to the external gene. The second level is a mature mRNA molecule containing overlapping ORFs or an ORF with an alternative-start codon. In this review we will focus on the properties of "matreshka" genes of the second type and methods for their detection and verification. Particular attention is paid to the biological properties of the polypeptides encoded by these genes. PMID:27215029

  10. Alternate nozzle ablative materials program

    NASA Technical Reports Server (NTRS)

    Kimmel, N. A.

    1984-01-01

    Four subscale solid rocket motor tests were conducted successfully to evaluate alternate nozzle liner, insulation, and exit cone structural overwrap components for possible application to the Space Shuttle Solid Rocket Motor (SRM) nozzle asasembly. The 10,000 lb propellant motor tests were simulated, as close as practical, the configuration and operational environment of the full scale SRM. Fifteen PAN based and three pitch based materials had no filler in the phenolic resin, four PAN based materials had carbon microballoons in the resin, and the rest of the materials had carbon powder in the resin. Three nozzle insulation materials were evaluated; an aluminum oxide silicon oxide ceramic fiber mat phenolic material with no resin filler and two E-glass fiber mat phenolic materials with no resin filler. It was concluded by MTI/WD (the fabricator and evaluator of the test nozzles) and NASA-MSFC that it was possible to design an alternate material full scale SRM nozzle assembly, which could provide an estimated 360 lb increased payload capability for Space Shuttle launches over that obtainable with the current qualified SRM design.

  11. Alternative Programs and Desegregation in Flint, Michigan

    ERIC Educational Resources Information Center

    Kugler, Marianne Russell

    1978-01-01

    Discusses the results of the Flint, Michigan Board of Education's decision to include extensive development of alternative programs as part of the Quality Education/Desegregation Plan developed for the Flint schools. (Author/RK)

  12. Bridge Program: An Alternative Curricular Model

    ERIC Educational Resources Information Center

    George, Deborah A.

    2012-01-01

    With the motivation for career advancement, many adult learners have chosen to return to graduate education or professional programs. The bridge program is one relatively new alternative curricular model available for adult learners who wish to build on their education within their chosen profession. Evidence on the effectiveness of such programs…

  13. An alternative splicing program promotes adipose tissue thermogenesis

    PubMed Central

    Vernia, Santiago; Edwards, Yvonne JK; Han, Myoung Sook; Cavanagh-Kyros, Julie; Barrett, Tamera; Kim, Jason K; Davis, Roger J

    2016-01-01

    Alternative pre-mRNA splicing expands the complexity of the transcriptome and controls isoform-specific gene expression. Whether alternative splicing contributes to metabolic regulation is largely unknown. Here we investigated the contribution of alternative splicing to the development of diet-induced obesity. We found that obesity-induced changes in adipocyte gene expression include alternative pre-mRNA splicing. Bioinformatics analysis associated part of this alternative splicing program with sequence specific NOVA splicing factors. This conclusion was confirmed by studies of mice with NOVA deficiency in adipocytes. Phenotypic analysis of the NOVA-deficient mice demonstrated increased adipose tissue thermogenesis and improved glycemia. We show that NOVA proteins mediate a splicing program that suppresses adipose tissue thermogenesis. Together, these data provide quantitative analysis of gene expression at exon-level resolution in obesity and identify a novel mechanism that contributes to the regulation of adipose tissue function and the maintenance of normal glycemia. DOI: http://dx.doi.org/10.7554/eLife.17672.001 PMID:27635635

  14. Implementing English Programs in Alternative Schools.

    ERIC Educational Resources Information Center

    Verner, Zenobia Brown; Conley, Houston

    The purpose of this study was to survey alternative schools to determine what their English programs are like, what kinds of problems and successes have been encountered by their English teachers, and what suggestions they have for others who encounter similar problems. Questionnaires were sent to administrators and English teachers in a number of…

  15. Indiana University Alternative School Teacher Education Program.

    ERIC Educational Resources Information Center

    Indiana Univ., Bloomington. School of Education.

    As public school districts have begun to develop optional alternative schools, a common concern has been where to find trained teachers to staff the schools. For the past four years Indiana University has worked closely with several of these school districts in developing a field-based teacher education program to prepare new teachers for these…

  16. School Counseling in Disciplinary Alternative Education Programs

    ERIC Educational Resources Information Center

    Mullen, Patrick R.; Lambie, Glenn W.

    2013-01-01

    Disciplinary alternative education programs (DAEP) service many students; however, limited literature is published for school counselors working in these schools. Therefore, this manuscript provides a conceptual foundation for counselors working with students attending DAEPs. Specifically, the manuscript (a) reviews the types of alternative…

  17. Alternative promoters of gene MAGE4a

    SciTech Connect

    De Plaen, E.; Naerhuyzen, B.; De Smet, C.

    1997-03-01

    Gene MAGE-4 (HGMW-approved symbol MAGE4) is expressed in several types of tumors, but not in normal tissues, except testis and placenta. The 5{prime} end of this gene contains eight homologous exons spread over a 5.8-kb region. These exons are alternatively spliced to a unique second exon and a unique third exon, which encodes a protein of 317 amino acids. The analysis of transcripts found in testis, placenta, and a sarcoma cell line showed that each of the alternative first exons is used in at least one of these tissues. Various regions of the promoter of the fifth alternative exon (1.5) were cloned in a luciferase reporter plasmid, and the constructs were transfected in a sarcoma cell line that expresses MAGE-4. Two Ets motifs located between positions -70 and -29 relative to the transcription start site were found to drive 55% of the promoter activity. A region containing an Sp1 consensus binding site located upstream of the two Ets motifs was found to be responsible for 44% of the transcriptional activity. MAGE-4a promoters 1.4 and 1.6, which also contain the Sp1 and the two Ets binding motifs, supported a level of transcription comparable to that of promoter 1.5, whereas promoter 1.1, which contains only one Ets binding site, was sixfold less active. In line with observations made with gene MAGE-1 (HGMW-approved symbol MAGE1), we found that promoter 1.5 stimulated a high level of transcription in a melanoma cell line that does not express MAGE-4. This suggests that the tumor-specific expression of MAGE genes is not determined by the presence of specific transcription factors. 26 refs., 7 figs., 2 tabs.

  18. Vials: Visualizing Alternative Splicing of Genes

    PubMed Central

    Strobelt, Hendrik; Alsallakh, Bilal; Botros, Joseph; Peterson, Brant; Borowsky, Mark; Pfister, Hanspeter; Lex, Alexander

    2016-01-01

    Alternative splicing is a process by which the same DNA sequence is used to assemble different proteins, called protein isoforms. Alternative splicing works by selectively omitting some of the coding regions (exons) typically associated with a gene. Detection of alternative splicing is difficult and uses a combination of advanced data acquisition methods and statistical inference. Knowledge about the abundance of isoforms is important for understanding both normal processes and diseases and to eventually improve treatment through targeted therapies. The data, however, is complex and current visualizations for isoforms are neither perceptually efficient nor scalable. To remedy this, we developed Vials, a novel visual analysis tool that enables analysts to explore the various datasets that scientists use to make judgments about isoforms: the abundance of reads associated with the coding regions of the gene, evidence for junctions, i.e., edges connecting the coding regions, and predictions of isoform frequencies. Vials is scalable as it allows for the simultaneous analysis of many samples in multiple groups. Our tool thus enables experts to (a) identify patterns of isoform abundance in groups of samples and (b) evaluate the quality of the data. We demonstrate the value of our tool in case studies using publicly available datasets. PMID:26529712

  19. Alternative Learning Programs Evaluation: Part 3 Report. Case Studies of Alternative Schools and Programs.

    ERIC Educational Resources Information Center

    Cobb, Caronly; Brewer, Delores; Bauman, Amy; Groves, Paula; Rayle, Joesph; Noblit, George

    In 1996, North Carolina began a 5-year evaluation of alternative learning programs (ALPs). This report contains in-depth case studies of four ALPs during the 1996-97 school year. The ALPs were selected to represent different types of programs in the state, and include one middle school, two high school, and one elementary school programs. The case…

  20. Alternative-splicing-mediated gene expression

    NASA Astrophysics Data System (ADS)

    Wang, Qianliang; Zhou, Tianshou

    2014-01-01

    Alternative splicing (AS) is a fundamental process during gene expression and has been found to be ubiquitous in eukaryotes. However, how AS impacts gene expression levels both quantitatively and qualitatively remains to be fully explored. Here, we analyze two common models of gene expression, each incorporating a simple splice mechanism that a pre-mRNA is spliced into two mature mRNA isoforms in a probabilistic manner. In the constitutive expression case, we show that the steady-state molecular numbers of two mature mRNA isoforms follow mutually independent Poisson distributions. In the bursting expression case, we demonstrate that the tail decay of the steady-state distribution for both mature mRNA isoforms that in general are not mutually independent can be characterized by the product of mean burst size and splicing probability. In both cases, we find that AS can efficiently modulate both the variability (measured by variance) and the noise level of the total mature mRNA, and in particular, the latter is always lower than the noise level of the pre-mRNA, implying that AS always reduces the noise. These results altogether reveal that AS is a mechanism of efficiently controlling the gene expression noise.

  1. Bacteria in gene therapy: bactofection versus alternative gene therapy.

    PubMed

    Pálffy, R; Gardlík, R; Hodosy, J; Behuliak, M; Resko, P; Radvánský, J; Celec, P

    2006-01-01

    Recent advances in gene therapy can be attributed to improvements of gene delivery vectors. New viral and nonviral transport vehicles that considerably increase the efficiency of transfection have been prepared. However, these vectors still have many disadvantages that are difficult to overcome, thus, a new approach is needed. The approach of bacterial delivery could in the future be important for gene therapy applications. In this article we try to summarize the most important modifications that are used for the preparation of applied strains, difficulties that are related with bacterial gene delivery and the current use of bactofection in animal experiments and clinical trials. Important differences to the alternative gene therapy (AGT) are discussed. AGT resembles bacteria-mediated protein delivery, as the therapeutical proteins are produced not by host cells but by the bacteria in situ and the expression can be regulated exogenously. Although the procedure of bacterial gene delivery is far from being definitely solved, bactofection remains a promising technique for transfection in human gene therapy.

  2. Impact of Alternative Programs on an Urban School District.

    ERIC Educational Resources Information Center

    Vincenzi, Harry; Fishman, Roger J.

    The number of secondary alternative programs in the school district of Philadelphia has grown to 75 giving it one of the largest networks of alternative programs in the country. The object of this paper is to report on the impact of those programs. The programs are divided into four categories: (1) disruptive/ truant programs, (2) career programs,…

  3. Evolution of alternative splicing in newly evolved genes of Drosophila.

    PubMed

    Zhan, Zubing; Ren, Juan; Zhang, Yue; Zhao, Ruoping; Yang, Shuang; Wang, Wen

    2011-01-01

    New gene origination is a fundamental process underlying evolution of biological diversity. Although new genes usually evolve rapidly in sequences, structure and expression, the evolutionary pattern of alternative splicing (AS) in new genes and the molecular mechanisms involved in this alternation remain to be explored. Here, we used the new genes identified in the Drosophila melanogaster lineage to study alternation of AS and the possible functional consequences of these genes. We found that new genes tended to exhibit low degree of AS, though a few new genes were alternatively spliced. Interestingly loss of introns in retroposed new genes can only account for one third of the low-level AS in new genes, while partial gene duplication without AS exons and mutations in the duplicated AS exons/introns together have resulted in two-third AS losses in new genes, indicating that reducing the degree of AS is a general trend in all categories of new genes. Further investigations on tissue expression patterns of these new genes showed that those with AS alternation had a relatively lower expression level, were expressed in fewer tissues and tended to be more likely expressed in testis than their parental genes. All these observations imply that these new genes may have gained diverged structures and expression patterns from their parental genes after AS alternation.

  4. 76 FR 11310 - Alternatives Analysis Program Discretionary Funding Allocations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-01

    ... Federal Transit Administration Alternatives Analysis Program Discretionary Funding Allocations AGENCY... Notice of Funding Availability (NOFA) on May 28, 2010. The Alternatives Analysis Program assists... address transportation needs in a defined travel corridor. Through these funding awards, FTA will...

  5. Alternative Education Guidelines, Model Middle School Alternative Education Program. Workshop II. Prevention Programs & Funding.

    ERIC Educational Resources Information Center

    National Association of School Security Directors, Bellevue, WA.

    These workshop materials are the guidelines Broward County (Florida) has established to carry out the state legislative mandate authorizing school boards to establish educational alternative programs to meet the individual needs and interests of students who are disruptive, unsucessful, or disinterested in the normal school environment. Included…

  6. An Analysis of State Policies Connected with Alternative School Programs

    ERIC Educational Resources Information Center

    Bielefeld, William C.; Stubblefield, Anna; Templeton, Zach

    2009-01-01

    Many school districts offer alternative education programs for their students who do not succeed in the regular classroom. At the high school level, many of these programs are separated from the regular schools. It seemed that many districts were establishing alternative education programs, but there were differences in the types of programs that…

  7. Current and Needed Research on Alternative Certification Programs

    ERIC Educational Resources Information Center

    Ham, Edward

    2010-01-01

    With alternative certification programs gaining popularity in teacher education, the need to evaluate these programs has become much more necessary. Without strict guidelines to classify alternative certification programs, it is difficult to make generalizations about these programs because of different requirements for completion and…

  8. 7 CFR 58.141 - Alternate quality control program.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Service 1 Quality Specifications for Raw Milk § 58.141 Alternate quality control program. When a plant has... outlined above for milk or cream, then such a program may be accepted in lieu of the program...

  9. 7 CFR 58.141 - Alternate quality control program.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Service 1 Quality Specifications for Raw Milk § 58.141 Alternate quality control program. When a plant has... outlined above for milk or cream, then such a program may be accepted in lieu of the program...

  10. 7 CFR 58.141 - Alternate quality control program.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... Service 1 Quality Specifications for Raw Milk § 58.141 Alternate quality control program. When a plant has... outlined above for milk or cream, then such a program may be accepted in lieu of the program...

  11. 7 CFR 58.141 - Alternate quality control program.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Service 1 Quality Specifications for Raw Milk § 58.141 Alternate quality control program. When a plant has... outlined above for milk or cream, then such a program may be accepted in lieu of the program...

  12. 7 CFR 58.141 - Alternate quality control program.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... Service 1 Quality Specifications for Raw Milk § 58.141 Alternate quality control program. When a plant has... outlined above for milk or cream, then such a program may be accepted in lieu of the program...

  13. Fourth annual report to Congress, Federal Alternative Motor Fuels Programs

    SciTech Connect

    1995-07-01

    This annual report to Congress presents the current status of the alternative fuel vehicle programs being conducted across the country in accordance with the Alternative Motor Fuels Act of 1988. These programs, which represent the most comprehensive data collection effort ever undertaken on alternative fuels, are beginning their fifth year. This report summarizes tests and results from the fourth year.

  14. Evaluating Organizational Training Programs: Alternatives and Criteria for Selection.

    ERIC Educational Resources Information Center

    Marth, Joseph; And Others

    Managers and program sponsors are often unaware of possible alternatives to costly training evaluation procedures and do not have criteria for selecting alternatives. What is needed is an understanding of the various levels of evaluating training programs, feasible alternatives, and decision criteria for choosing the right system. It is proposed…

  15. The Role of Alternative Programming in College Radio.

    ERIC Educational Resources Information Center

    Sauls, Samuel J.

    College radio is quite often viewed as the true alternative to commercial radio. However, what is alternative radio and how does college radio factor into the ideal? To further understand this concept, this paper focuses on the role of alternative programming in college radio. Areas discussed include alternative radio as a non-mainstream form of…

  16. EPAct Alternative Fuel Transporation Program - State and Alternative Fuel Provider Fleets: Frequently Asked Questions

    SciTech Connect

    2010-03-01

    Factsheet answering frequently asked questions about the U.S. Department of Energy's Alternative Fuel Transportation Program (the Program) that implements provisions of Titles III–V of the Energy Policy Act of 1992 (EPAct). Answers to questions that are frequently asked about the Program by managers of state government and alternative fuel provider fleets are provided in the factsheet.

  17. 77 FR 31756 - Energy Conservation Program: Alternative Efficiency Determination Methods and Alternative Rating...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-30

    ... Parts 429, 430, and 431 RIN 1904-AC46 Energy Conservation Program: Alternative Efficiency Determination Methods and Alternative Rating Methods: Public Meeting AGENCY: Office of Energy Efficiency and Renewable... proposed modifications to the regulations authorizing the use of alternative methods of determining...

  18. Toward a New Era: Alternatives for Revitalizing Student Services Programs.

    ERIC Educational Resources Information Center

    Deegan, William L.

    Alternatives for revitalizing the programs and management of student services in community colleges are reviewed in this paper. First, alternatives related to student services programs are considered, including: (1) the increased use of computer-assisted counseling to integrate student services more fully with mainstream academic activities; (2)…

  19. 24 CFR 7.26 - EEO Alternative Dispute Resolution Program.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false EEO Alternative Dispute Resolution...-Complaint Processing § 7.26 EEO Alternative Dispute Resolution Program. (a) The aggrieved person may elect... resolution is reached under the EEO ADR Program, or if the matter has not been resolved 90 days from...

  20. 33 CFR 104.140 - Alternative Security Programs.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Alternative Security Programs. 104.140 Section 104.140 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY MARITIME SECURITY MARITIME SECURITY: VESSELS General § 104.140 Alternative Security Programs. A...

  1. 33 CFR 105.140 - Alternative Security Program.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Alternative Security Program. 105.140 Section 105.140 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY MARITIME SECURITY MARITIME SECURITY: FACILITIES General § 105.140 Alternative Security Program. (a)...

  2. Alternative Schools and Programs: Five Descriptions. Technical Assistance Bulletin 37.

    ERIC Educational Resources Information Center

    National School Resource Network, Washington, DC.

    During the past ten years, many school districts have established alternative schools or programs for students who are seriously disruptive and academically unsuccessful. This bulletin describes five different types of alternative programs that have been effective in dealing with disruptive youth. They include the Tri-C Community Centered…

  3. Retrenchment: Alternatives for Teacher Education Programs.

    ERIC Educational Resources Information Center

    Kossack, Sharon W.; Greenberg, Barry

    1983-01-01

    Faced with declining enrollments, teacher education institutions must seek new approaches that either maintain present programs or encourage new programs in nontraditional areas. Results of a study of retrenchment strategies presently in use are reported. Implications for the quality of teacher education programs are also discussed. (PP)

  4. Cloning and expression of the potato alternative oxidase gene

    SciTech Connect

    Hiser, C.; McIntosh, L. Michigan State Univ., East Lansing )

    1990-05-01

    Mitochondria from 24-hour-aged potato slices possess an alternative path capacity and a 36kD protein not present in fresh potato mitochondria. This 36kD protein was identified by a monoclonal antibody against the Sauromatum guttatum alternative oxidase. These results suggest de novo synthesis of the 36kD protein during the aging process. To investigate this phenomenon, a clone containing a potato alternative oxidase gene was isolated from a cDNA library using the S. guttatum gene as a probe. This clone shows areas of high homology to the S. guttatum gene. Norther blots of RNA from fresh and 24-hour-aged potato slices are being probed with the potato gene to examine its expression in relation to the appearance of the 36kD protein.

  5. External Degree Programs: An Educational Alternative for Women.

    ERIC Educational Resources Information Center

    Desmonde, Sue Sommer; Harms, Delores

    Since 1970, external degree programs (programs for adult students who cannot attend on-campus courses on a regular basis) have become an educational alternative for the adult woman returning to or entering an educational setting. These innovative programs are ideal for the woman who must integrate the roles of worker, mother and student. A pilot…

  6. Spaces of Difference: The Contradictions of Alternative Educational Programs

    ERIC Educational Resources Information Center

    Vadeboncoeur, Jennifer A.

    2009-01-01

    Drawing upon the concept of "thirdspace" (Soja 1996), this article extends sociocultural theorizations of space in relation to alternative educational programs: programs designed to re-engage youth who have been pushed out of mainstream schools. Snapshots of educational programs, provided by ethnographic research gathered in the United States,…

  7. Alternative Route Special Education Teacher Preparation Programs Guidelines

    ERIC Educational Resources Information Center

    Wasburn-Moses, Leah; Rosenberg, Michael S.

    2008-01-01

    With the proliferation of alternative route (AR) special education teacher preparation programs, many teacher educators are likely to be involved in AR program design and implementation. Unfortunately, few resources have focused on best practices for program developers to prepare the nontraditional participants who typically populate their…

  8. Alternatives for Financing School Energy Savings Programs.

    ERIC Educational Resources Information Center

    Esteves, Rich

    1983-01-01

    This report compares shared-savings programs with financing through the use of internal funds, loans, leases, and lease purchase plans for financing energy conservation in nonprofit buildings. The shared savings option was found to offer the greatest benefits to the customer. (MLF)

  9. Degree program alternatives for fulltime employees

    SciTech Connect

    Strong, K.; Thayer, M.

    1992-01-01

    Los Alamos National Laboratory supports and sponsors degree programs for employees in order to help attract and retain the staff required to succeed in its mission. The support for these programs is provided by the Employee and Organization Development Group (HRD-3) which oversees the development, implementation, and delivery. This paper defines successful programs and suggests techniques to achieve a quality product. In order to attract the staff that it needs, the Laboratory has long recognized that educational opportunities must be available to its employees. To meet this need, the University of New Mexico (UNM) Los Alamos Center for Graduate Studies (LACGS) was established in 1956 and represents a unique cooperative venture between the Laboratory and UNM. The LACGS is funded primarily from the Laboratory. Over the years the LACGS has been a primary source of graduate degree programs for Laboratory employees, but until recently most offerings were not systematic or sequential. Nor was there any method to increase the variety of degree options.

  10. Degree program alternatives for fulltime employees

    SciTech Connect

    Strong, K.; Thayer, M.

    1992-03-01

    Los Alamos National Laboratory supports and sponsors degree programs for employees in order to help attract and retain the staff required to succeed in its mission. The support for these programs is provided by the Employee and Organization Development Group (HRD-3) which oversees the development, implementation, and delivery. This paper defines successful programs and suggests techniques to achieve a quality product. In order to attract the staff that it needs, the Laboratory has long recognized that educational opportunities must be available to its employees. To meet this need, the University of New Mexico (UNM) Los Alamos Center for Graduate Studies (LACGS) was established in 1956 and represents a unique cooperative venture between the Laboratory and UNM. The LACGS is funded primarily from the Laboratory. Over the years the LACGS has been a primary source of graduate degree programs for Laboratory employees, but until recently most offerings were not systematic or sequential. Nor was there any method to increase the variety of degree options.

  11. Another Alternative: A Ninety-Day Contractual Detoxification Treatment Program

    ERIC Educational Resources Information Center

    Kahn, Robert B.; And Others

    1976-01-01

    In May, 1974, Fresno County's Narcotic Abuse Treatment Program began a twenty-one-day outpatient methadone detoxification treatment modality. The results of the evaluation suggested an alternative treatment modality. The purpose of this paper is to examine this alternative treatment modality, its characteristics, its therapeutic outcomes and the…

  12. EPAct Alternative Fuel Transportation Program: Success Story (Fact Sheet)

    SciTech Connect

    Not Available

    2010-08-01

    This success story highlights the EPAct Alternative Fuel Transportation Program's series of workshops that bring fleets regulated under the Energy Policy Act of 1992 (EPAct) together with Clean Cities stakeholders and fuel providers to form and strengthen regional partnerships and initiate projects that will deploy more alternative fuel infrastructure.

  13. Evaluation of the Union County Alternative to Suspension Program

    ERIC Educational Resources Information Center

    Dunlap, Joyce Ann

    2010-01-01

    The schools in Union County have undergone a tremendous amount of growth in the past decade. The growth in the county has led to an increase in discipline problems. In order to provide suspended students a second chance, Union County Public Schools implemented an alternative to suspension program, the Union County Alternative to Suspension Program…

  14. 33 CFR 101.125 - Approved Alternative Security Programs.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Approved Alternative Security Programs. 101.125 Section 101.125 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY MARITIME SECURITY MARITIME SECURITY: GENERAL General § 101.125 Approved Alternative...

  15. 33 CFR 155.5061 - Alternative Training and Exercise Program.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... how the Alternative Training and Exercise Program addresses the requirements of 33 CFR 155.1055(b) through (f) and 33 CFR 155.1060; and (3) An explanation of how vessel owners or operators must implement... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Alternative Training and...

  16. 24 CFR 7.26 - EEO Alternative Dispute Resolution Program.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 1 2011-04-01 2011-04-01 false EEO Alternative Dispute Resolution...-Complaint Processing § 7.26 EEO Alternative Dispute Resolution Program. (a) The aggrieved person may elect... chosen, the EEO Counselor shall advise the aggrieved person that if the dispute is resolved during...

  17. Evaluating Alternative High Schools: Program Evaluation in Action

    ERIC Educational Resources Information Center

    Hinds, Drew Samuel Wayne

    2013-01-01

    Alternative high schools serve some of the most vulnerable students and their programs present a significant challenge to evaluate. Determining the impact of an alternative high school that serves mostly at-risk students presented a significant research problem. Few studies exist that dig deeper into the characteristics and strategies of…

  18. Fifth annual report to congress. Federal alternative motor fuels programs

    SciTech Connect

    1996-09-01

    This report presents the status of the US Department of Energy`s alternative fuel vehicle demonstration and performance tracking programs being conducted in accordance with the Energy Policy and Conservation Act. These programs comprise the most comprehensive data collection effort ever undertaken on alternative transportation fuels and alternative fuel vehicles. The report summarizes tests and results from the fifth year. Electric vehicles are not included in these programs, and the annual report does not include information on them. Since the inception of the programs, great strides have been made in developing commercially viable alternative fuel vehicle technologies. However, as is the case in the commercialization of all new technologies, some performance problems have been experienced on vehicles involved in early demonstration efforts. Substantial improvements have been recorded in vehicle practicality, safety, and performance in real-world demonstrations. An aspect of particular interest is emissions output. Results from light duty alternative fuel vehicles have demonstrated superior inservice emissions performance. Heavy duty alternative fuel vehicles have demonstrated dramatic reductions in particulate emissions. However, emissions results from vehicles converted to run on alternative fuel have not been as promising. Although the technologies available today are commercially viable in some markets, further improvements in infrastructure and economics will result in greater market expansion. Information is included in this report on light and heavy duty vehicles, transit buses, vehicle conversions, safety, infrastructure support, vehicle availability, and information dissemination.

  19. Hawaii alternative fuels utilization program. Phase 3, final report

    SciTech Connect

    Kinoshita, C.M.; Staackmann, M.

    1996-08-01

    The Hawaii Alternative Fuels Utilization Program originated as a five-year grant awarded by the US Department of Energy (USDOE) to the Hawaii Natural Energy Institute (HNEI) of the University of Hawaii at Manoa. The overall program included research and demonstration efforts aimed at encouraging and sustaining the use of alternative (i.e., substitutes for gasoline and diesel) ground transportation fuels in Hawaii. Originally, research aimed at overcoming technical impediments to the widespread adoption of alternative fuels was an important facet of this program. Demonstration activities centered on the use of methanol-based fuels in alternative fuel vehicles (AFVs). In the present phase, operations were expanded to include flexible fuel vehicles (FFVs) which can operate on M85 or regular unleaded gasoline or any combination of these two fuels. Additional demonstration work was accomplished in attempting to involve other elements of Hawaii in the promotion and use of alcohol fuels for ground transportation in Hawaii.

  20. Abnormalities in Alternative Splicing of Apoptotic Genes and Cardiovascular Diseases

    PubMed Central

    Dlamini, Zodwa; Tshidino, Shonisani C.; Hull, Rodney

    2015-01-01

    Apoptosis is required for normal heart development in the embryo, but has also been shown to be an important factor in the occurrence of heart disease. Alternative splicing of apoptotic genes is currently emerging as a diagnostic and therapeutic target for heart disease. This review addresses the involvement of abnormalities in alternative splicing of apoptotic genes in cardiac disorders including cardiomyopathy, myocardial ischemia and heart failure. Many pro-apoptotic members of the Bcl-2 family have alternatively spliced isoforms that lack important active domains. These isoforms can play a negative regulatory role by binding to and inhibiting the pro-apoptotic forms. Alternative splicing is observed to be increased in various cardiovascular diseases with the level of alternate transcripts increasing elevated in diseased hearts compared to healthy subjects. In many cases these isoforms appear to be the underlying cause of the disease, while in others they may be induced in response to cardiovascular pathologies. Regardless of this, the detection of alternate splicing events in the heart can serve as useful diagnostic or prognostic tools, while those splicing events that seem to play a causative role in cardiovascular disease make attractive future drug targets. PMID:26580598

  1. Alternative splicing of inner-ear-expressed genes.

    PubMed

    Wang, Yanfei; Liu, Yueyue; Nie, Hongyun; Ma, Xin; Xu, Zhigang

    2016-09-01

    Alternative splicing plays a fundamental role in the development and physiological function of the inner ear. Inner-ear-specific gene splicing is necessary to establish the identity and maintain the function of the inner ear. For example, exon 68 of Cadherin 23 (Cdh23) gene is subject to inner-ear-specific alternative splicing, and as a result, Cdh23(+ 68) is only expressed in inner ear hair cells. Alternative splicing along the tonotopic axis of the cochlea contributes to frequency tuning, particularly in lower vertebrates, such as chickens and turtles. Differential splicing of Kcnma1, which encodes for the α subunit of the Ca(2+)-activated K(+) channel (BK channel), has been suggested to affect the channel gating properties and is important for frequency tuning. Consequently, deficits in alternative splicing have been shown to cause hearing loss, as we can observe in Bronx Waltzer (bv) mice and Sfswap mutant mice. Despite the advances in this field, the regulation of alternative splicing in the inner ear remains elusive. Further investigation is also needed to clarify the mechanism of hearing loss caused by alternative splicing deficits. PMID:27376950

  2. 45 CFR 400.69 - Alternative RCA programs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 2 2010-10-01 2010-10-01 false Alternative RCA programs. 400.69 Section 400.69 Public Welfare Regulations Relating to Public Welfare OFFICE OF REFUGEE RESETTLEMENT, ADMINISTRATION FOR CHILDREN AND FAMILIES, DEPARTMENT OF HEALTH AND HUMAN SERVICES REFUGEE RESETTLEMENT PROGRAM Refugee...

  3. 76 FR 55136 - Implementation of the Alternative Dispute Resolution Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-06

    ... COMMISSION Implementation of the Alternative Dispute Resolution Program AGENCY: Nuclear Regulatory Commission... Resolution (ADR) Program in the Office of Enforcement (OE). The meeting will be composed of panel discussions... contacted by mail at the U.S. Nuclear Regulatory Commission, Office of Enforcement, Concerns...

  4. 45 CFR 400.69 - Alternative RCA programs.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 2 2011-10-01 2011-10-01 false Alternative RCA programs. 400.69 Section 400.69 Public Welfare Regulations Relating to Public Welfare OFFICE OF REFUGEE RESETTLEMENT, ADMINISTRATION FOR CHILDREN AND FAMILIES, DEPARTMENT OF HEALTH AND HUMAN SERVICES REFUGEE RESETTLEMENT PROGRAM Refugee...

  5. Program Health Indicators: An Alternative Approach to Program Review.

    ERIC Educational Resources Information Center

    Morton, John F.

    For the past 20 years, the University of Hawaii Community Colleges have had a formal process for the review of educational programs, requiring that each program undergo a systematic review at least once every 5 years. The result tended to be a lengthy document that chronicled the history of the previous 5 years and was far more descriptive than…

  6. Monitoring Alternative Splicing Changes in Arabidopsis Circadian Clock Genes.

    PubMed

    Simpson, Craig G; Fuller, John; Calixto, Cristiane P G; McNicol, Jim; Booth, Clare; Brown, John W S; Staiger, Dorothee

    2016-01-01

    Posttranscriptional control makes an important contribution to circadian regulation of gene expression. In higher plants, alternative splicing is particularly prevalent upon abiotic and biotic stress and in the circadian system. Here we describe in detail a high-resolution reverse transcription-PCR based panel (HR RT-PCR) to monitor alternative splicing events. The use of the panel allows the quantification of changes in the proportion of splice isoforms between different samples, e.g., different time points, different tissues, genotypes, ecotypes, or treatments. PMID:26867620

  7. Alternative management and funding options for aeronautics programs, Task 1

    NASA Technical Reports Server (NTRS)

    1975-01-01

    Research and technology will be at lower program levels with basic military research for aviation decreasing as fewer aircraft programs are initiated and the present new aircraft programs move into the prototype and production status. The key question is can industry take on the management and financing role and meet the criteria and characteristics considered essential for a viable research and technology program. The criteria for evaluating alternative approaches include an examination of the nature of the product to be provided, responsiveness to changing needs, efficiency in terms of costs, ability to provide leadership, and to provide impartial and independent evaluation of approaches, and to provide technological inputs for regulating functions.

  8. Intrasplicing coordinates alternative first exons with alternative splicing in the protein 4.1R gene

    SciTech Connect

    Conboy, John G.; Parra, Marilyn K.; Tan, Jeff S.; Mohandas, Narla; Conboy, John G.

    2008-11-07

    In the protein 4.1R gene, alternative first exons splice differentially to alternative 3' splice sites far downstream in exon 2'/2 (E2'/2). We describe a novel intrasplicing mechanism by which exon 1A (E1A) splices exclusively to the distal E2'/2 acceptor via two nested splicing reactions regulated by novel properties of exon 1B (E1B). E1B behaves as an exon in the first step, using its consensus 5' donor to splice to the proximal E2'/2 acceptor. A long region of downstream intron is excised, juxtaposing E1B with E2'/2 to generate a new composite acceptor containing the E1B branchpoint/pyrimidine tract and E2 distal 3' AG-dinucleotide. Next, the upstream E1A splices over E1B to this distal acceptor, excising the remaining intron plus E1B and E2' to form mature E1A/E2 product. We mapped branch points for both intrasplicing reactions and demonstrated that mutation of the E1B 5' splice site or branchpoint abrogates intrasplicing. In the 4.1R gene, intrasplicing ultimately determines N-terminal protein structure and function. More generally, intrasplicing represents a new mechanism whereby alternative promoters can be coordinated with downstream alternative splicing.

  9. Alternative Route Programs for Certification in Special Education: Program Infrastructure Instructional Delivery, and Participant Characteristics

    ERIC Educational Resources Information Center

    Rosenberg, Michael S.; Boyer, K. Lynn; Sindelar, Paul T.; Misra, Sunil K.

    2007-01-01

    This study describes special education alternative route (AR) teacher preparation programs. The authors developed a national database of programs and collected information on program sponsorship, length and intensity, features, and participant demographics. Most of the 235 programs in the database were in states that had significant shortages of…

  10. Another Alternative: A 90-Day Contractual Detoxification Treatment Program

    ERIC Educational Resources Information Center

    Kahn, Robert B.; And Others

    1978-01-01

    In May 1974, Fresno County's Narcotic Abuse Treatment Program began a 21-day outpatient methadone detoxification treatment modality. The purpose of this paper is to examine this alternative treatment modality, its characteristics, its therapeutic outcomes and the rationale for its use. (Author)

  11. State and local government guide to environmental program funding alternatives

    SciTech Connect

    Not Available

    1994-01-01

    The booklet provides an overview of traditional funding mechanisms and introduces state and local governments to innovative alternatives to traditional funding. The focus is on nonpoint source pollution, but funding sources and mechanisms can be applied to environmental programs in general. A list of contacts and references is included at the back of the booklet to answer questions and provide additional information.

  12. Alternate Learning Center. Abstracts of Inservice Training Programs.

    ERIC Educational Resources Information Center

    Rhode Island State Dept. of Education, Providence. Div. of Development and Operations.

    This booklet is a collection of abstracts describing the 18 programs offered at the Alternate Learning Center of the Rhode Island Teacher Center which has as its Primary function school based inservice training for local teachers and administrators. Each project is described in detail, including course goals, specific objectives, training…

  13. 33 CFR 106.135 - Alternative Security Program.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Alternative Security Program. 106.135 Section 106.135 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY MARITIME SECURITY MARINE SECURITY: OUTER CONTINENTAL SHELF (OCS) FACILITIES General § 106.135...

  14. 6 CFR 27.235 - Alternative security program.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... facilities may submit an Alternate Security Program (ASP) pursuant to the requirements of this section. The... submit an ASP in lieu of a Security Vulnerability Assessment, Site Security Plan, or both. (2) Tier 1, Tier 2, or Tier 3 facilities may submit an ASP in lieu of a Site Security Plan. Tier 1, Tier 2,...

  15. 6 CFR 27.235 - Alternative security program.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... facilities may submit an Alternate Security Program (ASP) pursuant to the requirements of this section. The... submit an ASP in lieu of a Security Vulnerability Assessment, Site Security Plan, or both. (2) Tier 1, Tier 2, or Tier 3 facilities may submit an ASP in lieu of a Site Security Plan. Tier 1, Tier 2,...

  16. 6 CFR 27.235 - Alternative security program.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... facilities may submit an Alternate Security Program (ASP) pursuant to the requirements of this section. The... submit an ASP in lieu of a Security Vulnerability Assessment, Site Security Plan, or both. (2) Tier 1, Tier 2, or Tier 3 facilities may submit an ASP in lieu of a Site Security Plan. Tier 1, Tier 2,...

  17. 6 CFR 27.235 - Alternative security program.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... facilities may submit an Alternate Security Program (ASP) pursuant to the requirements of this section. The... submit an ASP in lieu of a Security Vulnerability Assessment, Site Security Plan, or both. (2) Tier 1, Tier 2, or Tier 3 facilities may submit an ASP in lieu of a Site Security Plan. Tier 1, Tier 2,...

  18. 6 CFR 27.235 - Alternative security program.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... facilities may submit an Alternate Security Program (ASP) pursuant to the requirements of this section. The... submit an ASP in lieu of a Security Vulnerability Assessment, Site Security Plan, or both. (2) Tier 1, Tier 2, or Tier 3 facilities may submit an ASP in lieu of a Site Security Plan. Tier 1, Tier 2,...

  19. Educational Alternatives for Boating Safety Programs. Final Report.

    ERIC Educational Resources Information Center

    Sager, E.; And Others

    The Coast Guard, in efforts to improve the safety of recreational boating, undertook research to identify educational alternatives in boating safety programs. Background research was done to assess materials from areas of boating education and education in comparable recreational areas. Research was also conducted to review educational and mass…

  20. 33 CFR 106.135 - Alternative Security Program.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Alternative Security Program. 106.135 Section 106.135 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY MARITIME SECURITY MARINE SECURITY: OUTER CONTINENTAL SHELF (OCS) FACILITIES General § 106.135...

  1. An Alternative Undergraduate Teacher Preparation Program in Early Childhood Education

    ERIC Educational Resources Information Center

    Xu, Yaoying; Gelfer, Jeffrey; Filler, John

    2003-01-01

    The realities of a multi-racial, multi-ethnic, and multi-ability student population demand a unique and nontraditional approach characterized by an individualization sensitive to group identity. The primary goal of this alternative Early Childhood Studies/Education Program with a degree of Bachelor of Science is to provide a comprehensive…

  2. 33 CFR 106.135 - Alternative Security Program.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Alternative Security Program. 106.135 Section 106.135 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY MARITIME SECURITY MARINE SECURITY: OUTER CONTINENTAL SHELF (OCS) FACILITIES General § 106.135...

  3. Evaluation of Clark County School District's Alternative Route to Licensure Program from the Program Participants' Perspectives

    ERIC Educational Resources Information Center

    Kenyon, James J., Jr.

    2013-01-01

    This evaluation assesses the Alternative Route to Licensure (ARL) program of the Clark County School District (CCSD), in Clark County, Nevada from the program participants' perspectives. The program was implemented to reduce teacher shortages in the school district and allow persons with non-education-related Bachelor's Degrees to obtain teaching…

  4. Alternative fuels for vehicles fleet demonstration program. Volume 1. Summary

    SciTech Connect

    Bechtold, R.L.

    1997-03-01

    Volume 1 of this report provides: (1) information about the purpose and scope of the Alternative Fuels for Vehicles Fleet Demonstration Program (AFV-FDP); (2) summary of AFV-FDP findings, organized on the basis of vehicle type and fuel type; (3) a short review of the status of AFV technology developments, including examples of companies in New York State that are active in developing AFVs and AFV components; and (4) a brief overview of AFV deployment status in New York State.

  5. Evaluating the prevention through alternative learning styles program.

    PubMed

    Huber, Mary J; Workman, Judson; Ford, Jo Ann; Moore, Dennis; Mayer, Theresa

    2009-01-01

    This article reports on the evaluation of a two-year alcohol, tobacco and other drug (ATOD) intervention, the Prevention through Alternative Learning Styles (PALS) program, targeting both teachers and middle-school students. Teachers are taught to recognize students' unique learning styles in the context of the ATOD curriculum and adapt the ATOD messages to these learning styles. The student curriculum consists of 5 topic areas with two lessons per topic area. Student goals include enhancing students' knowledge of the effects of ATOD, promoting students' use of refusal skills and decreasing students' intentions to use ATOD. The program was implemented in school dis-tricts in the greater Dayton Ohio area. Support was found for the intervention's overall effectiveness in both years, with statistically significant improvements demonstrated by the students who participated in the PALS program. Students had an increase in their knowledge of ATOD topic areas and a decrease in their intentions to use ATOD.

  6. Feelings of Preparedness among Alternatively Certified Teachers: What Is the Role of Program Features?

    ERIC Educational Resources Information Center

    Kee, Ayana N.

    2012-01-01

    In the United States, about one third of new teachers being hired are drawn from alternative certification programs. One way to address controversy about the differences among the training experiences of teachers in traditional certification programs, fast-track alternative programs, and residency alternative programs is to examine teacher reports…

  7. Alternative polyadenylation and gene expression regulation in plants.

    PubMed

    Xing, Denghui; Li, Qingshun Quinn

    2011-01-01

    Functioning as an essential step of pre-mRNA processing, polyadenylation has been realized in recent years to play an important regulatory role during eukaryotic gene expression. Such regulation occurs mostly through the use of alternative polyadenylation (APA) sites and generates different transcripts with altered coding capacity for proteins and/or RNA. However, the molecular mechanisms that underlie APAs are poorly understood. Besides APA cases demonstrated in animal embryo development, cancers, and other diseases, there are a number of APA examples reported in plants. The best-known ones are related to flowering time control pathways and stress responses. Genome-wide studies have revealed that plants use APA extensively to generate diversity in their transcriptomes. Although each transcript produced by RNA polymerase II has a poly(A) tail, over 50% of plant genes studied possess multiple APA sites in their transcripts. The signals defining poly(A) sites in plants were mostly studied through classical genetic means. Our understanding of these poly(A) signals is enhanced by the tallies of whole plant transcriptomes. The profiles of these signals have been used to build computer models that can predict poly(A) sites in newly sequenced genomes, potential APA sites in genes of interest, and/or to identify, and then mutate, unwanted poly(A) sites in target transgenes to facilitate crop improvements. In this review, we provide readers an update on recent research advances that shed light on the understanding of polyadenylation, APA, and its role in gene expression regulation in plants.

  8. Organization of potential alternative nitrogenase genes from Clostridium pasteurianum.

    PubMed

    Zinoni, F; Robson, R M; Robson, R L

    1993-07-18

    A 3.3 kb HindIII genomic DNA fragment from Clostridium pasteurianum ATCC 6013 which hybridized to the anfDGK genes for the Fe-only 'alternative' nitrogenase from Azotobacter vinelandii was cloned. Open reading frames (ORFs D, G, and K) with high sequence identity to anfD, anfG, and part of anfK were located in the nucleotide sequence obtained for 2494 bp of this fragment. In C. pasteurianum, ORFD maps approximately 1.8 kb downstream of nifH3 and is transcribed in the same direction. There was no evidence for additional copies of ORFDGK-like sequences in the genome of C. pasteurianum, other than those encoding the Mo-nitrogenase. Physiological and biochemical studies suggest that a nitrogenase not requiring molybdenum may occur in C. pasteurianum. This enzyme is probably encoded by nifH3 and ORFs D, G, and K identified here. PMID:8334167

  9. Alternative pre-mRNA splicing switches modulate gene expression in late erythropoiesis

    SciTech Connect

    Yamamoto, Miki L.; Clark, Tyson A.; Gee, Sherry L.; Kang, Jeong-Ah; Schweitzer, Anthony C.; Wickrema, Amittha; Conboy, John G.

    2009-02-03

    Differentiating erythroid cells execute a unique gene expression program that insures synthesis of the appropriate proteome at each stage of maturation. Standard expression microarrays provide important insight into erythroid gene expression but cannot detect qualitative changes in transcript structure, mediated by RNA processing, that alter structure and function of encoded proteins. We analyzed stage-specific changes in the late erythroid transcriptome via use of high-resolution microarrays that detect altered expression of individual exons. Ten differentiation-associated changes in erythroblast splicing patterns were identified, including the previously known activation of protein 4.1R exon 16 splicing. Six new alternative splicing switches involving enhanced inclusion of internal cassette exons were discovered, as well as 3 changes in use of alternative first exons. All of these erythroid stage-specific splicing events represent activated inclusion of authentic annotated exons, suggesting they represent an active regulatory process rather than a general loss of splicing fidelity. The observation that 3 of the regulated transcripts encode RNA binding proteins (SNRP70, HNRPLL, MBNL2) may indicate significant changes in the RNA processing machinery of late erythroblasts. Together, these results support the existence of a regulated alternative pre-mRNA splicing program that is critical for late erythroid differentiation.

  10. Alternative Basic Comprehensive Program (Project A.B.C.). Special Alternative Instructional Program. 1991-92 Final Evaluation Profile. OREA Report.

    ERIC Educational Resources Information Center

    Wallace, Cyril

    The Alternative Basic Comprehensive Program (Project ABC) was a special alternative program for bilingual high school students in New York City. The project targeted two high schools with an influx of newly arrived immigrant students from Cambodia, Vietnam, and Spanish-speaking countries of the Caribbean and South America. The program was designed…

  11. Radiopharmaceutical and Gene Therapy Program

    SciTech Connect

    Buchsbaum, Donald J.

    2006-02-09

    The objective of our research program was to determine whether novel receptors can be induced in solid cancers as a target for therapy with radiolabeled unmodified peptides that bind to the receptors. The hypothesis was that induction of a high number of receptors on the surface of these cancer cells would result in an increased uptake of the radiolabeled monomeric peptides as compared to published results with radiolabeled antibodies or peptides to naturally expressed antigens or receptors, and therefore a better therapeutic outcome. The following is a summary of published results.

  12. "Programmed packaging" for gene delivery.

    PubMed

    Hyodo, M; Sakurai, Y; Akita, H; Harashima, H

    2014-11-10

    We report on the development of a multifunctional envelope-type nano device (MEND) based on our packaging concept "Programmed packaging" to control not only intracellular trafficking but also the biodistribution of encapsulated compounds such as nucleic acids/proteins/peptides. Our strategy for achieving this is based on molecular mechanisms of cell biology such as endocytosis, vesicular trafficking, etc. In this review, we summarize the concept of programmed packaging and discuss some of our recent successful examples of using MENDs. Systematic evolution of ligands by exponential enrichment (SELEX) was applied as a new methodology for identifying a new ligand toward cell or mitochondria. The delivery of siRNA to tumors and the tumor vasculature was achieved using pH sensitive lipid (YSK05), which was newly designed and optimized under in vivo conditions. The efficient delivery of pDNA to immune cells such as dendritic cells has also been developed using the KALA ligand, which can be a breakthrough technology for DNA vaccine. Finally, ss-cleavable and pH-activated lipid-like surfactant (ssPalm) which is a lipid like material with pH-activatable and SS-cleavable properties is also introduced as a proof of our concept. PMID:24780263

  13. ISO New England: Results of Ancillary Service Pilot Programs, Alternative Technology Regulation Pilot Program and Demand Response Reserves Pilot Program

    SciTech Connect

    Lowell, Jon; Yoshimura, Henry

    2011-10-26

    This PowerPoint presentation compares performance of pilot program assets and generation resources in alternative technology regulation and demand response reserves for flywheels and residential electric thermal storage.

  14. Federal Alternative Fuel Program light duty vehicle operation

    SciTech Connect

    Not Available

    1992-03-01

    This annual report to Congress details the first year of the Federal light duty vehicle operations as required by Section 400AA(b)(1)(B) of the Energy Policy and Conservation Act (EPCA). Alternative Motors Fuels Act (AMFA) encourages the use and production of AFVs that use methanol, ethanol, and natural gas. The Congress has recognized that displacement of energy derived from imported oil with alternative fuels will help to achieve energy security and improve air quality. In passing this Act, the Federal Government is assisting clean-burning, non-petroleum transportation fuels to reach a threshold level of commercial application and consumer acceptability at which they can successfully compete with petroleum-base transportation fuels. The objectives of the program are to demonstrate the environmental, economic, and performance characteristics of alternative fuel fleet vehicles and to provide information or engine/vehicle manufacturers as well as the general public. This report details the first year of the Federal light duty vehicle operations, from January 1991 through September 1991. The Federal test vehicles are composed of 65 M85 fuel and 16 conventional gasoline fuel vehicles. The following sections discuss the vehicle operation and performance characteristics of the AMFA test vehicles in a fleet environment.

  15. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    SciTech Connect

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R

    2007-12-10

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  16. ASPic-GeneID: A Lightweight Pipeline for Gene Prediction and Alternative Isoforms Detection

    PubMed Central

    Alioto, Tyler; Picardi, Ernesto; Guigó, Roderic

    2013-01-01

    New genomes are being sequenced at an increasingly rapid rate, far outpacing the rate at which manual gene annotation can be performed. Automated genome annotation is thus necessitated by this growth in genome projects; however, full-fledged annotation systems are usually home-grown and customized to a particular genome. There is thus a renewed need for accurate ab initio gene prediction methods. However, it is apparent that fully ab initio methods fall short of the required level of sensitivity and specificity for a quality annotation. Evidence in the form of expressed sequences gives the single biggest improvement in accuracy when used to inform gene predictions. Here, we present a lightweight pipeline for first-pass gene prediction on newly sequenced genomes. The two main components are ASPic, a program that derives highly accurate, albeit not necessarily complete, EST-based transcript annotations from EST alignments, and GeneID, a standard gene prediction program, which we have modified to take as evidence intron annotations. The introns output by ASPic CDS predictions is given to GeneID to constrain the exon-chaining process and produce predictions consistent with the underlying EST alignments. The pipeline was successfully tested on the entire C. elegans genome and the 44 ENCODE human pilot regions. PMID:24308000

  17. Innovation in two alternative elementary school programs: why it works.

    PubMed

    Dyson, B; O'Sullivan, M

    1998-09-01

    The purpose of this paper was to describe and interpret the factors that supported and maintained curricular innovation at two alternative elementary schools. The two schools have Project Adventure as their curriculum focus and use the concepts of risk, challenge, trust, cooperation, and problem solving; briefing and debriefing; and personal goal-setting contracts as part of their schoolwide curriculum (Project Adventure, 1991). Data were collected through formal interviews with the physical education teachers, the principals, and four classroom teachers at each school. Nonparticipant observation, field notes, informal interviews, and document analysis were also conducted. Inductive analysis and constant comparison were used to analyze and organize the data throughout the research process. Five factors emerged that supported the implementation of this innovative physical education program: a shared vision, external support for the schools' programs, curricula integration, centrality of physical education, and shared decision making. Project Adventure at these schools provides an example of substantive curricular reform where physical education was a critical element in the school programs.

  18. The Evolutionary Fate of Alternatively Spliced Homologous Exons after Gene Duplication

    PubMed Central

    Abascal, Federico; Tress, Michael L.; Valencia, Alfonso

    2015-01-01

    Alternative splicing and gene duplication are the two main processes responsible for expanding protein functional diversity. Although gene duplication can generate new genes and alternative splicing can introduce variation through alternative gene products, the interplay between the two processes is complex and poorly understood. Here, we have carried out a study of the evolution of alternatively spliced exons after gene duplication to better understand the interaction between the two processes. We created a manually curated set of 97 human genes with mutually exclusively spliced homologous exons and analyzed the evolution of these exons across five distantly related vertebrates (lamprey, spotted gar, zebrafish, fugu, and coelacanth). Most of these exons had an ancient origin (more than 400 Ma). We found examples supporting two extreme evolutionary models for the behaviour of homologous axons after gene duplication. We observed 11 events in which gene duplication was accompanied by splice isoform separation, that is, each paralog specifically conserved just one distinct ancestral homologous exon. At other extreme, we identified genes in which the homologous exons were always conserved within paralogs, suggesting that the alternative splicing event cannot easily be separated from the function in these genes. That many homologous exons fall in between these two extremes highlights the diversity of biological systems and suggests that the subtle balance between alternative splicing and gene duplication is adjusted to the specific cellular context of each gene. PMID:25931610

  19. Parallel Alternate Curriculum--A Mainstreaming Implementation Program at the Secondary Level: Alternative Teaching Strategies Combined with Basic Skills.

    ERIC Educational Resources Information Center

    Smith, Gayle

    The Parallel Alternate Curriculum (PAC), a model providng regular content courses, in regular classes, to secondary students with learning problems, combines basic skill instruction with alternative teaching strategies. PAC, a mainstreaming implementation program, is designed to provide inservice training emphasizing the process of how students…

  20. Two Alternating Motor Programs Drive Navigation in Drosophila Larva

    PubMed Central

    Klein, Mason; Tang, Anji; Kane, Elizabeth; Gershow, Marc; Garrity, Paul; Samuel, Aravinthan D. T.

    2011-01-01

    When placed on a temperature gradient, a Drosophila larva navigates away from excessive cold or heat by regulating the size, frequency, and direction of reorientation maneuvers between successive periods of forward movement. Forward movement is driven by peristalsis waves that travel from tail to head. During each reorientation maneuver, the larva pauses and sweeps its head from side to side until it picks a new direction for forward movement. Here, we characterized the motor programs that underlie the initiation, execution, and completion of reorientation maneuvers by measuring body segment dynamics of freely moving larvae with fluorescent muscle fibers as they were exposed to temporal changes in temperature. We find that reorientation maneuvers are characterized by highly stereotyped spatiotemporal patterns of segment dynamics. Reorientation maneuvers are initiated with head sweeping movement driven by asymmetric contraction of a portion of anterior body segments. The larva attains a new direction for forward movement after head sweeping movement by using peristalsis waves that gradually push posterior body segments out of alignment with the tail (i.e., the previous direction of forward movement) into alignment with the head. Thus, reorientation maneuvers during thermotaxis are carried out by two alternating motor programs: (1) peristalsis for driving forward movement and (2) asymmetric contraction of anterior body segments for driving head sweeping movement. PMID:21858019

  1. Towards a Typology of Alternative Education Programs: A Compilation of Elements from the Literature.

    ERIC Educational Resources Information Center

    Aron, Laudan Y.

    This paper synthesizes existing knowledge, definitions, and themes about alternative education programs, based on a review of literature and reports, focusing on common terminologies to characterize the various kinds of alternative education programs. It seeks to develop a typology of existing alternative education by focusing on certain common…

  2. 5 CFR 2425.8 - Collaboration and Alternative Dispute Resolution Program.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... AWARDS § 2425.8 Collaboration and Alternative Dispute Resolution Program. The parties may request assistance from the Collaboration and Alternative Dispute Resolution Program (CADR) to attempt to resolve the... 5 Administrative Personnel 3 2011-01-01 2011-01-01 false Collaboration and Alternative...

  3. 5 CFR 2424.10 - Collaboration and Alternative Dispute Resolution Program.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Alternative Dispute Resolution; Requesting and Providing Allegations Concerning the Duty To Bargain § 2424.10 Collaboration and Alternative Dispute Resolution Program. Where an exclusive representative and an agency are... and Alternative Dispute Resolution Program (CADR). Upon request, and as agreed upon by the...

  4. Return to the fetal gene program

    PubMed Central

    Taegtmeyer, Heinrich; Sen, Shiraj; Vela, Deborah

    2013-01-01

    A hallmark of cardiac metabolism before birth is the predominance of carbohydrate use for energy provision. After birth, energy substrate metabolism rapidly switches to the oxidation of fatty acids. This switch accompanies the expression of “adult” isoforms of metabolic enzymes and other proteins. However, in a variety of pathophysiologic conditions, including hypoxia, ischemia, hypertrophy, atrophy, diabetes, and hypothyroidism, the postnatal heart returns to the “fetal” gene program. These adaptive mechanisms are also a feature of the failing heart muscle, where at a certain point this fetal-like reprogramming no longer suffices to support cardiac structure and function. We advance the hypothesis that in the postnatal heart, metabolic remodeling triggers the process through glycosylation of transcription factors, potentially protecting the stressed heart from irreversible functional impairment and programmed cell death. In other words, we propose a metabolic link to gene expression in the heart. PMID:20201903

  5. Alternatives Analysis for the Resumption of Transient Testing Program

    SciTech Connect

    Lee Nelson

    2013-11-01

    An alternatives analysis was performed for resumption of transient testing. The analysis considered eleven alternatives – including both US international facilities. A screening process was used to identify two viable alternatives from the original eleven. In addition, the alternatives analysis includes a no action alternative as required by the National Environmental Policy Act (NEPA). The alternatives considered in this analysis included: 1. Restart the Transient Reactor Test Facility (TREAT) 2. Modify the Annular Core Research Reactor (ACRR) which includes construction of a new hot cell and installation of a new hodoscope. 3. No Action

  6. An extensive program of periodic alternative splicing linked to cell cycle progression

    PubMed Central

    Dominguez, Daniel; Tsai, Yi-Hsuan; Weatheritt, Robert; Wang, Yang; Blencowe, Benjamin J; Wang, Zefeng

    2016-01-01

    Progression through the mitotic cell cycle requires periodic regulation of gene function at the levels of transcription, translation, protein-protein interactions, post-translational modification and degradation. However, the role of alternative splicing (AS) in the temporal control of cell cycle is not well understood. By sequencing the human transcriptome through two continuous cell cycles, we identify ~1300 genes with cell cycle-dependent AS changes. These genes are significantly enriched in functions linked to cell cycle control, yet they do not significantly overlap genes subject to periodic changes in steady-state transcript levels. Many of the periodically spliced genes are controlled by the SR protein kinase CLK1, whose level undergoes cell cycle-dependent fluctuations via an auto-inhibitory circuit. Disruption of CLK1 causes pleiotropic cell cycle defects and loss of proliferation, whereas CLK1 over-expression is associated with various cancers. These results thus reveal a large program of CLK1-regulated periodic AS intimately associated with cell cycle control. DOI: http://dx.doi.org/10.7554/eLife.10288.001 PMID:27015110

  7. Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal

    PubMed Central

    Holm, Frida; Hellqvist, Eva; Mason, Cayla N.; Ali, Shawn A.; Delos-Santos, Nathaniel; Barrett, Christian L.; Chun, Hye-Jung; Minden, Mark D.; Moore, Richard A.; Marra, Marco A.; Runza, Valeria; Frazer, Kelly A.; Sadarangani, Anil; Jamieson, Catriona H. M.

    2015-01-01

    Formative research suggests that a human embryonic stem cell-specific alternative splicing gene regulatory network, which is repressed by Muscleblind-like (MBNL) RNA binding proteins, is involved in cell reprogramming. In this study, RNA sequencing, splice isoform-specific quantitative RT-PCR, lentiviral transduction, and in vivo humanized mouse model studies demonstrated that malignant reprogramming of progenitors into self-renewing blast crisis chronic myeloid leukemia stem cells (BC LSCs) was partially driven by decreased MBNL3. Lentiviral knockdown of MBNL3 resulted in reversion to an embryonic alternative splice isoform program typified by overexpression of CD44 transcript variant 3, containing variant exons 8–10, and BC LSC proliferation. Although isoform-specific lentiviral CD44v3 overexpression enhanced chronic phase chronic myeloid leukemia (CML) progenitor replating capacity, lentiviral shRNA knockdown abrogated these effects. Combined treatment with a humanized pan-CD44 monoclonal antibody and a breakpoint cluster region - ABL proto-oncogene 1, nonreceptor tyrosine kinase (BCR-ABL1) antagonist inhibited LSC maintenance in a niche-dependent manner. In summary, MBNL3 down-regulation–related reversion to an embryonic alternative splicing program, typified by CD44v3 overexpression, represents a previously unidentified mechanism governing malignant progenitor reprogramming in malignant microenvironments and provides a pivotal opportunity for selective BC LSC detection and therapeutic elimination. PMID:26621726

  8. Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal.

    PubMed

    Holm, Frida; Hellqvist, Eva; Mason, Cayla N; Ali, Shawn A; Delos-Santos, Nathaniel; Barrett, Christian L; Chun, Hye-Jung; Minden, Mark D; Moore, Richard A; Marra, Marco A; Runza, Valeria; Frazer, Kelly A; Sadarangani, Anil; Jamieson, Catriona H M

    2015-12-15

    Formative research suggests that a human embryonic stem cell-specific alternative splicing gene regulatory network, which is repressed by Muscleblind-like (MBNL) RNA binding proteins, is involved in cell reprogramming. In this study, RNA sequencing, splice isoform-specific quantitative RT-PCR, lentiviral transduction, and in vivo humanized mouse model studies demonstrated that malignant reprogramming of progenitors into self-renewing blast crisis chronic myeloid leukemia stem cells (BC LSCs) was partially driven by decreased MBNL3. Lentiviral knockdown of MBNL3 resulted in reversion to an embryonic alternative splice isoform program typified by overexpression of CD44 transcript variant 3, containing variant exons 8-10, and BC LSC proliferation. Although isoform-specific lentiviral CD44v3 overexpression enhanced chronic phase chronic myeloid leukemia (CML) progenitor replating capacity, lentiviral shRNA knockdown abrogated these effects. Combined treatment with a humanized pan-CD44 monoclonal antibody and a breakpoint cluster region - ABL proto-oncogene 1, nonreceptor tyrosine kinase (BCR-ABL1) antagonist inhibited LSC maintenance in a niche-dependent manner. In summary, MBNL3 down-regulation-related reversion to an embryonic alternative splicing program, typified by CD44v3 overexpression, represents a previously unidentified mechanism governing malignant progenitor reprogramming in malignant microenvironments and provides a pivotal opportunity for selective BC LSC detection and therapeutic elimination. PMID:26621726

  9. 78 FR 45253 - National Toxicology Program Scientific Advisory Committee on Alternative Toxicological Methods...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-26

    ... HUMAN SERVICES National Institutes of Health National Toxicology Program Scientific Advisory Committee on Alternative Toxicological Methods; Announcement of Meeting; Request for Comments SUMMARY: This notice announces a meeting of the Scientific Advisory Committee on Alternative Toxicological...

  10. Alternate Assessment Manual for the Arizona Student Achievement Program

    ERIC Educational Resources Information Center

    Arizona Department of Education, 2005

    2005-01-01

    The Alternate Assessment Code of Ethics informs school personnel involved in alternate assessments of ethical, nondiscriminatory assessment practices and underscores the diligence necessary to provide accurate assessment data for instructional decision-making. The importance of commitment and adherence to the Alternate Assessment Code of Ethics by…

  11. 19 CFR 101.9 - Test programs or procedures; alternate requirements.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 19 Customs Duties 1 2012-04-01 2012-04-01 false Test programs or procedures; alternate... SECURITY; DEPARTMENT OF THE TREASURY GENERAL PROVISIONS § 101.9 Test programs or procedures; alternate requirements. (a) General testing. For purposes of conducting a test program or procedure designed to...

  12. Perception of Preparedness of Novice Teachers from Alternative and Traditional Licensing Programs

    ERIC Educational Resources Information Center

    Buchanan, Tenielle; Lang, Nathan; Morin, Laura-Lee

    2013-01-01

    Alternative teacher licensing programs have become very popular; however, very little research has been conducted on the efficacy of the programs. Alternative licensing programs (ALPs) have evolved and multiplied rapidly over the last few decades. The Tennessee Independent Colleges and Universities Association (TICUA) is attempting to determine…

  13. Backgrounds, Teaching Responsibilities, and Motivations of Music Education Candidates Enrolled in Alternative Certification Music Education Programs

    ERIC Educational Resources Information Center

    Hellman, Daniel; McDowell, Carol

    2011-01-01

    The purpose of this study was to examine the factors associated with enrolling, continuing, and completing alternative certification programs in music education. Data were collected via surveys and semi-structured interviews of music teacher candidates from 43 program completers from seven alternative certification programs in three states. In…

  14. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis.

    PubMed

    Pimentel, Harold; Parra, Marilyn; Gee, Sherry L; Mohandas, Narla; Pachter, Lior; Conboy, John G

    2016-01-29

    Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentally-dynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ∼50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclear-localized. Splice site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. We conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.

  15. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

    SciTech Connect

    Pimentel, Harold; Parra, Marilyn; Gee, Sherry L.; Mohandas, Narla; Pachter, Lior; Conboy, John G.

    2015-11-03

    Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentallydynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ~50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclearlocalized. Splice site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. Finally, we conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.

  16. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

    PubMed Central

    Pimentel, Harold; Parra, Marilyn; Gee, Sherry L.; Mohandas, Narla; Pachter, Lior; Conboy, John G.

    2016-01-01

    Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentally-dynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ∼50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclear-localized. Splice site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. We conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease. PMID:26531823

  17. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

    DOE PAGESBeta

    Pimentel, Harold; Parra, Marilyn; Gee, Sherry L.; Mohandas, Narla; Pachter, Lior; Conboy, John G.

    2015-11-03

    Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentallydynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ~50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclearlocalized. Splicemore » site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. Finally, we conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.« less

  18. Computational Analysis of an Evolutionarily Conserved VertebrateMuscle Alternative Splicing Program

    SciTech Connect

    Das, Debopriya; Clark, Tyson A.; Schweitzer, Anthony; Marr,Henry; Yamamoto, Miki L.; Parra, Marilyn K.; Arribere, Josh; Minovitsky,Simon; Dubchak, Inna; Blume, John E.; Conboy, John G.

    2006-06-15

    A novel exon microarray format that probes gene expression with single exon resolution was employed to elucidate critical features of a vertebrate muscle alternative splicing program. A dataset of 56 microarray-defined, muscle-enriched exons and their flanking introns were examined computationally in order to investigate coordination of the muscle splicing program. Candidate intron regulatory motifs were required to meet several stringent criteria: significant over-representation near muscle-enriched exons, correlation with muscle expression, and phylogenetic conservation among genomes of several vertebrate orders. Three classes of regulatory motifs were identified in the proximal downstream intron, within 200nt of the target exons: UGCAUG, a specific binding site for Fox-1 related splicing factors; ACUAAC, a novel branchpoint-like element; and UG-/UGC-rich elements characteristic of binding sites for CELF splicing factors. UGCAUG was remarkably enriched, being present in nearly one-half of all cases. These studies suggest that Fox and CELF splicing factors play a major role in enforcing the muscle-specific alternative splicing program, facilitating expression of a set of unique isoforms of cytoskeletal proteins that are critical to muscle cell differentiation. Supplementary materials: There are four supplementary tables and one supplementary figure. The tables provide additional detailed information concerning the muscle-enriched datasets, and about over-represented oligonucleotide sequences in the flanking introns. The supplementary figure shows RT-PCR data confirming the muscle-enriched expression of exons predicted from the microarray analysis.

  19. Alternatives for Young Americans: A Catalog of Drug Abuse Prevention Programs.

    ERIC Educational Resources Information Center

    Applied Management Sciences, Inc., Silver Spring, MD.

    This reference book contains resumes of program descriptions geared toward youth and adults who need or want information on drug abuse prevention programs, locally or nationally. Several major entries include: (1) national program models; (2) evaluated alternative programs from all states; and (3) descriptions of prevention programs. All section…

  20. School District Program Cost Accounting: An Alternative Approach

    ERIC Educational Resources Information Center

    Hentschke, Guilbert C.

    1975-01-01

    Discusses the value for school districts of a program cost accounting system and examines different approaches to generating program cost data, with particular emphasis on the "cost allocation to program system" (CAPS) and the traditional "transaction-based system." (JG)

  1. Alternative filtration testing program: Pre-evaluation of test results

    SciTech Connect

    Georgeton, G.K.; Poirier, M.R.

    1990-09-28

    Based on results of testing eight solids removal technologies and one pretreatment option, it is recommended that a centrifugal ultrafilter and polymeric ultrafilter undergo further testing as possible alternatives to the Norton Ceramic filters. Deep bed filtration should be considered as a third alternative, if a backwashable cartridge filter is shown to be inefficient in separate testing.

  2. Supports and Enhancements Designed for Alternative School Programming

    ERIC Educational Resources Information Center

    Menendez, Anthony L.

    2007-01-01

    In this informational survey, the author briefly explores the needs of professional staff and administrators who serve students in alternative educational settings and special education and provides a listing of helpful Internet resources. Initially, the author provides general information concerning the current state of alternative education…

  3. 78 FR 62472 - Energy Conservation Program: Alternative Efficiency Determination Methods, Basic Model Definition...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-22

    ...; ] DEPARTMENT OF ENERGY 10 CFR Parts 429 and 431 RIN 1904-AC46 Energy Conservation Program: Alternative... alternatives to testing for the purposes of certifying compliance with the applicable energy conservation..., U.S. Department of Energy, Building Technologies Office, Mailstop EE-2J, Alternative...

  4. Functional Dissection of an Alternatively Spliced Herpesvirus Gene by Splice Site Mutagenesis

    PubMed Central

    Schommartz, Tim; Loroch, Stefan; Alawi, Malik; Grundhoff, Adam; Sickmann, Albert

    2016-01-01

    ABSTRACT Herpesviruses have large and complex DNA genomes. The largest among the herpesviruses, those of the cytomegaloviruses, include over 170 genes. Although most herpesvirus gene products are expressed from unspliced transcripts, a substantial number of viral transcripts are spliced. Some viral transcripts are subject to alternative splicing, which leads to the expression of several proteins from a single gene. Functional analysis of individual proteins derived from an alternatively spliced gene is difficult, as deletion and nonsense mutagenesis, both common methods used in the generation of viral gene knockout mutants, affect several or all gene products at the same time. Here, we show that individual gene products of an alternatively spliced herpesvirus gene can be inactivated selectively by mutagenesis of the splice donor or acceptor site and by intron deletion or substitution mutagenesis. We used this strategy to dissect the essential M112/113 gene of murine cytomegalovirus (MCMV), which encodes the MCMV Early 1 (E1) proteins. The expression of each of the four E1 protein isoforms was inactivated individually, and the requirement for each isoform in MCMV replication was analyzed in fibroblasts, endothelial cells, and macrophages. We show that the E1 p87 isoform, but not the p33, p36, and p38 isoforms, is essential for viral replication in cell culture. Moreover, the presence of one of the two medium-size isoforms (p36 or p38) and the presence of intron 1, but not its specific sequence, are required for viral replication. This study demonstrates the usefulness of splice site mutagenesis for the functional analysis of alternatively spliced herpesvirus genes. IMPORTANCE Herpesviruses include up to 170 genes in their DNA genomes. The functions of most viral gene products remain poorly defined. The construction of viral gene knockout mutants has thus been an important tool for functional analysis of viral proteins. However, this strategy is of limited use when

  5. Considerations for Coursework and Mentoring in an Alternative-Route-to- Licensure Program for STEM Teachers

    ERIC Educational Resources Information Center

    Burbank, Mary D.; Shooter, Wynn; Groth, Cori A

    2014-01-01

    The purpose of this project was to investigate stakeholders' perspectives on coursework and the role of mentors within a unique teacher education program for prospective teachers of mathematics in an alternative-route-to-licensure program. The alternative route reflects a partnership between an institution of higher education, a state office…

  6. Interweaving Teaching and Emotional Support for Novice Special Educators in Alternative Certification Programs

    ERIC Educational Resources Information Center

    Ricci, Leila Ansari; Zetlin, Andrea G.

    2013-01-01

    As the shortage of special education teachers has led to increasing numbers of teacher candidates enrolled in alternative certification programs, there is a need to provide systematic mentoring and coaching. The relationship between support providers and novice teachers enrolled in an alternative certification program in a diverse, urban…

  7. A Meta-Analytic Assessment of Delinquency-Related Outcomes of Alternative Education Programs.

    ERIC Educational Resources Information Center

    Cox, Stephen M.; And Others

    1995-01-01

    Reports results of meta-analysis to quantitatively summarize prior empirical research on alternative schools. Alternative education programs have a small overall effect on school performance, attitudes toward school, and self-esteem, but no effect on delinquency. Programs that target a specific population of at-risk youth produce larger effects…

  8. A Gene Regulatory Program in Human Breast Cancer.

    PubMed

    Li, Renhua; Campos, John; Iida, Joji

    2015-12-01

    Molecular heterogeneity in human breast cancer has challenged diagnosis, prognosis, and clinical treatment. It is well known that molecular subtypes of breast tumors are associated with significant differences in prognosis and survival. Assuming that the differences are attributed to subtype-specific pathways, we then suspect that there might be gene regulatory mechanisms that modulate the behavior of the pathways and their interactions. In this study, we proposed an integrated methodology, including machine learning and information theory, to explore the mechanisms. Using existing data from three large cohorts of human breast cancer populations, we have identified an ensemble of 16 master regulator genes (or MR16) that can discriminate breast tumor samples into four major subtypes. Evidence from gene expression across the three cohorts has consistently indicated that the MR16 can be divided into two groups that demonstrate subtype-specific gene expression patterns. For example, group 1 MRs, including ESR1, FOXA1, and GATA3, are overexpressed in luminal A and luminal B subtypes, but lowly expressed in HER2-enriched and basal-like subtypes. In contrast, group 2 MRs, including FOXM1, EZH2, MYBL2, and ZNF695, display an opposite pattern. Furthermore, evidence from mutual information modeling has congruently indicated that the two groups of MRs either up- or down-regulate cancer driver-related genes in opposite directions. Furthermore, integration of somatic mutations with pathway changes leads to identification of canonical genomic alternations in a subtype-specific fashion. Taken together, these studies have implicated a gene regulatory program for breast tumor progression.

  9. Structure of the human myelin/oligodendrocyte glycoprotein gene and multiple alternative spliced isoforms

    SciTech Connect

    Pham-Dinh, D.; Gaspera, D.B.; Dautigny, A.

    1995-09-20

    Myelin/oligodendrocyte glycoprotein (MOG), a special component of the central nervous system localization on the outermost lamellae of mature myelin, is a member of the immunoglobulin superfamily. We report here the organization of the human MOG gene, which spans approximately 17 kb, and the characterization of six MOG mRNA splicing variants. The intron/exon structure of the human MOG gene confirmed the splicing pattern, supporting the hypothesis that mRNA isoforms could arise by alternative splicing of a single gene. In addition to the eight exons coding for the major MOG isoform, the human MOG gene also contains 3` region, a previously unknown alternatively spliced coding exon, VIA. Alternative utilization of two acceptor splicing sites for exon VIII could produce two different C-termini. The nucleotide sequences presented here may be a useful tool to study further possible involvement if the MOG gene in hereditary neurological disorders. 23 refs., 5 figs.

  10. Alternative Transposition Generates New Chimeric Genes and Segmental Duplications at the Maize p1 Locus.

    PubMed

    Wang, Dafang; Yu, Chuanhe; Zuo, Tao; Zhang, Jianbo; Weber, David F; Peterson, Thomas

    2015-11-01

    The maize Ac/Ds transposon family was the first transposable element system identified and characterized by Barbara McClintock. Ac/Ds transposons belong to the hAT family of class II DNA transposons. We and others have shown that Ac/Ds elements can undergo a process of alternative transposition in which the Ac/Ds transposase acts on the termini of two separate, nearby transposons. Because these termini are present in different elements, alternative transposition can generate a variety of genome alterations such as inversions, duplications, deletions, and translocations. Moreover, Ac/Ds elements transpose preferentially into genic regions, suggesting that structural changes arising from alternative transposition may potentially generate chimeric genes at the rearrangement breakpoints. Here we identified and characterized 11 independent cases of gene fusion induced by Ac alternative transposition. In each case, a functional chimeric gene was created by fusion of two linked, paralogous genes; moreover, each event was associated with duplication of the ∼70-kb segment located between the two paralogs. An extant gene in the maize B73 genome that contains an internal duplication apparently generated by an alternative transposition event was also identified. Our study demonstrates that alternative transposition-induced duplications may be a source for spontaneous creation of diverse genome structures and novel genes in maize. PMID:26434719

  11. Alternative Transposition Generates New Chimeric Genes and Segmental Duplications at the Maize p1 Locus.

    PubMed

    Wang, Dafang; Yu, Chuanhe; Zuo, Tao; Zhang, Jianbo; Weber, David F; Peterson, Thomas

    2015-11-01

    The maize Ac/Ds transposon family was the first transposable element system identified and characterized by Barbara McClintock. Ac/Ds transposons belong to the hAT family of class II DNA transposons. We and others have shown that Ac/Ds elements can undergo a process of alternative transposition in which the Ac/Ds transposase acts on the termini of two separate, nearby transposons. Because these termini are present in different elements, alternative transposition can generate a variety of genome alterations such as inversions, duplications, deletions, and translocations. Moreover, Ac/Ds elements transpose preferentially into genic regions, suggesting that structural changes arising from alternative transposition may potentially generate chimeric genes at the rearrangement breakpoints. Here we identified and characterized 11 independent cases of gene fusion induced by Ac alternative transposition. In each case, a functional chimeric gene was created by fusion of two linked, paralogous genes; moreover, each event was associated with duplication of the ∼70-kb segment located between the two paralogs. An extant gene in the maize B73 genome that contains an internal duplication apparently generated by an alternative transposition event was also identified. Our study demonstrates that alternative transposition-induced duplications may be a source for spontaneous creation of diverse genome structures and novel genes in maize.

  12. Alternative Transposition Generates New Chimeric Genes and Segmental Duplications at the Maize p1 Locus

    PubMed Central

    Wang, Dafang; Yu, Chuanhe; Zuo, Tao; Zhang, Jianbo; Weber, David F.; Peterson, Thomas

    2015-01-01

    The maize Ac/Ds transposon family was the first transposable element system identified and characterized by Barbara McClintock. Ac/Ds transposons belong to the hAT family of class II DNA transposons. We and others have shown that Ac/Ds elements can undergo a process of alternative transposition in which the Ac/Ds transposase acts on the termini of two separate, nearby transposons. Because these termini are present in different elements, alternative transposition can generate a variety of genome alterations such as inversions, duplications, deletions, and translocations. Moreover, Ac/Ds elements transpose preferentially into genic regions, suggesting that structural changes arising from alternative transposition may potentially generate chimeric genes at the rearrangement breakpoints. Here we identified and characterized 11 independent cases of gene fusion induced by Ac alternative transposition. In each case, a functional chimeric gene was created by fusion of two linked, paralogous genes; moreover, each event was associated with duplication of the ∼70-kb segment located between the two paralogs. An extant gene in the maize B73 genome that contains an internal duplication apparently generated by an alternative transposition event was also identified. Our study demonstrates that alternative transposition-induced duplications may be a source for spontaneous creation of diverse genome structures and novel genes in maize. PMID:26434719

  13. Design and Implementation Considerations for Alternative Teacher Compensation Programs

    ERIC Educational Resources Information Center

    Brodsky, Andrew; DeCesare, Dale; Kramer-Wine, Jennifer

    2010-01-01

    Over the past decade, educators and policymakers have used a variety of approaches to designing and implementing teacher compensation programs. These approaches include federal incentive funds, state-level programs, and district initiatives. This article reviews 6 such programs in order to identify themes and draw conclusions relevant to…

  14. Brayton heat exchanger unit development program (alternate design)

    NASA Technical Reports Server (NTRS)

    Duncan, J. D.; Gibson, J. C.; Graves, R. F.; Morse, C. J.; Richard, C. E.

    1973-01-01

    A Brayton Heat Exchanger Unit Alternate Design (BHXU-Alternate) consisting of a recuperator, a heat sink heat exchanger, and a gas ducting system, was designed and fabricated. The design was formulated to provide a high performance unit suitable for use in a long-life Brayton-cycle powerplant. Emphasis was on double containment against external leakage and leakage of the organic coolant into the gas stream. A parametric analysis and design study was performed to establish the optimum component configurations to achieve low weight and size and high reliability, while meeting the requirements of high effectiveness and low pressure drop. Layout studies and detailed mechanical and structural design were performed to obtain a flight-type packaging arrangement, including the close-coupled integration of the BHXU-Alternate with the Brayton Rotating Unit (BRU).

  15. Gene, Stem Cell, and Alternative Therapies for SCA 1

    PubMed Central

    Wagner, Jacob L.; O'Connor, Deirdre M.; Donsante, Anthony; Boulis, Nicholas M.

    2016-01-01

    Spinocerebellar ataxia 1 is an autosomal dominant disease characterized by neurodegeneration and motor dysfunction. In disease pathogenesis, polyglutamine expansion within Ataxin-1, a gene involved in transcriptional repression, causes protein nuclear inclusions to form. Most notably, neuronal dysfunction presents in Purkinje cells. However, the effect of mutant Ataxin-1 is not entirely understood. Two mouse models are employed to represent spinocerebellar ataxia 1, a B05 transgenic model that specifically expresses mutant Ataxin-1 in Purkinje cells, and a Sca1 154Q/2Q model that inserts the polyglutamine expansion into the mouse Ataxin-1 locus so that the mutant Ataxin-1 is expressed in all cells that express Ataxin-1. This review aims to summarize and evaluate the wide variety of therapies proposed for spinocerebellar ataxia 1, specifically gene and stem cell therapies. PMID:27570504

  16. Gene, Stem Cell, and Alternative Therapies for SCA 1.

    PubMed

    Wagner, Jacob L; O'Connor, Deirdre M; Donsante, Anthony; Boulis, Nicholas M

    2016-01-01

    Spinocerebellar ataxia 1 is an autosomal dominant disease characterized by neurodegeneration and motor dysfunction. In disease pathogenesis, polyglutamine expansion within Ataxin-1, a gene involved in transcriptional repression, causes protein nuclear inclusions to form. Most notably, neuronal dysfunction presents in Purkinje cells. However, the effect of mutant Ataxin-1 is not entirely understood. Two mouse models are employed to represent spinocerebellar ataxia 1, a B05 transgenic model that specifically expresses mutant Ataxin-1 in Purkinje cells, and a Sca1 154Q/2Q model that inserts the polyglutamine expansion into the mouse Ataxin-1 locus so that the mutant Ataxin-1 is expressed in all cells that express Ataxin-1. This review aims to summarize and evaluate the wide variety of therapies proposed for spinocerebellar ataxia 1, specifically gene and stem cell therapies. PMID:27570504

  17. Alternative splicing of the FMR1 gene in human fetal brain neurons

    SciTech Connect

    Tao Huang; Yan Shen; Xue-bin Qin; Guan-Yun Wu

    1996-08-09

    The alternative splicing expression of the FMR1 gene was reported in several human and mouse tissues. Five regions of FMR1 gene can be alternatively spliced, but the combination of them has not been investigated fully. We reported here the analysis of alternative splicing pattern of the FMR1 gene in cultured fetal human neurons, using a RT-PCR and cloning strategy. Eleven splicing types were cloned and different isoforms were not equally represented. The dominant isoform represents nearly 40%, and the other isoforms were relatively rare. One isoform has a different carboxyl-terminus. Most of the alternative spliced regions appear hydrophilic; thus, they may locate on the surface of the FMR1 protein. 16 refs., 2 figs.

  18. Heat-inducible gene expression system by applying alternating magnetic field to magnetic nanoparticles.

    PubMed

    Yamaguchi, Masaki; Ito, Akira; Ono, Akihiko; Kawabe, Yoshinori; Kamihira, Masamichi

    2014-05-16

    By combining synthetic biology with nanotechnology, we demonstrate remote controlled gene expression using a magnetic field. Magnetite nanoparticles, which generate heat under an alternating magnetic field, have been developed to label cells. Magnetite nanoparticles and heat-induced therapeutic genes were introduced into tumor xenografts. The magnetically triggered gene expression resulted in tumor growth inhibition. This system shows great potential for controlling target gene expression in a space and time selective manner and may be used for remote control of cell functions via gene expression. PMID:24144205

  19. Personality Types of Interns in Alternative Teacher Certification Programs.

    ERIC Educational Resources Information Center

    Meisgeier, Charles H.; Richardson, Rita C.

    1996-01-01

    Alternative teacher certification interns in special education (n=92) completed the Myers Briggs Type Indicator (MBTI), and results were used to develop a personality profile of types useful for the development of teacher training. Use of the MBTI also exposed interns to understanding the personality types of the children they will be teaching.…

  20. 24 CFR 7.5 - EEO Alternative Dispute Resolution Program.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... Statement regarding Alternative Dispute Resolution (ADR) located on the Department's website and 29 CFR 1614... 29 CFR 1614.105(c). The aggrieved person's election to proceed through ADR instead of EEO counseling... terms, the aggrieved person or Complainant may exercise the right of appeal pursuant to 29 CFR...

  1. 24 CFR 7.5 - EEO Alternative Dispute Resolution Program.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... Statement regarding Alternative Dispute Resolution (ADR) located on the Department's website and 29 CFR 1614... 29 CFR 1614.105(c). The aggrieved person's election to proceed through ADR instead of EEO counseling... terms, the aggrieved person or Complainant may exercise the right of appeal pursuant to 29 CFR...

  2. 24 CFR 7.5 - EEO Alternative Dispute Resolution Program.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... Statement regarding Alternative Dispute Resolution (ADR) located on the Department's website and 29 CFR 1614... 29 CFR 1614.105(c). The aggrieved person's election to proceed through ADR instead of EEO counseling... terms, the aggrieved person or Complainant may exercise the right of appeal pursuant to 29 CFR...

  3. 24 CFR 7.5 - EEO Alternative Dispute Resolution Program.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... Statement regarding Alternative Dispute Resolution (ADR) located on the Department's website and 29 CFR 1614... 29 CFR 1614.105(c). The aggrieved person's election to proceed through ADR instead of EEO counseling... terms, the aggrieved person or Complainant may exercise the right of appeal pursuant to 29 CFR...

  4. 24 CFR 7.5 - EEO Alternative Dispute Resolution Program.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... Statement regarding Alternative Dispute Resolution (ADR) located on the Department's website and 29 CFR 1614... 29 CFR 1614.105(c). The aggrieved person's election to proceed through ADR instead of EEO counseling... terms, the aggrieved person or Complainant may exercise the right of appeal pursuant to 29 CFR...

  5. ORNL Research Programs related to chlorofluorocarbon (CFC) alternatives. [Chlorofluorocarbons

    SciTech Connect

    Fairchild, P.D.

    1987-05-13

    Testimony covered: uses and control impacts; federal/Department of Energy role; and relevant DOE research and development (absorption cycle technology, advanced insulation, novel thermodynamic cycles, fluid substitutes and recovery technology, development of replacement chemicals, development of recycling and recovery practices, development of alternative technologies, and resource requirements and schedules for accomplishment). (PSB)

  6. 76 FR 77716 - Alternate Passenger Rail Service Pilot Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-14

    ... proposed rulemaking (NPRM) published on September 7, 2011 (76 FR 55335), FRA proposed an alternate... 44 FR 11034; February 26, 1979. FRA has prepared and placed in the docket a regulatory impact... jurisdictions that serve populations of 50,000 or less. See 68 FR 24891 (May 9, 2003) (codified at Appendix C...

  7. Survey and Analysis of Alternative Education Programs II

    ERIC Educational Resources Information Center

    Hosley, Nathaniel S.; Hosley, Jessica; Thein, Myint

    2009-01-01

    This research is a follow up to a similar study published by the Center for Rural Pennsylvania in 2003 in which researchers examined alternative education policies and practices among Pennsylvania school districts. The current study extended the previous research to include information on the perceptions of administrators and teachers on the…

  8. Alternative Education and Employment Preparation for Youth. The Eidos Program.

    ERIC Educational Resources Information Center

    Boyd, Sheila; Regner, Christine

    The Eidos Program, sponsored by the Idyllic Foundation, is a private community-based organization that, with schools and other cooperating agencies and sponsors, helps young people whose needs are not adequately met by existing instituions. The program, which was funded for six months by the Job Training Partnership Act, provided educational and…

  9. An Economic Analysis of Alternative Programs to Finance Higher Education.

    ERIC Educational Resources Information Center

    Mathematica, Inc., Bethesda, MD.

    The Federal government operates several programs that provide money, either as loans or as a combination of grants and loans, to students. This paper attempts to clarify the economic and budgetary implications associated with continuing these existing programs, and discusses the differing economic consequences that would follow if some alternative…

  10. Newcomer Programs: An Educational Alternative for Secondary Immigrant Students.

    ERIC Educational Resources Information Center

    Short, Deborah J.

    2002-01-01

    Examines the small but growing presence of newcomer programs being implemented in urban middle and high schools, providing the rationale for newcomer schools for recent, limited-English-speaking immigrants and summarizing data collected from a national study. Describes program designs in urban schools and their educational goals, instructional…

  11. Development and Delivery of an FCS Alternative Program for License

    ERIC Educational Resources Information Center

    Larson, Marsha L.

    2013-01-01

    When addressing the ongoing shortage of family and consumer sciences (FCS) teachers, it is important to accommodate those unable to follow a traditional college program. This article describes a program that is beneficial to practicing professionals; it utilizes technology to aid in effective communication and efficiency of content delivery.…

  12. Digital-computer program for design analysis of salient, wound pole alternators

    NASA Technical Reports Server (NTRS)

    Repas, D. S.

    1973-01-01

    A digital computer program for analyzing the electromagnetic design of salient, wound pole alternators is presented. The program, which is written in FORTRAN 4, calculates the open-circuit saturation curve, the field-current requirements at rated voltage for various loads and losses, efficiency, reactances, time constants, and weights. The methods used to calculate some of these items are presented or appropriate references are cited. Instructions for using the program and typical program input and output for an alternator design are given, and an alphabetical list of most FORTRAN symbols and the complete program listing with flow charts are included.

  13. EPAct Alternative Fuel Transportation Program: State and Alternative Fuel Provider Fleet Compliance Annual Report; Fleet Compliance Results for MY 2013/FY 2014

    SciTech Connect

    2015-09-01

    Compliance rates for covered state government and alternative fuel provider fleets under the Alternative Fuel Transportation Program (pursuant to the Energy Policy Act or EPAct) are reported for MY 2013/FY 2014 in this publication.

  14. FEMP (Federal Energy Management Program) presents alternative financing guidance memoranda

    SciTech Connect

    1998-06-01

    Utility financing of energy efficient measures becomes easier to accomplish with the two new alternative financing guidance memoranda, released April 17, 1998, that address the use of utility incentives for Federal facilities. The memoranda have been approved by the Alternative Financing Guidance Committee on the Interagency Energy Management Task Force. The memoranda include: (1) Policy Statement No. 001: Authority to Sole Source Utility Service Contracts as Referenced in Section 152 of the Energy Policy Act (EPACT) of 1992; and (2) Policy Statement No. 002: Congressional Notification for Utility Projects Under the Authority of Section 152 of the Energy Policy Act (EPACT) of 1992. The purpose for developing the financing memoranda was to address specific issues within current Federal procurement regulations that require clarification or guidance. This new guidance will allow for increased use of utility incentives as a means of financing energy efficient and life cycle cost-effective projects in Federal facilities.

  15. An Alternative Kaposi's Sarcoma-Associated Herpesvirus Replication Program Triggered by Host Cell Apoptosis

    PubMed Central

    Prasad, Alka; Lu, Michael; Lukac, David M.

    2012-01-01

    Kaposi's sarcoma-associated herpesvirus (KSHV) is linked to several neoplastic diseases: Kaposi's sarcoma, primary effusion lymphoma (PEL), and multicentric Castleman's disease (MCD). KSHV replicates actively, via a controlled gene expression program, but can also remain latent. It had been thought that the transition from latent to lytic replication was controlled exclusively by the replication and transcription activator protein RTA (open reading frame 50 [ORF50] gene product). A dominant-negative (DN) ORF50 mutant, ORF50ΔSTAD, blocks gene expression and replication. We produced a PEL cell line derivative containing both latent KSHV genomes and an inducible ORF50ΔSTAD. We unexpectedly found that induction of apoptosis triggered high-level viral replication, even when DN ORF50ΔSTAD was present, suggesting that apoptosis triggers KSHV replication through a distinct RTA-independent pathway. We verified that apoptosis triggers KSHV replication independent of RTA using ORF50 small interfering RNA (siRNA) and also showed that caspase activity is required to trigger KSHV replication. We showed that when apoptosis triggers KSHV replication, the kinetics of late gene expression is accelerated by 12 to 24 h and that virus produced following apoptosis has reduced infectivity. KSHV therefore appears to replicate via two distinct pathways, a conventional pathway requiring RTA, with slower replication kinetics, producing virus with higher infectivity, and an alternative apoptosis-triggered pathway that does not require RTA, has faster replication kinetics, and produces virus with lower infectivity. The existence of a distinct apoptosis-triggered, accelerated replication pathway may have evolutionary advantages for the virus and clinical significance for the treatment of KSHV-associated neoplasms. It also provides further evidence that KSHV can sense and react to its environment. PMID:22345480

  16. What the Research Says about Alternative Teacher Certification Programs. Information Capsule. Volume 1104

    ERIC Educational Resources Information Center

    Blazer, Christie

    2012-01-01

    The shortage of qualified teachers across the U.S. has contributed to the popularity of alternative certification programs. These programs are designed to attract individuals into the teaching profession by allowing candidates to become certified without having to complete a traditional teacher education program. This Information Capsule reviewed…

  17. AB 3059: A Report to the Governor on the Alternative Child Care Programs, 1976-80.

    ERIC Educational Resources Information Center

    Hailey, Jack

    This publication of the California Governor's Committee on Child Development Programs focuses on the Alternative Child Care Program in California (AB 3059). The report looks back over four years of the AB 3059, reviews the goals of that legislation, and measures the program's accomplishments against those goals. In early 1976, the Governor's…

  18. Alternate bearing design fabrication and test program, exhibit B

    NASA Technical Reports Server (NTRS)

    1978-01-01

    A 50 ft-lb-sec (FPS) reaction wheel was modified with an ironless armature brushless dc motor and a magnetic bearing suspension. The purpose was to demonstrate the performance of an alternate bearing concept, i.e., a magnetic bearing suspension, which could be used in Skylab type CMG's to meet the attitude control requirements of long term space stations. A magnetic suspension was built, installed and tested in the 50 FPS reaction wheel. A secondary effort included the build and test of a compatible reaction wheel motor. Performance characteristics of both are presented and discussed.

  19. An Alternative Preparation Program in Early Childhood Education: Description and Comparison of Alternative and Traditional Students.

    ERIC Educational Resources Information Center

    Guyton, Edith; And Others

    1993-01-01

    Students entering traditional and nontraditional early childhood teacher preparation programs completed the Educational Attitudes Inventory, Teacher Certification Test, and Efficacy Scale. Mean personal teaching efficacy scores were significantly higher for traditional students. Nontraditional students tended to be males, minorities, and older,…

  20. SELENIUM TREATMENT/REMOVAL ALTERNATIVES DEMONSTRATION PROJECT - MINE WASTE TECHNOLOGY PROGRAM ACTIVITY III, PROJECT 20

    EPA Science Inventory

    This document is the final report for EPA's Mine WAste Technology Program (MWTP) Activity III, Project 20--Selenium Treatment/Removal Alternatives Demonstration project. Selenium contamination originates from many sources including mining operations, mineral processing, abandoned...

  1. Pacific area wide program for methyl bromide alternatives – Ornamentals

    Technology Transfer Automated Retrieval System (TEKTRAN)

    During the past 5 years the following field trials have been conducted as part of the Pacific Area-Wide program for cut flowers and ornamentals using various combinations of 1, 3-dichloropropene, chloropicrin, and metam: 1) Drip demonstration trial with field-grown calla lilies at Golden State Bulb ...

  2. 36 CFR 800.14 - Federal agency program alternatives.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... historic properties are similar and repetitive or are multi-State or regional in scope; (ii) When effects... participation in consultation or Council signature. (c) Exempted categories—(1) Criteria for establishing. The... criteria: (i) The actions within the program or category would otherwise qualify as “undertakings”...

  3. Alternative Loan Programs: A Comparison of Various Features.

    ERIC Educational Resources Information Center

    New York State Higher Education Services Corp., Albany.

    This report provides comparative data on various features of 36 student loan programs available to undergraduate and/or graduate students in New York. Presented in a table format, the report provides information on loan type, lender, maximum limit, minimum limit, interest rate/payment, fees, repayment guidelines, eligibility, disbursement, and…

  4. Clarendon Alternative School Japanese Bilingual Bicultural Program: Curriculum Sampler.

    ERIC Educational Resources Information Center

    San Francisco Unified School District, CA.

    Sample lessons and instructional materials from a Japanese bilingual/bicultural elementary school program are presented. The lessons are designed to integrate Japanese language instruction with content instruction, using thematic units related to the core curriculum. The ten lessons are organized by target grade (K-5), and describe classroom…

  5. 76 FR 64124 - Implementation of the Alternative Dispute Resolution Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-17

    ... INFORMATION: I. Background On September 6, 2011 (76 FR 55136), the NRC announced its intention to hold a... the program's effectiveness, transparency, and efficiency, as well as several specific questions that... environment by facilitating timely and amicable resolution of discrimination concerns without resorting...

  6. Virginia Alternative Assessment Program: Implementation Manual (Revised 2002).

    ERIC Educational Resources Information Center

    Virginia State Dept. of Education, Richmond.

    The Individuals with Disabilities Education Act requires state programs to adopt standards for all children, including those with disabilities, in state and district-wide assessments with the provision of appropriate and necessary accommodations. For students who cannot participate in state and district-wide assessments, the law requires that…

  7. Alternative Programs for At-Risk Students: Wolves in Sheep's Clothing?

    ERIC Educational Resources Information Center

    Sagor, Richard

    1997-01-01

    Provides a critique of alternative education and details the disadvantages of segregated schooling. Discusses the problems associated with labeling children as "problem students" and outlines ways in which equitable alternative programs can be devised. Gives a case study as an example. (RJM)

  8. Alternative Break Programs: From Isolated Enthusiasm to Best Practices--The Haiti Compact

    ERIC Educational Resources Information Center

    Piacitelli, Jill; Barwick, Molly; Doerr, Elizabeth; Porter, Melody; Sumka, Shoshanna

    2013-01-01

    Alternative break programs, which are short-term service-learning trips, immerse students in direct service and education, resulting in the creation of active citizens who think and act critically around the root causes of social issues. Over the last 20 years, domestic alternative breaks have effectively created strong community partnerships and…

  9. 76 FR 72493 - ITS Joint Program Office Webinar on Alternative Organizational Structures for a Certificate...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-23

    ... ITS Joint Program Office Webinar on Alternative Organizational Structures for a Certificate Management...:00-3 p.m. (EST) to seek input on a set of high-level, alternative organizational structures for a... rapid and secure wireless communications and trusted data exchanges among vehicles,...

  10. Inclusion of Alternative and Complementary Therapies in CACREP Training Programs: A Survey

    ERIC Educational Resources Information Center

    Lumadue, Christine A.; Munk, Melanie; Wooten, H. Ray

    2005-01-01

    Given a heightened focus within the mental health profession on creative, complementary, and alternative practices, the authors surveyed CACREP programs with respect to their inclusion of such approaches in counselor training. For the purpose of this study, these approaches were designated as complementary and alternative methods (CAM) and defined…

  11. Educational Alternatives for Vulnerable Youth: Student Needs, Program Types, and Research Directions

    ERIC Educational Resources Information Center

    Aron, Laudan Y.; Zweig, Janine M.

    2003-01-01

    Chapter 1 of this document examines the need for alternative education among vulnerable youth by reviewing the numbers and characteristics of youth who disconnect from mainstream developmental pathways in various ways. The second chapter examines the question of "what is an alternative education school or program" and draws on a variety…

  12. Factors Associated with Student Resilience: Perspectives of Graduates of Alternative Education Programs

    ERIC Educational Resources Information Center

    Zolkoski, Staci M.; Bullock, Lyndal M.; Gable, Robert A.

    2016-01-01

    Many students with emotional and behavioral disorders placed in alternative education settings lack resilience and are likely to experience failure in school and beyond without carefully designed intervention programs. Although researchers have examined both resilience in children and youth and their placement in alternative education settings,…

  13. 5 CFR 2424.10 - Collaboration and Alternative Dispute Resolution Program.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 3 2010-01-01 2010-01-01 false Collaboration and Alternative Dispute... Collaboration and Alternative Dispute Resolution Program. Where an exclusive representative and an agency are unable to resolve disputes that arise under this part, they may request assistance from the...

  14. Reconstruction and minimal gene requirements for the alternative iron-only nitrogenase in Escherichia coli

    PubMed Central

    Yang, Jianguo; Xie, Xiaqing; Wang, Xia; Dixon, Ray; Wang, Yi-Ping

    2014-01-01

    All diazotrophic organisms sequenced to date encode a molybdenum-dependent nitrogenase, but some also have alternative nitrogenases that are dependent on either vanadium (VFe) or iron only (FeFe) for activity. In Azotobacter vinelandii, expression of the three different types of nitrogenase is regulated in response to metal availability. The majority of genes required for nitrogen fixation in this organism are encoded in the nitrogen fixation (nif) gene clusters, whereas genes specific for vanadium- or iron-dependent diazotophy are encoded by the vanadium nitrogen fixation (vnf) and alternative nitrogen fixation (anf) genes, respectively. Due to the complexities of metal-dependent regulation and gene redundancy in A. vinelandii, it has been difficult to determine the precise genetic requirements for alternative nitrogen fixation. In this study, we have used Escherichia coli as a chassis to build an artificial iron-only (Anf) nitrogenase system composed of defined anf and nif genes. Using this system, we demonstrate that the pathway for biosynthesis of the iron-only cofactor (FeFe-co) is likely to be simpler than the pathway for biosynthesis of the molybdenum-dependent cofactor (FeMo-co) equivalent. A number of genes considered to be essential for nitrogen fixation by FeFe nitrogenase, including nifM, vnfEN, and anfOR, are not required for the artificial Anf system in E. coli. This finding has enabled us to engineer a minimal FeFe nitrogenase system comprising the structural anfHDGK genes and the nifBUSV genes required for metallocluster biosynthesis, with nifF and nifJ providing electron transport to the alternative nitrogenase. This minimal Anf system has potential implications for engineering diazotrophy in eukaryotes, particularly in compartments (e.g., organelles) where molybdenum may be limiting. PMID:25139995

  15. Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array

    PubMed Central

    Singer, Gregory AC; Wu, Jiejun; Yan, Pearlly; Plass, Christoph; Huang, Tim HM; Davuluri, Ramana V

    2008-01-01

    Background Independent lines of evidence suggested that a large fraction of human genes possess multiple promoters driving gene expression from distinct transcription start sites. Understanding which promoter is employed in which cellular context is required to unravel gene regulatory networks within the cell. Results We have developed a custom microarray platform that tiles roughly 35,000 alternative putative promoters from nearly 7,000 genes in the human genome. To demonstrate the utility of this array platform, we have analyzed the patterns of promoter usage in 17β-estradiol (E2)-treated and untreated MCF7 cells and show widespread usage of alternative promoters. Most intriguingly, we show that the downstream promoter in E2-sensitive multiple promoter genes tends to be very close to the 3'-terminus of the gene, suggesting exotic mechanisms of expression regulation in these genes. Conclusion The usage of alternative promoters greatly multiplies the transcriptional complexity available within the human genome. The fact that many of these promoters are incapable of driving the synthesis of a meaningful protein-encoding transcript further complicates the story. PMID:18655706

  16. Update from the NREL Alternative Fuel Transit Bus Evaluation Program

    SciTech Connect

    Chandler, K.; Norton, P.; Clark, N.

    1999-05-01

    The object of this project, which is supported by the U.S. Department of Energy (DOE) through the National Renewable Energy Laboratory (NREL), is to provide a comprehensive comparison of heavy-duty urban transit buses operating on alternative fuels and diesel fuel. Final reports from this project were produced in 1996 from data collection and evaluation of 11 transit buses from eight transit sites. With the publication of these final reports, three issues were raised that needed further investigation: (1) the natural gas engines studied were older, open-loop control engines; (2) propane was not included in the original study; and (3) liquefied natural gas (LNG) was found to be in the early stages of deployment in transit applications. In response to these three issues, the project has continued by emissions testing newer natural gas engines and adding two new data collection sites to study the newer natural gas technology and specifically to measure new technology LNG buses.

  17. Prokaryotic origins for the mitochondrial alternative oxidase and plastid terminal oxidase nuclear genes.

    PubMed

    Finnegan, Patrick M; Umbach, Ann L; Wilce, Jackie A

    2003-12-18

    The mitochondrial alternative oxidase is a diiron carboxylate quinol oxidase (Dox) found in plants and some fungi and protists, but not animals. The plastid terminal oxidase is distantly related to alternative oxidase and is most likely also a Dox protein. Database searches revealed that the alpha-proteobacterium Novosphingobium aromaticivorans and the cyanobacteria Nostoc sp. PCC7120, Synechococcus sp. WH8102 and Prochlorococcus marinus subsp. pastoris CCMP1378 each possess a Dox homolog. Each prokaryotic protein conforms to the current structural models of the Dox active site and phylogenetic analyses suggest that the eukaryotic Dox genes arose from an ancestral prokaryotic gene.

  18. Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation of paralogous genes in Daphnia.

    PubMed

    Asselman, Jana; Pfrender, Michael E; Lopez, Jacqueline A; De Coninck, Dieter I M; Janssen, Colin R; Shaw, Joseph R; De Schamphelaere, Karel A C

    2015-04-01

    Despite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli. Daphnia were exposed to five different treatments, each consisting of a diet supplemented with one of five cyanobacterial species, and a control treatment consisting of a diet of only green algae. Differential gene expression profiles of Daphnia exposed to each of these five cyanobacterial species showed that genes with known functions are more likely to be shared by different expression profiles, whereas genes specific to the lineage of Daphnia are more likely to be unique to a given expression profile. Furthermore, while only a small number of nonlineage-specific genes were conserved across treatment type, there was a high degree of overlap in expression profiles at the functional level. The conservation of functional responses across the different cyanobacterial treatments can be attributed to the treatment-specific expression of different paralogous genes within the same gene family. Comparison with available gene expression data in the literature suggests differences in nutritional composition in diets with cyanobacterial species compared to diets of green algae as a primary driver for cyanobacterial effects on Daphnia. We conclude that conserved functional responses in Daphnia across different cyanobacterial treatments are mediated through alternate regulation of paralogous gene families.

  19. A dynamic programming algorithm for finding alternative RNA secondary structures.

    PubMed

    Williams, A L; Tinoco, I

    1986-01-10

    Dynamic programming algorithms that predict RNA secondary structure by minimizing the free energy have had one important limitation. They were able to predict only one optimal structure. Given the uncertainties of the thermodynamic data and the effects of proteins and other environmental factors on structure, the optimal structure predicted by these methods may not have biological significance. We present a dynamic programming algorithm that can determine optimal and suboptimal secondary structures for an RNA. The power and utility of the method is demonstrated in the folding of the intervening sequence of the rRNA of Tetrahymena. By first identifying the major secondary structures corresponding to the lowest free energy minima, a secondary structure of possible biological significance is derived.

  20. Multidimensional Programming Methods for Energy Facility Siting: Alternative Approaches

    NASA Technical Reports Server (NTRS)

    Solomon, B. D.; Haynes, K. E.

    1982-01-01

    The use of multidimensional optimization methods in solving power plant siting problems, which are characterized by several conflicting, noncommensurable objectives is addressed. After a discussion of data requirements and exclusionary site screening methods for bounding the decision space, classes of multiobjective and goal programming models are discussed in the context of finite site selection. Advantages and limitations of these approaches are highlighted and the linkage of multidimensional methods with the subjective, behavioral components of the power plant siting process is emphasized.

  1. Coordinately Regulated Alternative Splicing of Genes Involved in Cholesterol Biosynthesis and Uptake

    PubMed Central

    Naidoo, Devesh; Rudel, Lawrence L.; Temel, Ryan E.; McDaniel, Allison L.; Marshall, Stephanie M.; Krauss, Ronald M.

    2011-01-01

    Genes involved in cholesterol biosynthesis and uptake are transcriptionally regulated in response to cellular sterol content in a coordinated manner. A number of these genes, including 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR) and LDL receptor (LDLR), undergo alternative splicing, resulting in reductions of enzyme or protein activity. Here we demonstrate that cellular sterol depletion suppresses, and sterol loading induces, alternative splicing of multiple genes involved in the maintenance of cholesterol homeostasis including HMGCR and LDLR, the key regulators of cellular cholesterol biosynthesis and uptake, respectively. These changes were observed in both in vitro studies of the HepG2 human hepatoma derived cell line, as well as in vivo studies of St. Kitts vervets, also known as African green monkeys, a commonly used primate model for investigating cholesterol metabolism. These effects are mediated in part by sterol regulation of polypyrimidine tract binding protein 1 (PTBP1), since knock-down of PTBP1 eliminates sterol induced changes in alternative splicing of several of these genes. Single nucleotide polymorphisms (SNPs) that influence HMGCR and LDLR alternative splicing (rs3846662 and rs688, respectively), have been associated with variation in plasma LDL-cholesterol levels. Sterol-induced changes in alternative splicing are blunted in carriers of the minor alleles for each of these SNPs, indicating an interaction between genetic and non-genetic regulation of this process. Our results implicate alternative splicing as a novel mechanism of enhancing the robust transcriptional response to conditions of cellular cholesterol depletion or accumulation. Thus coordinated regulation of alternative splicing may contribute to cellular cholesterol homeostasis as well as plasma LDL levels. PMID:21559365

  2. Global variability in gene expression and alternative splicing is modulated by mitochondrial content.

    PubMed

    Guantes, Raul; Rastrojo, Alberto; Neves, Ricardo; Lima, Ana; Aguado, Begoña; Iborra, Francisco J

    2015-05-01

    Noise in gene expression is a main determinant of phenotypic variability. Increasing experimental evidence suggests that genome-wide cellular constraints largely contribute to the heterogeneity observed in gene products. It is still unclear, however, which global factors affect gene expression noise and to what extent. Since eukaryotic gene expression is an energy demanding process, differences in the energy budget of each cell could determine gene expression differences. Here, we quantify the contribution of mitochondrial variability (a natural source of ATP variation) to global variability in gene expression. We find that changes in mitochondrial content can account for ∼50% of the variability observed in protein levels. This is the combined result of the effect of mitochondria dosage on transcription and translation apparatus content and activities. Moreover, we find that mitochondrial levels have a large impact on alternative splicing, thus modulating both the abundance and type of mRNAs. A simple mathematical model in which mitochondrial content simultaneously affects transcription rate and splicing site choice can explain the alternative splicing data. The results of this study show that mitochondrial content (and/or probably function) influences mRNA abundance, translation, and alternative splicing, which ultimately affects cellular phenotype.

  3. Global variability in gene expression and alternative splicing is modulated by mitochondrial content

    PubMed Central

    Guantes, Raul; Rastrojo, Alberto; Neves, Ricardo; Lima, Ana; Aguado, Begoña; Iborra, Francisco J.

    2015-01-01

    Noise in gene expression is a main determinant of phenotypic variability. Increasing experimental evidence suggests that genome-wide cellular constraints largely contribute to the heterogeneity observed in gene products. It is still unclear, however, which global factors affect gene expression noise and to what extent. Since eukaryotic gene expression is an energy demanding process, differences in the energy budget of each cell could determine gene expression differences. Here, we quantify the contribution of mitochondrial variability (a natural source of ATP variation) to global variability in gene expression. We find that changes in mitochondrial content can account for ∼50% of the variability observed in protein levels. This is the combined result of the effect of mitochondria dosage on transcription and translation apparatus content and activities. Moreover, we find that mitochondrial levels have a large impact on alternative splicing, thus modulating both the abundance and type of mRNAs. A simple mathematical model in which mitochondrial content simultaneously affects transcription rate and splicing site choice can explain the alternative splicing data. The results of this study show that mitochondrial content (and/or probably function) influences mRNA abundance, translation, and alternative splicing, which ultimately affects cellular phenotype. PMID:25800673

  4. Global variability in gene expression and alternative splicing is modulated by mitochondrial content.

    PubMed

    Guantes, Raul; Rastrojo, Alberto; Neves, Ricardo; Lima, Ana; Aguado, Begoña; Iborra, Francisco J

    2015-05-01

    Noise in gene expression is a main determinant of phenotypic variability. Increasing experimental evidence suggests that genome-wide cellular constraints largely contribute to the heterogeneity observed in gene products. It is still unclear, however, which global factors affect gene expression noise and to what extent. Since eukaryotic gene expression is an energy demanding process, differences in the energy budget of each cell could determine gene expression differences. Here, we quantify the contribution of mitochondrial variability (a natural source of ATP variation) to global variability in gene expression. We find that changes in mitochondrial content can account for ∼50% of the variability observed in protein levels. This is the combined result of the effect of mitochondria dosage on transcription and translation apparatus content and activities. Moreover, we find that mitochondrial levels have a large impact on alternative splicing, thus modulating both the abundance and type of mRNAs. A simple mathematical model in which mitochondrial content simultaneously affects transcription rate and splicing site choice can explain the alternative splicing data. The results of this study show that mitochondrial content (and/or probably function) influences mRNA abundance, translation, and alternative splicing, which ultimately affects cellular phenotype. PMID:25800673

  5. Analysis of Genes Encoding an Alternative Nitrogenase in the Archaeon Methanosarcina barkeri 227

    PubMed Central

    Chien, Yueh-Tyng; Auerbuch, Victoria; Brabban, Andrew D.; Zinder, Stephen H.

    2000-01-01

    Methanosarcina barkeri 227 possesses two clusters of genes potentially encoding nitrogenases. We have previously demonstrated that one cluster, called nif2, is expressed under molybdenum (Mo)-sufficient conditions, and the deduced amino acid sequences for nitrogenase structural genes in that cluster most closely resemble those for the Mo nitrogenase of the gram-positive eubacterium Clostridium pasteurianum. The previously cloned nifH1 from M. barkeri shows phylogenetic relationships with genes encoding components of eubacterial Mo-independent eubacterial alternative nitrogenases and other methanogen nitrogenases. In this study, we cloned and sequenced nifD1 and part of nifK1 from M. barkeri 227. The deduced amino acid sequence encoded by nifD1 from M. barkeri showed great similarity with vnfD gene products from vanadium (V) nitrogenases, with an 80% identity at the amino acid level with the vnfD gene product from Anabaena variabilis. Moreover, there was a small open reading frame located between nifD1 and nifK1 with clear homology to vnfG, a hallmark of eubacterial alternative nitrogenases. Stimulation of diazotrophic growth of M. barkeri 227 by V in the absence of Mo was demonstrated. The unusual complement of nif genes in M. barkeri 227, with one cluster resembling that from a gram-positive eubacterium and the other resembling a eubacterial V nitrogenase gene cluster, suggests horizontal genetic transfer of those genes. PMID:10809706

  6. Quality Practices of Alternative Education Learning Environments as Represented in Virginia's Individual Student Alternative Education Plan (ISAEP) Program

    ERIC Educational Resources Information Center

    Feltman, Doris R.

    2013-01-01

    The purpose of this study was to analyze a prominent alternative education practice in the Commonwealth of Virginia through an analysis of the Virginia Department of Education's Individual Student Alternative Education Plan (ISAEP) program and the alternative education environment it provides. This was a descriptive study using…

  7. Gene structure, chromosomal location, and basis for alternative mRNA splicing of the human VCAM1 gene

    SciTech Connect

    Cybulsky, M.I.; Fries, J.W.U.; Williams, A.J.; Sultan, P.; Gimbrone, M.A. Jr.; Collins, T. ); Eddy, R.; Byers, M.; Shows, T. )

    1991-09-01

    Vascular cell adhesion molecule 1 (VCAM-1) is a cell surface glycoprotein adhesive for certain blood leukocytes and tumor cells, which is expressed by activated endothelium in a variety of pathologic conditions including atherosclerosis. Genomic clones encoding the VCAM1 gene were isolated and the organization of the gene was determined. The gene, which is present in a single copy in the human genome, contains 9 exons spanning {approx}25 kilobases of DNA. Exons 2-8 contain C2 or H-type immunoglobulin domains. At least two different VCAM-1 precursors can be generated from the human gene as a result of alternative mRNA splicing events, which include or exclude exon 5. A consensus TATAA element is located upstream of the transcriptional start site. The VCAM1 promoter contains consensus binding sites for NF-{kappa}B, the GATA family of transcription factors, as well as an AP1 site. The VCAM1 gene was assigned to the 1p31-32 region of chromosome 1 based on the analysis of human-mouse hybrid cell lines and in situ hybridization. Structural analysis of the human VCAM1 gene provides the basis for alternative mRNA splicing and an initial approach to elucidating the regulation of VCAM-1 expression.

  8. Daemen Alternative Energy/Geothermal Technologies Demonstration Program Erie County

    SciTech Connect

    Beiswanger, Jr, Robert C

    2010-05-20

    The purpose of the Daemen Alternative Energy/Geothermal Technologies Demonstration Project is to demonstrate the use of geothermal technology as model for energy and environmental efficiency in heating and cooling older, highly inefficient buildings. The former Marian Library building at Daemen College is a 19,000 square foot building located in the center of campus. Through this project, the building was equipped with geothermal technology and results were disseminated. Gold LEED certification for the building was awarded. 1) How the research adds to the understanding of the area investigated. This project is primarily a demonstration project. Information about the installation is available to other companies, organizations, and higher education institutions that may be interested in using geothermal energy for heating and cooling older buildings. 2) The technical effectiveness and economic feasibility of the methods or techniques investigated or demonstrated. According to the modeling and estimates through Stantec, the energy-efficiency cost savings is estimated at 20%, or $24,000 per year. Over 20 years this represents $480,000 in unrestricted revenue available for College operations. See attached technical assistance report. 3) How the project is otherwise of benefit to the public. The Daemen College Geothermal Technologies Ground Source Heat Pumps project sets a standard for retrofitting older, highly inefficient, energy wasting and environmentally irresponsible buildings quite typical of many of the buildings on the campuses of regional colleges and universities. As a model, the project serves as an energy-efficient system with significant environmental advantages. Information about the energy-efficiency measures is available to other colleges and universities, organizations and companies, students, and other interested parties. The installation and renovation provided employment for 120 individuals during the award period. Through the new Center, Daemen will

  9. 7 CFR 58.149 - Alternate quality control programs for dairy products.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Alternate quality control programs for dairy products... FOR GRADES OF DAIRY PRODUCTS 1 General Specifications for Dairy Plants Approved for USDA Inspection... for dairy products. (a) When a plant has in operation an acceptable quality control program which...

  10. 7 CFR 58.149 - Alternate quality control programs for dairy products.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 3 2013-01-01 2013-01-01 false Alternate quality control programs for dairy products... FOR GRADES OF DAIRY PRODUCTS 1 General Specifications for Dairy Plants Approved for USDA Inspection... for dairy products. (a) When a plant has in operation an acceptable quality control program which...

  11. 7 CFR 58.149 - Alternate quality control programs for dairy products.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 3 2014-01-01 2014-01-01 false Alternate quality control programs for dairy products... FOR GRADES OF DAIRY PRODUCTS 1 General Specifications for Dairy Plants Approved for USDA Inspection... for dairy products. (a) When a plant has in operation an acceptable quality control program which...

  12. 7 CFR 58.149 - Alternate quality control programs for dairy products.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 3 2012-01-01 2012-01-01 false Alternate quality control programs for dairy products... FOR GRADES OF DAIRY PRODUCTS 1 General Specifications for Dairy Plants Approved for USDA Inspection... for dairy products. (a) When a plant has in operation an acceptable quality control program which...

  13. 7 CFR 58.149 - Alternate quality control programs for dairy products.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 3 2011-01-01 2011-01-01 false Alternate quality control programs for dairy products... FOR GRADES OF DAIRY PRODUCTS 1 General Specifications for Dairy Plants Approved for USDA Inspection... for dairy products. (a) When a plant has in operation an acceptable quality control program which...

  14. Dumping Ground or Effective Alternative: Dropout Prevention Programs in Urban Schools.

    ERIC Educational Resources Information Center

    Groth, Cori

    1998-01-01

    An alternative dropout-prevention program is examined from the students' perspectives. Findings from interviews and observations suggest that the program is effective in keeping the students in school but does little to help the students develop daily living and social skills. Policy implications are discussed and suggestions for future research…

  15. An Alternative School Teacher Education Program. Teacher Education Forum; Volume 3, Number 7.

    ERIC Educational Resources Information Center

    Barr, Robert D.

    The Alternative School Teacher Education Program, cooperatively developed by participating public schools and Indiana University, is a field-based masters degree program designed for completion in one calendar year. Students spend two summers on campus pursuing graduate course work. During the academic year between these summers, students earn…

  16. Program Evaluation of Alternative Schools in North Carolina: A Companion Dissertation

    ERIC Educational Resources Information Center

    Jones, Michael O.

    2013-01-01

    The purpose of the evaluation was to evaluate two alternative programs in a North Carolina (NC) and South Carolina (SC) public school district to determine if they are effective in delivering constructive interventions that modify student behavior once students have left the programs and have returned to their regular learning environments. This…

  17. A Comparison of Technology Experiences Included in Alternative and Traditional Teacher Education Programs

    ERIC Educational Resources Information Center

    Strycker, Jesse D.

    2011-01-01

    Though an educational technology experience is required as part of a traditional teacher education program student's educational preparation, research has been limited into the experiences had by alternative teacher education program students. Similarly, little research has been done comparing technology experiences between both types of teacher…

  18. Yoga for Stress Management Program as a Complementary Alternative Counseling Resource in a University Counseling Center

    ERIC Educational Resources Information Center

    Milligan, Colleen K.

    2006-01-01

    A Yoga for Stress Management Program (YSMP) that served as a complementary alternative therapy resource was successfully implemented at a midsize, predominantly undergraduate university. It was offered in addition to traditional treatments for student mental health. Counselors, Residence Life staff, and faculty found that the program was useful…

  19. Development of Mathematics and Science Teacher Efficacy during an Alternative Middle Grades Certification Program

    ERIC Educational Resources Information Center

    Ketelhut, Diane Jass; Newton, Kristie Jones

    2011-01-01

    As part of a grant-funded project, the authors have designed an alternative certification program, E = mc[superscript 2], funded by U.S. Department of Education under its Transition to Teaching Program. Before beginning their student teaching, participants conduct observations, interviews, tutoring, small group instruction, and isolated whole…

  20. A Person-Oriented Approach to Characterizing Beginning Teachers in Alternative Certification Programs

    ERIC Educational Resources Information Center

    Chin, Elaine; Young, John W.

    2007-01-01

    In this article, the authors argue for the use of ecological models of development in studies of teachers prepared through alternative certification (AC) programs. Previous studies of candidates in AC programs have focused on variables that describe their demographic characteristics. An ecological approach focuses on persons and situates their…

  1. Transitioning from School to Work: Programming for an Alternative School for At-Risk Adolescents.

    ERIC Educational Resources Information Center

    Lister, Robert

    The Portsmouth (New Hampshire) Alternative Secondary School (PASS) has been developed for at-risk students who need a self-contained educational program with a community educational approach. This model program is based on the need for students to experience individual growth and success in the areas of academics, therapeutics, behavior…

  2. Does Teaching Experience Matter? Examining Biology Teachers' Prior Knowledge for Teaching in an Alternative Certification Program

    ERIC Educational Resources Information Center

    Friedrichsen, Patricia J.; Abell, Sandra K.; Pareja, Enrique M.; Brown, Patrick L.; Lankford, Deanna M.; Volkmann, Mark J.

    2009-01-01

    Alternative certification programs (ACPs) have been proposed as a viable way to address teacher shortages, yet we know little about how teacher knowledge develops within such programs. The purpose of this study was to investigate prior knowledge for teaching among students entering an ACP, comparing individuals with teaching experience to those…

  3. A Comparison of the Alternative and Traditional Licensure Programs at Metropolitan State College of Denver.

    ERIC Educational Resources Information Center

    Heyman, Ernest L.

    This study evaluated Metropolitan State College of Denver's Teacher-in-Residence (TiR) alternative licensure program. To participate, teacher candidates must possess a baccalaureate degree, have a teaching contract in a participating local school district, enroll in the TiR program, and pass a state content test. This study examined what Metro…

  4. "Special Delivery": Case Studies in Alternative Teacher Licensure Programs for Students of Color.

    ERIC Educational Resources Information Center

    Hasslen, Robin; Green, Les

    St. Cloud State University's Teacher of Color project provides alternate licensure for degreed individuals needing only to complete their teacher education core and subject area coursework. It offers minority students on- and off-campus programs, financial support, flexible hours, and a compressed program. Researchers examined participating…

  5. How Induction Programs Affect the Decision of Alternate Route Urban Teachers to Remain Teaching

    ERIC Educational Resources Information Center

    LoCascio, Steven J.; Smeaton, Patricia S.; Waters, Faith H.

    2016-01-01

    This mixed-methods study analyzes the induction programs for alternate route beginning teachers in low socioeconomic, urban schools. The researcher surveyed 53 teachers at the end of their first year and conducted six in-depth follow-up interviews. The study found that half the teachers did not receive an induction program congruent with state…

  6. Comparative Evaluation of AB 3059 Alternative Child Care Programs. Summary Report.

    ERIC Educational Resources Information Center

    Warner, Donna D.; And Others

    Findings from the evaluation of the AB 3059 alternative child care programs are presented in this report. (AB 3059 child care programs were mandated by the California legislature in 1976 with the goals of assessing features that might reduce child care costs, ensuring maximum parental choice among facilities, addressing unmet child care needs…

  7. Mentor & Intern Teacher Boundary Practices: Integrating Theory and Practice in Effective Alternative Certification Programs

    ERIC Educational Resources Information Center

    Tompkins, R Page, II.

    2011-01-01

    Alternative certification programs for primary and secondary school teachers face a difficult challenge: they must develop highly qualified and high quality teachers while adapting to the unique on-the-job training needs of their participants. Research literature indicates that many programs suffer from a lack of cohesion between coursework and…

  8. Do Alternative Teacher Education Programs Manage to Attract Different Candidates and Students?

    ERIC Educational Resources Information Center

    Donitsa-Schmidt, Smadar; Weinberger, Yehudith

    2014-01-01

    During 2009, three alternative teacher retraining programs in English as a Foreign Language, mathematics and biology were launched for the first time in one of Israel's largest teacher education colleges. The programs, which offered varied economic incentives to participants, were initiated by the state owing to shortages of teachers in these…

  9. 19 CFR 101.9 - Test programs or procedures; alternate requirements.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Test programs or procedures; alternate requirements. 101.9 Section 101.9 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY GENERAL PROVISIONS § 101.9 Test programs or procedures;...

  10. 19 CFR 101.9 - Test programs or procedures; alternate requirements.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 19 Customs Duties 1 2011-04-01 2011-04-01 false Test programs or procedures; alternate requirements. 101.9 Section 101.9 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY GENERAL PROVISIONS § 101.9 Test programs or procedures;...

  11. 19 CFR 101.9 - Test programs or procedures; alternate requirements.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 19 Customs Duties 1 2014-04-01 2014-04-01 false Test programs or procedures; alternate requirements. 101.9 Section 101.9 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY GENERAL PROVISIONS § 101.9 Test programs or procedures;...

  12. 19 CFR 101.9 - Test programs or procedures; alternate requirements.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 19 Customs Duties 1 2013-04-01 2013-04-01 false Test programs or procedures; alternate requirements. 101.9 Section 101.9 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY GENERAL PROVISIONS § 101.9 Test programs or procedures;...

  13. Effectiveness of an Alternative Certification Program for the Preparation of Elementary Teachers

    ERIC Educational Resources Information Center

    Follo, Eric J.; Rivard, James J.

    2009-01-01

    This study focuses on the effectiveness of the alternative elementary teacher certification program at Oakland University in Rochester, Michigan. The program was developed in response to the projected teacher shortage, the need for teachers in subjects such as mathematics and science, the need for teachers in urban schools, and the need for…

  14. Alternatives Drug and Alcohol Prevention Program. Self Evaluation, 1981-82.

    ERIC Educational Resources Information Center

    Blangiardo, John; Gold, Judith

    Alternatives, the Drug and Alcohol Prevention Program of Community School District 22 in Brooklyn, N.Y., is a broad-based substance abuse prevention program funded by the state that provides direct services to students and their families through three service modalities. These are prevention services, which provide students, parents, and the…

  15. Evaluating Selected Perceptions of Science and Mathematics Teachers in an Alternative Certification Program

    ERIC Educational Resources Information Center

    Boone, William J.; Abell, Sandra K.; Volkmann, Mark J.; Arbaugh, Fran; Lannin, John K.

    2011-01-01

    In 2003 the University of Missouri (with the aid of US National Science Foundation funding) initiated an alternative certification program (CAP) to address the well-documented need in the US for increasing the quantity and quality of mathematics and science teachers for the middle and secondary levels. Nationwide current certification programs do…

  16. Transcriptome Analysis Indicates Considerable Divergence in Alternative Splicing Between Duplicated Genes in Arabidopsis thaliana

    PubMed Central

    Tack, David C.; Pitchers, William R.; Adams, Keith L.

    2014-01-01

    Gene and genome duplication events have created a large number of new genes in plants that can diverge by evolving new expression profiles and functions (neofunctionalization) or dividing extant ones (subfunctionalization). Alternative splicing (AS) generates multiple types of mRNA from a single type of pre-mRNA by differential intron splicing. It can result in new protein isoforms or downregulation of gene expression by transcript decay. Using RNA-seq, we investigated the degree to which alternative splicing patterns are conserved between duplicated genes in Arabidopsis thaliana. Our results revealed that 30% of AS events in α-whole-genome duplicates and 33% of AS events in tandem duplicates are qualitatively conserved within leaf tissue. Loss of ancestral splice forms, as well as asymmetric gain of new splice forms, may account for this divergence. Conserved events had different frequencies, as only 31% of shared AS events in α-whole-genome duplicates and 41% of shared AS events in tandem duplicates had similar frequencies in both paralogs, indicating considerable quantitative divergence. Analysis of published RNA-seq data from nonsense-mediated decay (NMD) mutants indicated that 85% of α-whole-genome duplicates and 89% of tandem duplicates have diverged in their AS-induced NMD. Our results indicate that alternative splicing shows a high degree of divergence between paralogs such that qualitatively conserved alternative splicing events tend to have quantitative divergence. Divergence in AS patterns between duplicates may be a mechanism of regulating expression level divergence. PMID:25326238

  17. Alternative splicing of the beta A4 amyloid gene of Alzheimer's disease in cortex of control and Alzheimer's disease patients.

    PubMed

    König, G; Salbaum, J M; Wiestler, O; Lang, W; Schmitt, H P; Masters, C L; Beyreuther, K

    1991-02-01

    An S1 nuclease protection assay was designed to study the splicing pattern of the alternatively spliced beta A4 amyloid gene (APP gene) of Alzheimer's disease (AD). We determined the splicing pattern of the APP gene in fetal, adult, aged adult and AD human cortex. The results suggest that alternative splicing of the APP gene in AD is not significantly different from age-matched controls, but distinct from the developing fetal brain.

  18. Using the baseline environmental management report (BEMR) to examine alternate program scenarios

    SciTech Connect

    Kristofferson, K.

    1995-12-01

    The US Department of Energy`s (DOE) Office of Environmental Management (EM) released the first Baseline Environmental Management Report (BEMR) in March, 1995. The Congressionally-mandated report provides life-cycle cost estimates, tentative schedules, and projected activities necessary to complete DOE`s Environmental Management Program. This ``base case`` estimate is based on current program assumptions and the most likely set of activities. However, since the future course of the Environmental Management Program depends upon a number of fundamental technical and policy choices, alternate program scenarios were developed. These alternate cases show the potential cost impacts of changing assumptions in four key areas: future land use, program funding and scheduling, technology development, and waste management configurations. Several cost and program evaluation tools were developed to support the analysis of these alternate cases. The objective of this paper is to describe the analytical tool kit developed to support the development of the 1995 Baseline Report and to discuss the application of these tools to evaluate alternate program scenarios.

  19. Processes and Outcomes from a Medical Student Research Training Program in Integrative, Complementary, and Alternative Medicine.

    PubMed

    Dicianno, Brad E; Glick, Ronald M; Sowa, Gwendolyn A; Boninger, Michael L

    2016-10-01

    In response to the growing need to train a new generation of clinician scientists, a research program was developed to train medical students in integrative, complementary, and alternative medicine (ICAM) research early in their careers. A total of 25 students (100%) successfully completed a 10-week program. Students reported significantly increased levels of knowledge in all 7 integrative, complementary, and alternative medicine topics at the conclusion of the program. All students presented their work at one or more local research symposia. In addition, the average number of quality research outputs, which included manuscripts, awards, and abstracts presented at national and international meetings, was 1.5 per student, which exceeded benchmarks based on prior program outcomes. Results from this program may be useful when planning larger or longer-term projects aimed at attracting physicians who will become our next generation of academicians, researchers, and healers.

  20. Stress-induced alternative gene splicing in mind-body medicine.

    PubMed

    Rossi, Ernest Lawrence

    2004-01-01

    Recent research documents how psychosocial stress can alter the expression of the acetylcholinesterase gene to generate at least 3 alternative proteins that are implicated in a wide variety of normal mind-body functions, as well as pathologies. These range from early embryological development, plasticity of the brain in adulthood, post-traumatic stress disorder (PTSD), and stress-associated dysfunctions of the central nervous, endocrine, and immune systems, to age-related neuropathologies. Such stress-induced alternative gene splicing is proposed here as a major mind-body pathway of psychosocial genomics-the modulation of gene expression by creative psychological, social, and cultural processes. We explore the types of research that are now needed to investigate how stress-induced alternative splicing of the acetylcholinesterase gene may play a pivotal role in the deep psychobiology of psychotherapy, meditation, spiritual rituals, and the experiencing of positive humanistic values that have been associated with mind-body medicine, such as compassion, beneficence, serenity, forgiveness, and gratitude.

  1. Alternative splicing of the tuberous sclerosis 2 (TSC2) gene in human and mouse tissues

    SciTech Connect

    Xu, Lin; Sterner, C.; Maheshwar, M.M.

    1995-06-10

    The recently isolated gene for tuberous sclerosis 2 (TSC2) encodes a 5.5.kb transcript that is widely expressed. The TSC2 gene product, named tuberin, is a 1784-amino-acid protein that shows a small stretch of homology to the GTPase activating protein rap1GAP. We have detected a novel variant of the TSC2 mRNA lacking 129 nucleotides, predicting an in-frame deletion of 43 amino acids spanning codons 946-988 of tuberin. This 129-bp deletion precisely corresponds to exon 25 of the TSC2 gene suggesting that alternative splicing leads to production of two forms of transcripts designated isoforms 1 and 2. Further molecular analysis revealed a third isoform exhibiting a deletion of 44 amino acids spanning codons 946-989 of tuberin. Amino acid 989 is a Ser residue encoded by the first codon of exon 26. The two isoforms also exist in newborn and adult mouse tissues, reinforcing the potential functional importance of these alternatively spliced products. These alternative isoforms should have implications for efforts aimed at identifying mutations in TSC patients. The distinct polypeptides encoded by the TSC2 gene may have different targets as well as functions involved in the regulation of cell growth. 26 refs., 4 figs.

  2. Stress-induced alternative gene splicing in mind-body medicine.

    PubMed

    Rossi, Ernest Lawrence

    2004-01-01

    Recent research documents how psychosocial stress can alter the expression of the acetylcholinesterase gene to generate at least 3 alternative proteins that are implicated in a wide variety of normal mind-body functions, as well as pathologies. These range from early embryological development, plasticity of the brain in adulthood, post-traumatic stress disorder (PTSD), and stress-associated dysfunctions of the central nervous, endocrine, and immune systems, to age-related neuropathologies. Such stress-induced alternative gene splicing is proposed here as a major mind-body pathway of psychosocial genomics-the modulation of gene expression by creative psychological, social, and cultural processes. We explore the types of research that are now needed to investigate how stress-induced alternative splicing of the acetylcholinesterase gene may play a pivotal role in the deep psychobiology of psychotherapy, meditation, spiritual rituals, and the experiencing of positive humanistic values that have been associated with mind-body medicine, such as compassion, beneficence, serenity, forgiveness, and gratitude. PMID:15356952

  3. A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice.

    PubMed

    Li, Jigang; Li, Xiaojuan; Guo, Lei; Lu, Feng; Feng, Xiaojie; He, Kun; Wei, Liping; Chen, Zhangliang; Qu, Li-Jia; Gu, Hongya

    2006-01-01

    MYB transcription factor genes play important roles in many developmental processes and in various defence responses of plants. Two Arabidopsis R2R3-type MYB genes, AtMYB59 and AtMYB48, were found to undergo similar alternative splicing. Both genes have four distinctively spliced transcripts that encode either MYB-related proteins or R2R3-MYB proteins. An extensive BLAST search of the GenBank database resulted in finding and cloning two rice homologues, both of which were also found to share a similar alternative splicing pattern. In a semi-quantitative study, the expression of one splice variant of AtMYB59 was found to be differentially regulated in treatments with different phytohormones and stresses. GFP fusion protein analysis revealed that both of the two predicted nuclear localization signals (NLSs) in the R3 domain are required for localizing to the nucleus. Promoter-GUS analysis in transgenic plants showed that 5'-UTR is sufficient for the translation initiation of type 3 transcripts (encoding R2R3-MYB proteins), but not for type 2 transcripts (encoding MYB-related proteins). Moreover, a new type of non-canonical intron, with the same nucleotide repeats at the 5' and 3' splice sites, was identified. Thirty-eight Arabidopsis and rice genes were found to have this type of non-canonical intron, most of which undergo alternative splicing. These data suggest that this subgroup of transcription factor genes may be involved in multiple biological processes and may be transcriptionally regulated by alternative splicing. PMID:16531467

  4. Alternative fuels for vehicles fleet demonstration program. Final report, volume 2: Appendices

    SciTech Connect

    1997-06-01

    The Alternative Fuels for Vehicles Fleet Demonstration Program (AFV-FDP) was a multiyear effort to collect technical data for use in determining the costs and benefits of alternative-fuel vehicles (AFVs) in typical applications in New York State. This report, Volume 2, includes 13 appendices to Volume 1 that expand upon issues raised therein. Volume 1 provides: (1) Information about the purpose and scope of the AFV-FDP; (2) A summary of AFV-FDP findings organized on the basis of vehicle type and fuel type; (3) A short review of the status of AFV technology development, including examples of companies in the State that are active in developing AFVs and AFV components; and (4) A brief overview of the status of AFV deployment in the State. Volume 3 provides expanded reporting of AFV-FDP technical details, including the complete texts of the brochure Garage Guidelines for Alternative Fuels and the technical report Fleet Experience Survey Report, plus an extensive glossary of AFV terminology. The appendices cover a wide range of issues including: emissions regulations in New York State; production and health effects of ozone; vehicle emissions and control systems; emissions from heavy-duty engines; reformulated gasoline; greenhouse gases; production and characteristics of alternative fuels; the Energy Policy Act of 1992; the Clean Fuel Fleet Program; garage design guidelines for alternative fuels; surveys of fleet managers using alternative fuels; taxes on conventional and alternative fuels; and zero-emission vehicle technology.

  5. Final priority; Rehabilitation Services Administration--Assistive Technology Alternative Financing Program. Final priority.

    PubMed

    2014-08-14

    The Assistant Secretary for Special Education and Rehabilitative Services announces a priority under the Assistive Technology Alternative Financing Program administered by the Rehabilitation Services Administration (RSA). The Assistant Secretary may use this priority for competitions in fiscal year (FY) 2014 and later years. This priority is designed to ensure that the Department funds high-quality assistive technology (AT) alternative financing programs (AFPs) that meet rigorous standards in order to enable individuals with disabilities to access and acquire assistive technology devices and services necessary to achieve education, community living, and employment goals.

  6. Alternative-fueled truck demonstration natural gas program: Caterpillar G3406LE development and demonstration

    SciTech Connect

    1995-06-01

    In 1990, the California Energy Commission, the South Coast Air Quality Management District, and the Southern California Gas Company joined together to sponsor the development and demonstration of compressed natural gas engines for Class 8 heavy-duty line-haul trucking applications. This program became part of an overall Alternative-Fueled Truck Demonstration Program, with the goal of advancing the technological development of alternative-fueled engines. The demonstration showed natural gas to be a technically viable fuel for Class 8 truck engines.

  7. Data collection plan for Phase 2 Alternative Fuels Bus Data Collection Program. Final report

    SciTech Connect

    Krenelka, T

    1993-07-01

    This document constitutes the plan for collecting and reporting data associated with a special set of transit bus demonstrations to be conducted under the Urban Bus Program of the Alternative Motor Fuels Act (AMFA) of 1988. This program, called the Phase 2 Bus Data Collection Program, serves as an adjunct to the Phase I Bus Data Collection Program, collecting detailed data on just a few buses to augment and enhance the Phase 1 data in fulfilling the urban bus requirements of AMFA. Demonstrations will be conducted at a few transit system locations throughout the US and will use alternative fuels and associated technologies to reduce undesirable transit bus exhaust emissions. Several organizations will be involved in the data collection; NREL will manage the program, analyze and store vehicle data, and make these data available through the Alternative Fuels Data Center. This information will enable transit agencies, equipment manufacturers, fuel suppliers, and government policy makers to make informed decisions about buying and using alternative fuels.

  8. The neurofibromatosis 2 (NF2) tumor suppressor gene encodes multiple alternatively spliced transcripts.

    PubMed

    Pykett, M J; Murphy, M; Harnish, P R; George, D L

    1994-04-01

    Neurofibromatosis type 2 (NF2) is an autosomal dominantly-inherited disorder predisposing affected individuals to tumors of multiple cell types in the central nervous system, including meningiomas. A candidate tumor suppressor gene for this disorder has recently been cloned; the protein product of this gene has a predicted role in linking integral membrane proteins with the cytoskeleton. Utilizing reverse transcription-polymerase chain reaction (RT-PCR) analyses, we have identified a number of alternatively spliced transcription products encoded by the NF2 gene. These alternative splice variants were detected in RNA isolated from several sources, including primary leptomeningeal tissue and an established line of leptomeningeal cells (LMC). Several of these variants delete previously identified coding regions of this gene. Moreover, two of these splice variants add previously unrecognized exons to the NF2 coding region. These identified splice forms will serve as natural reagents for the functional dissection of the NF2 protein product(s). They also should be considered in studies investigating mutations of this gene in members of NF2 families and in tumor analyses.

  9. Subfunctionalization of duplicate mitf genes associated with differential degeneration of alternative exons in fish.

    PubMed Central

    Altschmied, Joachim; Delfgaauw, Jacqueline; Wilde, Brigitta; Duschl, Jutta; Bouneau, Laurence; Volff, Jean-Nicolas; Schartl, Manfred

    2002-01-01

    The microphthalmia-associated transcription factor (MITF) exists in at least four isoforms. These are generated in higher vertebrates using alternative 5' exons and promoters from a single gene. Two separate genes (mitf-m and mitf-b), however, are present in different teleost fish species including the poeciliid Xiphophorus, the pufferfishes Fugu rubripes and Tetraodon nigroviridis, and the zebrafish Danio rerio. Fish proteins MITF-m and MITF-b correspond at both the structural and the expression levels to one particular bird/mammalian MITF isoform. In the teleost lineage subfunctionalization of mitf genes after duplication at least 100 million years ago is associated with the degeneration of alternative exons and, probably, regulatory elements and promoters. For example, a remnant of the first exon specific for MITF-m is detected within the pufferfish gene encoding MITF-b. Retracing the evolutionary history of mitf genes in vertebrates uncovered the differential recruitment of new introns specific for either the teleost or the bird/mammalian lineage. PMID:12019239

  10. Ubiquitously expressed genes participate in cell-specific functions via alternative promoter usage.

    PubMed

    Feng, Guihai; Tong, Man; Xia, Baolong; Luo, Guan-Zheng; Wang, Meng; Xie, Dongfang; Wan, Haifeng; Zhang, Ying; Zhou, Qi; Wang, Xiu-Jie

    2016-09-01

    How do different cell types acquire their specific identities and functions is a fundamental question of biology. Previously significant efforts have been devoted to search for cell-type-specifically expressed genes, especially transcription factors, yet how do ubiquitously expressed genes participate in the formation or maintenance of cell-type-specific features remains largely unknown. Here, we have identified 110 mouse embryonic stem cell (mESC) specifically expressed transcripts with cell-stage-specific alternative transcription start sites (SATS isoforms) from 104 ubiquitously expressed genes, majority of which have active epigenetic modification- or stem cell-related functions. These SATS isoforms are specifically expressed in mESCs, and tend to be transcriptionally regulated by key pluripotency factors through direct promoter binding. Knocking down the SATS isoforms of Nmnat2 or Usp7 leads to differentiation-related phenotype in mESCs. These results demonstrate that cell-type-specific transcription factors are capable to produce cell-type-specific transcripts with alternative transcription start sites from ubiquitously expressed genes, which confer ubiquitously expressed genes novel functions involved in the establishment or maintenance of cell-type-specific features. PMID:27466324

  11. Dispositions and Perceived Preparedness of Teacher Candidates in Traditional Undergraduate Teacher Education, Master's with Licensure, and Alternative Licensure Programs

    ERIC Educational Resources Information Center

    Iyer, Nithya Narayanaswamy; Soled, Suzanne Wegener

    2007-01-01

    This study compares the dispositions and perceived preparedness of three teacher preparation programs: traditional, masters, and alternative licensure. We specifically investigated whether teachers in alternative licensure programs have the dispositions and perceived preparation essential for teaching. Each program was examined to identify…

  12. A cell-based in vitro alternative to identify skin sensitizers by gene expression

    SciTech Connect

    Hooyberghs, Jef Schoeters, Elke; Lambrechts, Nathalie; Nelissen, Inge; Witters, Hilda; Schoeters, Greet; Heuvel, Rosette van den

    2008-08-15

    The ethical and economic burden associated with animal testing for assessment of skin sensitization has triggered intensive research effort towards development and validation of alternative methods. In addition, new legislation on the registration and use of cosmetics and chemicals promote the use of suitable alternatives for hazard assessment. Our previous studies demonstrated that human CD34{sup +} progenitor-derived dendritic cells from cord blood express specific gene profiles upon exposure to low molecular weight sensitizing chemicals. This paper presents a classification model based on this cell type which is successful in discriminating sensitizing chemicals from non-sensitizing chemicals based on transcriptome analysis of 13 genes. Expression profiles of a set of 10 sensitizers and 11 non-sensitizers were analyzed by RT-PCR using 9 different exposure conditions and a total of 73 donor samples. Based on these data a predictive dichotomous classifier for skin sensitizers has been constructed, which is referred to as . In a first step the dimensionality of the input data was reduced by selectively rejecting a number of exposure conditions and genes. Next, the generalization of a linear classifier was evaluated by a cross-validation which resulted in a prediction performance with a concordance of 89%, a specificity of 97% and a sensitivity of 82%. These results show that the present model may be a useful human in vitro alternative for further use in a test strategy towards the reduction of animal use for skin sensitization.

  13. Alternative processing of scrambled genes generates protein diversity in the ciliate Chilodonella uncinata.

    PubMed

    Katz, Laura A; Kovner, Alexandra M

    2010-09-15

    In ciliates, chromosomal rearrangements occur during the development of the somatic macronuclear genome from the germline micronuclear genome. These rearrangements are extensive in three ciliate classes-Armophorea, Spirotrichea, and Phyllopharyngea-generating a macronucleus with up to 20,000,000 gene-sized chromosomes. Earlier, we have shown that these three classes also share elevated rates of protein evolution relative to other ciliates. To assess the evolution of germline-limited sequences in the class Phyllopharyngea, we used a combination of traditional and walking PCR to analyze micronuclear copies of multiple genes from two lines of the morphospecies Chilodonella uncinata for which we had previously characterized macronuclear sequences. Analyses of the resulting data yield three main results: (1) conserved macronuclear (somatic) regions are found within rapidly evolving micronuclear (germline) regions; (2) gene scrambling exists within this ciliate lineage; and (3) alternative processing of micronuclear regions yields diverse macronuclear beta-tubulin paralogs. To our knowledge, this is the first study to demonstrate gene scrambling outside the nonsister class Spirotrichea, and to show that alternative processing of scrambled genes generates diversity in gene families. Intriguingly, the Spirotrichea and Phyllopharyngea are also united in having transient "giant" polytene chromosomes, gene-sized somatic chromosomes, and elevated rates of protein evolution. We hypothesize that this suite of characters enables these ciliates to enjoy the benefits of asexuality while still maintaining the ability to go through sexual cycles. The data presented here add to the growing evidence of the dynamic nature of eukaryotic genomes within diverse lineages across the tree of life. PMID:20700892

  14. Alternative activation deprives macrophages of a coordinated defense program to Mycobacterium tuberculosis.

    PubMed

    Kahnert, Antje; Seiler, Peter; Stein, Maik; Bandermann, Silke; Hahnke, Karin; Mollenkopf, Hans; Kaufmann, Stefan H E

    2006-03-01

    A potent Th1 immune response is critical to the control of tuberculosis. The impact of an additive Th2 response on the course of disease has so far been insufficiently characterized, despite increased morbidity after co-infection with Mycobacterium tuberculosis and Th2-eliciting helminths and possible involvement of Th2 polarization in reactivation of latent tuberculosis. Here, we describe the gene expression profile of murine bone marrow-derived macrophages alternatively activated by IL-4 in response to infection with M. tuberculosis. Comparison of transcriptional profiles of infected IL-4- and IFN-gamma-activated macrophages revealed delayed and partially diminished responses to intracellular bacteria in alternatively activated macrophages, characterized by reduced exposure to nitrosative stress and increased iron availability, respectively. Alternative activation of host macrophages correlated with elevated expression of the M. tuberculosis iron storage protein bacterioferritin as well as reduced expression of the mycobactin synthesis genes mbtI and mbtJ. The extracellular matrix-remodeling enzyme matrix metalloproteinase (MMP)-12 was induced in alternatively activated macrophages in vitro, and MMP-12-expressing macrophages were abundant at late, but not early, stages of tuberculosis in murine lungs. Our findings emphasize that alternative activation deprives macrophages of control mechanisms that limit mycobacterial growth in vivo, thus supporting intracellular persistence of M. tuberculosis. PMID:16479545

  15. Alternative Break Programs and the Factors that Contribute to Changes in Students' Lives

    ERIC Educational Resources Information Center

    Niehaus, Elizabeth Kathleen

    2012-01-01

    The purpose of this study was to explore the extent to and ways in which student participants in Alternative Break (AB) programs report that their AB experience influenced their intentions or plans to volunteer, engage in advocacy, or study or travel abroad, or their major or career plans. Additional analysis explored the specific program…

  16. 78 FR 79579 - Energy Conservation Program: Alternative Efficiency Determination Methods, Basic Model Definition...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-31

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY 10 CFR Parts 429 and 431 RIN 1904-AC46 Energy Conservation Program: Alternative Efficiency Determination... AGENCY: Office of Energy Efficiency and Renewable Energy, Department of Energy. ACTION: Final...

  17. Supporting First Year Alternatively Certified Urban and Rural Intern Teachers through a Multicomponent Distance Induction Program

    ERIC Educational Resources Information Center

    Gresko, Jennifer A.

    2013-01-01

    The pathway for entering the K-12 classroom as a teacher varies compared to what was once the traditional model of teacher preparation. In this mixed-methods action research study, I explore supporting first year alternatively certified urban and rural intern teachers through a multicomponent distance induction program. The induction model in this…

  18. Examining Incoming Identities in an Alternative Certification Program in Mathematics and Science

    ERIC Educational Resources Information Center

    Friedrichsen, Patricia; Lannin, John; Abell, Sandra; Arbaugh, Fran; Volkmann, Mark

    2008-01-01

    In response to the shortage of qualified secondary mathematics and science teachers in the United States, alternative certification programs (ACPs) are proliferating. This study used identity as a theoretical lens to examine the incoming identities of 19 participants with post-baccalaureate degrees who entered an ACP. Within this cohort, the…

  19. 46 CFR 115.650 - Alternative Hull Examination (AHE) Program options: Divers or underwater ROV.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 4 2012-10-01 2012-10-01 false Alternative Hull Examination (AHE) Program options: Divers or underwater ROV. 115.650 Section 115.650 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY... underwater visibility is poor, to provide the camera with a clear view of the hull. (b) You may use...

  20. 46 CFR 176.650 - Alternative Hull Examination Program options: Divers or underwater ROV.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 7 2013-10-01 2013-10-01 false Alternative Hull Examination Program options: Divers or underwater ROV. 176.650 Section 176.650 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED... as a clear box, if underwater visibility is poor, to provide the camera with a clear view of the...

  1. 46 CFR 115.650 - Alternative Hull Examination (AHE) Program options: Divers or underwater ROV.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 4 2013-10-01 2013-10-01 false Alternative Hull Examination (AHE) Program options: Divers or underwater ROV. 115.650 Section 115.650 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY... underwater visibility is poor, to provide the camera with a clear view of the hull. (b) You may use...

  2. 46 CFR 115.650 - Alternative Hull Examination (AHE) Program options: Divers or underwater ROV.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 4 2011-10-01 2011-10-01 false Alternative Hull Examination (AHE) Program options: Divers or underwater ROV. 115.650 Section 115.650 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY... underwater visibility is poor, to provide the camera with a clear view of the hull. (b) You may use...

  3. 46 CFR 176.650 - Alternative Hull Examination Program options: Divers or underwater ROV.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 7 2011-10-01 2011-10-01 false Alternative Hull Examination Program options: Divers or underwater ROV. 176.650 Section 176.650 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED... as a clear box, if underwater visibility is poor, to provide the camera with a clear view of the...

  4. 46 CFR 176.650 - Alternative Hull Examination Program options: Divers or underwater ROV.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 7 2012-10-01 2012-10-01 false Alternative Hull Examination Program options: Divers or underwater ROV. 176.650 Section 176.650 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED... as a clear box, if underwater visibility is poor, to provide the camera with a clear view of the...

  5. 46 CFR 115.650 - Alternative Hull Examination (AHE) Program options: Divers or underwater ROV.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 4 2014-10-01 2014-10-01 false Alternative Hull Examination (AHE) Program options: Divers or underwater ROV. 115.650 Section 115.650 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY... underwater visibility is poor, to provide the camera with a clear view of the hull. (b) You may use...

  6. 46 CFR 176.650 - Alternative Hull Examination Program options: Divers or underwater ROV.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 7 2014-10-01 2014-10-01 false Alternative Hull Examination Program options: Divers or underwater ROV. 176.650 Section 176.650 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED... as a clear box, if underwater visibility is poor, to provide the camera with a clear view of the...

  7. Clarendon Alternative School. Japanese Bilingual Bicultural Program. Curriculum Sampler II: Science.

    ERIC Educational Resources Information Center

    Choy, V. Kanani, Ed.; And Others

    A sampler of thematic science lessons from the Japanese bilingual/bicultural education program of the Clarendon Alternative School, a California elementary school, is presented. The lessons are designed to integrate Japanese instruction with the core science curriculum. Each lesson contains this information: the grade level, teacher(s), and…

  8. Perceptions of Educators Regarding the Effectiveness of Alternative Programs in a Southern State

    ERIC Educational Resources Information Center

    Roberson, Lydia

    2015-01-01

    At-risk students are engaged in dangerous behaviors that lead them to become involved in the juvenile justice system and cause the feeling of low self-worth. This eventually causes at-risk youths to drop out of school and engage in detrimental behaviors that meddle in their academic success. The alternative education program provides these at-risk…

  9. Total Program Efficacy: A Comparison of Traditionally and Alternatively Certified Agriculture Teachers

    ERIC Educational Resources Information Center

    Duncan, Dennis W.; Ricketts, John C.

    2008-01-01

    The purpose of this study was to determine agriculture teachers' perceived levels of efficacy as they relate to managing the total program of agricultural education, both for traditionally and alternatively certified teachers. The constructs used in this study were technical content, FFA/leadership development/SAE, teaching and learning, and…

  10. The Effects of a Violence Prevention Program on Alternative High School Students

    ERIC Educational Resources Information Center

    Triplett, Carla A.

    2013-01-01

    This study addressed the effectiveness of a violence prevention program in an inner-city alternative school setting. The researcher, an administrator at the school, used a prepackaged curriculum targeting lessons on violence in an eight-week study with the entire school population. Students met bi-weekly with a team of two teachers to review and…

  11. A Study of the Effect of Alternative Programs on the Potential Dropout.

    ERIC Educational Resources Information Center

    Gloria, Cyril; Karr-Kidwell, PJ

    Educators are very concerned about the problem of students dropping out of school. The reasons for students dropping out vary from social to economic causes. Alternative programs or schools have been used since the 1960s to try to keep students in school. This study involved a literature review of research on the identification and remediation of…

  12. 77 FR 22321 - National Toxicology Program (NTP) Interagency Center for the Evaluation of Alternative...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-13

    ... HUMAN SERVICES National Toxicology Program (NTP) Interagency Center for the Evaluation of Alternative Toxicological Methods: Call for Nominations of High Throughput Screening (HTS) Assays for the Tox21 Initiative... Sciences (NIEHS), National Institutes of Health (NIH). ACTION: Call for nominations. SUMMARY:...

  13. 46 CFR 8.420 - Classification society authorization to participate in the Alternate Compliance Program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... recognition to the Commandant in writing in accordance with 46 CFR 1.03-15(h)(4). (e) The Coast Guard will... 46 Shipping 1 2010-10-01 2010-10-01 false Classification society authorization to participate in... § 8.420 Classification society authorization to participate in the Alternate Compliance Program....

  14. 46 CFR 8.420 - Classification society authorization to participate in the Alternate Compliance Program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... recognition to the Commandant in writing in accordance with 46 CFR 1.03-15(h)(4). (e) The Coast Guard will... 46 Shipping 1 2011-10-01 2011-10-01 false Classification society authorization to participate in... § 8.420 Classification society authorization to participate in the Alternate Compliance Program....

  15. 46 CFR 8.420 - Classification society authorization to participate in the Alternate Compliance Program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... recognition to the Commandant in writing in accordance with 46 CFR 1.03-15(h)(4). (e) The Coast Guard will... 46 Shipping 1 2013-10-01 2013-10-01 false Classification society authorization to participate in... § 8.420 Classification society authorization to participate in the Alternate Compliance Program....

  16. 46 CFR 8.420 - Classification society authorization to participate in the Alternate Compliance Program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... recognition to the Commandant in writing in accordance with 46 CFR 1.03-15(h)(4). (e) The Coast Guard will... 46 Shipping 1 2012-10-01 2012-10-01 false Classification society authorization to participate in... § 8.420 Classification society authorization to participate in the Alternate Compliance Program....

  17. 46 CFR 8.420 - Classification society authorization to participate in the Alternate Compliance Program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... recognition to the Commandant in writing in accordance with 46 CFR 1.03-15(h)(4). (e) The Coast Guard will... 46 Shipping 1 2014-10-01 2014-10-01 false Classification society authorization to participate in... § 8.420 Classification society authorization to participate in the Alternate Compliance Program....

  18. Accelerating the commercialization on new technologies. [free market operation of federal alternate energy sources programs

    NASA Technical Reports Server (NTRS)

    Kuehn, T. J.; Nawrocki, P. M.

    1978-01-01

    It is suggested that federal programs for hastening the adoption of alternative energy sources must operate within the free market structure. Five phases of the free market commercialization process are described. Federal role possibilities include information dissemination and funding to stimulate private sector activities within these five phases, and federally sponsored procedures for accelerating commercialization of solar thermal small power systems are considered.

  19. Recruitment and Selection of Mathematics and Science Teaching Candidates for an Alternative Teacher Certification Program.

    ERIC Educational Resources Information Center

    Denton, Jon J.; Morris, John E.

    1991-01-01

    Examines how an alternative certification program for secondary teachers was developed and implemented to address local teacher shortages in mathematics and science in Texas. Topics discussed are the policy context, course offerings, the recruitment and selection process, developing an applicant pool, screening of applicants, and placement of…

  20. 46 CFR 115.650 - Alternative Hull Examination (AHE) Program options: Divers or underwater ROV.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...: Divers or underwater ROV. 115.650 Section 115.650 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY... Alternative Hull Examination (AHE) Program options: Divers or underwater ROV. To complete your underwater survey, you may use divers or an underwater remotely operated vehicle (ROV). (a) If you use divers...

  1. Alternatives to Social Promotion Program at Grades 7 & 8. Final Report.

    ERIC Educational Resources Information Center

    Wircenski, Jerry L.; Sarkees, Michelle D.

    This final report and curriculum guide are products of a project conducted to improve existing at-risk programs through cooperation between vocational and academic personnel by coordinating lesson plans. The following project activities are described: (1) a literature review on the diverse needs of at-risk students enrolled in an alternative to…

  2. 78 FR 52116 - Request for Public Comment on a Review Level Alternative Dispute Resolution Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-22

    ... HEALTH REVIEW COMMISSION 29 CFR Part 2200 Request for Public Comment on a Review Level Alternative Dispute Resolution Program AGENCY: Occupational Safety and Health Review Commission. ACTION: Request for comment. SUMMARY: The Occupational Safety and Health Review Commission invites the public to comment...

  3. A Critical Examination of the Process of Modifying the Curriculum of Alternative Secondary Educational Programs

    ERIC Educational Resources Information Center

    Ross, Michael

    2014-01-01

    This study, "A Critical Examination of the Process of Modifying the Curriculum of Alternative Secondary Educational Programs," was done with the use of action research to study (a) whether students currently participating in a continuation school believe their educational and career needs are presently being met; (b) the types of career…

  4. Concept Mapping: An Approach for Evaluating a Public Alternative School Program

    ERIC Educational Resources Information Center

    Streeter, Calvin L.; Franklin, Cynthia; Kim, Johnny S.; Tripodi, Stephen J.

    2011-01-01

    This article describes how concept mapping techniques were applied to evaluate the development of a solution-focused, public alternative school program. Concept Systems software was used to create 15 cluster maps based on statements generated from students, teachers, and school staff. In addition, pattern matches were analyzed to examine the…

  5. Alternative splicing in the 5' moiety of the H-2Kd gene transcript.

    PubMed Central

    Transy, C; Lalanne, J L; Kourilsky, P

    1984-01-01

    The H-2Kd gene, which encodes a mouse major transplantation antigen, was transfected into L TK- mouse fibroblasts. Two transcripts of the gene were detected by S1 nuclease mapping analysis. They correspond to two previously characterized cDNA clones isolated from DBA/2 mouse liver RNA, leading to the conclusion that the H-2Kd gene gives rise to two distinct transcripts through an alternate use of splicing sites. The non-canonical RNA potentially encodes a so far undescribed H-2Kd-like molecule. It is present in all tissues tested (liver, spleen, thymus, kidney) albeit in lower amounts (approximately 10-fold less) than the canonical RNA coding for H-2Kd. Images Fig. 2. Fig. 3. PMID:6094182

  6. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

    PubMed Central

    Kalyna, Maria; Simpson, Craig G.; Syed, Naeem H.; Lewandowska, Dominika; Marquez, Yamile; Kusenda, Branislav; Marshall, Jacqueline; Fuller, John; Cardle, Linda; McNicol, Jim; Dinh, Huy Q.; Barta, Andrea; Brown, John W. S.

    2012-01-01

    Alternative splicing (AS) coupled to nonsense-mediated decay (NMD) is a post-transcriptional mechanism for regulating gene expression. We have used a high-resolution AS RT–PCR panel to identify endogenous AS isoforms which increase in abundance when NMD is impaired in the Arabidopsis NMD factor mutants, upf1-5 and upf3-1. Of 270 AS genes (950 transcripts) on the panel, 102 transcripts from 97 genes (32%) were identified as NMD targets. Extrapolating from these data around 13% of intron-containing genes in the Arabidopsis genome are potentially regulated by AS/NMD. This cohort of naturally occurring NMD-sensitive AS transcripts also allowed the analysis of the signals for NMD in plants. We show the importance of AS in introns in 5′ or 3′UTRs in modulating NMD-sensitivity of mRNA transcripts. In particular, we identified upstream open reading frames overlapping the main start codon as a new trigger for NMD in plants and determined that NMD is induced if 3′-UTRs were >350 nt. Unexpectedly, although many intron retention transcripts possess NMD features, they are not sensitive to NMD. Finally, we have shown that AS/NMD regulates the abundance of transcripts of many genes important for plant development and adaptation including transcription factors, RNA processing factors and stress response genes. PMID:22127866

  7. RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum

    PubMed Central

    2013-01-01

    Background The genome of Fusarium graminearum has been sequenced and annotated previously, but correct gene annotation remains a challenge. In addition, posttranscriptional regulations, such as alternative splicing and RNA editing, are poorly understood in F. graminearum. Here we took advantage of RNA-Seq to improve gene annotations and to identify alternative splicing and RNA editing in F. graminearum. Results We identified and revised 655 incorrectly predicted gene models, including revisions of intron predictions, intron splice sites and prediction of novel introns. 231 genes were identified with two or more alternative splice variants, mostly due to intron retention. Interestingly, the expression ratios between different transcript isoforms appeared to be developmentally regulated. Surprisingly, no RNA editing was identified in F. graminearum. Moreover, 2459 novel transcriptionally active regions (nTARs) were identified and our analysis indicates that many of these could be missed genes. Finally, we identified the 5′ UTR and/or 3′ UTR sequences of 7666 genes. A number of representative novel gene models and alternatively spliced genes were validated by reverse transcription polymerase chain reaction and sequencing of the generated amplicons. Conclusions We have developed novel and efficient strategies to identify alternatively spliced genes and incorrect gene models based on RNA-Seq data. Our study identified hundreds of alternatively spliced genes in F. graminearum and for the first time indicated that alternative splicing is developmentally regulated in filamentous fungi. In addition, hundreds of incorrect predicted gene models were identified and revised and thousands of nTARs were discovered in our study, which will be helpful for the future genomic and transcriptomic studies in F. graminearum. PMID:23324402

  8. Sperm is epigenetically programmed to regulate gene transcription in embryos.

    PubMed

    Teperek, Marta; Simeone, Angela; Gaggioli, Vincent; Miyamoto, Kei; Allen, George E; Erkek, Serap; Kwon, Taejoon; Marcotte, Edward M; Zegerman, Philip; Bradshaw, Charles R; Peters, Antoine H F M; Gurdon, John B; Jullien, Jerome

    2016-08-01

    For a long time, it has been assumed that the only role of sperm at fertilization is to introduce the male genome into the egg. Recently, ideas have emerged that the epigenetic state of the sperm nucleus could influence transcription in the embryo. However, conflicting reports have challenged the existence of epigenetic marks on sperm genes, and there are no functional tests supporting the role of sperm epigenetic marking on embryonic gene expression. Here, we show that sperm is epigenetically programmed to regulate embryonic gene expression. By comparing the development of sperm- and spermatid-derived frog embryos, we show that the programming of sperm for successful development relates to its ability to regulate transcription of a set of developmentally important genes. During spermatid maturation into sperm, these genes lose H3K4me2/3 and retain H3K27me3 marks. Experimental removal of these epigenetic marks at fertilization de-regulates gene expression in the resulting embryos in a paternal chromatin-dependent manner. This demonstrates that epigenetic instructions delivered by the sperm at fertilization are required for correct regulation of gene expression in the future embryos. The epigenetic mechanisms of developmental programming revealed here are likely to relate to the mechanisms involved in transgenerational transmission of acquired traits. Understanding how parental experience can influence development of the progeny has broad potential for improving human health. PMID:27034506

  9. Sperm is epigenetically programmed to regulate gene transcription in embryos

    PubMed Central

    Teperek, Marta; Simeone, Angela; Gaggioli, Vincent; Miyamoto, Kei; Allen, George E.; Erkek, Serap; Kwon, Taejoon; Marcotte, Edward M.; Zegerman, Philip; Bradshaw, Charles R.; Peters, Antoine H.F.M.; Gurdon, John B.; Jullien, Jerome

    2016-01-01

    For a long time, it has been assumed that the only role of sperm at fertilization is to introduce the male genome into the egg. Recently, ideas have emerged that the epigenetic state of the sperm nucleus could influence transcription in the embryo. However, conflicting reports have challenged the existence of epigenetic marks on sperm genes, and there are no functional tests supporting the role of sperm epigenetic marking on embryonic gene expression. Here, we show that sperm is epigenetically programmed to regulate embryonic gene expression. By comparing the development of sperm- and spermatid-derived frog embryos, we show that the programming of sperm for successful development relates to its ability to regulate transcription of a set of developmentally important genes. During spermatid maturation into sperm, these genes lose H3K4me2/3 and retain H3K27me3 marks. Experimental removal of these epigenetic marks at fertilization de-regulates gene expression in the resulting embryos in a paternal chromatin-dependent manner. This demonstrates that epigenetic instructions delivered by the sperm at fertilization are required for correct regulation of gene expression in the future embryos. The epigenetic mechanisms of developmental programming revealed here are likely to relate to the mechanisms involved in transgenerational transmission of acquired traits. Understanding how parental experience can influence development of the progeny has broad potential for improving human health. PMID:27034506

  10. Innovative Program Targets Five Common Pain Syndromes With Non-opioid Alternatives.

    PubMed

    2016-06-01

    To combat the prescription opioid problem, St. Joseph's Healthcare System in Paterson, NJ, has developed a new program that gives providers options they can use to effectively alleviate pain without resorting to highly addictive medication. Launched in January 2016 in the ED at St. Joseph's Regional Medical Center (SJRMC), the Alternatives to Opioids (ALTO) program utilizes protocols that primarily target five common conditions: renal colic, sciatica, headaches, musculoskeletal pain, and extremity fractures. Administrators say they have successfully treated more than 300 patients under the new program, and they see ALTO as a model other hospitals can duplicate. Among the alternative therapies called for in the ALTO program are trigger point injections, nitrous oxide, and ultrasound-guided nerve blocks. ALTO medications are specifically chosen because of how they affect the pain receptor sites for each different pain syndrome. While the primary goal of the program is to use alternatives to opioids when-ever possible, another important underlying goal is to stop acute pain from becoming chronic. While ALTO therapies typically take a bit longer to deliver than prescribing opioids, administrators note that this has not adversely affected patient flow in the ED. PMID:27295817

  11. Innovative Program Targets Five Common Pain Syndromes With Non-opioid Alternatives.

    PubMed

    2016-06-01

    To combat the prescription opioid problem, St. Joseph's Healthcare System in Paterson, NJ, has developed a new program that gives providers options they can use to effectively alleviate pain without resorting to highly addictive medication. Launched in January 2016 in the ED at St. Joseph's Regional Medical Center (SJRMC), the Alternatives to Opioids (ALTO) program utilizes protocols that primarily target five common conditions: renal colic, sciatica, headaches, musculoskeletal pain, and extremity fractures. Administrators say they have successfully treated more than 300 patients under the new program, and they see ALTO as a model other hospitals can duplicate. Among the alternative therapies called for in the ALTO program are trigger point injections, nitrous oxide, and ultrasound-guided nerve blocks. ALTO medications are specifically chosen because of how they affect the pain receptor sites for each different pain syndrome. While the primary goal of the program is to use alternatives to opioids when-ever possible, another important underlying goal is to stop acute pain from becoming chronic. While ALTO therapies typically take a bit longer to deliver than prescribing opioids, administrators note that this has not adversely affected patient flow in the ED.

  12. Alternative splicing and genomic structure of the Wilms tumor gene WT1.

    PubMed Central

    Haber, D A; Sohn, R L; Buckler, A J; Pelletier, J; Call, K M; Housman, D E

    1991-01-01

    The chromosome 11p13 Wilms tumor susceptibility gene WT1 appears to play a crucial role in regulating the proliferation and differentiation of nephroblasts and gonadal tissue. The WT1 gene consists of 10 exons, encoding a complex pattern of mRNA species: four distinct transcripts are expressed, reflecting the presence or absence of two alternative splices. Splice I consists of a separate exon, encoding 17 amino acids, which is inserted between the proline-rich amino terminus and the zinc finger domains. Splice II arises from the use of an alternative 5' splice junction and results in the insertion of 3 amino acids between zinc fingers 3 and 4. RNase protection analysis demonstrates that the most prevalent splice variant in both human and mouse is that which contains both alternative splices, whereas the least common is the transcript missing both splices. The relative distribution of splice variants is highly conserved between normal fetal kidney tissue and Wilms tumors that have intact WT1 transcripts. The ratio of these different WT1 mRNA species is also maintained as a function of development in the mouse kidney and in various mouse tissues expressing WT1. The conservation in structure and relative levels of each of the four WT1 mRNA species suggests that each encoded polypeptide makes a significant contribution to normal gene function. The control of cellular proliferation and differentiation exerted by the WT1 gene products may involve interactions between four polypeptides with distinct targets and functions. Images PMID:1658787

  13. Alternative life histories shape brain gene expression profiles in males of the same population.

    PubMed

    Aubin-Horth, Nadia; Landry, Christian R; Letcher, Benjamin H; Hofmann, Hans A

    2005-08-22

    Atlantic salmon (Salmo salar) undergo spectacular marine migrations before homing to spawn in natal rivers. However, males that grow fastest early in life can adopt an alternative 'sneaker' tactic by maturing earlier at greatly reduced size without leaving freshwater. While the ultimate evolutionary causes have been well studied, virtually nothing is known about the molecular bases of this developmental plasticity. We investigate the nature and extent of coordinated molecular changes that accompany such a fundamental transformation by comparing the brain transcription profiles of wild mature sneaker males to age-matched immature males (future large anadromous males) and immature females. Of the ca. 3000 genes surveyed, 15% are differentially expressed in the brains of the two male types. These genes are involved in a wide range of processes, including growth, reproduction and neural plasticity. Interestingly, despite the potential for wide variation in gene expression profiles among individuals sampled in nature, consistent patterns of gene expression were found for individuals of the same reproductive tactic. Notably, gene expression patterns in immature males were different both from immature females and sneakers, indicating that delayed maturation and sea migration by immature males, the 'default' life cycle, may actually result from an active inhibition of development into a sneaker.

  14. Alternative life histories shape brain gene expression profiles in males of the same population

    USGS Publications Warehouse

    Aubin-Horth, N.; Landry, C.R.; Letcher, B.H.; Hofmann, H.A.

    2005-01-01

    Atlantic salmon (Salmo salar) undergo spectacular marine migrations before homing to spawn in natal rivers. However, males that grow fastest early in life can adopt an alternative 'sneaker' tactic by maturing earlier at greatly reduced size without leaving freshwater. While the ultimate evolutionary causes have been well studied, virtually nothing is known about the molecular bases of this developmental plasticity. We investigate the nature and extent of coordinated molecular changes that accompany such a fundamental transformation by comparing the brain transcription profiles of wild mature sneaker males to age-matched immature males (future large anadromous males) and immature females. Of the ca. 3000 genes surveyed, 15% are differentially expressed in the brains of the two male types. These genes are involved in a wide range of processes, including growth, reproduction and neural plasticity. Interestingly, despite the potential for wide variation in gene expression profiles among individuals sampled in nature, consistent patterns of gene expression were found for individuals of the same reproductive tactic. Notably, gene expression patterns in immature males were different both from immature females and sneakers, indicating that delayed maturation and sea migration by immature males, the 'default' life cycle, may actually result from an active inhibition of development into a sneaker. ?? 2005 The Royal Society.

  15. Myocardial alternative RNA splicing and gene expression profiling in early stage hypoplastic left heart syndrome.

    PubMed

    Ricci, Marco; Xu, Yanji; Hammond, Harriet L; Willoughby, David A; Nathanson, Lubov; Rodriguez, Maria M; Vatta, Matteo; Lipshultz, Steven E; Lincoln, Joy

    2012-01-01

    Hypoplastic Left Heart Syndrome (HLHS) is a congenital defect characterized by underdevelopment of the left ventricle and pathological compensation of the right ventricle. If untreated, HLHS is invariably lethal due to the extensive increase in right ventricular workload and eventual failure. Despite the clinical significance, little is known about the molecular pathobiological state of HLHS. Splicing of mRNA transcripts is an important regulatory mechanism of gene expression. Tissue specific alterations of this process have been associated with several cardiac diseases, however, transcriptional signature profiles related to HLHS are unknown. In this study, we performed genome-wide exon array analysis to determine differentially expressed genes and alternatively spliced transcripts in the right ventricle (RV) of six neonates with HLHS, compared to the RV and left ventricle (LV) from non-diseased control subjects. In HLHS, over 180 genes were differentially expressed and 1800 were differentially spliced, leading to changes in a variety of biological processes involving cell metabolism, cytoskeleton, and cell adherence. Additional hierarchical clustering analysis revealed that differential gene expression and mRNA splicing patterns identified in HLHS are unique compared to non-diseased tissue. Our findings suggest that gene expression and mRNA splicing are broadly dysregulated in the RV myocardium of HLHS neonates. In addition, our analysis identified transcriptome profiles representative of molecular biomarkers of HLHS that could be used in the future for diagnostic and prognostic stratification to improve patient outcome.

  16. Structure of the human laminin {gamma}2 chain gene (LAMC2): Alternative splicing with different tissue distribution of two transcripts

    SciTech Connect

    Airenne, T.; Haakana, H.; Kallunki, T.

    1996-02-15

    This article discusses the exon-intron structure and tissue distribution of the laminin {gamma}2 chain (LAMC2) gene, which is mutated in some cases of junctional epidermolysis bullosa. The article also discusses the transcription and splicing of this gene, which result in alternative uses of the last two exons of the gene. The different tissue distributions of the transcripts indicate different functions for the gene in vivo. 36 refs., 8 figs., 3 tabs.

  17. Development Of Educational Programs In Renewable And Alternative Energy Processing: The Case Of Russia

    NASA Astrophysics Data System (ADS)

    Svirina, Anna; Shindor, Olga; Tatmyshevsky, Konstantin

    2014-12-01

    The paper deals with the main problems of Russian energy system development that proves necessary to provide educational programs in the field of renewable and alternative energy. In the paper the process of curricula development and defining teaching techniques on the basis of expert opinion evaluation is defined, and the competence model for renewable and alternative energy processing master students is suggested. On the basis of a distributed questionnaire and in-depth interviews, the data for statistical analysis was obtained. On the basis of this data, an optimization of curricula structure was performed, and three models of a structure for optimizing teaching techniques were developed. The suggested educational program structure which was adopted by employers is presented in the paper. The findings include quantitatively estimated importance of systemic thinking and professional skills and knowledge as basic competences of a masters' program graduate; statistically estimated necessity of practice-based learning approach; and optimization models for structuring curricula in renewable and alternative energy processing. These findings allow the establishment of a platform for the development of educational programs.

  18. Organization, structure and alternate splicing of the murine RFC-1 gene encoding a folate transporter.

    PubMed

    Tolner, B; Roy, K; Sirotnak, F M

    1997-04-11

    The structural organization of the murine RFC-1 gene encoding a folate transporter has been determined. The entire nucleotide sequence of the L1210 cell RFC-1 cDNA, the 3'- and 5'-untranslated regions and the coding sequence were found to be distributed in eight exons, including six primary exons and alternates to exon 1 and exon 5, spanning 10.4 kb. Splice variants were identified in an L1210 cell cDNA library. The most common incorporates exons 1 through 6, encoding a 58-kDa polypeptide. The two least common incorporate exons 1 and 2, a truncated version of exon 3 and exons 4 through 6; or exons 1 through 4, an alternate to exon 5, and exon 6, encoding polypeptides of 53.6 and 43.4 kDa, respectively. A fourth variant reported earlier (GenBank/EMBL accession No. L36539) by others incorporates what we have found to be an alternate of exon 1 and exons 2 through 6. A relatively GC-rich region of the genome just 5' of exon 1 as well as exon 1a appears to be distinctly promoter-like and encodes a number of putative cis-acting elements. The findings pertaining to alternates of exon 1 suggest that the transcription of RFC-1 variants results from two different promoters.

  19. Alternative haplotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution.

    PubMed

    McConnell, Sean C; Hernandez, Kyle M; Wcisel, Dustin J; Kettleborough, Ross N; Stemple, Derek L; Yoder, Jeffrey A; Andrade, Jorge; de Jong, Jill L O

    2016-08-23

    Antigen processing and presentation genes found within the MHC are among the most highly polymorphic genes of vertebrate genomes, providing populations with diverse immune responses to a wide array of pathogens. Here, we describe transcriptome, exome, and whole-genome sequencing of clonal zebrafish, uncovering the most extensive diversity within the antigen processing and presentation genes of any species yet examined. Our CG2 clonal zebrafish assembly provides genomic context within a remarkably divergent haplotype of the core MHC region on chromosome 19 for six expressed genes not found in the zebrafish reference genome: mhc1uga, proteasome-β 9b (psmb9b), psmb8f, and previously unknown genes psmb13b, tap2d, and tap2e We identify ancient lineages for Psmb13 within a proteasome branch previously thought to be monomorphic and provide evidence of substantial lineage diversity within each of three major trifurcations of catalytic-type proteasome subunits in vertebrates: Psmb5/Psmb8/Psmb11, Psmb6/Psmb9/Psmb12, and Psmb7/Psmb10/Psmb13. Strikingly, nearby tap2 and MHC class I genes also retain ancient sequence lineages, indicating that alternative lineages may have been preserved throughout the entire MHC pathway since early diversification of the adaptive immune system ∼500 Mya. Furthermore, polymorphisms within the three MHC pathway steps (antigen cleavage, transport, and presentation) are each predicted to alter peptide specificity. Lastly, comparative analysis shows that antigen processing gene diversity is far more extensive than previously realized (with ancient coelacanth psmb8 lineages, shark psmb13, and tap2t and psmb10 outside the teleost MHC), implying distinct immune functions and conserved roles in shaping MHC pathway evolution throughout vertebrates. PMID:27493218

  20. Description of the Prometheus Program Alternator/Thruster Integration Laboratory (ATIL)

    NASA Technical Reports Server (NTRS)

    Baez, Anastacio N.; Birchenough, Arthur G.; Lebron-Velilla, Ramon C.; Gonzalez, Marcelo C.

    2005-01-01

    The Project Prometheus Alternator Electric Thruster Integration Laboratory's (ATIL) primary two objectives are to obtain test data to influence the power conversion and electric propulsion systems design, and to assist in developing the primary power quality specifications prior to system Preliminary Design Review (PDR). ATIL is being developed in stages or configurations of increasing fidelity and complexity in order to support the various phases of the Prometheus program. ATIL provides a timely insight of the electrical interactions between a representative Permanent Magnet Generator, its associated control schemes, realistic electric system loads, and an operating electric propulsion thruster. The ATIL main elements are an electrically driven 100 kWe Alternator Test Unit (ATU), an alternator controller using parasitic loads, and a thruster Power Processing Unit (PPU) breadboard. This paper describes the ATIL components, its development approach, preliminary integration test results, and current status.

  1. Neural Progenitors Adopt Specific Identities by Directly Repressing All Alternative Progenitor Transcriptional Programs.

    PubMed

    Kutejova, Eva; Sasai, Noriaki; Shah, Ankita; Gouti, Mina; Briscoe, James

    2016-03-21

    In the vertebrate neural tube, a morphogen-induced transcriptional network produces multiple molecularly distinct progenitor domains, each generating different neuronal subtypes. Using an in vitro differentiation system, we defined gene expression signatures of distinct progenitor populations and identified direct gene-regulatory inputs corresponding to locations of specific transcription factor binding. Combined with targeted perturbations of the network, this revealed a mechanism in which a progenitor identity is installed by active repression of the entire transcriptional programs of other neural progenitor fates. In the ventral neural tube, sonic hedgehog (Shh) signaling, together with broadly expressed transcriptional activators, concurrently activates the gene expression programs of several domains. The specific outcome is selected by repressive input provided by Shh-induced transcription factors that act as the key nodes in the network, enabling progenitors to adopt a single definitive identity from several initially permitted options. Together, the data suggest design principles relevant to many developing tissues. PMID:26972603

  2. Identification of new alternative splice events in the TCIRG1 gene in different human tissues

    SciTech Connect

    Smirnova, Anna S.; Morgun, Andrey . E-mail: anemorgun@hotmail.com; Shulzhenko, Natalia; Silva, Ismael D.C.G.; Gerbase-DeLima, Maria

    2005-05-13

    Two transcript variants (TV) of the T cell immune regulator gene 1 (TCIRG1) have already been characterized. TV1 encodes a subunit of the osteoclast vacuolar proton pump and TV2 encodes a T cell inhibitory receptor. Based on the search in dbEST, we validated by RT-PCR six new alternative splice events in TCIRG1 in most of the 28 human tissues studied. In addition, we observed that transcripts using the TV1 transcription start site and two splice forms previously described in a patient with infantile malignant osteopetrosis are also expressed in various tissues of healthy individuals. Studies of these nine splice forms in cytoplasmic RNA of peripheral blood mononuclear cells showed that at least six of them could be efficiently exported from the nucleus. Since various products with nearly ubiquitous tissue distribution are generated from TCIRG1, this gene may be involved in other processes besides immune response and bone resorption.

  3. Radiolabeled semi-quantitative RT-PCR assay for the analysis of alternative splicing of interleukin genes.

    PubMed

    Shakola, Felitsiya; Byrne, Stephen; Javed, Kainaat; Ruggiu, Matteo

    2014-01-01

    Alternative splicing evolved as a very efficient way to generate proteome diversity from a limited number of genes, while at the same time modulating posttranscriptional events of gene expression-such as stability, turnover, subcellular localization, binding properties, and general activity of both mRNAs and proteins. Since the vast majority of human genes undergo alternative splicing, it comes to no surprise that interleukin genes also show extensive alternative splicing. In fact, there is a growing body of evidence indicating that alternative splicing plays a central role in modulating the pleiotropic functions of cytokines, and aberrant expression of alternatively spliced interleukin mRNAs has been linked to disease. However, while several interleukin splice variants have been described, their function is still poorly understood. This is particularly relevant, since alternatively spliced cytokine isoforms can act both as disease biomarkers and as candidate entry points for therapeutic intervention. In this chapter we describe a protocol that uses radiolabeled semi-quantitative RT-PCR to efficiently detect, analyze, and quantify alternative splicing patterns of cytokine genes. PMID:24908320

  4. Radiolabeled semi-quantitative RT-PCR assay for the analysis of alternative splicing of interleukin genes.

    PubMed

    Shakola, Felitsiya; Byrne, Stephen; Javed, Kainaat; Ruggiu, Matteo

    2014-01-01

    Alternative splicing evolved as a very efficient way to generate proteome diversity from a limited number of genes, while at the same time modulating posttranscriptional events of gene expression-such as stability, turnover, subcellular localization, binding properties, and general activity of both mRNAs and proteins. Since the vast majority of human genes undergo alternative splicing, it comes to no surprise that interleukin genes also show extensive alternative splicing. In fact, there is a growing body of evidence indicating that alternative splicing plays a central role in modulating the pleiotropic functions of cytokines, and aberrant expression of alternatively spliced interleukin mRNAs has been linked to disease. However, while several interleukin splice variants have been described, their function is still poorly understood. This is particularly relevant, since alternatively spliced cytokine isoforms can act both as disease biomarkers and as candidate entry points for therapeutic intervention. In this chapter we describe a protocol that uses radiolabeled semi-quantitative RT-PCR to efficiently detect, analyze, and quantify alternative splicing patterns of cytokine genes.

  5. Aerosol delivery of programmed cell death protein 4 using polysorbitol-based gene delivery system for lung cancer therapy.

    PubMed

    Kim, You-Kyoung; Xing, Lei; Chen, Bao-An; Xu, Fengguo; Jiang, Hu-Lin; Zhang, Can

    2014-11-01

    The development of a safe and effective gene delivery system is the most challenging obstacle to the broad application of gene therapy in the clinic. In this study, we report the development of a polysorbitol-based gene delivery system as an alternative gene carrier for lung cancer therapy. The copolymer was prepared by a Michael addition reaction between sorbitol diacrylate (SD) and spermine (SPE); the SD-SPE copolymer effectively condenses with DNA on the nanoscale and protects it from nucleases. SD-SPE/DNA complexes showed excellent transfection with low toxicity both in vitro and in vivo, and aerosol delivery of SD-SPE complexes with programmed cell death protein 4 DNA significantly suppressed lung tumorigenesis in K-ras(LA1) lung cancer model mice. These results demonstrate that SD-SPE has great potential as a gene delivery system based on its excellent biocompatibility and high gene delivery efficiency for lung cancer gene therapy. PMID:24983766

  6. Alternative promoter usage and differential expression of multiple transcripts of mouse Prkar1a gene.

    PubMed

    Banday, Abdul Rouf; Azim, Shafquat; Tabish, Mohammad

    2011-11-01

    Prkar1a gene encodes regulatory type 1 alpha subunit (RIα) of cAMP-dependent protein kinase (PKA) in mouse. The role of this gene has been implicated in Carney complex and many cancer types that suggest its involvement in physiological processes like cell cycle regulation, growth and/or proliferation. We have identified and sequenced partial cDNA clones encoding four alternatively spliced transcripts of mouse Prkar1a gene. These transcripts have alternate 5' UTR structure which results from splicing of three exons (designated as E1a, E1b, and E1c) to canonical exon 2. The designated transcripts T1, T2, T3, and T4 contain 5' UTR exons as E1c, E1a + E1b, E1a, and E1b, respectively. The transcript T1 corresponded to earlier reported transcript in GenBank. In silico study of genomic DNA sequence revealed three distinct promoter regions namely, P1, P2, and P3 upstream of the exons E1a, E1b, and E1c, respectively. P1 is non-CpG-related promoter but P2 and P3 are CpG-related promoters; however, all three are TATA less. RT-PCR analysis demonstrated the expression of all four transcripts in late postnatal stages; however, these were differentially regulated in early postnatal stages of 0.5 day, 3 day, and 15 day mice in different tissue types. Variations in expression of Prkar1a gene transcripts suggest their regulation from multiple promoters that respond to a variety of signals arising in or out of the cell in tissue and developmental stage-specific manner. PMID:21638026

  7. Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes

    PubMed Central

    Huang, Yuheng; Agrawal, Aneil F.

    2016-01-01

    Little is known of how gene expression and its plasticity evolves as populations adapt to different environmental regimes. Expression is expected to evolve adaptively in all populations but only those populations experiencing environmental heterogeneity are expected to show adaptive evolution of plasticity. We measured the transcriptome in a cadmium-enriched diet and a salt-enriched diet for experimental populations of Drosophila melanogaster that evolved for ~130 generations in one of four selective regimes: two constant regimes maintained in either cadmium or salt diets and two heterogeneous regimes that varied either temporally or spatially between the two diets. For populations evolving in constant regimes, we find a strong signature of counter-gradient evolution; the evolved expression differences between populations adapted to alternative diets is opposite to the plastic response of the ancestral population that is naïve to both diets. Based on expression patterns in the ancestral populations, we identify a set of genes for which we predict selection in heterogeneous regimes to result in increases in plasticity and we find the expected pattern. In contrast, a set of genes where we predicted reduced plasticity did not follow expectation. Nonetheless, both gene sets showed a pattern consistent with adaptive expression evolution in heterogeneous regimes, highlighting the difference between observing “optimal” plasticity and improvements in environment-specific expression. Looking across all genes, there is evidence in all regimes of differences in biased allele expression across environments (“allelic plasticity”) and this is more common among genes with plasticity in total expression. PMID:27661078

  8. The Gene Expression Program for the Formation of Wing Cuticle in Drosophila

    PubMed Central

    Adler, Paul N.

    2016-01-01

    The cuticular exoskeleton of insects and other arthropods is a remarkably versatile material with a complex multilayer structure. We made use of the ability to isolate cuticle synthesizing cells in relatively pure form by dissecting pupal wings and we used RNAseq to identify genes expressed during the formation of the adult wing cuticle. We observed dramatic changes in gene expression during cuticle deposition, and combined with transmission electron microscopy, we were able to identify candidate genes for the deposition of the different cuticular layers. Among genes of interest that dramatically change their expression during the cuticle deposition program are ones that encode cuticle proteins, ZP domain proteins, cuticle modifying proteins and transcription factors, as well as genes of unknown function. A striking finding is that mutations in a number of genes that are expressed almost exclusively during the deposition of the envelope (the thin outermost layer that is deposited first) result in gross defects in the procuticle (the thick chitinous layer that is deposited last). An attractive hypothesis to explain this is that the deposition of the different cuticle layers is not independent with the envelope instructing the formation of later layers. Alternatively, some of the genes expressed during the deposition of the envelope could form a platform that is essential for the deposition of all cuticle layers. PMID:27232182

  9. The Gene Expression Program for the Formation of Wing Cuticle in Drosophila.

    PubMed

    Sobala, Lukasz F; Adler, Paul N

    2016-05-01

    The cuticular exoskeleton of insects and other arthropods is a remarkably versatile material with a complex multilayer structure. We made use of the ability to isolate cuticle synthesizing cells in relatively pure form by dissecting pupal wings and we used RNAseq to identify genes expressed during the formation of the adult wing cuticle. We observed dramatic changes in gene expression during cuticle deposition, and combined with transmission electron microscopy, we were able to identify candidate genes for the deposition of the different cuticular layers. Among genes of interest that dramatically change their expression during the cuticle deposition program are ones that encode cuticle proteins, ZP domain proteins, cuticle modifying proteins and transcription factors, as well as genes of unknown function. A striking finding is that mutations in a number of genes that are expressed almost exclusively during the deposition of the envelope (the thin outermost layer that is deposited first) result in gross defects in the procuticle (the thick chitinous layer that is deposited last). An attractive hypothesis to explain this is that the deposition of the different cuticle layers is not independent with the envelope instructing the formation of later layers. Alternatively, some of the genes expressed during the deposition of the envelope could form a platform that is essential for the deposition of all cuticle layers. PMID:27232182

  10. Role of Energy Metabolism in the Brown Fat Gene Program

    PubMed Central

    Nam, Minwoo; Cooper, Marcus P.

    2015-01-01

    In murine and human brown adipose tissue (BAT), mitochondria are powerful generators of heat that safely metabolize fat, a feature that has great promise in the fight against obesity and diabetes. Recent studies suggest that the actions of mitochondria extend beyond their conventional role as generators of heat. There is mounting evidence that impaired mitochondrial respiratory capacity is accompanied by attenuated expression of Ucp1 and other BAT-selective genes, implying that mitochondria exert transcriptional control over the brown fat gene program. In this review, we discuss the current understanding of brown fat mitochondria, their potential role in transcriptional control of the brown fat gene program, and potential strategies to treat obesity in humans by leveraging thermogenesis in brown adipocytes. PMID:26175716

  11. Alternative splicing, a new target to block cellular gene expression by poliovirus 2A protease

    SciTech Connect

    Alvarez, Enrique; Castello, Alfredo; Carrasco, Luis; Izquierdo, Jose M.

    2011-10-14

    Highlights: {yields} Novel role for poliovirus 2A protease as splicing modulator. {yields} Poliovirus 2A protease inhibits the alternative splicing of pre-mRNAs. {yields} Poliovirus 2A protease blocks the second catalytic step of splicing. -- Abstract: Viruses have developed multiple strategies to interfere with the gene expression of host cells at different stages to ensure their own survival. Here we report a new role for poliovirus 2A{sup pro} modulating the alternative splicing of pre-mRNAs. Expression of 2A{sup pro} potently inhibits splicing of reporter genes in HeLa cells. Low amounts of 2A{sup pro} abrogate Fas exon 6 skipping, whereas higher levels of protease fully abolish Fas and FGFR2 splicing. In vitro splicing of MINX mRNA using nuclear extracts is also strongly inhibited by 2A{sup pro}, leading to accumulation of the first exon and the lariat product containing the unspliced second exon. These findings reveal that the mechanism of action of 2A{sup pro} on splicing is to selectively block the second catalytic step.

  12. TASR-1 regulates alternative splicing of collagen genes in chondrogenic cells.

    PubMed

    Matsushita, Hiroshi; Blackburn, Michael L; Klineberg, Eric; Zielinska-Kwiatkowska, Anna; Bolander, Mark E; Sarkar, Gobinda; Suva, Larry J; Chansky, Howard A; Yang, Liu

    2007-05-01

    During the differentiation of chondroprogenitors into mature chondrocytes, the alternative splicing of collagen genes switches from longer isoforms to shorter ones. To investigate the underlying mechanisms, we infected mouse ATDC5 chondroprogenitor cells with retrovirus for stable expression of two closely related SR splicing factors. RT-PCR analysis revealed that TASR-1, but not TASR-2, influenced alternative splicing of type II and type XI collagens in ATDC5 cells. The effect of TASR-1 on splicing could be reversed with the addition of insulin. Results from our microarray analysis of ATDC5 cells showed that TASR-1 and TASR-2 differentially affect genes involved in the differentiation of chondrocytes. Of special interest is the finding that TASR-1 could down-regulate expression of type X collagen, a hallmark of hypertrophic chondrocytes. Immunohistostaining demonstrated that TASR-1 protein is more abundantly expressed than TASR-2 in mouse articular chondrocytes, raising the possibility that TASR-1 might be involved in phenotype maintenance of articular chondrocytes. PMID:17367759

  13. TASR-1 regulates alternative splicing of collagen genes in chondrogenic cells.

    PubMed

    Matsushita, Hiroshi; Blackburn, Michael L; Klineberg, Eric; Zielinska-Kwiatkowska, Anna; Bolander, Mark E; Sarkar, Gobinda; Suva, Larry J; Chansky, Howard A; Yang, Liu

    2007-05-01

    During the differentiation of chondroprogenitors into mature chondrocytes, the alternative splicing of collagen genes switches from longer isoforms to shorter ones. To investigate the underlying mechanisms, we infected mouse ATDC5 chondroprogenitor cells with retrovirus for stable expression of two closely related SR splicing factors. RT-PCR analysis revealed that TASR-1, but not TASR-2, influenced alternative splicing of type II and type XI collagens in ATDC5 cells. The effect of TASR-1 on splicing could be reversed with the addition of insulin. Results from our microarray analysis of ATDC5 cells showed that TASR-1 and TASR-2 differentially affect genes involved in the differentiation of chondrocytes. Of special interest is the finding that TASR-1 could down-regulate expression of type X collagen, a hallmark of hypertrophic chondrocytes. Immunohistostaining demonstrated that TASR-1 protein is more abundantly expressed than TASR-2 in mouse articular chondrocytes, raising the possibility that TASR-1 might be involved in phenotype maintenance of articular chondrocytes.

  14. A functional alternative splicing mutation in AIRE gene causes autoimmune polyendocrine syndrome type 1.

    PubMed

    Zhang, Junyu; Liu, Hongbin; Liu, Zhiyuan; Liao, Yong; Guo, Luo; Wang, Honglian; He, Lin; Zhang, Xiaodong; Xing, Qinghe

    2013-01-01

    Autoimmune polyendocrine syndrome type 1 (APS-1) is a rare autosomal recessive disease defined by the presence of two of the three conditions: mucocutaneous candidiasis, hypoparathyroidism, and Addison's disease. Loss-of-function mutations of the autoimmune regulator (AIRE) gene have been linked to APS-1. Here we report mutational analysis and functional characterization of an AIRE mutation in a consanguineous Chinese family with APS-1. All exons of the AIRE gene and adjacent exon-intron sequences were amplified by PCR and subsequently sequenced. We identified a homozygous missense AIRE mutation c.463G>A (p.Gly155Ser) in two siblings with different clinical features of APS-1. In silico splice-site prediction and minigene analysis were carried out to study the potential pathological consequence. Minigene splicing analysis and subsequent cDNA sequencing revealed that the AIRE mutation potentially compromised the recognition of the splice donor of intron 3, causing alternative pre-mRNA splicing by intron 3 retention. Furthermore, the aberrant AIRE transcript was identified in a heterozygous carrier of the c.463G>A mutation. The aberrant intron 3-retaining transcript generated a truncated protein (p.G155fsX203) containing the first 154 AIRE amino acids and followed by 48 aberrant amino acids. Therefore, our study represents the first functional characterization of the alternatively spliced AIRE mutation that may explain the pathogenetic role in APS-1.

  15. Alternative Splicing in Adhesion- and Motility-Related Genes in Breast Cancer

    PubMed Central

    Aversa, Rosanna; Sorrentino, Anna; Esposito, Roberta; Ambrosio, Maria Rosaria; Amato, Angela; Zambelli, Alberto; Ciccodicola, Alfredo; D’Apice, Luciana; Costa, Valerio

    2016-01-01

    Breast cancer is the most common tumor and the second leading cause of cancer death among woman, mainly caused by the metastatic spread. Tumor invasiveness is due to an altered expression of adhesion molecules. Among them, semaphorins are of peculiar interest. Cancer cells can manipulate alternative splicing patterns to modulate the expression of adhesion- and motility-related molecules, also at the isoform level. In this study, combining RNA-Sequencing on MCF-7 to targeted experimental validations—in human breast cell lines and breast tumor biopsies—we identified 12 new alternative splicing transcripts in genes encoding adhesion- and motility-related molecules, including semaphorins, their receptors and co-receptors. Among them, a new SEMA3F transcript is expressed in all breast cell lines and breast cancer biopsies, and is translated into a new semaphorin 3F isoform. In silico analysis predicted that most of the new putative proteins lack functional domains, potentially missing some functions and acquiring new ones. Our findings better describe the extent of alternative splicing in breast cancer and highlight the need to further investigate adhesion- and motility-related molecules to gain insights into breast cancer progression. PMID:26784191

  16. Alternative Splicing of Rice WRKY62 and WRKY76 Transcription Factor Genes in Pathogen Defense.

    PubMed

    Liu, Jiqin; Chen, Xujun; Liang, Xiaoxing; Zhou, Xiangui; Yang, Fang; Liu, Jia; He, Sheng Yang; Guo, Zejian

    2016-06-01

    The WRKY family of transcription factors (TFs) functions as transcriptional activators or repressors in various signaling pathways. In this study, we discovered that OsWRKY62 and OsWRKY76, two genes of the WRKY IIa subfamily, undergo constitutive and inducible alternative splicing. The full-length OsWRKY62.1 and OsWRKY76.1 proteins formed homocomplexes and heterocomplexes, and the heterocomplex dominates in the nuclei when analyzed in Nicotiana benthamiana leaves. Transgenic overexpression of OsWRKY62.1 and OsWRKY76.1 in rice (Oryza sativa) enhanced plant susceptibility to the blast fungus Magnaporthe oryzae and the leaf blight bacterium Xanthomonas oryzae pv oryzae, whereas RNA interference and loss-of-function knockout plants exhibited elevated resistance. The dsOW62/76 and knockout lines of OsWRKY62 and OsWRKY76 also showed greatly increased expression of defense-related genes and the accumulation of phytoalexins. The ratio of full-length versus truncated transcripts changed in dsOW62/76 plants as well as in response to pathogen infection. The short alternative OsWRKY62.2 and OsWRKY76.2 isoforms could interact with each other and with full-length proteins. OsWRKY62.2 showed a reduced repressor activity in planta, and two sequence determinants required for the repressor activity were identified in the amino terminus of OsWRKY62.1. The amino termini of OsWRKY62 and OsWRKY76 splice variants also showed reduced binding to the canonical W box motif. These results not only enhance our understanding of the DNA-binding property, the repressor sequence motifs, and the negative feedback regulation of the IIa subfamily of WRKYs but also provide evidence for alternative splicing of WRKY TFs during the plant defense response. PMID:27208272

  17. Implementation of alternative bio-based fuels in aviation: The Clean Airports Program

    SciTech Connect

    Shauck, M.E.; Zanin, M.G.

    1997-12-31

    The Renewable Aviation Fuels Development Center at Baylor University in Waco, Texas, was designated, in March 1996, by the US Department of Energy (US DOE) as the national coordinator of the Clean Airports Program. This program, a spin-off of the Clean Cities Program, was initiated to increase the use of alternative fuels in aviation. There are two major fuels used in aviation today, the current piston engine aviation gasoline, and the current turbine engine fuel. The environmental impact of each of these fuels is significant. Aviation Gasoline (100LL), currently used in the General Aviation piston engine fleet, contributes 100% of the emissions containing lead in the USA today. In the case of the turbine engine fuel (Jet fuel), there are two major environmental impacts to be considered: the local, in the vicinity of the airports, and the global impact on climate change. The Clean Airports Program was established to promote the use of clean burning fuels in order to achieve and maintain clean air at and in the vicinities of airports through the use of alternative fuel-powered air and ground transportation vehicles.

  18. Dysregulation of Autoantigen Genes in ANCA-Associated Vasculitis Involves Alternative Transcripts and New Protein Synthesis

    PubMed Central

    McInnis, Elizabeth A.; Badhwar, Anshul K.; Muthigi, Akhil; Lardinois, Olivier M.; Allred, S. Colby; Yang, Jiajin; Free, Meghan E.; Jennette, J. Charles; Preston, Gloria A.; Falk, Ronald J.

    2015-01-01

    Proteinase 3 (PR3) and myeloperoxidase (MPO) are two major autoantigens in patients with vasculitis with ANCA. The genes encoding these autoantigens are abnormally expressed in peripheral granulocytes of patients with active ANCA-associated vasculitis. This study provides evidence that this transcriptional dysregulation results in a variety of mRNA processing events from the PRTN3 gene locus. In addition to elevated levels of PR3 message, leukocyte RNA from patients contained PR3 transcripts with an alternative 3′ untranslated region. Furthermore, we detected usage of an alternative transcription start site within intron 1 of the PRTN3 gene locus that coincided with active disease (odds ratio, 3.3; 95% confidence interval, 1.3 to 8.4; P=0.01). This promoter may be developmentally regulated, because it was active in normal human bone marrow, multiple leukemia cell lines, MCF-7 cells, and subjects after GM-CSF treatment but not subjects with a neutrophil left shift. This transcript, which lacks exon 1 of PRTN3, encodes a 24-kD protein (p24PR3/MBN) with a sequence similar to that previously described for myeloblastin. Notably, PR3, p24PR3/MBN, and MPO were synthesized in cultured neutrophils from patients with active ANCA-associated vasculitis, indicating that increased transcription results in newly synthesized autoantigens in peripheral neutrophils of patients. The synthesis of p24PR3/MBN seems to expand the autoantigen repertoire, because immunoblots showed that sera from patients recognized p24PR3/MBN. These findings emphasize the importance of transcriptional dysregulation of the autoantigen in autoimmune disease. PMID:25060059

  19. Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes.

    PubMed

    Zhang, Chengjun; Gschwend, Andrea R; Ouyang, Yidan; Long, Manyuan

    2014-05-01

    The structure of eukaryotic genes evolves extensively by intron loss or gain. Previous studies have revealed two models for gene structure evolution through the loss of introns: RNA-based gene conversion, dubbed the Fink model and retroposition model. However, retrogenes that experienced both intron loss and intron-retaining events have been ignored; evolutionary processes responsible for the variation in complex exon-intron structure were unknown. We detected hundreds of retroduplication-derived genes in human (Homo sapiens), fly (Drosophila melanogaster), rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) and categorized them either as duplicated genes that have all introns lost or as duplicated genes that have at least lost one and retained one intron compared with the parental copy (intron-retaining [IR] type). Our new model attributes intron retention alternative splicing to the generation of these IR-type gene pairs. We presented 25 parental genes that have an intron retention isoform and have retained introns in the same locations in the IR-type duplicate genes, which directly support our hypothesis. Our alternative-splicing-based model in conjunction with the retroposition and Fink models can explain the IR-type gene observed. We discovered a greater percentage of IR-type genes in plants than in animals, which may be due to the abundance of intron retention cases in plants. Given the prevalence of intron retention in plants, this new model gives a support that plant genomes have very complex gene structures.

  20. Differential gene expression and alternative splicing between diploid and tetraploid watermelon

    PubMed Central

    Saminathan, Thangasamy; Nimmakayala, Padma; Manohar, Sumanth; Malkaram, Sridhar; Almeida, Aldo; Cantrell, Robert; Tomason, Yan; Abburi, Lavanya; Rahman, Mohammad A.; Vajja, Venkata G.; Khachane, Amit; Kumar, Brajendra; Rajasimha, Harsha K.; Levi, Amnon; Wehner, Todd; Reddy, Umesh K.

    2015-01-01

    The exploitation of synthetic polyploids for producing seedless fruits is well known in watermelon. Tetraploid progenitors of triploid watermelon plants, compared with their diploid counterparts, exhibit wide phenotypic differences. Although many factors modulate alternative splicing (AS) in plants, the effects of autopolyploidization on AS are still unknown. In this study, we used tissues of leaf, stem, and fruit of diploid and tetraploid sweet watermelon to understand changes in gene expression and the occurrence of AS. RNA-sequencing analysis was performed along with reverse transcription quantitative PCR and rapid amplification of cDNA ends (RACE)-PCR to demonstrate changes in expression and splicing. All vegetative tissues except fruit showed an increased level of AS in the tetraploid watermelon throughout the growth period. The ploidy levels of diploids and the tetraploid were confirmed using a ploidy analyser. We identified 5362 and 1288 genes that were up- and downregulated, respectively, in tetraploid as compared with diploid plants. We further confirmed that 22 genes underwent AS events across tissues, indicating possibilities of generating different protein isoforms with altered functions of important transcription factors and transporters. Arginine biosynthesis, chlorophyllide synthesis, GDP mannose biosynthesis, trehalose biosynthesis, and starch and sucrose degradation pathways were upregulated in autotetraploids. Phloem protein 2, chloroplastic PGR5-like protein, zinc-finger protein, fructokinase-like 2, MYB transcription factor, and nodulin MtN21 showed AS in fruit tissues. These results should help in developing high-quality seedless watermelon and provide additional transcriptomic information related to other cucurbits. PMID:25520388

  1. Differential gene expression and alternative splicing between diploid and tetraploid watermelon.

    PubMed

    Saminathan, Thangasamy; Nimmakayala, Padma; Manohar, Sumanth; Malkaram, Sridhar; Almeida, Aldo; Cantrell, Robert; Tomason, Yan; Abburi, Lavanya; Rahman, Mohammad A; Vajja, Venkata G; Khachane, Amit; Kumar, Brajendra; Rajasimha, Harsha K; Levi, Amnon; Wehner, Todd; Reddy, Umesh K

    2015-03-01

    The exploitation of synthetic polyploids for producing seedless fruits is well known in watermelon. Tetraploid progenitors of triploid watermelon plants, compared with their diploid counterparts, exhibit wide phenotypic differences. Although many factors modulate alternative splicing (AS) in plants, the effects of autopolyploidization on AS are still unknown. In this study, we used tissues of leaf, stem, and fruit of diploid and tetraploid sweet watermelon to understand changes in gene expression and the occurrence of AS. RNA-sequencing analysis was performed along with reverse transcription quantitative PCR and rapid amplification of cDNA ends (RACE)-PCR to demonstrate changes in expression and splicing. All vegetative tissues except fruit showed an increased level of AS in the tetraploid watermelon throughout the growth period. The ploidy levels of diploids and the tetraploid were confirmed using a ploidy analyser. We identified 5362 and 1288 genes that were up- and downregulated, respectively, in tetraploid as compared with diploid plants. We further confirmed that 22 genes underwent AS events across tissues, indicating possibilities of generating different protein isoforms with altered functions of important transcription factors and transporters. Arginine biosynthesis, chlorophyllide synthesis, GDP mannose biosynthesis, trehalose biosynthesis, and starch and sucrose degradation pathways were upregulated in autotetraploids. Phloem protein 2, chloroplastic PGR5-like protein, zinc-finger protein, fructokinase-like 2, MYB transcription factor, and nodulin MtN21 showed AS in fruit tissues. These results should help in developing high-quality seedless watermelon and provide additional transcriptomic information related to other cucurbits.

  2. Alternatives for management of wastes generated by the formerly utilized sites remedial action program and supplement

    SciTech Connect

    Gilbert, T.L.; Peterson, J.M.; Vocke, R.W.; Alexander, J.K.

    1983-03-01

    Alternatives for disposal or stabilization of the wastes generated by the US Department of Energy's Formerly Utilized Sites Remedial Action Program (FUSRAP) are identified and compared, with emphasis on the long-term aspects. These wastes consist of soil material and rubble containing trace amounts of radionuclides. A detailed pathway analysis for the dose to the maximally exposed individual is carried out using an adaptation of the natural analogue method. Comparisons of the different alternatives, based on the results of the pathway analysis and qualitative cost considerations, indicate that, if the hazard is such that the wastes must be removed and disposed of rather than stabilized in place, disposal by immediate dispersal is preferable to containment, and containment followed by slow planned dispersal is preferable to containment without dispersal. The Supplement presents refinements of work that was reported at the 1982 International Decommissioning Symposium. The new material consists of revisions of the estimates of the predicted potential dose to the maximally exposed individual and a more detailed comparative assessment of the radiological impacts of alternatives for management of wastes generated by the US Department of Energy's Formerly Utilized Sites Remedial Action Program (FUSRAP).

  3. A framework program for the teaching of alternative methods (replacement, reduction, refinement) to animal experimentation.

    PubMed

    Daneshian, Mardas; Akbarsha, Mohammad A; Blaauboer, Bas; Caloni, Francesca; Cosson, Pierre; Curren, Rodger; Goldberg, Alan; Gruber, Franz; Ohl, Frauke; Pfaller, Walter; van der Valk, Jan; Vinardell, Pilar; Zurlo, Joanne; Hartung, Thomas; Leist, Marcel

    2011-01-01

    Development of improved communication and education strategies is important to make alternatives to the use of animals, and the broad range of applications of the 3Rs concept better known and understood by different audiences. For this purpose, the Center for Alternatives to Animal Testing in Europe (CAAT-Europe) together with the Transatlantic Think Tank for Toxicology (t(4)) hosted a three-day workshop on "Teaching Alternative Methods to Animal Experimentation". A compilation of the recommendations by a group of international specialists in the field is summarized in this report. Initially, the workshop participants identified the different audience groups to be addressed and also the communication media that may be used. The main outcome of the workshop was a framework for a comprehensive educational program. The modular structure of the teaching program presented here allows adaptation to different audiences with their specific needs; different time schedules can be easily accommodated on this basis. The topics cover the 3Rs principle, basic research, toxicological applications, method development and validation, regulatory aspects, case studies and ethical aspects of 3Rs approaches. This expert consortium agreed to generating teaching materials covering all modules and providing them in an open access online repository.

  4. Evaluation of the Courtlink Auto Crime Prevention Program (CACPP) for Senior Elementary and Alternative School Students in British Columbia.

    ERIC Educational Resources Information Center

    Curtis, Charles K.; Meehan, George

    This study evaluated the Courtlink Auto Crime Prevention Program (CACPP), a 13-hour curriculum for senior elementary school and secondary school alternative program at-risk students in British Columbia, Canada. The program provides students with information about automobile crime and its costs, consequences, and prevention. It promotes positive…

  5. 46 CFR 176.620 - Description of the Alternative Hull Examination (AHE) Program for certain passenger vessels.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Description of the Alternative Hull Examination (AHE... completed using only divers, this program has four steps: the application process, the preliminary... program, or if a remotely operated vehicle (ROV) is used during the program, the preliminary exam step...

  6. Perspectives on Best Practices for Gene Therapy Programs

    PubMed Central

    Cheever, Thomas R.; Berkley, Dale; Braun, Serge; Brown, Robert H.; Byrne, Barry J.; Chamberlain, Jeffrey S.; Cwik, Valerie; Duan, Dongsheng; Federoff, Howard J.; High, Katherine A.; Kaspar, Brian K.; Klinger, Katherine W.; Larkindale, Jane; Lincecum, John; Mavilio, Fulvio; McDonald, Cheryl L.; McLaughlin, James; Weiss McLeod, Bonnie; Mendell, Jerry R.; Nuckolls, Glen; Stedman, Hansell H.; Tagle, Danilo A.; Vandenberghe, Luk H.; Wang, Hao; Wernett, Pamela J.; Wilson, James M.; Porter, John D.

    2015-01-01

    Abstract With recent successes in gene therapy trials for hemophilia and retinal diseases, the promise and prospects for gene therapy are once again garnering significant attention. To build on this momentum, the National Institute of Neurological Disorders and Stroke and the Muscular Dystrophy Association jointly hosted a workshop in April 2014 on “Best Practices for Gene Therapy Programs,” with a focus on neuromuscular disorders. Workshop participants included researchers from academia and industry as well as representatives from the regulatory, legal, and patient advocacy sectors to cover the gamut from preclinical optimization to intellectual property concerns and regulatory approval. The workshop focused on three key issues in the field: (1) establishing adequate scientific premise for clinical trials in gene therapy, (2) addressing regulatory process issues, and (3) intellectual property and commercialization issues as they relate to gene therapy. The outcomes from the discussions at this workshop are intended to provide guidance for researchers and funders in the gene therapy field. PMID:25654329

  7. Signals Regulating the Expression of the Nuclear Gene Encoding Alternative Oxidase of Plant Mitochondria.

    PubMed

    Vanlerberghe, G. C.; McLntosh, L.

    1996-06-01

    Suspension cells of tobacco (Nicotiana tabacum L. cv Bright Yellow) were used to investigate signals regulating the expression of the nuclear gene Aox1 encoding the mitochondrial alternative oxidase (AOX) protein responsible for cyanide-resistant respiration in plants. We found that an increase in the tricarboxylic acid cycle intermediate citrate (either after its exogenous supply to cells or after inhibition of aconitase by monofluoroacetate) caused a rapid and dramatic increase in the steady-state level of Aox1 mRNA and AOX protein. This led to a large increase in the capacity for AOX respiration, defined as the amount of salicylhydroxamic acid-sensitive O2 uptake by cells in the presence of potassium cyanide. The results indicate that citrate may be an important signal metabolite regulating Aox1 gene expression. A number of other treatments were also identified that rapidly induced the level of Aox1 mRNA and AOX capacity. These included short-term incubation of cells with 10 mM acetate, 2 [mu]M antimycin A, 5 mM H2O2, or 1 mM cysteine. For some of these treatments, induction of AOX occurred without an increase in cellular citrate level, indicating that other signals (possibly related to oxidative stress conditions) are also important in regulating Aox1 gene expression. The signals influencing Aox1 gene expression are discussed with regard to the potential function(s) of AOX to modulate tricarboxylic acid cycle metabolism and/or to prevent the generation of active oxygen species by the mitochondrial electron transport chain. PMID:12226312

  8. Signals Regulating the Expression of the Nuclear Gene Encoding Alternative Oxidase of Plant Mitochondria.

    PubMed Central

    Vanlerberghe, G. C.; McLntosh, L.

    1996-01-01

    Suspension cells of tobacco (Nicotiana tabacum L. cv Bright Yellow) were used to investigate signals regulating the expression of the nuclear gene Aox1 encoding the mitochondrial alternative oxidase (AOX) protein responsible for cyanide-resistant respiration in plants. We found that an increase in the tricarboxylic acid cycle intermediate citrate (either after its exogenous supply to cells or after inhibition of aconitase by monofluoroacetate) caused a rapid and dramatic increase in the steady-state level of Aox1 mRNA and AOX protein. This led to a large increase in the capacity for AOX respiration, defined as the amount of salicylhydroxamic acid-sensitive O2 uptake by cells in the presence of potassium cyanide. The results indicate that citrate may be an important signal metabolite regulating Aox1 gene expression. A number of other treatments were also identified that rapidly induced the level of Aox1 mRNA and AOX capacity. These included short-term incubation of cells with 10 mM acetate, 2 [mu]M antimycin A, 5 mM H2O2, or 1 mM cysteine. For some of these treatments, induction of AOX occurred without an increase in cellular citrate level, indicating that other signals (possibly related to oxidative stress conditions) are also important in regulating Aox1 gene expression. The signals influencing Aox1 gene expression are discussed with regard to the potential function(s) of AOX to modulate tricarboxylic acid cycle metabolism and/or to prevent the generation of active oxygen species by the mitochondrial electron transport chain. PMID:12226312

  9. Geothermal Reservoir Insurance Program: Evaluation of Alternatives and Assessment of Needs

    SciTech Connect

    Golabi, Kamal

    1980-12-16

    In this paper we present some thoughts on a study that would help in laying the groundwork for drafting regulations for the geothermal reservoir insurance program. The objectives of this study would be 1) to assess the likelihood and the financial consequences of premature depletion of reservoirs 2) to evaluate the advantages and shortcomings of alternative schemes for reducing the financial risks of geothermal development 3) to assess the need for government-sponsored reservoir insurance programs, and 4) to delineate the areas and conditions under which a reservoir insurance program would be most useful in promoting national goals . In view of the importance of the government-funded reservoir insurance program and the complex nature of the problem, four issues must be considered in defining the scope and objectives of this study. First, the goals and expectations of the government must be specifically defined and a procedure be developed to allow for measuring the achievement of these goals. Second, the reservoir-related risk should be assessed and a framework should be developed for resolution of differences among the views expressed by segments of the industry on the likelihood of premature reservoir depletion and the financial consequences of such events. Third, given the diversity of opinion among interest groups, it is important that the viewpoints of various segments of industry and the public be sought and incorporated into the study. Fourth, the study should avoid recommending a policy that would be "optimal" from an overall point of view yet would involve so many compromises that no group would consider it beneficial. With these points in mind, we propose the following four steps: DEFINING THE GOALS OF THE GEOTHERMAL DEVELOPMENT PROGRAM; ASSESSING THE RISK OF PREMATURE RESERVOIR DEPLETION; EVALUATING ALTERNATIVE SCHEMES; ACHIEVING CONSENSUS AND RECOMMENDING GUIDELINES.

  10. Community-based home-care program for the management of pre-eclampsia: an alternative.

    PubMed Central

    Helewa, M; Heaman, M; Robinson, M A; Thompson, L

    1993-01-01

    OBJECTIVE: To evaluate the safety, acceptability and cost of a community-based home-care program for the management of mild pre-eclampsia. DESIGN: A descriptive study of outcomes between Apr. 1, 1985, and Dec. 31, 1989. SETTING: St. Boniface General Hospital, Winnipeg. PATIENTS: Urban Winnipeg residents between 27 and 40 weeks' gestation with mild pre-eclampsia who demonstrated acceptance and compliance with home-care management; 321 patients of 1330 were enrolled in the program. INTERVENTIONS: Bed rest at home with daily biochemical and biophysical follow-up protocol and weekly clinic visits; patient education; hospital admission for labour, induction, worsening pre-eclampsia or noncompliance with rest at home. OUTCOME MEASURES: Patterns of referral to the program; clinical, biochemical and biophysical profiles; incidence of severe complications; reduction in total hospital stay and cost analysis. RESULTS: As many women were referred from physicians' offices as were referred from the hospital's antepartum unit, the average gestational age at referral being 36 weeks. Most (205 [64%]) of the women were nulliparous. The average length of stay in the program was 11.5 days. The program's availability resulted in a reduction of 2 days (from 5.7 days to 3.7 days) on average in the length of hospital stay when analysed for all 1330 women with pre-eclampsia. Of the 321 patients in the program 137 (43%) were admitted to hospital for worsening pre-eclampsia; severe pre-eclampsia developed 4 days after admission in 9. No patient suffered eclampsia, disseminated intravascular coagulopathy, abruption or fetal loss related to pre-eclampsia while in the program. The estimated cost saving in the management of pre-eclampsia was over $700,000 over the study period. CONCLUSION: The community-based home-care program is a safe, feasible and less costly alternative to hospital admission in the management of mild pre-eclampsia. PMID:8374846

  11. Global Gene Expression Profiling and Alternative Splicing Events during the Chondrogenic Differentiation of Human Cartilage Endplate-Derived Stem Cells

    PubMed Central

    Shang, Jin; Fan, Xin; Shangguan, Lei; Liu, Huan; Zhou, Yue

    2015-01-01

    Low back pain (LBP) is a very prevalent disease and degenerative disc diseases (DDDs) usually account for the LBP. However, the pathogenesis of DDDs is complicated and difficult to elucidate. Alternative splicing is a sophisticated regulatory process which greatly increases cellular complexity and phenotypic diversity of eukaryotic organisms. In addition, the cartilage endplate-derived stem cells have been discovered and identified by our research group. In this paper, we continue to investigate gene expression profiling and alternative splicing events during chondrogenic differentiation of cartilage endplate-derived stem cells. We adopted Affymetrix Human Transcriptome Array 2.0 (HTA 2.0) to compare the transcriptional and splicing changes between the control and differentiated samples. RT-PCR and quantitative PCR are used to validate the microarray results. The GO and KEGG pathway analysis was also performed. After bioinformatics analysis of the data, we detected 1953 differentially expressed genes. In terms of alternative splicing, the Splicing Index algorithm was used to select alternatively spliced genes. We detected 4411 alternatively spliced genes. GO and KEGG pathway analysis also revealed several functionally involved biological processes and signaling pathways. To our knowledge, this is the first study to investigate the alternative splicing mechanisms in chondrogenic differentiation of stem cells on a genome-wide scale. PMID:26649308

  12. Alternative Education: A Comparative Case Study of the Behavior Modification Programs of Two Upstate South Carolina Alternative Schools for Youth Who Exhibit Behavior That Is Disruptive

    ERIC Educational Resources Information Center

    Scipio, Timothy Lamont

    2013-01-01

    This study examined behavior modification programs in schools designed to focus on discipline and that aim to reform disruptive behavior in students, usually over a limited period of time. This was a comparative case study of two type II alternative schools in the Upstate of South Carolina. The findings contributed to the research base regarding…

  13. Conserved Gene Expression Programs in Developing Roots from Diverse Plants.

    PubMed

    Huang, Ling; Schiefelbein, John

    2015-08-01

    The molecular basis for the origin and diversification of morphological adaptations is a central issue in evolutionary developmental biology. Here, we defined temporal transcript accumulation in developing roots from seven vascular plants, permitting a genome-wide comparative analysis of the molecular programs used by a single organ across diverse species. The resulting gene expression maps uncover significant similarity in the genes employed in roots and their developmental expression profiles. The detailed analysis of a subset of 133 genes known to be associated with root development in Arabidopsis thaliana indicates that most of these are used in all plant species. Strikingly, this was also true for root development in a lycophyte (Selaginella moellendorffii), which forms morphologically different roots and is thought to have evolved roots independently. Thus, despite vast differences in size and anatomy of roots from diverse plants, the basic molecular mechanisms employed during root formation appear to be conserved. This suggests that roots evolved in the two major vascular plant lineages either by parallel recruitment of largely the same developmental program or by elaboration of an existing root program in the common ancestor of vascular plants.

  14. High gene flow between alternative morphs and the evolutionary persistence of facultative paedomorphosis

    PubMed Central

    Oromi, Neus; Michaux, Johan; Denoël, Mathieu

    2016-01-01

    Paedomorphosis and metamorphosis are two major developmental processes that characterize the evolution of complex life cycles in many lineages. Whereas these processes were fixed in some taxa, they remained facultative in others, with alternative phenotypes expressed in the same populations. From a genetic perspective, it is still unknown whether such phenotypes form a single population or whether they show some patterns of isolation in syntopy. This has deep implications for understanding the evolution of the phenotypes, i.e. towards their persistence or their fixation and speciation. Newts and salamanders are excellent models to test this hypothesis because they exhibit both developmental processes in their populations: the aquatic paedomorphs retain gills, whereas the metamorphs are able to colonize land. Using microsatellite data of coexisting paedomorphic and metamorphic palmate newts (Lissotriton helveticus), we found that they formed a panmictic population, which evidences sexual compatibility between the two phenotypes. The high gene flow could be understood as an adaptation to unstable habitats in which phenotypic plasticity is favored over the fixation of developmental alternatives. This makes then possible the persistence of a polyphenism: only metamorphosis could be maintained in case of occasional drying whereas paedomorphosis could offer specific advantages in organisms remaining in water. PMID:27534370

  15. High gene flow between alternative morphs and the evolutionary persistence of facultative paedomorphosis.

    PubMed

    Oromi, Neus; Michaux, Johan; Denoël, Mathieu

    2016-01-01

    Paedomorphosis and metamorphosis are two major developmental processes that characterize the evolution of complex life cycles in many lineages. Whereas these processes were fixed in some taxa, they remained facultative in others, with alternative phenotypes expressed in the same populations. From a genetic perspective, it is still unknown whether such phenotypes form a single population or whether they show some patterns of isolation in syntopy. This has deep implications for understanding the evolution of the phenotypes, i.e. towards their persistence or their fixation and speciation. Newts and salamanders are excellent models to test this hypothesis because they exhibit both developmental processes in their populations: the aquatic paedomorphs retain gills, whereas the metamorphs are able to colonize land. Using microsatellite data of coexisting paedomorphic and metamorphic palmate newts (Lissotriton helveticus), we found that they formed a panmictic population, which evidences sexual compatibility between the two phenotypes. The high gene flow could be understood as an adaptation to unstable habitats in which phenotypic plasticity is favored over the fixation of developmental alternatives. This makes then possible the persistence of a polyphenism: only metamorphosis could be maintained in case of occasional drying whereas paedomorphosis could offer specific advantages in organisms remaining in water. PMID:27534370

  16. Advanced Transportation System Studies. Technical Area 3: Alternate Propulsion Subsystems Concepts. Volume 3; Program Cost Estimates

    NASA Technical Reports Server (NTRS)

    Levack, Daniel J. H.

    2000-01-01

    The objective of this contract was to provide definition of alternate propulsion systems for both earth-to-orbit (ETO) and in-space vehicles (upper stages and space transfer vehicles). For such propulsion systems, technical data to describe performance, weight, dimensions, etc. was provided along with programmatic information such as cost, schedule, needed facilities, etc. Advanced technology and advanced development needs were determined and provided. This volume separately presents the various program cost estimates that were generated under three tasks: the F- IA Restart Task, the J-2S Restart Task, and the SSME Upper Stage Use Task. The conclusions, technical results , and the program cost estimates are described in more detail in Volume I - Executive Summary and in individual Final Task Reports.

  17. Molecular cloning and functional characterization of a mouse gene upregulated by lipopolysaccharide treatment reveals alternative splicing

    SciTech Connect

    Du, Kejun; Chen, Yaoming; Dai, Zongming; Bi, Yuan; Cai, Tongjian; Hou, Lichao; Chai, Yubo; Song, Qinghe; Chen, Sumin; Luo, Wenjing; Chen, Jingyuan

    2010-01-01

    Treatment of mouse cells with lipopolysaccharide (LPS) potently initiates an inflammatory response, but the underlying mechanisms are unclear. We therefore sought to characterize cDNA sequences of a new mouse LPS-responsive gene, and to evaluate the effects of MLrg. Full-length cDNAs were obtained from LPS-treated NIH3T3 cells. We report that the MLrg gene produces two alternative splice products (GenBank Accession Nos. (DQ316984) and (DQ320011)), respectively, encoding MLrgW and MLrgS polypeptides. Both proteins contain zinc finger and leucine zipper domains and are thus potential regulators of transcription. Expression of MLrgW and MLrgS were robustly upregulated following LPS treatment, and the proteins were localized predominantly in the nuclear membrane and cytoplasm. In stable transfectants over-expressing MLrgW the proportion of cells in G1 phase was significantly reduced, while in cells over-expressing MLrgS the proportion of cells in G2 was significantly increased; both proteins are thus potential regulators of cell cycle progression. Upregulation of MLrgW and MLrgS may be an important component of the LPS inflammatory pathway and of the host response to infection with GNB.

  18. The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators

    PubMed Central

    Llorian, Miriam; Gooding, Clare; Bellora, Nicolas; Hallegger, Martina; Buckroyd, Adrian; Wang, Xiao; Rajgor, Dipen; Kayikci, Melis; Feltham, Jack; Ule, Jernej; Eyras, Eduardo; Smith, Christopher W.J.

    2016-01-01

    Alternative splicing (AS) is a key component of gene expression programs that drive cellular differentiation. Smooth muscle cells (SMCs) are important in the function of a number of physiological systems; however, investigation of SMC AS has been restricted to a handful of events. We profiled transcriptome changes in mouse de-differentiating SMCs and observed changes in hundreds of AS events. Exons included in differentiated cells were characterized by particularly weak splice sites and by upstream binding sites for Polypyrimidine Tract Binding protein (PTBP1). Consistent with this, knockdown experiments showed that that PTBP1 represses many smooth muscle specific exons. We also observed coordinated splicing changes predicted to downregulate the expression of core components of U1 and U2 snRNPs, splicing regulators and other post-transcriptional factors in differentiated cells. The levels of cognate proteins were lower or similar in differentiated compared to undifferentiated cells. However, levels of snRNAs did not follow the expression of splicing proteins, and in the case of U1 snRNP we saw reciprocal changes in the levels of U1 snRNA and U1 snRNP proteins. Our results suggest that the AS program in differentiated SMCs is orchestrated by the combined influence of auxiliary RNA binding proteins, such as PTBP1, along with altered activity and stoichiometry of the core splicing machinery. PMID:27317697

  19. Characterization of the interferon genes in homozygous rainbow trout reveals two novel genes, alternate splicing and differential regulation of duplicated genes

    USGS Publications Warehouse

    Purcell, M.K.; Laing, K.J.; Woodson, J.C.; Thorgaard, G.H.; Hansen, J.D.

    2009-01-01

    The genes encoding the type I and type II interferons (IFNs) have previously been identified in rainbow trout and their proteins partially characterized. These previous studies reported a single type II IFN (rtIFN-??) and three rainbow trout type I IFN genes that are classified into either group I (rtIFN1, rtIFN2) or group II (rtIFN3). In this present study, we report the identification of a novel IFN-?? gene (rtIFN-??2) and a novel type I group II IFN (rtIFN4) in homozygous rainbow trout and predict that additional IFN genes or pseudogenes exist in the rainbow trout genome. Additionally, we provide evidence that short and long forms of rtIFN1 are actively and differentially transcribed in homozygous trout, and likely arose due to alternate splicing of the first exon. Quantitative reverse transcriptase PCR (qRT-PCR) assays were developed to systematically profile all of the rainbow trout IFN transcripts, with high specificity at an individual gene level, in na??ve fish and after stimulation with virus or viral-related molecules. Cloned PCR products were used to ensure the specificity of the qRT-PCR assays and as absolute standards to assess transcript abundance of each gene. All IFN genes were modulated in response to Infectious hematopoietic necrosis virus (IHNV), a DNA vaccine based on the IHNV glycoprotein, and poly I:C. The most inducible of the type I IFN genes, by all stimuli tested, were rtIFN3 and the short transcript form of rtIFN1. Gene expression of rtIFN-??1 and rtIFN-??2 was highly up-regulated by IHNV infection and DNA vaccination but rtIFN-??2 was induced to a greater magnitude. The specificity of the qRT-PCR assays reported here will be useful for future studies aimed at identifying which cells produce IFNs at early time points after infection. ?? 2008 Elsevier Ltd.

  20. Determination of ligand-binding specificity by alternative splicing: Two distinct growth factor receptors encoded by a single gene

    SciTech Connect

    Miki, T.; Bottaro, D.P.; Fleming, T.P.; Smith, C.L.; Chan, A.M.L.; Aaronson, S.A. ); Burgess, W.H. )

    1992-01-01

    Expression cDNA cloning and structural analysis of the human keratinocyte growth factor receptor (KGFR) revealed identity with one of the fibroblast growth factor (FGF) receptors encoded by the bek gene (FGFR-2), except for a divergent stretch of 49 amino acids in their extracellular domains. Binding assays demonstrated that the KGFR was a high-affinity receptor for both KGF and acidic FGF, while FGFR-2 showed high affinity for basic and acidic FGF but no detectable binding by KGF. Genomic analysis of the bek gene revealed two alternative exons responsible for the region of divergence between the two receptors. The KGFR transcript was specific to epithelial cells, and it appeared to be differentially regulated with respect to the alternative FGFR-2 transcript. Thus, two growth factor receptors with different ligand-binding specificities and expression patterns are encoded by alternative transcripts of the same gene.

  1. Structure and expression of the human L-myc gene reveal a complex pattern of alternative mRNA processing

    SciTech Connect

    Kaye, F.; Battey, J.; Nau, M.; Brooks, B.; Seifter, E.; De Greve, J.; Birrer, M.; Sausville, E.; Minna, J.

    1988-01-01

    The authors' analyzed in detail the structure of the L-myc gene isolated from human placental DNA and characterized its expression in several small-cell lung cancer cell lines. The gene is composed of three exons and two introns spanning 6.6 kilobases in human DNA. Several distinct mRNA species are produced in all small-cell lung cancer cell lines that express L-myc. These transcripts are generated from a single gene by alternative splicing of introns 1 and 2 and by use of alternative polyadenylation signals. In some mRNAs that is a long open reading frame with a predicted translated protein of 364 residues. Amino acid sequence comparison with c-myc and N-myc demonstrated multiple discrete regions with extensive homology. In contrast, other mRNA transcripts, generated by alternative processing, could encode a truncated protein with a novel carboxy-terminal end.

  2. Federal Alternative Fuel Program light duty vehicle operation. First annual report to Congress, fiscal year 1991

    SciTech Connect

    Not Available

    1992-03-01

    This annual report to Congress details the first year of the Federal light duty vehicle operations as required by Section 400AA(b)(1)(B) of the Energy Policy and Conservation Act (EPCA). Alternative Motors Fuels Act (AMFA) encourages the use and production of AFVs that use methanol, ethanol, and natural gas. The Congress has recognized that displacement of energy derived from imported oil with alternative fuels will help to achieve energy security and improve air quality. In passing this Act, the Federal Government is assisting clean-burning, non-petroleum transportation fuels to reach a threshold level of commercial application and consumer acceptability at which they can successfully compete with petroleum-base transportation fuels. The objectives of the program are to demonstrate the environmental, economic, and performance characteristics of alternative fuel fleet vehicles and to provide information or engine/vehicle manufacturers as well as the general public. This report details the first year of the Federal light duty vehicle operations, from January 1991 through September 1991. The Federal test vehicles are composed of 65 M85 fuel and 16 conventional gasoline fuel vehicles. The following sections discuss the vehicle operation and performance characteristics of the AMFA test vehicles in a fleet environment.

  3. Fruit regulates seasonal expression of flowering genes in alternate-bearing ‘Moncada’ mandarin

    PubMed Central

    Muñoz-Fambuena, Natalia; Mesejo, Carlos; Carmen González-Mas, M.; Primo-Millo, Eduardo; Agustí, Manuel; Iglesias, Domingo J.

    2011-01-01

    Background and Aims The presence of fruit has been widely reported to act as an inhibitor of flowering in fruit trees. This study is an investigation into the effect of fruit load on flowering of ‘Moncada’ mandarin and on the expression of putative orthologues of genes involved in flowering pathways to provide insight into the molecular mechanisms underlying alternate bearing in citrus. Methods The relationship between fruit load and flowering intensity was examined first. Defruiting experiments were further conducted to demonstrate the causal effect of fruit removal upon flowering. Finally, the activity of flowering-related genes was investigated to determine the extent to which their seasonal expression is affected by fruit yield. Key Results First observations and defruiting experiments indicated a significant inverse relationship between preceding fruit load and flowering intensity. Moreover, data indicated that when fruit remained on the tree from November onwards, a dramatic inhibition of flowering occurred the following spring. The study of the expression pattern of flowering-genes of on (fully loaded) and off (without fruits) trees revealed that homologues of FLOWERING LOCUS T (FT), SUPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), APETALA1 (AP1) and LEAFY (LFY) were negatively affected by fruit load. Thus, CiFT expression showed a progressive increase in leaves from off trees through the study period, the highest differences found from December onwards (10-fold). Whereas differences in the relative expression of SOC1 only reached significance from September to mid-December, CsAP1 expression was constantly higher in those trees through the whole study period. Significant variations in CsLFY expression only were found in late February (close to 20 %). On the other hand, the expression of the homologues of TERMINAL FLOWER 1 (TFL1) and FLOWERING LOCUS C (FLC) did not appear to be related to fruit load. Conclusions These results suggest for the first time

  4. Alternative splicing of the AGAMOUS orthologous gene in double flower of Magnolia stellata (Magnoliaceae).

    PubMed

    Zhang, Bo; Liu, Zhi-Xiong; Ma, Jiang; Song, Yi; Chen, Fa-Ju

    2015-12-01

    Magnolia stellata is a woody ornamental shrub with more petaloid tepals than related plants from family Magnoliaceae. Recent studies revealed that expression changes in an AGAMOUS (AG) orthologous gene could resulted in double flowers with increased numbers of petals. We isolated three transcripts encoding different isoforms of a single AG orthologous gene, MastAG, mastag_2 and mastag_3, from M. stellata. Sequence alignments and Southern blot analyses suggested that MastAG was a single-copy gene in M. stellata genomes, and that mastag_2 and mastag_3 were abnormally spliced isoforms of MastAG. An 144bp exon skipping in MastAG results in the truncated mastag_2 protein lacking the completely I domain and 18 aa of the K1 subdomain, whereas an 165bp exon skipping of MastAG produces a truncated mastag_3 protein lacking 6 aa of the K3 subdomain and the completely C terminal region. Expression analyses showed that three alternative splicing (AS) isoforms expressed only in developing stamens and carpels. Functional analyses revealed that MastAG could mimic the endogenous AG to specify carpel identity, but failed to regulate stamen development in an Arabidopsis ag-1 mutant. Moreover, the key domain or subdomain deletions represented by mastag_2 and mastag_3 resulted in loss of C-function. However, ectopic expression of mastag_2 in Arabidopsis produced flowers with sepals converted into carpeloid organs, but without petals and stamens, whereas ectopic expression of mastag_3 in Arabidopsis could mimic the flower phenotype of the ag mutant and produced double flowers with homeotic transformation of stamens into petals and carpels into another ag flower. Our results also suggest that mastag_3 holds some potential for biotechnical engineering to create multi-petal phenotypes in commercial ornamental cultivars.

  5. Alternative splicing of the AGAMOUS orthologous gene in double flower of Magnolia stellata (Magnoliaceae).

    PubMed

    Zhang, Bo; Liu, Zhi-Xiong; Ma, Jiang; Song, Yi; Chen, Fa-Ju

    2015-12-01

    Magnolia stellata is a woody ornamental shrub with more petaloid tepals than related plants from family Magnoliaceae. Recent studies revealed that expression changes in an AGAMOUS (AG) orthologous gene could resulted in double flowers with increased numbers of petals. We isolated three transcripts encoding different isoforms of a single AG orthologous gene, MastAG, mastag_2 and mastag_3, from M. stellata. Sequence alignments and Southern blot analyses suggested that MastAG was a single-copy gene in M. stellata genomes, and that mastag_2 and mastag_3 were abnormally spliced isoforms of MastAG. An 144bp exon skipping in MastAG results in the truncated mastag_2 protein lacking the completely I domain and 18 aa of the K1 subdomain, whereas an 165bp exon skipping of MastAG produces a truncated mastag_3 protein lacking 6 aa of the K3 subdomain and the completely C terminal region. Expression analyses showed that three alternative splicing (AS) isoforms expressed only in developing stamens and carpels. Functional analyses revealed that MastAG could mimic the endogenous AG to specify carpel identity, but failed to regulate stamen development in an Arabidopsis ag-1 mutant. Moreover, the key domain or subdomain deletions represented by mastag_2 and mastag_3 resulted in loss of C-function. However, ectopic expression of mastag_2 in Arabidopsis produced flowers with sepals converted into carpeloid organs, but without petals and stamens, whereas ectopic expression of mastag_3 in Arabidopsis could mimic the flower phenotype of the ag mutant and produced double flowers with homeotic transformation of stamens into petals and carpels into another ag flower. Our results also suggest that mastag_3 holds some potential for biotechnical engineering to create multi-petal phenotypes in commercial ornamental cultivars. PMID:26706078

  6. The evolution of novelty in conserved genes; evidence of positive selection in the Drosophila fruitless gene is localised to alternatively spliced exons

    PubMed Central

    Parker, D J; Gardiner, A; Neville, M C; Ritchie, M G; Goodwin, S F

    2014-01-01

    There has been much debate concerning whether cis-regulatory or coding changes are more likely to produce evolutionary innovation or adaptation in gene function, but an additional complication is that some genes can dramatically diverge through alternative splicing, increasing the diversity of gene function within a locus. The fruitless gene is a major transcription factor with a wide range of pleiotropic functions, including a fundamental conserved role in sexual differentiation, species-specific morphology and an important influence on male sexual behaviour. Here, we examine the structure of fruitless in multiple species of Drosophila, and determine the patterns of selective constraint acting across the coding region. We found that the pattern of selection, estimated from the ratio of non-synonymous to synonymous substitutions, varied considerably across the gene, with most regions of the gene evolutionarily conserved but with several regions showing evidence of divergence as a result of positive selection. The regions that showed evidence of positive selection were found to be localised to relatively consistent regions across multiple speciation events, and are associated with alternative splicing. Alternative splicing may thus provide a route to gene diversification in key regulatory loci. PMID:24149653

  7. Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine.

    PubMed

    Sheng, Zhen; Sun, Yi; Zhu, Ruixin; Jiao, Na; Tang, Kailin; Cao, Zhiwei; Ma, Chao

    2015-01-01

    Berberine has been identified with anti-proliferative effects on various cancer cells. Many researchers have been trying to elucidate the anti-cancer mechanisms of berberine based on differentially expressed genes. However, differentially alternative splicing genes induced by berberine might also contribute to its pharmacological actions and have not been reported yet. Moreover, the potential functional cross-talking between the two sets of genes deserves further exploration. In this study, RNA-seq technology was used to detect the differentially expressed genes and differentially alternative spliced genes in BEL-7402 cancer cells induced by berberine. Functional enrichment analysis indicated that these genes were mainly enriched in the p53 and cell cycle signalling pathway. In addition, it was statistically proven that the two sets of genes were locally co-enriched along chromosomes, closely connected to each other based on protein-protein interaction and functionally similar on Gene Ontology tree. These results suggested that the two sets of genes regulated by berberine might be functionally cross-talked and jointly contribute to its cell cycle arresting effect. It has provided new clues for further researches on the pharmacological mechanisms of berberine as well as the other botanical drugs.

  8. Biodiesel Drives Florida Power & Light's EPAct Alternative Compliance Strategy; EPAct Alternative Fuel Transportation Program: Success Story (Fact Sheet)

    SciTech Connect

    Not Available

    2010-05-01

    This success story highlights how Florida Power & Light Company has successfully complied with the Energy Policy Act of 1992 (EPAct) through Alternative Compliance using biodiesel technologies and how it has become a biofuel leader, reducing petroleum use and pollutant emissions throughout Florida.

  9. MYCN controls an alternative RNA splicing program in high-risk metastatic neuroblastoma.

    PubMed

    Zhang, Shile; Wei, Jun S; Li, Samuel Q; Badgett, Tom C; Song, Young K; Agarwal, Saurabh; Coarfa, Cristian; Tolman, Catherine; Hurd, Laura; Liao, Hongling; He, Jianbin; Wen, Xinyu; Liu, Zhihui; Thiele, Carol J; Westermann, Frank; Asgharzadeh, Shahab; Seeger, Robert C; Maris, John M; Guidry Auvil, Jamie M; Smith, Malcolm A; Kolaczyk, Eric D; Shohet, Jason; Khan, Javed

    2016-02-28

    The molecular mechanisms underlying the aggressive behavior of MYCN driven neuroblastoma (NBL) is under intense investigation; however, little is known about the impact of this family of transcription factors on the splicing program. Here we used high-throughput RNA sequencing to systematically study the expression of RNA isoforms in stage 4 MYCN-amplified NBL, an aggressive subtype of metastatic NBL. We show that MYCN-amplified NBL tumors display a distinct gene splicing pattern affecting multiple cancer hallmark functions. Six splicing factors displayed unique differential expression patterns in MYCN-amplified tumors and cell lines, and the binding motifs for some of these splicing factors are significantly enriched in differentially-spliced genes. Direct binding of MYCN to promoter regions of the splicing factors PTBP1 and HNRNPA1 detected by ChIP-seq demonstrates that MYCN controls the splicing pattern by direct regulation of the expression of these key splicing factors. Furthermore, high expression of PTBP1 and HNRNPA1 was significantly associated with poor overall survival of stage4 NBL patients (p ≤ 0.05). Knocking down PTBP1, HNRNPA1 and their downstream target PKM2, an isoform of pro-tumor-growth, result in repressed growth of NBL cells. Therefore, our study reveals a novel role of MYCN in controlling global splicing program through regulation of splicing factors in addition to its well-known role in the transcription program. These findings suggest a therapeutically potential to target the key splicing factors or gene isoforms in high-risk NBL with MYCN-amplification.

  10. In Vivo Programmed Gene Expression Based on Artificial Quorum Networks

    PubMed Central

    Chu, Teng; Huang, Yajun; Hou, Mingyu; Wang, Qiyao; Xiao, Jingfan; Zhang, Yuanxing

    2015-01-01

    The quorum sensing (QS) system, as a well-functioning population-dependent gene switch, has been widely applied in many gene circuits in synthetic biology. In our work, an efficient cell density-controlled expression system (QS) was established via engineering of the Vibrio fischeri luxI-luxR quorum sensing system. In order to achieve in vivo programmed gene expression, a synthetic binary regulation circuit (araQS) was constructed by assembling multiple genetic components, including the quorum quenching protein AiiA and the arabinose promoter ParaBAD, into the QS system. In vitro expression assays verified that the araQS system was initiated only in the absence of arabinose in the medium at a high cell density. In vivo expression assays confirmed that the araQS system presented an in vivo-triggered and cell density-dependent expression pattern. Furthermore, the araQS system was demonstrated to function well in different bacteria, indicating a wide range of bacterial hosts for use. To explore its potential applications in vivo, the araQS system was used to control the production of a heterologous protective antigen in an attenuated Edwardsiella tarda strain, which successfully evoked efficient immune protection in a fish model. This work suggested that the araQS system could program bacterial expression in vivo and might have potential uses, including, but not limited to, bacterial vector vaccines. PMID:25979894

  11. More than genes: the advanced fetal programming hypothesis.

    PubMed

    Hocher, Berthold

    2014-10-01

    Many lines of data, initial epidemiologic studies as well as subsequent extensive experimental studies, indicate that early-life events play a powerful role in influencing later suceptibility to certain chronic diseases. Such events might be over- or undernutrition, exposure to environmental toxins, but also changes in hormones, in particular stress hormones. Typically, those events are triggered by the environmental challenges of the mother. However, recent studies have shown that paternal environmental or nutritional factors affect the phenotype of the offspring as well. The maternal and paternal environmental factors act on the phenotype of the offspring via epigenetic modification of its genome. The advanced fetal programming hypothesis proposes an additional non-environmentally driven mechanism: maternal and also paternal genes may influence the maturating sperm, the oocyte, and later the embryo/fetus, leading to their epigenetic alteration. Thus, the observed phenotype of the offspring may be altered by maternal/paternal genes independent of the fetal genome. Meanwhile, several independent association studies in humans dealing with metabolic and neurological traits also suggest that maternal genes might affect the offspring phenotype independent of the transmission of that particular gene to the offspring. Considering the implications of this hypothesis, some conclusions drawn from transgenic or knockout animal models and based on the causality between a genetic alteration and a phenotype, need to be challenged. Possible implications for the development, diagnostic and therapy of human genetic diseases have to be investigated.

  12. Regulation of tissue-specific expression of alternative peripheral myelin protein-22 (PMP22) gene transcripts by two promoters

    SciTech Connect

    Patel, P.I.; Schoener-Scott, R.; Lupski, J.R.

    1994-09-01

    Mutations affecting the peripheral myelin protein-22 (PMP22) gene have been shown to be associated with inherited peripheral neuropathies. We have cloned and characterized the human PMP22 gene which spans approximately 40 kilobases and contains four coding exons. Towards developing gene therapy regimens for the associated peripheral neuropathies, we have initiated detailed analysis of the 5{prime} flanking region of the PMP22 gene and identified two alternatively transcribed, but untranslated exons. Mapping of separate PMP22 mRNA transcription initiation sites to each of these exons indicates that PMP22 expression is regulated by two alternatively used promoters. Both putative promoter sequences demonstrated the ability to drive expression of reporter genes in transfection experiments. Furthermore, the structure of the 5{prime} portion of the PMP22 gene appears to be identical in rat and human, supporting the biological significance of the observed arrangement of regulatory regions. The relative expression of the alternative PMP22 transcripts is tissue-specific and high levels of the exon 1A-containing transcript are tightly coupled to myelin formation. In contrast, exon 1B-containing transcripts are predominant in non-neural tissues and in growth-arrested primary fibroblasts. The observed regulation of the PMP22 by a complex molecular mechanism is consistent with the proposed dual role of PMP22 in neural and non-neural tissue.

  13. Comparative analysis of alternative splicing, alternative polyadenylation and the expression of the two KIN genes from cytoplasmic male sterility cabbage (Brassica oleracea L. var. capitata L.).

    PubMed

    Tao, Peng; Huang, Xiaoyun; Li, Biyuan; Wang, Wuhong; Yue, Zhichen; Lei, Juanli; Zhong, Xinmin

    2014-06-01

    The KIN genes are crucial members of the cold-regulated gene family. They play exclusive roles during the developmental processes of many organs and respond to various abiotic stresses in plants. However, little is known about the regulation of KIN gene expression in cytoplasmic male sterility (CMS) cabbages (Brassica oleracea L. var. capitata L.). We carried out a genome-wide analysis to identify the KIN genes in the CMS cabbage. Two non-redundant KIN genes, named BoKIN1 (Bol021262) and BoKIN2 (Bol030498), were identified. Reverse transcriptase PCR detected alternative splicing (AS) products of BoKIN1 (four AS products) and BoKIN2 (three AS products). In addition, alternative polyadenylation (APA) was observed for BoKIN1 and BoKIN2 in the CMS cabbage, resulting in variable 3'UTRs in their transcripts. Furthermore, the transcription levels of BoKIN1-0 and BoKIN2-0, the introns of which were spliced completely, were analyzed in various organs and young leaves treated by abiotic stresses. Our data indicated that BoKIN1-0 is highly expressed in various organs, whereas BoKIN2-0 is expressed exclusively in the stamen. Our study also suggested that BoKIN1-0 was upregulated significantly in young leaves of plants exposed to abscisic acid treatment, and cold and heat stress. BoKIN1 and BoKIN2 had differential AS and APA patterns in pre-mRNA processing, and showed differences in their expression patterns and transcript levels. BoKIN1 participates widely in organ development and responds to diverse abiotic stresses, whereas BoKIN2 plays a main role in stamen development in the CMS cabbage.

  14. Comparative analysis of alternative splicing, alternative polyadenylation and the expression of the two KIN genes from cytoplasmic male sterility cabbage (Brassica oleracea L. var. capitata L.).

    PubMed

    Tao, Peng; Huang, Xiaoyun; Li, Biyuan; Wang, Wuhong; Yue, Zhichen; Lei, Juanli; Zhong, Xinmin

    2014-06-01

    The KIN genes are crucial members of the cold-regulated gene family. They play exclusive roles during the developmental processes of many organs and respond to various abiotic stresses in plants. However, little is known about the regulation of KIN gene expression in cytoplasmic male sterility (CMS) cabbages (Brassica oleracea L. var. capitata L.). We carried out a genome-wide analysis to identify the KIN genes in the CMS cabbage. Two non-redundant KIN genes, named BoKIN1 (Bol021262) and BoKIN2 (Bol030498), were identified. Reverse transcriptase PCR detected alternative splicing (AS) products of BoKIN1 (four AS products) and BoKIN2 (three AS products). In addition, alternative polyadenylation (APA) was observed for BoKIN1 and BoKIN2 in the CMS cabbage, resulting in variable 3'UTRs in their transcripts. Furthermore, the transcription levels of BoKIN1-0 and BoKIN2-0, the introns of which were spliced completely, were analyzed in various organs and young leaves treated by abiotic stresses. Our data indicated that BoKIN1-0 is highly expressed in various organs, whereas BoKIN2-0 is expressed exclusively in the stamen. Our study also suggested that BoKIN1-0 was upregulated significantly in young leaves of plants exposed to abscisic acid treatment, and cold and heat stress. BoKIN1 and BoKIN2 had differential AS and APA patterns in pre-mRNA processing, and showed differences in their expression patterns and transcript levels. BoKIN1 participates widely in organ development and responds to diverse abiotic stresses, whereas BoKIN2 plays a main role in stamen development in the CMS cabbage. PMID:24488150

  15. Evolution of the CNS myelin gene regulatory program.

    PubMed

    Li, Huiliang; Richardson, William D

    2016-06-15

    Myelin is a specialized subcellular structure that evolved uniquely in vertebrates. A myelinated axon conducts action potentials many times faster than an unmyelinated axon of the same diameter; for the same conduction speed, the unmyelinated axon would need a much larger diameter and volume than its myelinated counterpart. Hence myelin speeds information transfer and saves space, allowing the evolution of a powerful yet portable brain. Myelination in the central nervous system (CNS) is controlled by a gene regulatory program that features a number of master transcriptional regulators including Olig1, Olig2 and Myrf. Olig family genes evolved from a single ancestral gene in non-chordates. Olig2, which executes multiple functions with regard to oligodendrocyte identity and development in vertebrates, might have evolved functional versatility through post-translational modification, especially phosphorylation, as illustrated by its evolutionarily conserved serine/threonine phospho-acceptor sites and its accumulation of serine residues during more recent stages of vertebrate evolution. Olig1, derived from a duplicated copy of Olig2 in early bony fish, is involved in oligodendrocyte development and is critical to remyelination in bony vertebrates, but is lost in birds. The origin of Myrf orthologs might be the result of DNA integration between an invading phage or bacterium and an early protist, producing a fusion protein capable of self-cleavage and DNA binding. Myrf seems to have adopted new functions in early vertebrates - initiation of the CNS myelination program as well as the maintenance of mature oligodendrocyte identity and myelin structure - by developing new ways to interact with DNA motifs specific to myelin genes. This article is part of a Special Issue entitled SI: Myelin Evolution.

  16. Narrative Non-Fiction Stories of the School-to-Prison Pipeline: Are Discipline Alternative Educational Programs the Pump Station?

    ERIC Educational Resources Information Center

    Knox, Ronny D.

    2013-01-01

    This research project used the Narrative Non-fiction method to examine the school-to-prison pipeline phenomenon through the experiences of four previously incarcerated adult males who had been placed in Discipline Alternative Educational Programs (DAEPs) during their public school education. In 1981, DAEPs were instituted as a pilot program to…

  17. Investigating the Effectiveness of a Reading Recovery Program for At-Risk Students in an Alternative School Setting

    ERIC Educational Resources Information Center

    Alderman, Clyde E.

    2008-01-01

    This applied dissertation was designed to evaluate a Reading Recovery program at an alternative school in Florida. The Reading Recovery program was used as an intervention for improving students' reading skills and performances on the Florida Comprehensive Assessment Test (FCAT) that is given each year to students in Grades 7 and 8. The…

  18. Genes encoding Cher-TPR fusion proteins are predominantly found in gene clusters encoding chemosensory pathways with alternative cellular functions.

    PubMed

    Muñoz-Martínez, Francisco; García-Fontana, Cristina; Rico-Jiménez, Miriam; Alfonso, Carlos; Krell, Tino

    2012-01-01

    Chemosensory pathways correspond to major signal transduction mechanisms and can be classified into the functional families flagellum-mediated taxis, type four pili-mediated taxis or pathways with alternative cellular functions (ACF). CheR methyltransferases are core enzymes in all of these families. CheR proteins fused to tetratricopeptide repeat (TPR) domains have been reported and we present an analysis of this uncharacterized family. We show that CheR-TPRs are widely distributed in GRAM-negative but almost absent from GRAM-positive bacteria. Most strains contain a single CheR-TPR and its abundance does not correlate with the number of chemoreceptors. The TPR domain fused to CheR is comparatively short and frequently composed of 2 repeats. The majority of CheR-TPR genes were found in gene clusters that harbor multidomain response regulators in which the REC domain is fused to different output domains like HK, GGDEF, EAL, HPT, AAA, PAS, GAF, additional REC, HTH, phosphatase or combinations thereof. The response regulator architectures coincide with those reported for the ACF family of pathways. Since the presence of multidomain response regulators is a distinctive feature of this pathway family, we conclude that CheR-TPR proteins form part of ACF type pathways. The diversity of response regulator output domains suggests that the ACF pathways form a superfamily which regroups many different regulatory mechanisms, in which all CheR-TPR proteins appear to participate. In the second part we characterize WspC of Pseudomonas putida, a representative example of CheR-TPR. The affinities of WspC-Pp for S-adenosylmethionine and S-adenosylhomocysteine were comparable to those of prototypal CheR, indicating that WspC-Pp activity is in analogy to prototypal CheRs controlled by product feed-back inhibition. The removal of the TPR domain did not impact significantly on the binding constants and consequently not on the product feed-back inhibition. WspC-Pp was found to be

  19. 75 FR 25867 - National Toxicology Program (NTP) Interagency Center for the Evaluation of Alternative...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-10

    ... new, revised, and alternative methods with regulatory applicability, and promotes the scientific... the Evaluation of Alternative Toxicological Methods (NICEATM): International Workshop on Alternative Methods To Reduce, Refine, and Replace the Use of Animals in Vaccine Potency and Safety Testing: State...

  20. THE GRK4 SUBFAMILY OF G PROTEIN-COUPLED RECEPTOR KINASES: ALTERNATIVE SPLICING, GENE ORGANIZATION, AND SEQUENCE CONSERVATION

    EPA Science Inventory

    The GRK4 subfamily of G protein-coupled receptor kinases. Alternative splicing, gene organization, and sequence conservation.

    Premont RT, Macrae AD, Aparicio SA, Kendall HE, Welch JE, Lefkowitz RJ.

    Department of Medicine, Howard Hughes Medical Institute, Duke Univer...

  1. Plant Gene and Alternatively Spliced Variant Annotator. A plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species.

    PubMed

    Chen, Feng-Chi; Wang, Sheng-Shun; Chaw, Shu-Miaw; Huang, Yao-Ting; Chuang, Trees-Juen

    2007-03-01

    The completion of the rice (Oryza sativa) genome draft has brought unprecedented opportunities for genomic studies of the world's most important food crop. Previous rice gene annotations have relied mainly on ab initio methods, which usually yield a high rate of false-positive predictions and give only limited information regarding alternative splicing in rice genes. Comparative approaches based on expressed sequence tags (ESTs) can compensate for the drawbacks of ab initio methods because they can simultaneously identify experimental data-supported genes and alternatively spliced transcripts. Furthermore, cross-species EST information can be used to not only offset the insufficiency of same-species ESTs but also derive evolutionary implications. In this study, we used ESTs from seven plant species, rice, wheat (Triticum aestivum), maize (Zea mays), barley (Hordeum vulgare), sorghum (Sorghum bicolor), soybean (Glycine max), and Arabidopsis (Arabidopsis thaliana), to annotate the rice genome. We developed a plant genome annotation pipeline, Plant Gene and Alternatively Spliced Variant Annotator (PGAA). Using this approach, we identified 852 genes (931 isoforms) not annotated in other widely used databases (i.e. the Institute for Genomic Research, National Center for Biotechnology Information, and Rice Annotation Project) and found 87% of them supported by both rice and nonrice EST evidence. PGAA also identified more than 44,000 alternatively spliced events, of which approximately 20% are not observed in the other three annotations. These novel annotations represent rich opportunities for rice genome research, because the functions of most of our annotated genes are currently unknown. Also, in the PGAA annotation, the isoforms with non-rice-EST-supported exons are significantly enriched in transporter activity but significantly underrepresented in transcription regulator activity. We have also identified potential lineage-specific and conserved isoforms, which are

  2. Alternative dispute resolution programs in health care: a study of organizational utilization.

    PubMed

    Rotarius, T M; Liberman, A; Osterman, K C; Putnam, P

    1999-03-01

    The hyperturbulence in today's health care environment acts as a primer that escalates the frequency and severity of business conflicts. Several alternative dispute resolution (ADR) programs are described, with ADR suggested as a viable approach in assisting organizations in resolving conflicts. The data indicate that all of the health care organizations surveyed utilize some form of ADR to resolve conflict. The most common conflict resolution objective found is win/win, and respondents felt that ADR effectively met intended objectives. While the data gathered for this study are from a limited geographic region in Central Florida, the results can likely be generalized to many socially and ethnically diverse regions of the country. PMID:10351047

  3. MSWT-01, an alternative in combining Production Based Education (PBE) and student CSR program in Polman

    NASA Astrophysics Data System (ADS)

    Ananto, Gamawan; Setiawan, Albertus B.; Z, Darman M.

    2014-06-01

    MSWT-01, Mobile Surface Water Treatment, producing 1m3 per hour, is an alternative for providing clean water in flood disaster areas, and was developed at Bandung State Polytechnic for Manufacturing (Polman) as a part of institution research project. The combination of cartridge or membrane technology such as carbon block, MF, UF and filtration media is used for this machine, instead of coagulation-flocculation with chemical addition, due to emergency purposes related with its treatment processing time. The idea is that MSWT could be combined with Production Based Education (PBE) concept in Polman as a vocational education institution and students 'CSR', students social activities. With the number of implementation trials in real flood area condition, MSWT will be developed further based on the technical output result. The manufacturing process for improving or adding necessary features could be implemented as a student's project in PBE system. This might be an ideal combination alternative for such vocational institution that students get the product media for their PBE program and implement their work as a defined social activity. They will learn and experience related technical matters and more social interactions with the people and other disaster stakeholder as well.

  4. The Anne Frank Haven: A case of an alternative educational program in an integrative Kibbutz setting

    NASA Astrophysics Data System (ADS)

    Ben-Peretz, Miriam; Giladi, Moshe; Dror, Yuval

    1992-01-01

    The essential features of the programme of the Anne Frank Haven are the complete integration of children from low SES and different cultural backgrounds with Kibbutz children; a holistic approach to education; and the involvement of the whole community in an "open" residential school. After 33 years, it is argued that the experiment has proved successful in absorbing city-born youth in the Kibbutz, enabling at-risk populations to reach significant academic achievements, and ensuring their continued participation in the dominant culture. The basic integration model consists of "layers" of concentric circles, in dynamic interaction. The innermost circle is the class, the learning community. The Kibbutz community and the foster parents form a supportive, enveloping circle, which enables students to become part of the outer community and to intervene in it. A kind of meta-environment, the inter-Kibbutz partnership and the Israeli educational system, influence the program through decision making and guidance. Some of the principles of the Haven — integration, community involvement, a year's induction for all new students, and open residential settings — could be useful for cultures and societies outside the Kibbutz. The real "secret" of success of an alternative educational program is the dedicated, motivated and highly trained staff.

  5. Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis.

    PubMed

    Puniya, Bhanwar Lal; Kulshreshtha, Deepika; Mittal, Inna; Mobeen, Ahmed; Ramachandran, Srinivasan

    2016-01-01

    Robustness of metabolic networks is accomplished by gene regulation, modularity, re-routing of metabolites and plasticity. Here, we probed robustness against perturbations of biochemical reactions of M. tuberculosis in the form of predicting compensatory trends. In order to investigate the transcriptional programming of genes associated with correlated fluxes, we integrated with gene co-expression network. Knock down of the reactions NADH2r and ATPS responsible for producing the hub metabolites, and Central carbon metabolism had the highest proportion of their associated genes under transcriptional co-expression with genes of their flux correlated reactions. Reciprocal gene expression correlations were observed among compensatory routes, fresh activation of alternative routes and in the multi-copy genes of Cysteine synthase and of Phosphate transporter. Knock down of 46 reactions caused the activation of Isocitrate lyase or Malate synthase or both reactions, which are central to the persistent state of M. tuberculosis. A total of 30 new freshly activated routes including Cytochrome c oxidase, Lactate dehydrogenase, and Glycine cleavage system were predicted, which could be responsible for switching into dormant or persistent state. Thus, our integrated approach of exploring transcriptional programming of flux correlated reactions has the potential to unravel features of system architecture conferring robustness. PMID:27000948

  6. Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis

    PubMed Central

    Puniya, Bhanwar Lal; Kulshreshtha, Deepika; Mittal, Inna; Mobeen, Ahmed; Ramachandran, Srinivasan

    2016-01-01

    Robustness of metabolic networks is accomplished by gene regulation, modularity, re-routing of metabolites and plasticity. Here, we probed robustness against perturbations of biochemical reactions of M. tuberculosis in the form of predicting compensatory trends. In order to investigate the transcriptional programming of genes associated with correlated fluxes, we integrated with gene co-expression network. Knock down of the reactions NADH2r and ATPS responsible for producing the hub metabolites, and Central carbon metabolism had the highest proportion of their associated genes under transcriptional co-expression with genes of their flux correlated reactions. Reciprocal gene expression correlations were observed among compensatory routes, fresh activation of alternative routes and in the multi-copy genes of Cysteine synthase and of Phosphate transporter. Knock down of 46 reactions caused the activation of Isocitrate lyase or Malate synthase or both reactions, which are central to the persistent state of M. tuberculosis. A total of 30 new freshly activated routes including Cytochrome c oxidase, Lactate dehydrogenase, and Glycine cleavage system were predicted, which could be responsible for switching into dormant or persistent state. Thus, our integrated approach of exploring transcriptional programming of flux correlated reactions has the potential to unravel features of system architecture conferring robustness. PMID:27000948

  7. Alternative fuels for vehicles fleet demonstration program final report. Volume 1: Summary

    SciTech Connect

    1997-03-01

    The Alternative Fuels for Vehicles Fleet Demonstration Program (AFV-FDP) was a multiyear effort to collect technical data for use in determining the costs and benefits of alternative-fuel vehicles in typical applications in New York State. During 3 years of collecting data, 7.3 million miles of driving were accumulated, 1,003 chassis-dynamometer emissions tests were performed, 862,000 gallons of conventional fuel were saved, and unique information was developed about garage safety recommendations, vehicle performance, and other topics. Findings are organized by vehicle and fuel type. For light-duty compressed natural gas (CNG) vehicles, technology has evolved rapidly and closed-loop, electronically-controlled fuel systems provide performance and emissions advantages over open-loop, mechanical systems. The best CNG technology produces consistently low tailpipe emissions versus gasoline, and can eliminate evaporative emissions. Reduced driving range remains the largest physical drawback. Fuel cost is low ($/Btu) but capital costs are high, indicating that economics are best with vehicles that are used intensively. Propane produces impacts similar to CNG and is less expensive to implement, but fuel cost is higher than gasoline and safety codes limit use in urban areas. Light-duty methanol/ethanol vehicles provide performance and emissions benefits over gasoline with little impact on capital costs, but fuel costs are high. Heavy-duty CNG engines are evolving rapidly and provide large reductions in emissions versus diesel. Capital costs are high for CNG buses and fuel efficiency is reduced, but the fuel is less expensive and overall operating costs are about equal to those of diesel buses. Methanol buses provide performance and emissions benefits versus diesel, but fuel costs are high. Other emerging technologies were also evaluated, including electric vehicles, hybrid-electric vehicles, and fuel cells.

  8. Pyramiding, alternating or mixing: comparative performances of deployment strategies of nematode resistance genes to promote plant resistance efficiency and durability

    PubMed Central

    2014-01-01

    Background Resistant cultivars are key elements for pathogen control and pesticide reduction, but their repeated use may lead to the emergence of virulent pathogen populations, able to overcome the resistance. Increased research efforts, mainly based on theoretical studies, explore spatio-temporal deployment strategies of resistance genes in order to maximize their durability. We evaluated experimentally three of these strategies to control root-knot nematodes: cultivar mixtures, alternating and pyramiding resistance genes, under controlled and field conditions over a 3-years period, assessing the efficiency and the durability of resistance in a protected crop rotation system with pepper as summer crop and lettuce as winter crop. Results The choice of the resistance gene and the genetic background in which it is introgressed, affected the frequency of resistance breakdown. The pyramiding of two different resistance genes in one genotype suppressed the emergence of virulent isolates. Alternating different resistance genes in rotation was also efficient to decrease virulent populations in fields due to the specificity of the virulence and the trapping effect of resistant plants. Mixing resistant cultivars together appeared as a less efficient strategy to control nematodes. Conclusions This work provides experimental evidence that, in a cropping system with seasonal sequences of vegetable species, pyramiding or alternating resistance genes benefit yields in the long-term by increasing the durability of resistant cultivars and improving the long-term control of a soil-borne pest. To our knowledge, this result is the first one obtained for a plant-nematode interaction, which helps demonstrate the general applicability of such strategies for breeding and sustainable management of resistant cultivars against pathogens. PMID:24559060

  9. TCERG1 Regulates Alternative Splicing of the Bcl-x Gene by Modulating the Rate of RNA Polymerase II Transcription

    PubMed Central

    Montes, Marta; Cloutier, Alexandre; Sánchez-Hernández, Noemí; Michelle, Laetitia; Lemieux, Bruno; Blanchette, Marco; Hernández-Munain, Cristina; Chabot, Benoit

    2012-01-01

    Complex functional coupling exists between transcriptional elongation and pre-mRNA alternative splicing. Pausing sites and changes in the rate of transcription by RNA polymerase II (RNAPII) may therefore have fundamental impacts in the regulation of alternative splicing. Here, we show that the elongation and splicing-related factor TCERG1 regulates alternative splicing of the apoptosis gene Bcl-x in a promoter-dependent manner. TCERG1 promotes the splicing of the short isoform of Bcl-x (Bcl-xs) through the SB1 regulatory element located in the first half of exon 2. Consistent with these results, we show that TCERG1 associates with the Bcl-x pre-mRNA. A transcription profile analysis revealed that the RNA sequences required for the effect of TCERG1 on Bcl-x alternative splicing coincide with a putative polymerase pause site. Furthermore, TCERG1 modifies the impact of a slow polymerase on Bcl-x alternative splicing. In support of a role for an elongation mechanism in the transcriptional control of Bcl-x alternative splicing, we found that TCERG1 modifies the amount of pre-mRNAs generated at distal regions of the endogenous Bcl-x. Most importantly, TCERG1 affects the rate of RNAPII transcription of endogenous human Bcl-x. We propose that TCERG1 modulates the elongation rate of RNAPII to relieve pausing, thereby activating the proapoptotic Bcl-xS 5′ splice site. PMID:22158966

  10. Mutational bias is the driving force for shaping the synonymous codon usage pattern of alternatively spliced genes in rice (Oryza sativa L.).

    PubMed

    Liu, Qingpo; Hu, Haichao; Wang, Hong

    2015-04-01

    Alternative splicing plays important roles in diverse aspects of plant development, metabolism, and stress responses. However, the regulatory mechanisms of alternative splicing of genes still remain incompletely elucidated, especially in plants. In this study, the synonymous codon usage pattern of alternatively spliced (AS) genes in rice was firstly explored using the combination of correspondence analysis (CA), internal CA, correlation and ANOVA analyses. The results show that alternatively and non-alternatively spliced (non-AS) genes have similar tendency for overall codon usage, but exhibit significant difference in 58 out of 64 codons. AS and non-AS genes are both under strong purifying selection, but the former ones have significant lower mutation rate and are prone to be enriched towards the chromosomal ends. In the group of AS genes, the variability in synonymous codon usage between genes is mainly due to the variations in GC content, CDS length, as well as gene functions. Mutational bias that accounts for 25.85 % of the total codon usage variability plays a major role in shaping the codon usage pattern of AS genes. In contrast, no obvious evidence is found for the contributions of translational selection, AS types, the conservation of AS events, and numbers of AS variants to the codon usage divergence between AS genes. These findings may be useful for further understanding the mechanisms of origination, differentiation and regulation of alternatively spliced genes in plants.

  11. Commute alternatives educational outreach. Transportation demand management resource program for the transportation professional. Report for July 1993-December 1994

    SciTech Connect

    Winters, P.L.; Rudge, D.E.

    1995-01-01

    This project is designed to aid in the planning, implementation, evaluation, and improvements of a (TDM) agency of program. Through the use of examples, the TDM professional can review innovative programs and initiatives throughout the United States, and model activities after these exhibits. The equations and benchmarks cited by this publication are other effective tools which offer insights into the relative success of TDM plan components in various environments. This report also introduces many of the traditional and innovative commute alternatives and discusses the benefits, obstacles, and goals of these initiatives. Strategies including carpooling, vanpooling, telecommuting, tax incentives, guaranteed ride home programs, bicycle and pedestrian facilities, transit, telecommuting, alternative work hour programs, and intermodalism are discussed and evaluated in real-world scenarios.

  12. Analysis of an alternatively spliced exon of the neurofibromatosis type 1 gene in cultured melanocytes from patients with neurofibromatosis 1.

    PubMed

    Eisenbarth, I; Hoffmeyer, S; Kaufmann, D; Assum, G; Krone, W

    1995-01-01

    Neurofibromatosis type 1 (NF1) is characterized by clinical features that primarily affect tissues derived from the neural crest (neurofibromas, café-aulait macules). Because aberrant regulation of alternative splicing in the NF1 gene transcript may be of functional significance, cultured melanocytes from café-aulait macules (CALM), as an example of benign NF1 lesions, were examined for the expression of the different alternative splice products of this gene. Both kinds of NF1 messengers (type 1 and 2) were found not only in CALM melanocytes but also in keratinocytes, fibroblasts and blood cells. Except in blood cells, there was a predominance of the type 2 transcript. Melanocytes from NF1 patients and healthy donors showed similar expression patterns under several culture conditions. Our results suggest that the development of CALM does not correlate with a switch in the ratio of type 1 to type 2 NF1 messenger RNA.

  13. Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

    PubMed Central

    Takeda, Jun-ichi; Suzuki, Yutaka; Nakao, Mitsuteru; Barrero, Roberto A.; Koyanagi, Kanako O.; Jin, Lihua; Motono, Chie; Hata, Hiroko; Isogai, Takao; Nagai, Keiichi; Otsuki, Tetsuji; Kuryshev, Vladimir; Shionyu, Masafumi; Yura, Kei; Go, Mitiko; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Wiemann, Stefan; Nomura, Nobuo; Sugano, Sumio; Gojobori, Takashi; Imanishi, Tadashi

    2006-01-01

    We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56 419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37 670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. We also identified interesting patterns of alternative splicing, in which two distinct genes seemed to be bridged, nested or having overlapping protein coding sequences (CDSs) of different reading frames (multiple CDS). In these cases, completely unrelated proteins are encoded by a single locus. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function, which is mediated by the fast expanding universe of alternative splicing variants. PMID:16914452

  14. EM-21 ALTERNATIVE ENHANCED CHEMICAL CLEANING PROGRAM FOR SLUDGE HEEL REMOVAL

    SciTech Connect

    Hay, M; King, W; Martino, C

    2009-12-18

    Preliminary studies in the EM-21 Alternative Chemical Cleaning Program have focused on understanding the dissolution of Hematite (a primary sludge heel phase) in oxalic acid, with a focus on minimizing oxalic acid usage. Literature reviews, thermodynamic modeling, and experimental results have all confirmed that pH control, preferably using a supplemental proton source, is critical to oxalate minimization. With pH control, iron concentrations as high as 0.103 M have been obtained in 0.11 M oxalic acid. This is consistent with the formation of a 1:1 (iron:oxalate) complex. The solubility of Hematite in oxalic acid has been confirmed to increase by a factor of 3 when the final solution pH decreases from 5 to below 1. This is consistent with literature predictions of a shift in speciation from a 1:3 to 1:1 as the pH is lowered. Above a solution pH of 6, little Hematite dissolves. These results emphasize the importance of pH control in optimizing Hematite dissolution in oxalic acid.

  15. Global transcription analysis of Krebs tricarboxylic acid cycle mutants reveals an alternating pattern of gene expression and effects on hypoxic and oxidative genes.

    PubMed

    McCammon, Mark T; Epstein, Charles B; Przybyla-Zawislak, Beata; McAlister-Henn, Lee; Butow, Ronald A

    2003-03-01

    To understand the many roles of the Krebs tricarboxylic acid (TCA) cycle in cell function, we used DNA microarrays to examine gene expression in response to TCA cycle dysfunction. mRNA was analyzed from yeast strains harboring defects in each of 15 genes that encode subunits of the eight TCA cycle enzymes. The expression of >400 genes changed at least threefold in response to TCA cycle dysfunction. Many genes displayed a common response to TCA cycle dysfunction indicative of a shift away from oxidative metabolism. Another set of genes displayed a pairwise, alternating pattern of expression in response to contiguous TCA cycle enzyme defects: expression was elevated in aconitase and isocitrate dehydrogenase mutants, diminished in alpha-ketoglutarate dehydrogenase and succinyl-CoA ligase mutants, elevated again in succinate dehydrogenase and fumarase mutants, and diminished again in malate dehydrogenase and citrate synthase mutants. This pattern correlated with previously defined TCA cycle growth-enhancing mutations and suggested a novel metabolic signaling pathway monitoring TCA cycle function. Expression of hypoxic/anaerobic genes was elevated in alpha-ketoglutarate dehydrogenase mutants, whereas expression of oxidative genes was diminished, consistent with a heme signaling defect caused by inadequate levels of the heme precursor, succinyl-CoA. These studies have revealed extensive responses to changes in TCA cycle function and have uncovered new and unexpected metabolic networks that are wired into the TCA cycle.

  16. Cloning and expression analysis of the ATP-binding cassette transporter gene MFABC1 and the alternative oxidase gene MfAOX1 from Monilinia fructicola.

    PubMed

    Schnabel, Guido; Dait, Qun; Paradkar, Manjiri R

    2003-10-01

    Brown rot, caused by Moniliniafructicola (G Wint) Honey, is a serious disease of peach in all commercial peach production areas in the USA, including South Carolina where it has been primarily controlled by pre-harvest application of 14-alpha demethylation (DMI) fungicides for more than 15 years. Recently, the Qo fungicide azoxystrobin was registered for brown rot control and is currently being investigated for its potential as a DMI fungicide rotation partner because of its different mode of action. In an effort to investigate molecular mechanisms of DMI and Qo fungicide resistance in M fructicola, the ABC transporter gene MfABC1 and the alternative oxidase gene MfAOX1 were cloned to study their potential role in conferring fungicide resistance. The MfABC1 gene was 4380 bp in length and contained one intron of 71 bp. The gene revealed high amino acid homologies with atrB from Aspergillus nidulans (Eidam) Winter, an ABC transporter conferring resistance to many fungicides, including DMI fungicides. MfABC1 gene expression was induced after myclobutanil and propiconazole treatment in isolates with low sensitivity to the same fungicides, and in an isolate with high sensitivity to propiconazole. The results suggest that the MfABC1 gene may be a DMI fungicide resistance determinant in M fructicola. The alternative oxidase gene MfAOX1 from M fructicola was cloned and gene expression was analyzed. The MfAOX1 gene was 1077 bp in length and contained two introns of 54 and 67 bp. The amino acid sequence was 63.8, 63.8 and 57.7% identical to alternative oxidases from Venturia inaequalis (Cooke) Winter, Aspergillus niger van Teighem and A nidulans, respectively. MfAOX1 expression in some but not all M fructicola isolates was induced in mycelia treated with azoxystrobin. Azoxystrobin at 2 microg ml(-1) significantly induced MfAOX1 expression in isolates with low MfAOX1 constitutive expression levels. PMID:14561072

  17. Alternatively Spliced Genes as Biomarkers for Schizophrenia, Bipolar Disorder and Psychosis: A Blood-Based Spliceome-Profiling Exploratory Study

    PubMed Central

    Glatt, S.J.; Chandler, S.D.; Bousman, C.A.; Chana, G.; Lucero, G.R.; Tatro, E.; May, T.; Lohr, J.B.; Kremen, W.S.; Everall, I.P.; Tsuang, M.T.

    2010-01-01

    Objective Transcriptomic biomarkers of psychiatric diseases obtained from a query of peripheral tissues that are clinically accessible (e.g., blood cells instead of post-mortem brain tissue) have substantial practical appeal to discern the molecular subtypes of common complex diseases such as major psychosis. To this end, spliceome-profiling is a new methodological approach that has considerable conceptual relevance for discovery and clinical translation of novel biomarkers for psychiatric illnesses. Advances in microarray technology now allow for improved sensitivity in measuring the transcriptome while simultaneously querying the “exome” (all exons) and “spliceome” (all alternatively spliced variants). The present study aimed to evaluate the feasibility of spliceome-profiling to discern transcriptomic biomarkers of psychosis. Methods We measured exome and spliceome expression in peripheral blood mononuclear cells from 13 schizophrenia patients, nine bipolar disorder patients, and eight healthy control subjects. Each diagnostic group was compared to each other, and the combined group of bipolar disorder and schizophrenia patients was also compared to the control group. Furthermore, we compared subjects with a history of psychosis to subjects without such history. Results After applying Bonferroni corrections for the 21,866 full-length gene transcripts analyzed, we found significant interactions between diagnostic group and exon identity, consistent with group differences in rates or types of alternative splicing. Relative to the control group, 18 genes in the bipolar disorder group, eight genes in the schizophrenia group, and 15 genes in the combined bipolar disorder and schizophrenia group appeared differentially spliced. Importantly, thirty-three genes showed differential splicing patterns between the bipolar disorder and schizophrenia groups. More frequent exon inclusion and/or over-expression was observed in psychosis. Finally, these observations are

  18. Lower East Side Prep: An Alternative to the Conventional High School Program. First Year of Operation, Final Report.

    ERIC Educational Resources Information Center

    Wohl, Seth F.

    This evaluation report of one alternative high school in New York City analyzes the academic achievement, attendance, testing, academic credit, English language proficiency, and attitudes of the sixty minority students who attended this urban prep school in Chinatown. Three fifths of the students in the program were recent Chinese immigrants. The…

  19. UNESCO Science Programs: Impacts of U.S. Withdrawal and Suggestions for Alternative Interim Arrangements. A Preliminary Assessment.

    ERIC Educational Resources Information Center

    National Academy of Sciences - National Research Council, Washington, DC. Office of International Affairs.

    This study was conducted to provide the U.S. Department of State with an assessment of the potential impacts on science of a United States withdrawal from UNESCO and to suggest possible alternative arrangements to maintain essential U.S. scientific contacts with UNESCO-sponsored programs in case the United States were no longer a member of UNESCO…

  20. Teacher and Parent Perceptions of Classroom Experiences of African American Male Students in a High School Alternative Program

    ERIC Educational Resources Information Center

    Johnson, Kimberly C.

    2013-01-01

    A major concern in the public schools is the low academic achievement of African American males. This mixed methods study examined the classroom experiences of African American male students in an alternative program. The dual purpose was to investigate the teachers' perceptions and their ability to provide best learning environments for…

  1. Capacity Building Special Alternatives Program Community School District 3. Final Evaluation Report, 1992-93. OREA Report.

    ERIC Educational Resources Information Center

    Tajbaksh, Kian

    The Capacity Building Alternatives Program, an Elementary and Secondary Education Act Title VII-funded project in its first year of operation functioned at 8 schools, serving 139 students of limited English proficiency whose home language was Albanian, Chinese, Haitian, Polish, Russian, or Serbo-Croatian. Students targeted showed an achievement…

  2. South Carolina's Program of Alternative Certification for Educators (PACE): Pedagogical Content Knowledge and Post-Employment Performance

    ERIC Educational Resources Information Center

    Burkett, Christopher; Gimbert, Belinda G.

    2009-01-01

    This research evaluated South Carolina's Program of Alternative Certification for Educators (PACE). Specifically, the study analyzed this nontraditional teacher preparation pathway's outcomes: to recruit, train, and retain effective beginning teachers who fill the growing teacher vacancies in rural South Carolina. From an in-depth review of the…

  3. Capacity Building Special Alternatives Program Community School District 3. Final Evaluation Report, 1993-94. OER Report.

    ERIC Educational Resources Information Center

    Duque, Diana L.

    The Capacity Building Special Alternatives Program, an Elementary and Secondary Education Act Title VII-funded project in its second year of operation, functioned at seven schools in a community school district of Manhattan (New York). The project served 195 students of limited English proficiency (LEP) whose native languages were Albanian,…

  4. Commission Recommendations Concerning Alternate Delivery Options for the State's Cal Grant Program. Commission Report 03-04

    ERIC Educational Resources Information Center

    California Postsecondary Education Commission, 2003

    2003-01-01

    In September 2002, the California Legislature adopted Supplemental Report Language (SRL) directing the California Postsecondary Education Commission (CPEC) to convene a task force to examine alternative delivery systems for the State's Cal Grant program. This report responds to that legislative request. The recommendations contained in this report…

  5. An Advanced Multiple Alternatives Modeling Formulation for Determining Graduated Fiscal Support Strategies for Operational and Planned Educational Programs.

    ERIC Educational Resources Information Center

    Wholeben, Brent Edward

    A rationale is presented for viewing the decision-making process inherent in determining budget reductions for educational programs as most effectively modeled by a graduated funding approach. The major tenets of the graduated budget reduction approach to educational fiscal policy include the development of multiple alternative reduction plans, or…

  6. When There Is No Blueprint: The Provision of Mental Health Services in Alternative School Programs for Suspended and Expelled Youth

    ERIC Educational Resources Information Center

    Goldenson, Julie

    2011-01-01

    A variety of alternative programs are being implemented in Canada and the United States for students who have exhibited conduct problems and who are suspended or expelled from their schools. Given the complexity of issues that these students frequently face, treatment must be multifaceted, wrap-around, delivered by trained professionals and be…

  7. An Interactive Microcomputer Program for Teaching the Impacts of Alternative Policy Sets in the Market for a Single Commodity.

    ERIC Educational Resources Information Center

    Li, Elton; Stoecker, Arthur

    1995-01-01

    Describes a computer software program where students define alternative policy sets and compare their effects on the welfare of consumers, producers, and the public sector. Policy sets may be a single tax or quota or a mix of taxes, subsidies, and/or price supports implemented in the marketing chain. (MJP)

  8. Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals.

    PubMed

    Olson, Evan J; Hartsough, Lucas A; Landry, Brian P; Shroff, Raghav; Tabor, Jeffrey J

    2014-04-01

    Gene circuits are dynamical systems that regulate cellular behaviors, often using protein signals as inputs and outputs. Here we have developed an optogenetic 'function generator' method for programming tailor-made gene expression signals in live bacterial cells. We designed precomputed light sequences based on experimentally calibrated mathematical models of light-switchable two-component systems and used them to drive intracellular protein levels to match user-defined reference time courses. We used this approach to generate accelerated and linearized dynamics, sinusoidal oscillations with desired amplitudes and periods, and a complex waveform, all with unprecedented accuracy and precision. We also combined the function generator with a dual fluorescent protein reporter system, analogous to a dual-channel oscilloscope, to reveal that a synthetic repressible promoter linearly transforms repressor signals with an approximate 7-min delay. Our approach will enable a new generation of dynamical analyses of synthetic and natural gene circuits, providing an essential step toward the predictive design and rigorous understanding of biological systems.

  9. [The teaching and application of alternative medicine in medical education programs].

    PubMed

    Chiang, Han-Sun

    2014-12-01

    The history of alternative medicine is perhaps as long as the history of human medicine. The development of evidence-based medicine has not annihilated alternative medicine. On the contrary, more people turn to alternative medicine because this approach to treatment serves as an effective remedial or supportive treatment when used in conjunction with evidence-based medicine. In contemporary healthcare, alternative medicine is now an essential part of integrated medicine. In Taiwan, most professional medical practitioners have not received proper education about alternative medicine and therefore generally lack comprehensive knowledge on this subject. While alternative medicine may be effective when used with some patients, it may also impart a placebo effect, which helps restore the body and soul of the patients. Medical staff with advanced knowledge of alternative medicine may not only help patients but also improve the doctor-patient relationship. There is great diversity in alternative medicine, with some alternative therapies supported by evidence and covered by insurance. However, there also remain fraudulent medical practices that may be harmful to health. Medical staff must be properly educated so that they can provide patients and their family a proper understanding and attitude toward alternative medicine. Therefore, alternative medicine should be included in the standard medical education curriculum. Offering classes on alternative medicine in university for more than 10 years, the author shares his experiences regarding potential content, lecture subjects, group experience exercises, and in-class activities. This article is intended to provide a reference to professors in university medical education and offer a possible model for alternative medicine education in Taiwan.

  10. Ligand-Bound GeneSwitch Causes Developmental Aberrations in Drosophila that Are Alleviated by the Alternative Oxidase

    PubMed Central

    Andjelković, Ana; Kemppainen, Kia K.; Jacobs, Howard T.

    2016-01-01

    Culture of Drosophila expressing the steroid-dependent GeneSwitch transcriptional activator under the control of the ubiquitous α-tubulin promoter was found to produce extensive pupal lethality, as well as a range of dysmorphic adult phenotypes, in the presence of high concentrations of the inducing drug RU486. Prominent among these was cleft thorax, seen previously in flies bearing mutant alleles of the nuclear receptor Ultraspiracle and many other mutants, as well as notched wings, leg malformations, and bristle abnormalities. Neither the α-tubulin-GeneSwitch driver nor the inducing drug on their own produced any of these effects. A second GeneSwitch driver, under the control of the daughterless promoter, which gave much lower and more tissue-restricted transgene expression, exhibited only mild bristle abnormalities in the presence of high levels of RU486. Coexpression of the alternative oxidase (AOX) from Ciona intestinalis produced a substantial shift in the developmental outcome toward a wild-type phenotype, which was dependent on the AOX expression level. Neither an enzymatically inactivated variant of AOX, nor GFP, or the alternative NADH dehydrogenase Ndi1 from yeast gave any such rescue. Users of the GeneSwitch system should be aware of the potential confounding effects of its application in developmental studies. PMID:27412986

  11. Ligand-Bound GeneSwitch Causes Developmental Aberrations in Drosophila that Are Alleviated by the Alternative Oxidase.

    PubMed

    Andjelković, Ana; Kemppainen, Kia K; Jacobs, Howard T

    2016-01-01

    Culture of Drosophila expressing the steroid-dependent GeneSwitch transcriptional activator under the control of the ubiquitous α-tubulin promoter was found to produce extensive pupal lethality, as well as a range of dysmorphic adult phenotypes, in the presence of high concentrations of the inducing drug RU486. Prominent among these was cleft thorax, seen previously in flies bearing mutant alleles of the nuclear receptor Ultraspiracle and many other mutants, as well as notched wings, leg malformations, and bristle abnormalities. Neither the α-tubulin-GeneSwitch driver nor the inducing drug on their own produced any of these effects. A second GeneSwitch driver, under the control of the daughterless promoter, which gave much lower and more tissue-restricted transgene expression, exhibited only mild bristle abnormalities in the presence of high levels of RU486. Coexpression of the alternative oxidase (AOX) from Ciona intestinalis produced a substantial shift in the developmental outcome toward a wild-type phenotype, which was dependent on the AOX expression level. Neither an enzymatically inactivated variant of AOX, nor GFP, or the alternative NADH dehydrogenase Ndi1 from yeast gave any such rescue. Users of the GeneSwitch system should be aware of the potential confounding effects of its application in developmental studies. PMID:27412986

  12. Alternative messenger RNA splicing of autophagic gene Beclin 1 in human B-cell acute lymphoblastic leukemia cells.

    PubMed

    Niu, Yu-Na; Liu, Qing-Qing; Zhang, Su-Ping; Yuan, Na; Cao, Yan; Cai, Jin-Yang; Lin, Wei-Wei; Xu, Fei; Wang, Zhi-Jian; Chen, Bo; Wang, Jian-Rong

    2014-01-01

    Beclin 1 is a key factor for initiation and regulation of autophagy, which is a cellular catabolic process involved in tumorigenesis. To investigate the role of alternative splicing of Beclin1 in the regulation of autophagy in leukemia cells, Beclin1 mRNA from 6 different types of cell lines and peripheral blood mononuclear cells from 2 healthy volunteers was reversely transcribed, subcloned, and screened for alternative splicing. New transcript variants were analyzed by DNA sequencing. A transcript variant of Beclin 1 gene carrying a deletion of exon 11, which encoded a C-terminal truncation of Beclin 1 isoform, was found. The alternative isoform was assessed by bioinformatics, immunoblotting and subcellular localization. The results showed that this variable transcript is generated by alternative 3' splicing, and its translational product displayed a reduced activity in induction of autophagy by starvation, indicating that the spliced isoform might function as a dominant negative modulator of autophagy. Our findings suggest that the alternative splicing of Beclin 1 might play important roles in leukemogenesis regulated by autophagy.

  13. Gene gun bombardment with DNA-coated gold particles is a potential alternative to hydrodynamics-based transfection for delivering genes into superficial hepatocytes.

    PubMed

    Chang, Ming-Ling; Chen, Jeng-Chang; Yeh, Chau-Ting; Chang, Ming-Yu; Liang, Chun-Kai; Chiu, Cheng-Tang; Lin, Deng-Yn; Liaw, Yun-Fan

    2008-04-01

    Although in vivo nonviral gene delivery to the liver is critical for hepatic gene therapy, there are a number of technical obstacles. Enhanced green fluorescent protein (EGFP)-encoding DNA was coated onto gold particles (gold-DNA), dissolved in phosphate-buffered saline (pure DNA), and prepared as a polymer adjuvant (jetPEI)-galactosidase solution (polymer-DNA). Murine liver transfection was attempted by nonviral approaches, which included hydrodynamics-based transfection (HBT) of pure DNA, transport and transhepatic injection of polymer-DNA, and gene gun bombardment with pure DNA, gold-DNA, and polymer-DNA. Only HBT and gene gun bombardment yielded significant numbers of EGFP(+) hepatocytes. With the exception of the edge of the liver, HBT had a whole-liver transfection rate of 20% under optimized conditions. HBT resulted in marked hepatic infarctions, most prominently at the edge of the liver. For gene gun bombardment, the transfection rate was pressure dependent and limited to 15% for gold-DNA. Triple or quadruple bombardment at 30 psi resulted in a transfection rate comparable to that of a single bombardment at higher pressure, but was associated with minimal scattered hepatic necrosis. The EGFP(+) hepatocytes were located mainly in the superficial layers. We conclude that both HBT and gene gun bombardment yielded efficient murine hepatocyte transfection in vivo. Severe hepatic infarction impedes foreign gene expression in the superficial hepatocytes after HBT. Repeated bombardment with gold-DNA, using an accelerated particle gene gun at 30 psi, is a potential alternative to HBT for delivering genes to superficial hepatocytes in vivo, although gold-related hepatic necrosis is a persistent problem. PMID:18366343

  14. Characterization of the Amicetin Biosynthesis Gene Cluster from Streptomyces vinaceusdrappus NRRL 2363 Implicates Two Alternative Strategies for Amide Bond Formation

    PubMed Central

    Zhang, Gaiyun; Zhang, Haibo; Li, Sumei; Xiao, Ji; Zhang, Guangtao; Zhu, Yiguang; Niu, Siwen; Ju, Jianhua

    2012-01-01

    Amicetin, an antibacterial and antiviral agent, belongs to a group of disaccharide nucleoside antibiotics featuring an α-(1→4)-glycoside bond in the disaccharide moiety. In this study, the amicetin biosynthesis gene cluster was cloned from Streptomyces vinaceusdrappus NRRL 2363 and localized on a 37-kb contiguous DNA region. Heterologous expression of the amicetin biosynthesis gene cluster in Streptomyces lividans TK64 resulted in the production of amicetin and its analogues, thereby confirming the identity of the ami gene cluster. In silico sequence analysis revealed that 21 genes were putatively involved in amicetin biosynthesis, including 3 for regulation and transportation, 10 for disaccharide biosynthesis, and 8 for the formation of the amicetin skeleton by the linkage of cytosine, p-aminobenzoic acid (PABA), and the terminal (+)-α-methylserine moieties. The inactivation of the benzoate coenzyme A (benzoate-CoA) ligase gene amiL and the N-acetyltransferase gene amiF led to two mutants that accumulated the same two compounds, cytosamine and 4-acetamido-3-hydroxybenzoic acid. These data indicated that AmiF functioned as an amide synthethase to link cytosine and PABA. The inactivation of amiR, encoding an acyl-CoA-acyl carrier protein transacylase, resulted in the production of plicacetin and norplicacetin, indicating AmiR to be responsible for attachment of the terminal methylserine moiety to form another amide bond. These findings implicated two alternative strategies for amide bond formation in amicetin biosynthesis. PMID:22267658

  15. Characterization of the amicetin biosynthesis gene cluster from Streptomyces vinaceusdrappus NRRL 2363 implicates two alternative strategies for amide bond formation.

    PubMed

    Zhang, Gaiyun; Zhang, Haibo; Li, Sumei; Xiao, Ji; Zhang, Guangtao; Zhu, Yiguang; Niu, Siwen; Ju, Jianhua; Zhang, Changsheng

    2012-04-01

    Amicetin, an antibacterial and antiviral agent, belongs to a group of disaccharide nucleoside antibiotics featuring an α-(1→4)-glycoside bond in the disaccharide moiety. In this study, the amicetin biosynthesis gene cluster was cloned from Streptomyces vinaceusdrappus NRRL 2363 and localized on a 37-kb contiguous DNA region. Heterologous expression of the amicetin biosynthesis gene cluster in Streptomyces lividans TK64 resulted in the production of amicetin and its analogues, thereby confirming the identity of the ami gene cluster. In silico sequence analysis revealed that 21 genes were putatively involved in amicetin biosynthesis, including 3 for regulation and transportation, 10 for disaccharide biosynthesis, and 8 for the formation of the amicetin skeleton by the linkage of cytosine, p-aminobenzoic acid (PABA), and the terminal (+)-α-methylserine moieties. The inactivation of the benzoate coenzyme A (benzoate-CoA) ligase gene amiL and the N-acetyltransferase gene amiF led to two mutants that accumulated the same two compounds, cytosamine and 4-acetamido-3-hydroxybenzoic acid. These data indicated that AmiF functioned as an amide synthethase to link cytosine and PABA. The inactivation of amiR, encoding an acyl-CoA-acyl carrier protein transacylase, resulted in the production of plicacetin and norplicacetin, indicating AmiR to be responsible for attachment of the terminal methylserine moiety to form another amide bond. These findings implicated two alternative strategies for amide bond formation in amicetin biosynthesis.

  16. Alternative splicing of RNAs transcribed from the human c- myb gene

    SciTech Connect

    Shen-Ong, G.L.C.; Skurla, R.M. Jr.; Owens, J.D.; Mushinski, J.F. )

    1990-06-01

    An alternative splicing event in which a portion of the intron bounded by the vE6 and vE7 exons with v-{ital myb} homology is included as an additional 363-nucleotide coding exon (termed E6A or coding exon 9A) has been described for normal and tumor murine cells that express {ital myb}. The authors show that this alternative splicing event is conserved in human c-{ital myb} transcripts. In addition, another novel exon (termed E7A or coding exon 10A) is identified in human c-{ital myb} mRNAs expressed in normal and tumor cells. Although the {ital myb} protein isoform encoded by murine E6A-containing mRNA is larger than the major c-{ital myb} protein, the predicted products of both forms of human alternatively spliced {ital myb} transcripts are 3{prime}-truncated {ital myb} proteins that terminate in the alternative exons. These proteins are predicted to lack the same carboxy-terminal domains as the viral {ital myb} proteins encoded by avian myeloblastosis virus and E26 virus. The junction sequences that flank these exons closely resemble the consensus splice donor and splice acceptor sequences, yet the alternative transcripts are less abundant than is the major form of c-{ital myb} transcripts. The contribution that alternative splicing events in c-{ital myb} expression may make on c-{ital myb} function remains to be elucidated.

  17. Characterization of genes for an alternative nitrogenase in the cyanobacterium Anabaena variabilis.

    PubMed Central

    Thiel, T

    1993-01-01

    Anabaena variabilis ATCC 29413 is a heterotrophic, nitrogen-fixing cyanobacterium that has been reported to fix nitrogen and reduce acetylene to ethane in the absence of molybdenum. DNA from this strain hybridized well at low stringency to the nitrogenase 2 (vnfDGK) genes of Azotobacter vinelandii. The hybridizing region was cloned from a lambda EMBL3 genomic library of A. variabilis, mapped, and sequenced. The deduced amino acid sequences of the vnfD and vnfK genes of A. variabilis showed only about 56% similarity to the nifDK genes of Anabaena sp. strain PCC 7120 but were 76 to 86% similar to the anfDK or vnfDK genes of A. vinelandii. The organization of the vnf gene cluster in A. variabilis was similar to that of A. vinelandii. However, in A. variabilis, the vnfG gene was fused to vnfD; hence, this gene is designated vnfDG. A vnfH gene was not contiguous with the vnfDG gene and has not yet been identified. A mutant strain, in which a neomycin resistance cassette was inserted into the vnf cluster, grew well in a medium lacking a source of fixed nitrogen in the presence of molybdenum but grew poorly when vanadium replaced molybdenum. In contrast, the parent strain grew equally well in media containing either molybdenum or vanadium. The vnf genes were transcribed in the absence of molybdenum, with or without vanadium. The vnf gene cluster did not hybridize to chromosomal DNA from Anabaena sp. strain PCC 7120 or from the heterotrophic strains, Nostoc sp. strain Mac and Nostoc sp. strain ATCC 29150. A hybridizing ClaI fragment very similar in size to the A. variabilis ClaI fragment was present in DNA isolated from several independent, cultured isolates of Anabaena sp. from the Azolla symbiosis. Images PMID:8407800

  18. Expression and alternative splicing of classical and nonclassical MHCI genes in the hippocampus and neuromuscular junction.

    PubMed

    Tetruashvily, Mazell M; Melson, John W; Park, Joseph J; Peng, Xiaoyu; Boulanger, Lisa M

    2016-04-01

    The major histocompatibility complex class I (MHCI) is a large gene family, with over 20 members in mouse. Some MHCIs are well-known for their critical roles in the immune response. Studies in mice which lack stable cell-surface expression of many MHCI proteins suggest that one or more MHCIs also play unexpected, essential roles in the establishment, function, and modification of neuronal synapses. However, there is little information about which genes mediate MHCI's effects in neurons. In this study, RT-PCR was used to simultaneously assess transcription of many MHCI genes in regions of the central and peripheral nervous system where MHCI has a known or suspected role. In the hippocampus, a part of the CNS where MHCI regulates synapse density, synaptic transmission, and plasticity, we found that more than a dozen MHCI genes are transcribed. Single-cell RT-PCR revealed that individual hippocampal neurons can express more than one MHCI gene, and that the MHCI gene expression profile of CA1 pyramidal neurons differs significantly from that of CA3 pyramidal neurons or granule cells of the dentate gyrus. MHCI gene expression was also assessed at the neuromuscular junction (NMJ), a part of the peripheral nervous system (PNS) where MHCI plays a role in developmental synapse elimination, aging-related synapse loss, and neuronal regeneration. Four MHCI genes are expressed at the NMJ at an age when synapse elimination is occurring in three different muscles. Several MHCI mRNA splice variants were detected in hippocampus, but not at the NMJ. Together, these results establish the first profile of MHCI gene expression at the developing NMJ, and demonstrate that MHCI gene expression is under tight spatial and temporal regulation in the nervous system. They also identify more than a dozen MHCIs that could play important roles in regulating synaptic transmission and plasticity in the central and peripheral nervous systems. PMID:26802536

  19. Serving a Higher Power: The Influence of Alternative Break Programs on Students' Religiousness

    ERIC Educational Resources Information Center

    Niehaus, Elizabeth; Rivera, Mark

    2016-01-01

    The purpose of this study was to explore the relationship between students' religiousness and participation in alternative breaks (ABs) using both survey and interview data from the National Survey of Alternative Breaks. Findings from this mixed methods study demonstrate the potential for ABs to facilitate religiousness and help students connect…

  20. Innovative and Alternative Technologies. Instructor Guide. Working for Clean Water: An Information Program for Advisory Groups.

    ERIC Educational Resources Information Center

    Cole, Charles A.

    Innovative and alternative methods of wastewater treatment can improve the efficiency and lower the cost of waste treatment procedures. Described in this instructor's guide is a one-hour learning session for citizens interested in improving water quality planning and decision making. Among the topics covered are the need for alternative wastewater…

  1. Mixed Results in a Transitional Planning Program for Alternative School Students

    ERIC Educational Resources Information Center

    Wolf, Elaine M.; Wolf, Douglas A.

    2008-01-01

    Disciplinary alternative schools have a reputation as gateways to the juvenile and criminal justice systems. The authors conducted an evaluation of an intervention (Strategies for Success) designed to divert seventh-, eighth-, and ninth-grade alternative school students from this gateway. They used propensity score matching and a multivariate…

  2. Characterization of the Tomato ARF Gene Family Uncovers a Multi-Levels Post-Transcriptional Regulation Including Alternative Splicing

    PubMed Central

    Chateigner-Boutin, Anne-Laure; Mila, Isabelle; Frasse, Pierre; Wang, Hua; Audran, Corinne; Roustan, Jean-Paul; Bouzayen, Mondher

    2014-01-01

    Background The phytohormone auxin is involved in a wide range of developmental processes and auxin signaling is known to modulate the expression of target genes via two types of transcriptional regulators, namely, Aux/IAA and Auxin Response Factors (ARF). ARFs play a major role in transcriptional activation or repression through direct binding to the promoter of auxin-responsive genes. The present study aims at gaining better insight on distinctive structural and functional features among ARF proteins. Results Building on the most updated tomato (Solanum lycopersicon) reference genome sequence, a comprehensive set of ARF genes was identified, extending the total number of family members to 22. Upon correction of structural annotation inconsistencies, renaming the tomato ARF family members provided a consensus nomenclature for all ARF genes across plant species. In silico search predicted the presence of putative target site for small interfering RNAs within twelve Sl-ARFs while sequence analysis of the 5′-leader sequences revealed the presence of potential small uORF regulatory elements. Functional characterization carried out by transactivation assay partitioned tomato ARFs into repressors and activators of auxin-dependent gene transcription. Expression studies identified tomato ARFs potentially involved in the fruit set process. Genome-wide expression profiling using RNA-seq revealed that at least one third of the gene family members display alternative splicing mode of regulation during the flower to fruit transition. Moreover, the regulation of several tomato ARF genes by both ethylene and auxin, suggests their potential contribution to the convergence mechanism between the signaling pathways of these two hormones. Conclusion All together, the data bring new insight on the complexity of the expression control of Sl-ARF genes at the transcriptional and post-transcriptional levels supporting the hypothesis that these transcriptional mediators might represent

  3. Non-proliferation, safeguards, and security for the fissile materials disposition program immobilization alternatives

    SciTech Connect

    Duggan, R.A.; Jaeger, C.D.; Tolk, K.M.; Moore, L.R.

    1996-05-01

    The Department of Energy is analyzing long-term storage and disposition alternatives for surplus weapons-usable fissile materials. A number of different disposition alternatives are being considered. These include facilities for storage, conversion and stabilization of fissile materials, immobilization in glass or ceramic material, fabrication of fissile material into mixed oxide (MOX) fuel for reactors, use of reactor based technologies to convert material into spent fuel, and disposal of fissile material using geologic alternatives. This paper will focus on how the objectives of reducing security and proliferation risks are being considered, and the possible facility impacts. Some of the areas discussed in this paper include: (1) domestic and international safeguards requirements, (2) non-proliferation criteria and measures, (3) the threats, and (4) potential proliferation, safeguards, and security issues and impacts on the facilities. Issues applicable to all of the possible disposition alternatives will be discussed in this paper. However, particular attention is given to the plutonium immobilization alternatives.

  4. Comprehensive gene expression analysis of rice aleurone cells: probing the existence of an alternative gibberellin receptor.

    PubMed

    Yano, Kenji; Aya, Koichiro; Hirano, Ko; Ordonio, Reynante Lacsamana; Ueguchi-Tanaka, Miyako; Matsuoka, Makoto

    2015-02-01

    Current gibberellin (GA) research indicates that GA must be perceived in plant nuclei by its cognate receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1). Recognition of GA by GID1 relieves the repression mediated by the DELLA protein, a model known as the GID1-DELLA GA perception system. There have been reports of potential GA-binding proteins in the plasma membrane that perceive GA and induce α-amylase expression in cereal aleurone cells, which is mechanistically different from the GID1-DELLA system. Therefore, we examined the expression of the rice (Oryza sativa) α-amylase genes in rice mutants impaired in the GA receptor (gid1) and the DELLA repressor (slender rice1; slr1) and confirmed their lack of response to GA in gid1 mutants and constitutive expression in slr1 mutants. We also examined the expression of GA-regulated genes by genome-wide microarray and quantitative reverse transcription-polymerase chain reaction analyses and confirmed that all GA-regulated genes are modulated by the GID1-DELLA system. Furthermore, we studied the regulatory network involved in GA signaling by using a set of mutants defective in genes involved in GA perception and gene expression, namely gid1, slr1, gid2 (a GA-related F-box protein mutant), and gamyb (a GA-related trans-acting factor mutant). Almost all GA up-regulated genes were regulated by the four named GA-signaling components. On the other hand, GA down-regulated genes showed different expression patterns with respect to GID2 and GAMYB (e.g. a considerable number of genes are not controlled by GAMYB or GID2 and GAMYB). Based on these observations, we present a comprehensive discussion of the intricate network of GA-regulated genes in rice aleurone cells.

  5. Network activity-independent coordinated gene expression program for synapse assembly

    PubMed Central

    Valor, Luis M.; Charlesworth, Paul; Humphreys, Lawrence; Anderson, Chris N. G.; Grant, Seth G. N.

    2007-01-01

    Global biological datasets generated by genomics, transcriptomics, and proteomics provide new approaches to understanding the relationship between the genome and the synapse. Combined transcriptome analysis and multielectrode recordings of neuronal network activity were used in mouse embryonic primary neuronal cultures to examine synapse formation and activity-dependent gene regulation. Evidence for a coordinated gene expression program for assembly of synapses was observed in the expression of 642 genes encoding postsynaptic and plasticity proteins. This synaptogenesis gene expression program preceded protein expression of synapse markers and onset of spiking activity. Continued expression was followed by maturation of morphology and electrical neuronal networks, which was then followed by the expression of activity-dependent genes. Thus, two distinct sequentially active gene expression programs underlie the genomic programs of synapse function. PMID:17360580

  6. Alternate Alternates: A Medley of Alternate Assessments.

    ERIC Educational Resources Information Center

    Burdette, Paula J.; Olsen, Ken

    This paper highlights eight states that have implemented alternate assessments for children with disabilities who cannot participate in their state and district-wide assessment programs. The alternate assessment systems in Delaware, Florida, Georgia, Indiana, Minnesota, North Dakota, Utah, and West Virginia are briefly described, along with their…

  7. Polymorphism, recombination and alternative unscrambling in the DNA polymerase alpha gene of the ciliate Stylonychia lemnae (Alveolata; class Spirotrichea).

    PubMed Central

    Ardell, David H; Lozupone, Catherine A; Landweber, Laura F

    2003-01-01

    DNA polymerase alpha is the most highly scrambled gene known in stichotrichous ciliates. In its hereditary micronuclear form, it is broken into >40 pieces on two loci at least 3 kb apart. Scrambled genes must be reassembled through developmental DNA rearrangements to yield functioning macronuclear genes, but the mechanism and accuracy of this process are unknown. We describe the first analysis of DNA polymorphism in the macronuclear version of any scrambled gene. Six functional haplotypes obtained from five Eurasian strains of Stylonychia lemnae were highly polymorphic compared to Drosophila genes. Another incompletely unscrambled haplotype was interrupted by frameshift and nonsense mutations but contained more silent mutations than expected by allelic inactivation. In our sample, nucleotide diversity and recombination signals were unexpectedly high within a region encompassing the boundary of the two micronuclear loci. From this and other evidence we infer that both members of a long repeat at the ends of the loci provide alternative substrates for unscrambling in this region. Incongruent genealogies and recombination patterns were also consistent with separation of the two loci by a large genetic distance. Our results suggest that ciliate developmental DNA rearrangements may be more probabilistic and error prone than previously appreciated and constitute a potential source of macronuclear variation. From this perspective we introduce the nonsense-suppression hypothesis for the evolution of ciliate altered genetic codes. We also introduce methods and software to calculate the likelihood of hemizygosity in ciliate haplotype samples and to correct for multiple comparisons in sliding-window analyses of Tajima's D. PMID:14704164

  8. Alternative gene expression in type I and type II cells may enable further nuclear changes during conjugation of Blepharisma japonicum.

    PubMed

    Sugiura, Mayumi; Tanaka, Yuri; Suzaki, Toshinobu; Harumoto, Terue

    2012-03-01

    In contrast to most ciliates, meiosis and successive nuclear changes during conjugation occur only in heterotypic pairs in Blepharisma. It has been suggested that homotypic pairs are ready for conjugation, but lack a trigger to initiate the nuclear changes, and the conjugation process is arrested before the onset of meiosis. To explore the possible nature of the trigger, we previously identified the genes BjCdk1 (homologous to cdk1/cdc2), Bj4HPPD (4-hydroxy-phenylpyruvate dioxygenase) and BjCks (cyclin dependent kinase regulatory subunit) whose expression is up-regulated in gamone1-treated type II cells. In this study, we investigated the molecular structures of these three genes, and compared their expression patterns in homotypic and heterotypic pairs, finding remarkable differences. BjCdk1, Bj4HPPD and BjCks were expressed specifically in gamone1-treated type II cells, but not in gamone2-treated type I cells. In heterotypic pairs, the expression of these genes stayed at the same level or gradually decreased throughout the entire process of conjugation, but it rapidly decreased and ceased after 10hours in homotypic pairs. These results indicate that some genes are expressed in a mating-type specific manner. Alternative gene expression in mating type I and type II cells and merging of individual factors in a heterotypic pair may induce nuclear changes including meiosis.

  9. Gene expression profiles underlying alternative caste phenotypes in a highly eusocial bee, Melipona quadrifasciata.

    PubMed

    Judice, C C; Carazzole, M F; Festa, F; Sogayar, M C; Hartfelder, K; Pereira, G A G

    2006-02-01

    To evaluate caste-biased gene expression in Melipona quadrifasciata, a stingless bee, we generated 1278 ESTs using Representational Difference Analysis. Most annotated sequences were similar to honey bee genes of unknown function. Only few queen-biased sequences had their putative function assigned by sequence comparison, contrasting with the worker-biased ESTs. The expression of six annotated genes connected to caste specificity was validated by real time PCR. Interestingly, queens that were developmentally induced by treatment with a juvenile hormone analogue displayed an expression profile clearly different from natural queens for this set of genes. In summary, this study represents an important first step in applying a comparative genomic approach to queen/worker polyphenism in the bee.

  10. NPY family genes respond negatively to alternative feedstuffs in channel catfish diets

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Of considerable importance in fish nutrition is the development of aquafeeds using alternative dietary ingredients which will allow aquaculture to grow globally, without putting excessive pressure on natural fisheries or adding considerable cost to production, while also addressing and maintaining t...

  11. A Feasibility Study to Assess Alternative Energy Program Development Potential at the Community College Level, October 1, 1983-June 30, 1984. Final Report.

    ERIC Educational Resources Information Center

    Blair, Brittain A.

    In 1983-84, a feasibility study was conducted to determine the viability of establishing a comprehensive alternative energy technology program at Southeastern Illinois College (SIC). The study involved an examination of a number of exemplary associate degree programs in alternative energy, through on-site visits and telephone surveys; a survey of…

  12. 20 CFR 411.710 - How will an alternate participant choose to participate as an EN in the Ticket to Work program?

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 20 Employees' Benefits 2 2011-04-01 2011-04-01 false How will an alternate participant choose to participate as an EN in the Ticket to Work program? 411.710 Section 411.710 Employees' Benefits SOCIAL... Alternate Participants Under the Programs For Payments For Vocational Rehabilitation Services § 411.710...

  13. Establishing a Program for Behaviorally Disordered Students: Alternatives to Consider, Components to Include, and Strategies for Building Support: Monograph 3. Monograph Series in Behavior Disorders.

    ERIC Educational Resources Information Center

    Heilman, Lanelle

    The types of programs that can be established for behaviorally disordered (BD) students are discussed, along with behavioral monitoring systems and approaches to establishing staff and administrative support for programs. In addition, a checklist of program components for BD students is included. The following program alternatives are described:…

  14. Alternation of apoptotic and implanting genes expression of mouse embryos after re-vitrification

    PubMed Central

    Majidi Gharenaz, Nasrin; Movahedin, Mansoureh; Mazaheri, Zohreh; Pour beiranvand, Shahram

    2016-01-01

    Background: Nowadays, oocytes and embryos vitrification has become a routine technique. Based on clinical judgment, re-vitrification maybe required. But little is known about re-vitrification impact on genes expression. Objective: The impact of re-vitrification on apoptotic and implanting genes, Bax, Bcl-2 and ErbB4, at compaction stage embryos were evaluated in this study. Materials and Methods: In this experimental study, 8 cell embryos (n=240) were collected from female mature mice, 60-62 hr post HCG injection. The embryos were divided randomly to 3 groups included: fresh (n=80), vitrified at 8 cell stage (n=80), vitrified at 8 cell stage thawed and re-vitrified at compaction stage (n=80). Embryos were vitrified by using cryolock, (open system) described by Kuwayama. Q-PCR was used to examine the expression of Bax, Bcl2 ErbB4 genes in derived blastocysts. Results: Our result showed that expanded blastocyst rate was similar between vitrified and re-vitrified groups, while re-vitrified embryos showed significant decrease in expanded blastocyst rate comparing with fresh embryos (p=0.03). In addition, significant difference was observed on apoptotic gene expression when comparing re-vitrified and fresh embryos (p=0.004), however expression of Bax and Bcl-2 (apoptotic) genes didn't demonstrate a significant difference between re-vitrified and vitrified groups. The expression rate of ErbB4, an implantation gene was decreased in re-vitrified embryos comparing with fresh embryos (p=0.003), but it was similar between re-vitrified and vitrified embryos. Conclusion: Re-vitrification can alter the expression of Bax, Bcl-2 and ErbB4 genes and developmental rate of mouse embryos in compaction stage. PMID:27679826

  15. Alternation of apoptotic and implanting genes expression of mouse embryos after re-vitrification

    PubMed Central

    Majidi Gharenaz, Nasrin; Movahedin, Mansoureh; Mazaheri, Zohreh; Pour beiranvand, Shahram

    2016-01-01

    Background: Nowadays, oocytes and embryos vitrification has become a routine technique. Based on clinical judgment, re-vitrification maybe required. But little is known about re-vitrification impact on genes expression. Objective: The impact of re-vitrification on apoptotic and implanting genes, Bax, Bcl-2 and ErbB4, at compaction stage embryos were evaluated in this study. Materials and Methods: In this experimental study, 8 cell embryos (n=240) were collected from female mature mice, 60-62 hr post HCG injection. The embryos were divided randomly to 3 groups included: fresh (n=80), vitrified at 8 cell stage (n=80), vitrified at 8 cell stage thawed and re-vitrified at compaction stage (n=80). Embryos were vitrified by using cryolock, (open system) described by Kuwayama. Q-PCR was used to examine the expression of Bax, Bcl2 ErbB4 genes in derived blastocysts. Results: Our result showed that expanded blastocyst rate was similar between vitrified and re-vitrified groups, while re-vitrified embryos showed significant decrease in expanded blastocyst rate comparing with fresh embryos (p=0.03). In addition, significant difference was observed on apoptotic gene expression when comparing re-vitrified and fresh embryos (p=0.004), however expression of Bax and Bcl-2 (apoptotic) genes didn't demonstrate a significant difference between re-vitrified and vitrified groups. The expression rate of ErbB4, an implantation gene was decreased in re-vitrified embryos comparing with fresh embryos (p=0.003), but it was similar between re-vitrified and vitrified embryos. Conclusion: Re-vitrification can alter the expression of Bax, Bcl-2 and ErbB4 genes and developmental rate of mouse embryos in compaction stage.

  16. Lifeline electric rates and alternative approaches to the problems of low-income ratepayers: ten case studies of rejected programs

    SciTech Connect

    Not Available

    1980-07-01

    This volume, Volume 3, contains ten case studies of non-implemented programs. It is noted that in Volume 2, the implemented lifeline programs, evolved as policy closely after the 1973 oil embargo; in contrast, the rejected programs were initiated about 4 years later and considered in a more-complex policy environment - after which time alternate methods of assisting low-income people had been developed. Specifically presented here are program summary, issue development, governmental process, and impact for the following: (a) Delaware Senate Bill 202; (b) Illinois House Bill 83; (c) Maine Legislative Document No. 1043; (d) Minnesota House File 1243; (e) New York Assembly Bill 12214; (f) New York Senate Bill 7013-A; (g) Rhode Island Resolution 79-H 5770-A; (h) South Dakota Senate Joint Resolution 9; (i) West Virginia House Bill 943; and (j) Wisconsin Assembly Bill 1250. 4 figures, 24 tables.

  17. Lifeline electric rates and alternative approaches to the problems of low-income ratepayers. Ten case studies of implemented programs

    SciTech Connect

    Not Available

    1980-07-01

    Program summaries, issue developments, governmental processes, and impacts are discussed for 10 case studies dealing with lifeline electric rates and alternative approaches to the problems of low-income ratepayers, namely; the Boston Edison rate freeze; the California lifeline; Florida Power and Light conservation rate; the Iowa-Illinois Gas and Electric small-use rate; the Maine demonstration lifeline program; the Massachusetts Electric Company A-65 rate; the Michigan optional senior citizen rate; the Narragansett Electric Company A-65 SSI rate; the Northern States Power Company conservation rate break; and the Potomac Electric Power Company rate freeze. (MCW)

  18. A Comparison of the Batterer Intervention and Prevention Program With Alternative Court Dispositions on 12-Month Recidivism.

    PubMed

    Boots, Denise Paquette; Wareham, Jennifer; Bartula, Aaron; Canas, Roberto

    2016-08-01

    Studies of batterer intervention and prevention programs (BIPPs) offer mixed results regarding their effect on recidivism. The purpose of this study was to examine the effectiveness of BIPP for cases assigned to a misdemeanor family court. This study focused on determining whether BIPP cases, compared with alternative sanctions, had significantly lower recidivism rates 12 months after program involvement. Findings indicated that BIPP was more effective than jail or regular dismissal in reducing the likelihood of future arrests, but not plea deferred adjudication and conditional dismissal. Results argue toward the efficacy of some form of treatment versus simply receiving jail time. PMID:26683096

  19. Nuclear proliferation and civilian nuclear power. Report of the Nonproliferation Alternative Systems Assessment Program. Volume IV. Commercial potential

    SciTech Connect

    Not Available

    1980-06-01

    This volume of the Nonproliferation Alternative Systems Assessment Program (NASAP) report provides time and cost estimates for positioning new nuclear power systems for commercial deployment. The assessment also estimates the rates at which the new systems might penetrate the domestic market, assuming the continuing viability of the massive light-water reactor network that now exists worldwide. This assessment does not recommend specific, detailed program plans and budgets for individual systems; however, it is clear from this analysis that any of the systems investigated could be deployed if dictated by national interest.

  20. A Comparative Study of Undergraduates in Three Alternative Degree Programs at the University of Minnesota.

    ERIC Educational Resources Information Center

    Peterson, Howard L.; Weidman, John C.

    Three nontraditional study programs at the University of Minnesota provide the setting of this study to determine what kinds of persons become students in a given program and what factors make their experience in a program a successful one. A questionnaire was distributed to students in the Experimental College, the University Without Walls, and…

  1. Presenting an Alternative Source Code Plagiarism Detection Framework for Improving the Teaching and Learning of Programming

    ERIC Educational Resources Information Center

    Hattingh, Frederik; Buitendag, Albertus A. K.; van der Walt, Jacobus S.

    2013-01-01

    The transfer and teaching of programming and programming related skills has become, increasingly difficult on an undergraduate level over the past years. This is partially due to the number of programming languages available as well as access to readily available source code over the Web. Source code plagiarism is common practice amongst many…

  2. Chicano Studies Programs at the Crossroads: Alternative Futures for the 1980s. Working Paper #103.

    ERIC Educational Resources Information Center

    Burrola, Luis Ramon; Rivera, Jose A.

    Fiscal reductions as well as growing conservatism may have a profound impact on many university programs, including Chicano Studies programs, which are expanding into research, publications, and other areas. To frame the issues of greatest concern to Chicano Studies programs, a small research effort at the University of New Mexico involved the…

  3. Characterization of a novel human breast cancer associated gene (BCA3) encoding an alternatively spliced proline-rich protein.

    PubMed

    Kitching, Richard; Li, Haoxia; Wong, Michael J; Kanaganayakam, Shankary; Kahn, Harriette; Seth, Arun

    2003-01-01

    As part of an integrated study of breast cancer gene expression, partial cDNAs were cloned from normal and tumor breast cells by subtractive-hybridization and differential display cloning. The DNA sequence for one of these breast cancer associated genes was used to construct the larger 1319 bp BCA3 cDNA sequence using ESTs without assigned names or functions. High-level BCA3 mRNA expression was found in breast and prostate tumor cell lines whereas normal breast and prostate tissues have low-level expression. Further analysis revealed possible functional domains and alternative splicing of BCA3 that we confirmed by RT-PCR analysis. Immunohistochemistry revealed that the protein is expressed in breast tumor cells in vivo, and not in surrounding stromal tissue. PMID:12527432

  4. The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA

    PubMed Central

    2014-01-01

    Background Retention of a subset of introns in spliced polyadenylated mRNA is emerging as a frequent, unexplained finding from RNA deep sequencing in mammalian cells. Results Here we analyze intron retention in T lymphocytes by deep sequencing polyadenylated RNA. We show a developmentally regulated RNA-binding protein, hnRNPLL, induces retention of specific introns by sequencing RNA from T cells with an inactivating Hnrpll mutation and from B lymphocytes that physiologically downregulate Hnrpll during their differentiation. In Ptprc mRNA encoding the tyrosine phosphatase CD45, hnRNPLL induces selective retention of introns flanking exons 4 to 6; these correspond to the cassette exons containing hnRNPLL binding sites that are skipped in cells with normal, but not mutant or low, hnRNPLL. We identify similar patterns of hnRNPLL-induced differential intron retention flanking alternative exons in 14 other genes, representing novel elements of the hnRNPLL-induced splicing program in T cells. Retroviral expression of a normally spliced cDNA for one of these targets, Senp2, partially corrects the survival defect of Hnrpll-mutant T cells. We find that integrating a number of computational methods to detect genes with differentially retained introns provides a strategy to enrich for alternatively spliced exons in mammalian RNA-seq data, when complemented by RNA-seq analysis of purified cells with experimentally perturbed RNA-binding proteins. Conclusions Our findings demonstrate that intron retention in mRNA is induced by specific RNA-binding proteins and suggest a biological significance for this process in marking exons that are poised for alternative splicing. PMID:24476532

  5. Two nifA-like genes required for expression of alternative nitrogenases by Azotobacter vinelandii.

    PubMed

    Joerger, R D; Jacobson, M R; Bishop, P E

    1989-06-01

    Two nifA-like genes, designated anfA and vnfA, have been identified in Azotobacter vinelandii. The anfA gene is located upstream from the nitrogenase-3 structural gene cluster (anfHDGK) and is preceded by a sequence that is potentially part of a ntrA-dependent promoter. The product of anfA appears to be required for expression of nitrogenase-3, since cells of the anfA deletion strain CA66 were unable to synthesize this nitrogenase when derepressed in N-free, Mo- and V-deficient medium. The vnfA gene was identified after determination of the nucleotide sequence of DNA flanking the Tn5 insertion in mutant strain CA46. Two open reading frames (ORF1 and ORF2) were found located upstream from the vnfA gene, and a nifE-like ORF, preceded by a possible ntrA-dependent promoter, was found downstream from this gene. It is not known whether vnfA is expressed only under N2-fixing conditions. However, potential ntrA-dependent promoters were found immediately upstream from vnfA (within the 3' end of ORF2) and immediately downstream from ORF1. The region spanning ORF1 and ORF2 contained an A + T-rich sequence that was also found immediately upstream from the potential ntrA-dependent promoter of anfA. The product of vnfA appears to be required for the synthesis of nitrogenase-2, since cells of strain CA46 synthesized only nitrogenase-1 and -3 but not nitrogenase-2 when grown in the presence of vanadium. The product of nifA, which is required for synthesis of nitrogenase-1, is not required for synthesis of either nitrogenase-2 or nitrogenase-3. However, growth data indicate that nifA is required for a factor (or factors) necessary for maximal diazotrophic growth under Mo- and V-deficient conditions.

  6. Differential Shannon entropy and differential coefficient of variation: alternatives and augmentations to differential expression in the search for disease-related genes

    PubMed Central

    Wang, Kai; Phillips, Charles A.; Rogers, Gary L.; Barrenas, Fredrik; Benson, Mikael; Langston, Michael A.

    2014-01-01

    Differential expression has been a standard tool for analysing case-control transcriptomic data since the advent of microarray technology. It has proved invaluable in characterising the molecular mechanisms of disease. Nevertheless, the expression profile of a gene across samples can be perturbed in ways that leave the expression level unaltered, while a biological effect is nonetheless present. This paper describes and analyses differential Shannon entropy and differential coefficient of variation, two alternate techniques for identifying genes of interest. Ontological analysis across 16 human disease datasets demonstrates that these alternatives are effective at identifying disease-related genes not found by mere differential expression alone. Because the two alternate techniques are based on somewhat different mathematical formulations, they tend to produce somewhat different gene lists. Moreover, each may pinpoint genes completely overlooked by the other. Thus, measures of entropy and variation can be used to replace or better yet augment standard differential expression computations. PMID:24878729

  7. Differential Shannon entropy and differential coefficient of variation: alternatives and augmentations to differential expression in the search for disease-related genes.

    PubMed

    Wang, Kai; Phillips, Charles A; Rogers, Gary L; Barrenas, Fredrik; Benson, Mikael; Langston, Michael A

    2014-01-01

    Differential expression has been a standard tool for analysing case-control transcriptomic data since the advent of microarray technology. It has proved invaluable in characterising the molecular mechanisms of disease. Nevertheless, the expression profile of a gene across samples can be perturbed in ways that leave the expression level unaltered, while a biological effect is nonetheless present. This paper describes and analyses differential Shannon entropy and differential coefficient of variation, two alternate techniques for identifying genes of interest. Ontological analysis across 16 human disease datasets demonstrates that these alternatives are effective at identifying disease-related genes not found by mere differential expression alone. Because the two alternate techniques are based on somewhat different mathematical formulations, they tend to produce somewhat different gene lists. Moreover, each may pinpoint genes completely overlooked by the other. Thus, measures of entropy and variation can be used to replace or better yet augment standard differential expression computations.

  8. Fork head alternative binding drives stage-specific gene expression in the silk gland of Bombyx mori.

    PubMed

    Julien, E; Bordeaux, M C; Garel, A; Couble, P

    2002-04-01

    Here, we identified the main transactivator of fhx, the gene encoding the silk protein fibrohexamerin in posterior silk gland cells (PSG), as the homeotic SGF1/fork head factor. The same factor also stimulates sericin-1, another silk protein encoding gene, in the middle silk gland cells. SGF1/fork head is present in the silk gland nuclei during the whole course of larval life, but its binding to the fhx promoter occurs at intermolt and not during molt, when fhx is respectively turned on and off. The alternative binding of the factor is associated with specific changes in the fhx chromatin topology in PSG cells. Taken together, our results show that stabilization of SGF1/fork head to its target sequence is critical to promote fhx transcription at each intermolt. We also found that fhx is characterized by a PSG-specific DNase I hypersensitive site in the first intron, present during molt and intermolt, i.e. independent of the transcriptional status of the gene. All these data suggest that differential chromatin accessibility and fork head activation are crucial in controlling the spatial and temporal regulation of the fhx gene in the posterior silk gland cells.

  9. Benefits and Costs of Aggressive Energy Efficiency Programs and the Impacts of Alternative Sources of Funding: Case Study of Massachusetts

    SciTech Connect

    Cappers, Peter; Satchwell, Andrew; Goldman, Charles; Schlegel, Jeff

    2010-08-06

    Increased interest by state (and federal) policymakers and regulatory agencies in pursuing aggressive energy efficiency efforts could deliver significant utility bill savings for customers while having long-term implications for ratepayers (e.g. potential rate impacts). Equity and distributional concerns associated with the authorized recovery of energy efficiency program costs may necessitate the pursuit of alternative program funding approaches. In 2008, Massachusetts passed the Green Communities Act which directed its energy efficiency (EE) program administrators to obtain all cost-effective EE resources. This goal has translated into achieving annual electric energy savings equivalent to a 2.4% reduction in retail sales from energy efficiency programs in 2012. Representatives of electricity consumer groups supported the new portfolio of EE programs (and the projected bill savings) but raised concerns about the potential rate impacts associated with achieving such aggressive EE goals, leading policymakers to seek out alternative funding sources which can potentially mitigate these effects. Utility administrators have also raised concerns about under-recovery of fixed costs when aggressive energy efficiency programs are pursued and have proposed ratemaking policies (e.g. decoupling) and business models that better align the utility's financial interests with the state's energy efficiency public policy goals. Quantifying these concerns and identifying ways they can be addressed are crucial steps in gaining the support of major stakeholder groups - lessons that can apply to other states looking to significantly increase savings targets that can be achieved from their own ratepayer-funded energy efficiency programs. We use a pro-forma utility financial model to quantify the bill and rate impacts on electricity customers when very aggressive annual energy efficiency savings goals ({approx}2.4%) are achieved over the long-term and also assess the impact of different

  10. Confirmatory and Competitive Evaluation of Alternative Gene-Environment Interaction Hypotheses

    ERIC Educational Resources Information Center

    Belsky, Jay; Pluess, Michael; Widaman, Keith F.

    2013-01-01

    Background: Most gene-environment interaction (GXE) research, though based on clear, vulnerability-oriented hypotheses, is carried out using exploratory rather than hypothesis-informed statistical tests, limiting power and making formal evaluation of competing GXE propositions difficult. Method: We present and illustrate a new regression technique…

  11. Assembling genes from predicted exons in linear time with dynamic programming.

    PubMed

    Guigó, R

    1998-01-01

    In a number of programs for gene structure prediction in higher eukaryotic genomic sequences, exon prediction is decoupled from gene assembly: a large pool of candidate exons is predicted and scored from features located in the query DNA sequence, and candidate genes are assembled from such a pool as sequences of nonoverlapping frame-compatible exons. Genes are scored as a function of the scores of the assembled exons, and the highest scoring candidate gene is assumed to be the most likely gene encoded by the query DNA sequence. Considering additive gene scoring functions, currently available algorithms to determine such a highest scoring candidate gene run in time proportional to the square of the number of predicted exons. Here, we present an algorithm whose running time grows only linearly with the size of the set of predicted exons. Polynomial algorithms rely on the fact that, while scanning the set of predicted exons, the highest scoring gene ending in a given exon can be obtained by appending the exon to the highest scoring among the highest scoring genes ending at each compatible preceding exon. The algorithm here relies on the simple fact that such highest scoring gene can be stored and updated. This requires scanning the set of predicted exons simultaneously by increasing acceptor and donor position. On the other hand, the algorithm described here does not assume an underlying gene structure model. Indeed, the definition of valid gene structures is externally defined in the so-called Gene Model. The Gene Model specifies simply which gene features are allowed immediately upstream which other gene features in valid gene structures. This allows for great flexibility in formulating the gene identification problem. In particular it allows for multiple-gene two-strand predictions and for considering gene features other than coding exons (such as promoter elements) in valid gene structures.

  12. Biological Activity of the Alternative Promoters of the Dictyostelium discoideum Adenylyl Cyclase A Gene

    PubMed Central

    Rodriguez-Centeno, Javier; Sastre, Leandro

    2016-01-01

    Amoebae of the Dictyostelium discoideum species form multicellular fruiting bodies upon starvation. Cyclic adenosine monophosphate (cAMP) is used as intercellular signalling molecule in cell-aggregation, cell differentiation and morphogenesis. This molecule is synthesized by three adenylyl cyclases, one of which, ACA, is required for cell aggregation. The gene coding for ACA (acaA) is transcribed from three different promoters that are active at different developmental stages. Promoter 1 is active during cell-aggregation, promoters 2 and 3 are active in prespore and prestalk tip cells at subsequent developmental stages. The biological relevance of acaA expression from each of the promoters has been studied in this article. The acaA gene was expressed in acaA-mutant cells, that do not aggregate, under control of each of the three acaA promoters. acaA expression under promoter 1 control induced cell aggregation although subsequent development was delayed, very small fruiting bodies were formed and cell differentiation genes were expressed at very low levels. Promoter 2-driven acaA expression induced the formation of small aggregates and small fruiting bodies were formed at the same time as in wild-type strains and differentiation genes were also expressed at lower levels. Expression of acaA from promoter 3 induced aggregates and fruiting bodies formation and their size and the expression of differentiation genes were more similar to that of wild-type cells. Expression of acaA from promoters 1 and 2 in AX4 cells also produced smaller structures. In conclusion, the expression of acaA under control of the aggregation-specific Promoter 1 is able to induce cell aggregation in acaA-mutant strains. Expression from promoters 2 and 3 also recovered aggregation and development although promoter 3 induced a more complete recovery of fruiting body formation. PMID:26840347

  13. ss-siRNAs allele selectively inhibit ataxin-3 expression: multiple mechanisms for an alternative gene silencing strategy.

    PubMed

    Liu, Jing; Yu, Dongbo; Aiba, Yuichiro; Pendergraff, Hannah; Swayze, Eric E; Lima, Walt F; Hu, Jiaxin; Prakash, Thazha P; Corey, David R

    2013-11-01

    Single-stranded silencing RNAs (ss-siRNAs) provide an alternative approach to gene silencing. ss-siRNAs combine the simplicity and favorable biodistribution of antisense oligonucleotides with robust silencing through RNA interference (RNAi). Previous studies reported potent and allele-selective inhibition of human huntingtin expression by ss-siRNAs that target the expanded CAG repeats within the mutant allele. Mutant ataxin-3, the genetic cause of Machado-Joseph Disease, also contains an expanded CAG repeat. We demonstrate here that ss-siRNAs are allele-selective inhibitors of ataxin-3 expression and then redesign ss-siRNAs to optimize their selectivity. We find that both RNAi-related and non-RNAi-related mechanisms affect gene expression by either blocking translation or affecting alternative splicing. These results have four broad implications: (i) ss-siRNAs will not always behave similarly to analogous RNA duplexes; (ii) the sequences surrounding CAG repeats affect allele-selectivity of anti-CAG oligonucleotides; (iii) ss-siRNAs can function through multiple mechanisms and; and (iv) it is possible to use chemical modification to optimize ss-siRNA properties and improve their potential for drug discovery.

  14. Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications

    PubMed Central

    Niklas, Karl J.; Bondos, Sarah E.; Dunker, A. Keith; Newman, Stuart A.

    2015-01-01

    Models for genetic regulation and cell fate specification characteristically assume that gene regulatory networks (GRNs) are essentially deterministic and exhibit multiple stable states specifying alternative, but pre-figured cell fates. Mounting evidence shows, however, that most eukaryotic precursor RNAs undergo alternative splicing (AS) and that the majority of transcription factors contain intrinsically disordered protein (IDP) domains whose functionalities are context dependent as well as subject to post-translational modification (PTM). Consequently, many transcription factors do not have fixed cis-acting regulatory targets, and developmental determination by GRNs alone is untenable. Modeling these phenomena requires a multi-scale approach to explain how GRNs operationally interact with the intra- and intercellular environments. Evidence shows that AS, IDP, and PTM complicate gene expression and act synergistically to facilitate and promote time- and cell-specific protein modifications involved in cell signaling and cell fate specification and thereby disrupt a strict deterministic GRN-phenotype mapping. The combined effects of AS, IDP, and PTM give proteomes physiological plasticity, adaptive responsiveness, and developmental versatility without inefficiently expanding genome size. They also help us understand how protein functionalities can undergo major evolutionary changes by buffering mutational consequences. PMID:25767796

  15. Regulation of Shootin1 Gene Expression Involves NGF-induced Alternative Splicing during Neuronal Differentiation of PC12 Cells

    PubMed Central

    Ergin, Volkan; Erdogan, Mutlu; Menevse, Adnan

    2015-01-01

    Shootin1 is a protein involved in neuronal polarization, and has been shown to be a key molecule for the positive/negative feedback loop for axon induction required during neuronal symmetry breaking. To better understand the molecular basis of shootin1 dynamics, we analysed the regulatory pathways and the expressional status of shootin1 gene during NGF-induced neuronal differentiation. We demonstrated that the isoform-1 and isoform-2 of shootin1 is differentially expressed during neuronal differentiation. By blocking individual downstream pathways of NGF signalling, we found that PI3K/Akt pathway plays a major role in the expression of shootin1 isoform-2. Western blot and RT-PCR results showed that the isoform-1 of shootin1 is constitutively expressed, while the isoform-2 is expressed in a manner that is strictly dependent on NGF-stimulation. Isoform-specific RT-PCR results demonstrated that the differential expression of the isoform-1 and isoform-2 of shootin1 is a consequence of alternative splicing of shootin1 pre-mRNA, in response to NGF-signalling. Collectively these findings provide the first information on the molecular mechanisms regulating the expression of shootin1 gene and represent the first example of NGF-induced alternative splicing process that has a regulatory role in neuritogenesis. PMID:26648138

  16. Alternatives to mammalian pain models 2: using Drosophila to identify novel genes involved in nociception.

    PubMed

    Caldwell, Jason C; Tracey, W Daniel

    2010-01-01

    Identification of the molecules involved in nociception is fundamental to our understanding of pain. Drosophila, with its short generation time, powerful genetics and capacity for rapid, genome-wide mutagenesis, represents an ideal invertebrate model organism to dissect nociception. The fly has already been used to identify factors that are involved in other sensory systems such as vision, chemosensation, and audition. Thus, the tiny fruit fly is a viable alternative to mammalian model organisms. Here we present a brief primer on techniques used in screening for thermal and/or mechanical nociception mutants using Drosophila. PMID:20336410

  17. Alternative Splicing of Rice WRKY62 and WRKY76 Transcription Factor Genes in Pathogen Defense1[OPEN

    PubMed Central

    Chen, Xujun; Zhou, Xiangui; Yang, Fang

    2016-01-01

    The WRKY family of transcription factors (TFs) functions as transcriptional activators or repressors in various signaling pathways. In this study, we discovered that OsWRKY62 and OsWRKY76, two genes of the WRKY IIa subfamily, undergo constitutive and inducible alternative splicing. The full-length OsWRKY62.1 and OsWRKY76.1 proteins formed homocomplexes and heterocomplexes, and the heterocomplex dominates in the nuclei when analyzed in Nicotiana benthamiana leaves. Transgenic overexpression of OsWRKY62.1 and OsWRKY76.1 in rice (Oryza sativa) enhanced plant susceptibility to the blast fungus Magnaporthe oryzae and the leaf blight bacterium Xanthomonas oryzae pv oryzae, whereas RNA interference and loss-of-function knockout plants exhibited elevated resistance. The dsOW62/76 and knockout lines of OsWRKY62 and OsWRKY76 also showed greatly increased expression of defense-related genes and the accumulation of phytoalexins. The ratio of full-length versus truncated transcripts changed in dsOW62/76 plants as well as in response to pathogen infection. The short alternative OsWRKY62.2 and OsWRKY76.2 isoforms could interact with each other and with full-length proteins. OsWRKY62.2 showed a reduced repressor activity in planta, and two sequence determinants required for the repressor activity were identified in the amino terminus of OsWRKY62.1. The amino termini of OsWRKY62 and OsWRKY76 splice variants also showed reduced binding to the canonical W box motif. These results not only enhance our understanding of the DNA-binding property, the repressor sequence motifs, and the negative feedback regulation of the IIa subfamily of WRKYs but also provide evidence for alternative splicing of WRKY TFs during the plant defense response. PMID:27208272

  18. Low Emissions Alternative Power (LEAP) Project Office Business Team of the Aeropropulsion Research Program Office (ARPO) Org. 0140

    NASA Technical Reports Server (NTRS)

    Buttler, Jennifer A.

    2004-01-01

    The program for which I am working at this summer is Propulsion and Power/Low Emissions Alternative Power (P&P/LEAP). It invests in a fundamental TRL 1-6 research and technology portfolio that will enable the future of: Alternative fuels and/or alternative propulsion systems, non-combustion (electric) propulsion systems. P&P/LEAP will identify and capitalize on the highest potential concepts generated both internal and external to the Agency. During my 2004 summer at NASA Glenn Research Center, I worked with my mentor Barbara Mader, in the Project Office with the Business Team completing various tasks for the project and personnel. The LEAP project is a highly matrixed organization. The Project Office is responsible for the goals advocacy and dollar (budget) of the LEAP project. The objectives of the LEAP Project are to discover new energy sources and develop unconventional engines and power systems directed towards greatly reduced emissions, enable new vehicle concepts for public mobility, new science missions and national security. The Propulsion and PowerLow Emissions Alternative Power directly supports the environmental, mobility, national security objectives of the Vehicle Systems Program and the Aeronautics Technology Theme. Technology deliverables include the demonstration through integrated ground tests, a constant volume combustor in an engine system, and UAV/small transport aircraft all electric power system. My mentor serves as a key member of the management team for the Aeropropulsion Research Program Office (ARPO). She has represented the office on numerous occasions, and is a member of a number of center-wide panels/teams, such as the Space management Committee and is chair to the Business Process Consolidation Team. She is responsible for the overall coordination of resources for the Propulsion and Power Project - from advocacy to implementation. The goal for my summer at NASA was to document processes and archive program documents from the past

  19. [Future cure of hearing disorders? Gene therapy and stem cell implantation are possible new therapeutic alternatives].

    PubMed

    Duan, M L; Ulfendahl, M; Ahlberg, A; Pyykkö, I; Borg, E

    2000-03-01

    Hearing loss is a very common disorder; nearly 10 per cent of the population is affected. Recently, a few findings such as the roles of neurotrophins, nitric oxide, reactive oxygen species and glutamate receptors in the peripheral hearing system have been highlighted. In this review, focus is set on possible mechanisms of peripheral hearing disorders, and on recent advances to prevent and treat hearing loss. Clinically useful treatment strategies, especially gene therapy and the use of embryonic stem cells, are particularly stressed.

  20. The Positive Alternative Learning Supports Program: Collaborating to Improve Student Success

    ERIC Educational Resources Information Center

    Arter, Patricia S.

    2007-01-01

    No Child Left Behind (NCLB) mandates that "all" students, not just well-behaved and academically motivated students, make academic progress. Unfortunately, about 10% of students with chronic behavior problems make this goal difficult for themselves and others (Sprague & Walker, 2000; Sugai, 2000). The Positive Alternative Learning Supports (PALS)…

  1. Program Evaluation in Alternative Education: An Annotated Bibliography. Teacher Education Forum; Volume 4, Number 17.

    ERIC Educational Resources Information Center

    Esp, Barbara

    The Forum Series is a collection of papers dealing with all phases of teacher education including inservice training and graduate study. This selection is an annotated bibliography in two parts: (1) Evaluation Issues and Methods; and (2) Studies of Alternative Environments. (DMT)

  2. Harvesting Alternative Credit Transfer Students: Redefining Selectivity in Your Online Learning Program Enrollment Leads

    ERIC Educational Resources Information Center

    Corlett, Bradly

    2014-01-01

    Several recent issues and trends in online education have resulted in consolidation of efforts for Massive Open Online Courses (MOOCs), increased Open Educational Resources (OER) in the form of asynchronous course repositories, with noticeable increases in governance and policy amplification. These emerging enrollment trends in alternative online…

  3. Identification and Analysis of the Alternatives for Achieving Greater Television Program Diversity in the United States.

    ERIC Educational Resources Information Center

    Dimling, John A., Jr.; And Others

    Several alternatives to the present television industry structure are considered in this study. They are: continuation of present policies, satellite-to-home broadcasting, and cable distribution of television. Trends noted are: the growth of commercial UHF (Ultra High Frequency) stations, the introduction of all-channel sets, population growth,…

  4. Analysis of Urban Teachers' First-Year Experiences in an Alternative Certification Program

    ERIC Educational Resources Information Center

    Ilmer, Steven; Nahan, Neva; Elliott, Sharon; Colombo, Marie; Snyder, Jo-Ann

    2005-01-01

    The demand to prepare increased numbers of qualified teachers for urban schools continues to represent a major challenge nationwide. In Michigan, Wayne State University, the Detroit Public Schools, the Michigan Department of Education, and the Detroit Federation of Teachers have collaborated to design and implement an alternative certification…

  5. 75 FR 32942 - National Toxicology Program (NTP); NTP Interagency Center for the Evaluation of Alternative...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-10

    ... validation and regulatory acceptance of toxicological test methods that more accurately assess the safety and.... Additional information about ICCVAM and NICEATM, guidelines for nomination of test methods for validation... Coordinating Committee on the Validation of Alternative Methods (ICCVAM) AGENCY: National Institute...

  6. The Relationship of Academic Achievement and Duration of Placement in Alternative Education Programming

    ERIC Educational Resources Information Center

    Elias, Janilyn

    2011-01-01

    Education agencies are driven by the need to remove disruptive and dangerous students from classrooms without suspending or expelling them to home or the streets (Bear, 1998). As stated in the National Association of State Boards of Education (1994), the term "alternative education" refers to nontraditional educational services ranging from…

  7. Disciplinary Alternative Education Programs in Texas--What Is Known; What Is Needed. A Policy Brief.

    ERIC Educational Resources Information Center

    Cortez, Albert; Robledo Montecel, Maria

    In 1995, the Texas legislature established a policy that each school district must have an "alternative educational setting for behavioral management." This policy brief examines the ways in which this idea has been implemented in Texas, using data from the Texas Education Agency. Findings show that, for the most part, these alternative…

  8. State High School Exit Exams: Trends in Test Programs, Alternate Pathways, and Pass Rates

    ERIC Educational Resources Information Center

    Zhang, Ying

    2009-01-01

    The report draws from Center on Education Policy's eight-year study of high school exit exams to identify long-term trends in state policies and student performance. It highlights a growing trend among states to establish alternate pathways to graduation for students who are struggling to pass exit exams. The report also analyzes exit exam pass…

  9. 75 FR 62845 - National Toxicology Program (NTP) Interagency Center for the Evaluation of Alternative...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-13

    ... workshops will help participants gain a practical understanding of the theory and application of available... will learn the strengths and weaknesses of available alternative test methods, become familiar with the types of data they provide, and learn how to use these data in regulatory safety assessments....

  10. Questioning Tradition: Alternative Safety Techniques and Procedures for Ropes Course and Climbing Programs.

    ERIC Educational Resources Information Center

    Hartley, Mike

    This paper examines current standards and procedures used in rope and climbing courses and offers alternatives to standard practices. The techniques and issues covered include belay techniques, belay signals, and the use of the initiative wall. Current techniques are often not the most efficient or even the safest, but they have stood the "test of…

  11. Alternatives to Custody: A Ten-Year Review of a Community-Based Program in Britain.

    ERIC Educational Resources Information Center

    Stevens, Barbara Christine

    1996-01-01

    Describes the development of a community forensic psychology service during its first 10 years of service. Service emphasizes cooperation among psychologists, probation officers, and others in establishing alternatives to custody for sex offenders, shoplifters, drug and alcohol abusers, and young criminals. Discusses theoretical orientation of the…

  12. Going Back to School: Why STEM Professionals Decide to Teach through Alternative Certification Programs

    ERIC Educational Resources Information Center

    Morettini, Brianne W.

    2014-01-01

    Prompted by the emergence of alternative pathways to teacher certification as well as federal, state, and local policy directives aimed at raising student achievement, this study explores the extent to which prospective teachers' reasons to teach have or have not changed since before the enactment of such changes in public schools. In addition,…

  13. 77 FR 5617 - Alternative Transportation in Parks and Public Lands Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-03

    ..., Efficient Transportation Equity Act--A Legacy for Users of 2005 (SAFETEA-LU) and its extensions, and... expenses for alternative transportation systems in parks and public lands. Federal land management agencies and State, tribal and local governments acting with the consent of a Federal land management...

  14. RNA-seq analysis of impact of PNN on gene expression and alternative splicing in corneal epithelial cells

    PubMed Central

    Akin, Debra; Newman, Jeremy R.B.; McIntyre, Lauren M.

    2016-01-01

    Purpose The specialized corneal epithelium requires differentiated properties, specific for its role at the anterior surface of the eye. Thus, tight maintenance of the differentiated qualities of the corneal epithelial is essential. Pinin (PNN) is an exon junction component (EJC) that has dramatic implications for corneal epithelial cell differentiation and may act as a stabilizer of the corneal epithelial cell phenotype. Our studies revealed that PNN is involved in transcriptional repression complexes and spliceosomal complexes, placing PNN at the fulcrum between chromatin and mRNA splicing. Transcriptome analysis of PNN-knockdown cells revealed clear and reproducible alterations in transcript profiles and splicing patterns of a subset of genes that would significantly impact the epithelial cell phenotype. We further investigated PNN’s role in the regulation of gene expression and alternative splicing (AS) in a corneal epithelial context. Methods Human corneal epithelial (HCET) cells that carry the doxycycline-inducible PNN-knockdown shRNA vector were used to perform RNA-seq to determine differential gene expression and differential AS events. Results Multiple genes and AS events were identified as differentially expressed between PNN-knockdown and control cells. Genes upregulated by PNN knockdown included a large proportion of genes that are associated with enhanced cell migration and ECM remodeling processes, such as MMPs, ADAMs, HAS2, LAMA3, CXCRs, and UNC5C. Genes downregulated in response to PNN depletion included IGFBP5, FGD3, FGFR2, PAX6, RARG, and SOX10. AS events in PNN-knockdown cells compared to control cells were also more likely to be detected, and upregulated. In particular, 60% of exon-skipping events, detected in only one condition, were detected in PNN-knockdown cells and of the shared exon-skipping events, 92% of those differentially expressed were more frequent in the PNN knockdown. Conclusions These data suggest that lowering of PNN levels in

  15. Fruit load modulates flowering-related gene expression in buds of alternate-bearing ‘Moncada’ mandarin

    PubMed Central

    Muñoz-Fambuena, Natalia; Mesejo, Carlos; González-Mas, M. Carmen; Primo-Millo, Eduardo; Agustí, Manuel; Iglesias, Domingo J.

    2012-01-01

    Background and Aims Gene determination of flowering is the result of complex interactions involving both promoters and inhibitors. In this study, the expression of flowering-related genes at the meristem level in alternate-bearing citrus trees is analysed, together with the interplay between buds and leaves in the determination of flowering. Methods First defruiting experiments were performed to manipulate blossoming intensity in ‘Moncada’ mandarin, Citrus clementina. Further defoliation was performed to elucidate the role leaves play in the flowering process. In both cases, the activity of flowering-related genes was investigated at the flower induction (November) and differentiation (February) stages. Key Results Study of the expression pattern of flowering-genes in buds from on (fully loaded) and off (without fruits) trees revealed that homologues of FLOWERING LOCUS T (CiFT), TWIN SISTER OF FT (TSF), APETALA1 (CsAP1) and LEAFY (CsLFY) were negatively affected by fruit load. CiFT and TSF activities showed a marked increase in buds from off trees through the study period (ten-fold in November). By contrast, expression of the homologues of the flowering inhibitors of TERMINAL FLOWER 1 (CsTFL), TERMINAL FLOWER 2 (TFL2) and FLOWERING LOCUS C (FLC) was generally lower in off trees. Regarding floral identity genes, the increase in CsAP1 expression in off trees was much greater in buds than in leaves, and significant variations in CsLFY expression (approx. 20 %) were found only in February. Defoliation experiments further revealed that the absence of leaves completely abolished blossoming and severely affected the expression of most of the flowering-related genes, particularly decreasing the activity of floral promoters and of CsAP1 at the induction stage. Conclusions These results suggest that the presence of fruit affects flowering by greatly altering gene-expression not only at the leaf but also at the meristem level. Although leaves are required for flowering to

  16. Admission to the Master of Business Administration Program: An Alternative for Savannah State University

    ERIC Educational Resources Information Center

    Dowling, Bill

    2009-01-01

    Traditionally, graduate programs in business administration have heavily relied on the Graduate Management Aptitude Test prepared and administered by the Educational Testing Service in the decision to admit a candidate to the program. The purpose of this paper is to review the literature regarding the statistical validity and statistical…

  17. 78 FR 14843 - Temporary Scope Expansion of the Post-Investigation Alternative Dispute Resolution Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-07

    ... August 14, 1992 (57 FR 36678), the NRC issued a general policy statement which supports and encourages... (ADAMS Accession No. ML040550473). The Commission approved the pilot ADR Program (August 13, 2004; 69 FR... program, including determining if it should be expanded. On September 6, 2011 (76 FR 55136), the...

  18. Reversing the Demise and Preventing the Apocalypse: Using Alternative Programs To Help African American Males.

    ERIC Educational Resources Information Center

    Gill, Walter

    1995-01-01

    Describes the Agriculture-Science Project, a program designed for inner-city African-American males to improve science grades, increase awareness of good health/safety practices, and increase awareness of science/health careers. Notes summer program results revealing significant differences in educational climate between summer and regular school,…

  19. Transcriptome Analysis in Rat Kidneys: Importance of Genes Involved in Programmed Hypertension

    PubMed Central

    Tain, You-Lin; Huang, Li-Tung; Chan, Julie Y. H.; Lee, Chien-Te

    2015-01-01

    Suboptimal conditions in pregnancy can elicit long-term effects on the health of offspring. The most common outcome is programmed hypertension. We examined whether there are common genes and pathways in the kidney are responsible for generating programmed hypertension among three different models using next generation RNA sequencing (RNA-Seq) technology. Pregnant Sprague-Dawley rats received dexamethasone (DEX, 0.1 mg/kg) from gestational day 16 to 22, 60% high-fructose (HF) diet, or NG-nitro-l-arginine-methyester (l-NAME, 60 mg/kg/day) to conduct DEX, HF, or l-NAME model respectively. All three models elicited programmed hypertension in adult male offspring. We observed five shared genes (Bcl6, Dmrtc1c, Egr1, Inmt, and Olr1668) among three different models. The identified differential genes (DEGs) that are related to regulation of blood pressure included Aqp2, Ptgs1, Eph2x, Hba-a2, Apln, Guca2b, Hmox1, and Npy. RNA-Seq identified genes in arachidonic acid metabolism are potentially gatekeeper genes contributing to programmed hypertension. In addition, HF and DEX increased expression and activity of soluble epoxide hydrolase (Ephx2 gene encoding protein). Conclusively, the DEGs in arachidonic acid metabolism are potentially gatekeeper genes in programmed hypertension. The roles of DEGs identified by the RNA-Seq in this study deserve further clarification, to develop the potential interventions in the prevention of programmed hypertension. PMID:25739086

  20. Identification of Coilin Mutants in a Screen for Enhanced Expression of an Alternatively Spliced GFP Reporter Gene in Arabidopsis thaliana

    PubMed Central

    Kanno, Tatsuo; Lin, Wen-Dar; Fu, Jason L.; Wu, Ming-Tsung; Yang, Ho-Wen; Lin, Shih-Shun; Matzke, Antonius J. M.; Matzke, Marjori

    2016-01-01

    Coilin is a marker protein for subnuclear organelles known as Cajal bodies, which are sites of various RNA metabolic processes including the biogenesis of spliceosomal small nuclear ribonucleoprotein particles. Through self-associations and interactions with other proteins and RNA, coilin provides a structural scaffold for Cajal body formation. However, despite a conspicuous presence in Cajal bodies, most coilin is dispersed in the nucleoplasm and expressed in cell types that lack these organelles. The molecular function of coilin, particularly of the substantial nucleoplasmic fraction, remains uncertain. We identified coilin loss-of-function mutations in a genetic screen for mutants showing either reduced or enhanced expression of an alternatively spliced GFP reporter gene in Arabidopsis thaliana. The coilin mutants feature enhanced GFP fluorescence and diminished Cajal bodies compared with wild-type plants. The amount of GFP protein is several-fold higher in the coilin mutants owing to elevated GFP transcript levels and more efficient splicing to produce a translatable GFP mRNA. Genome-wide RNA-sequencing data from two distinct coilin mutants revealed a small, shared subset of differentially expressed genes, many encoding stress-related proteins, and, unexpectedly, a trend toward increased splicing efficiency. These results suggest that coilin attenuates splicing and modulates transcription of a select group of genes. The transcriptional and splicing changes observed in coilin mutants are not accompanied by gross phenotypic abnormalities or dramatically altered stress responses, supporting a role for coilin in fine tuning gene expression. Our GFP reporter gene provides a sensitive monitor of coilin activity that will facilitate further investigations into the functions of this enigmatic protein. PMID:27317682

  1. Identification of Coilin Mutants in a Screen for Enhanced Expression of an Alternatively Spliced GFP Reporter Gene in Arabidopsis thaliana.

    PubMed

    Kanno, Tatsuo; Lin, Wen-Dar; Fu, Jason L; Wu, Ming-Tsung; Yang, Ho-Wen; Lin, Shih-Shun; Matzke, Antonius J M; Matzke, Marjori

    2016-08-01

    Coilin is a marker protein for subnuclear organelles known as Cajal bodies, which are sites of various RNA metabolic processes including the biogenesis of spliceosomal small nuclear ribonucleoprotein particles. Through self-associations and interactions with other proteins and RNA, coilin provides a structural scaffold for Cajal body formation. However, despite a conspicuous presence in Cajal bodies, most coilin is dispersed in the nucleoplasm and expressed in cell types that lack these organelles. The molecular function of coilin, particularly of the substantial nucleoplasmic fraction, remains uncertain. We identified coilin loss-of-function mutations in a genetic screen for mutants showing either reduced or enhanced expression of an alternatively spliced GFP reporter gene in Arabidopsis thaliana The coilin mutants feature enhanced GFP fluorescence and diminished Cajal bodies compared with wild-type plants. The amount of GFP protein is several-fold higher in the coilin mutants owing to elevated GFP transcript levels and more efficient splicing to produce a translatable GFP mRNA. Genome-wide RNA-sequencing data from two distinct coilin mutants revealed a small, shared subset of differentially expressed genes, many encoding stress-related proteins, and, unexpectedly, a trend toward increased splicing efficiency. These results suggest that coilin attenuates splicing and modulates transcription of a select group of genes. The transcriptional and splicing changes observed in coilin mutants are not accompanied by gross phenotypic abnormalities or dramatically altered stress responses, supporting a role for coilin in fine tuning gene expression. Our GFP reporter gene provides a sensitive monitor of coilin activity that will facilitate further investigations into the functions of this enigmatic protein. PMID:27317682

  2. Serial analysis of gene expression in sugarcane (Saccharum spp.) leaves revealed alternative C4 metabolism and putative antisense transcripts.

    PubMed

    Calsa, Tercilio; Figueira, Antonio

    2007-04-01

    Sugarcane (Saccharum spp.) is a highly efficient biomass and sugar producing crop. Leaf reactions have been considered as potential rate-limiting step for sucrose accumulation in sugarcane stalks. To characterize the sugarcane leaf transcriptome, field-grown mature leaves from cultivar "SP80-3280" were analyzed using Serial Analysis of Gene Expression (SAGE). From 480 sequenced clones, 9,482 valid tags were extracted, with 5,227 unique sequences, from which 3,659 (70%) matched at least a sugarcane assembled sequence (SAS) with putative function; while 872 tags (16.7%) matched SAS with unknown function; 523 (10%) matched SAS without a putative annotation; and only 173 (3.3%) did not match any sugarcane ESTs. Based on gene ontology (GO), photosystem (PS) I reaction center was identified as the most frequent gene product location, followed by the remaining sites of PS I, PS II and thylakoid complexes. For metabolic processes, photosynthesis light harvesting complexes; carbon fixation; and chlorophyll biosynthesis were the most enriched GO-terms. Considering the alternative photosynthetic C(4) cycles, tag frequencies related to phosphoenolpyruvate carboxykinase (PEPCK) and aspartate aminotransferase compared to those for NADP(+)-malic enzyme (NADP-ME) and NADP-malate dehydrogenase, suggested that PEPCK-type decarboxylation appeared to predominate over NADP-ME in mature leaves, although both may occur, opposite to currently assumed in sugarcane. From the unique tag set, 894 tags (17.1%) were assigned as potentially derived from antisense transcripts, while 73 tags (1.4%) were assigned to more than one SAS, suggesting the occurrence of alternative processing. The occurrence of antisense was validated by quantitative reverse transcription amplification. Sugarcane leaf transcriptome provided new insights for functional studies associated with sucrose synthesis and accumulation.

  3. Genetic programming as alternative for predicting development effort of individual software projects.

    PubMed

    Chavoya, Arturo; Lopez-Martin, Cuauhtemoc; Andalon-Garcia, Irma R; Meda-Campaña, M E

    2012-01-01

    Statistical and genetic programming techniques have been used to predict the software development effort of large software projects. In this paper, a genetic programming model was used for predicting the effort required in individually developed projects. Accuracy obtained from a genetic programming model was compared against one generated from the application of a statistical regression model. A sample of 219 projects developed by 71 practitioners was used for generating the two models, whereas another sample of 130 projects developed by 38 practitioners was used for validating them. The models used two kinds of lines of code as well as programming language experience as independent variables. Accuracy results from the model obtained with genetic programming suggest that it could be used to predict the software development effort of individual projects when these projects have been developed in a disciplined manner within a development-controlled environment.

  4. Genetic Programming as Alternative for Predicting Development Effort of Individual Software Projects

    PubMed Central

    Chavoya, Arturo; Lopez-Martin, Cuauhtemoc; Andalon-Garcia, Irma R.; Meda-Campaña, M. E.

    2012-01-01

    Statistical and genetic programming techniques have been used to predict the software development effort of large software projects. In this paper, a genetic programming model was used for predicting the effort required in individually developed projects. Accuracy obtained from a genetic programming model was compared against one generated from the application of a statistical regression model. A sample of 219 projects developed by 71 practitioners was used for generating the two models, whereas another sample of 130 projects developed by 38 practitioners was used for validating them. The models used two kinds of lines of code as well as programming language experience as independent variables. Accuracy results from the model obtained with genetic programming suggest that it could be used to predict the software development effort of individual projects when these projects have been developed in a disciplined manner within a development-controlled environment. PMID:23226305

  5. Evolutionary effects of alternative artificial propagation programs: implications for viability of endangered anadromous salmonids

    PubMed Central

    McClure, Michelle M; Utter, Fred M; Baldwin, Casey; Carmichael, Richard W; Hassemer, Peter F; Howell, Philip J; Spruell, Paul; Cooney, Thomas D; Schaller, Howard A; Petrosky, Charles E

    2008-01-01

    Most hatchery programs for anadromous salmonids have been initiated to increase the numbers of fish for harvest, to mitigate for habitat losses, or to increase abundance in populations at low abundance. However, the manner in which these programs are implemented can have significant impacts on the evolutionary trajectory and long-term viability of populations. In this paper, we review the potential benefits and risks of hatchery programs relative to the conservation of species listed under the US Endangered Species Act. To illustrate, we present the range of potential effects within a population as well as among populations of Chinook salmon (Oncorhynchus tshawytscha) where changes to major hatchery programs are being considered. We apply evolutionary considerations emerging from these examples to suggest broader principles for hatchery uses that are consistent with conservation goals. We conclude that because of the evolutionary risks posed by artificial propagation programs, they should not be viewed as a substitute for addressing other limiting factors that prevent achieving viability. At the population level, artificial propagation programs that are implemented as a short-term approach to avoid imminent extinction are more likely to achieve long-term population viability than approaches that rely on long-term supplementation. In addition, artificial propagation programs can have out-of-population impacts that should be considered in conservation planning. PMID:25567637

  6. Integrative analyses of RNA editing, alternative splicing, and expression of young genes in human brain transcriptome by deep RNA sequencing.

    PubMed

    Wu, Dong-Dong; Ye, Ling-Qun; Li, Yan; Sun, Yan-Bo; Shao, Yi; Chen, Chunyan; Zhu, Zhu; Zhong, Li; Wang, Lu; Irwin, David M; Zhang, Yong E; Zhang, Ya-Ping

    2015-08-01

    Next-generation RNA sequencing has been successfully used for identification of transcript assembly, evaluation of gene expression levels, and detection of post-transcriptional modifications. Despite these large-scale studies, additional comprehensive RNA-seq data from different subregions of the human brain are required to fully evaluate the evolutionary patterns experienced by the human brain transcriptome. Here, we provide a total of 6.5 billion RNA-seq reads from different subregions of the human brain. A significant correlation was observed between the levels of alternative splicing and RNA editing, which might be explained by a competition between the molecular machineries responsible for the splicing and editing of RNA. Young human protein-coding genes demonstrate biased expression to the neocortical and non-neocortical regions during evolution on the lineage leading to humans. We also found that a significantly greater number of young human protein-coding genes are expressed in the putamen, a tissue that was also observed to have the highest level of RNA-editing activity. The putamen, which previously received little attention, plays an important role in cognitive ability, and our data suggest a potential contribution of the putamen to human evolution.

  7. The subsidiary GntII system for gluconate metabolism in Escherichia coli: alternative induction of the gntV gene.

    PubMed

    Gómez, Keyla M; Rodríguez, Andrea; Rodriguez, Yesseima; Ramírez, Alvaro H; Istúriz, Tomás

    2011-01-01

    Two systems are involved in the transport and phosphorylation of gluconate in Escherichia coli. GntI, the main system, consists of high and low-affinity gluconate transporters and a thermoresistant gluconokinase for its phosphorylation. The corresponding genes, gntT, gntU and gntK at 76.5 min, are induced by gluconate. GntII, the subsidiary system, includes IdnT and GntV, which duplicate activities of transport and phosphorylation of gluconate, respectively. Gene gntV at 96.8 min is divergently transcribed from the idnDOTR operon involved in L-idonate metabolism. These genetic elements are induced by the substrate or 5-keto-D-gluconate. Because gntV is also induced in cells grown in gluconate, it was of interest to investigate its expression in this condition. E. coli gntK, idnOokan mutants were constructed to study this question. These idnO kan-cassete inserted mutants, unable to convert gluconate to 5-keto-D-gluconate, permitted examining gntV expression in the absence of this inducer and demonstrating that it is not required when the cells grow in gluconate. The results suggest that E. coli gntV gene is alternatively induced by 5-keto-D-gluconate or gluconate in cells cultivated either in idonate or gluconate. In this way, the control of gntV expression would seem to be involved in the efficient utilization of these substrates.

  8. Data and programs in support of network analysis of genes and their association with diseases.

    PubMed

    Kontou, Panagiota I; Pavlopoulou, Athanasia; Dimou, Niki L; Pavlopoulos, Georgios A; Bagos, Pantelis G

    2016-09-01

    The network-based approaches that were employed in order to depict the relationships between human genetic diseases and their associated genes are described. Towards this direction, monopartite disease-disease and gene-gene networks were constructed from bipartite gene-disease association networks. The latter were created by collecting and integrating data from three diverse resources, each one with different content, covering from rare monogenic disorders to common complex diseases. Moreover, topological and clustering graph analyses were performed. The methodology and the programs presented in this article are related to the research article entitled "Network analysis of genes and their association with diseases" [1]. PMID:27508260

  9. The CTFA Evaluation of Alternatives Program: an evaluation of in vitro alternatives to the Draize primary eye irritation test. (Phase II) oil/water emulsions.

    PubMed

    Gettings, S D; Dipasquale, L C; Bagley, D M; Casterton, P L; Chudkowski, M; Curren, R D; Demetrulias, J L; Feder, P I; Galli, C L; Gay, R

    1994-10-01

    The Cosmetic, Toiletry and Fragrance Association (CTFA) Evaluation of Alternatives Program is an evaluation of the relationship between Draize ocular safety test data and comparable data from a selection of in vitro tests. In Phase II, 18 representative oil/water-based personal-care formulations were subjected to the Draize primary eye safety test and 30 in vitro assay protocols (14 different types of in vitro endpoints were evaluated; the remainder were protocol variations). Correlation of in vitro with in vivo data was evaluated using analysis of sensitivity/specificity and statistical analysis of the relationship between maximum average Draize score (MAS) and in vitro endpoint. Regression modelling is the primary approach adopted in the CTFA Program for evaluating in vitro assay performance. The objective of regression analysis is to predict MAS for a given test material (and to place upper and lower prediction interval bounds on the range in which the MAS is anticipated to fall with high probability) conditional on observing an in vitro assay score for that material. The degree of confidence in prediction is quantified in terms of the relative widths of prediction intervals constructed about the fitted regression curves: the narrower the prediction interval, the more predictive of the Draize score is the in vitro test result. 16 assays were shown to have the greatest agreement with the Draize procedure and were therefore selected for regression analysis. Based on the magnitude of the 95% prediction bounds of each of the 16 selected assays over the range of test data, it may be inferred that prediction of MAS values from experimentally determined in vitro scores is more accurate for oil/water-based formulations with lower rather than higher irritancy potential. The assays selected for modelling in Phase II generally exhibited weaker relationships with MAS than those selected in Phase I (evaluated using hydroalcoholic formulations), even though several assays

  10. 20 CFR 411.710 - How will an alternate participant choose to participate as an EN in the Ticket to Work program?

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... participate as an EN in the Ticket to Work program? 411.710 Section 411.710 Employees' Benefits SOCIAL... will an alternate participant choose to participate as an EN in the Ticket to Work program? (a) When... in that State will be notified of its right to choose to participate as an EN in the program in...

  11. Analysis of the First Year of Operation of the Federal Alternative Financing Program for Individuals with Disabilities: Providing Low Cost Loans for the Purchase of Assistive Technology.

    ERIC Educational Resources Information Center

    RESNA: Association for the Advancement of Rehabilitation Technology, Arlington, VA.

    This report analyzes the first year of the Federal Alternative Financing Program (AFP), a program designed to help individuals with disabilities who need to purchase assistive technology (AT) find a way to pay for the equipment. The program receives funding under Title III of the Assistive Technology Act of 1998 and provides low-cost financing for…

  12. 77 FR 14587 - FY 2012 Discretionary Livability Funding Opportunity: Alternatives Analysis Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-12

    ... and value of such improvements. Livable Communities and Sustainable Development FTA has long fostered livable communities and sustainable development through its various transit ] programs and activities... Maintaining transit assets in a state of good repair, fostering livable communities and promoting...

  13. Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis.

    PubMed

    Charmpi, Konstantina; Ycart, Bernard

    2015-06-01

    Gene Set Enrichment Analysis (GSEA) is a basic tool for genomic data treatment. Its test statistic is based on a cumulated weight function, and its distribution under the null hypothesis is evaluated by Monte-Carlo simulation. Here, it is proposed to subtract to the cumulated weight function its asymptotic expectation, then scale it. Under the null hypothesis, the convergence in distribution of the new test statistic is proved, using the theory of empirical processes. The limiting distribution needs to be computed only once, and can then be used for many different gene sets. This results in large savings in computing time. The test defined in this way has been called Weighted Kolmogorov Smirnov (WKS) test. Using expression data from the GEO repository, tested against the MSig Database C2, a comparison between the classical GSEA test and the new procedure has been conducted. Our conclusion is that, beyond its mathematical and algorithmic advantages, the WKS test could be more informative in many cases, than the classical GSEA test.

  14. Space transportation alternatives for large space programs: The International Space University Summer Session, 1992

    NASA Astrophysics Data System (ADS)

    Palaszewski, Bryan A.

    1993-06-01

    In 1992, the International Space University (ISU) held its Summer Session in Kitakyushu, Japan. This paper summarizes and expands upon some aspects of space solar power and space transportation that were considered during that session. The issues discussed in this paper are the result of a 10-week study by the Space Solar Power Program design project members and the Space Transportation Group to investigate new paradigms in space propulsion and how those paradigms might reduce the costs for large space programs. The program plan was to place a series of power satellites in Earth orbit. Several designs were studied where many kW, MW, or GW of power would be transmitted to Earth or to other spacecraft in orbit. During the summer session, a space solar power system was also detailed and analyzed. A high-cost space transportation program is potentially the most crippling barrier to such a space power program. At ISU, the focus of the study was to foster and develop some of the new paradigms that may eliminate the barriers to low cost for space exploration and exploitation. Many international and technical aspects of a large multinational program were studied. Environmental safety, space construction and maintenance, legal and policy issues of frequency allocation, technology transfer and control and many other areas were addressed. Over 120 students from 29 countries participated in this summer session. The results discussed in this paper, therefore, represent the efforts of many nations.

  15. Space transportation alternatives for large space programs: The International Space University Summer Session, 1992

    NASA Technical Reports Server (NTRS)

    Palaszewski, Bryan A.

    1993-01-01

    In 1992, the International Space University (ISU) held its Summer Session in Kitakyushu, Japan. This paper summarizes and expands upon some aspects of space solar power and space transportation that were considered during that session. The issues discussed in this paper are the result of a 10-week study by the Space Solar Power Program design project members and the Space Transportation Group to investigate new paradigms in space propulsion and how those paradigms might reduce the costs for large space programs. The program plan was to place a series of power satellites in Earth orbit. Several designs were studied where many kW, MW, or GW of power would be transmitted to Earth or to other spacecraft in orbit. During the summer session, a space solar power system was also detailed and analyzed. A high-cost space transportation program is potentially the most crippling barrier to such a space power program. At ISU, the focus of the study was to foster and develop some of the new paradigms that may eliminate the barriers to low cost for space exploration and exploitation. Many international and technical aspects of a large multinational program were studied. Environmental safety, space construction and maintenance, legal and policy issues of frequency allocation, technology transfer and control and many other areas were addressed. Over 120 students from 29 countries participated in this summer session. The results discussed in this paper, therefore, represent the efforts of many nations.

  16. Nucleotide sequence and mutational analysis of the structural genes (anfHDGK) for the second alternative nitrogenase from Azotobacter vinelandii.

    PubMed Central

    Joerger, R D; Jacobson, M R; Premakumar, R; Wolfinger, E D; Bishop, P E

    1989-01-01

    The nucleotide sequence of a region of the Azotobacter vinelandii genome exhibiting sequence similarity to nifH has been determined. The order of open reading frames within this 6.1-kilobase-pair region was found to be anfH (alternative nitrogen fixation, nifH-like gene), anfD (nifD-like gene), anfG (potentially encoding a protein similar to the product of vnfG from Azotobacter chroococcum), anfK (nifK-like gene), followed by two additional open reading frames. The 5'-flanking region of anfH contains a nif promoter similar to that found in the A. vinelandii nifHDK gene cluster. The presumed products of anfH, anfD, and anfK are similar in predicted Mr and pI to the previously described subunits of nitrogenase 3. Deletion plus insertion mutations introduced into the anfHDGK region of wild-type strain A. vinelandii CA resulted in mutant strains that were unable to grow in Mo-deficient, N-free medium but grew in the presence of 1 microM Na2MoO4 or V2O5. Introduction of the same mutations into the nifHDK deletion strain CA11 resulted in strains that grew under diazotrophic conditions only in the presence of vanadium. The lack of nitrogenase 3 subunits in these mutant strains was demonstrated through two-dimensional gel analysis of protein extracts from cells derepressed for nitrogenase under Mo and V deficiency. These results indicate that anfH, anfD, and anfK encode structural proteins for nitrogenase 3. Images PMID:2644222

  17. Nucleotide sequence and mutational analysis of the structural genes (anfHDGK) for the second alternative nitrogenase from Azotobacter vinelandii.

    PubMed

    Joerger, R D; Jacobson, M R; Premakumar, R; Wolfinger, E D; Bishop, P E

    1989-02-01

    The nucleotide sequence of a region of the Azotobacter vinelandii genome exhibiting sequence similarity to nifH has been determined. The order of open reading frames within this 6.1-kilobase-pair region was found to be anfH (alternative nitrogen fixation, nifH-like gene), anfD (nifD-like gene), anfG (potentially encoding a protein similar to the product of vnfG from Azotobacter chroococcum), anfK (nifK-like gene), followed by two additional open reading frames. The 5'-flanking region of anfH contains a nif promoter similar to that found in the A. vinelandii nifHDK gene cluster. The presumed products of anfH, anfD, and anfK are similar in predicted Mr and pI to the previously described subunits of nitrogenase 3. Deletion plus insertion mutations introduced into the anfHDGK region of wild-type strain A. vinelandii CA resulted in mutant strains that were unable to grow in Mo-deficient, N-free medium but grew in the presence of 1 microM Na2MoO4 or V2O5. Introduction of the same mutations into the nifHDK deletion strain CA11 resulted in strains that grew under diazotrophic conditions only in the presence of vanadium. The lack of nitrogenase 3 subunits in these mutant strains was demonstrated through two-dimensional gel analysis of protein extracts from cells derepressed for nitrogenase under Mo and V deficiency. These results indicate that anfH, anfD, and anfK encode structural proteins for nitrogenase 3. PMID:2644222

  18. Nucleotide sequence and mutational analysis of the structural genes (anfHDGK) for the second alternative nitrogenase from Azotobacter vinelandii.

    PubMed

    Joerger, R D; Jacobson, M R; Premakumar, R; Wolfinger, E D; Bishop, P E

    1989-02-01

    The nucleotide sequence of a region of the Azotobacter vinelandii genome exhibiting sequence similarity to nifH has been determined. The order of open reading frames within this 6.1-kilobase-pair region was found to be anfH (alternative nitrogen fixation, nifH-like gene), anfD (nifD-like gene), anfG (potentially encoding a protein similar to the product of vnfG from Azotobacter chroococcum), anfK (nifK-like gene), followed by two additional open reading frames. The 5'-flanking region of anfH contains a nif promoter similar to that found in the A. vinelandii nifHDK gene cluster. The presumed products of anfH, anfD, and anfK are similar in predicted Mr and pI to the previously described subunits of nitrogenase 3. Deletion plus insertion mutations introduced into the anfHDGK region of wild-type strain A. vinelandii CA resulted in mutant strains that were unable to grow in Mo-deficient, N-free medium but grew in the presence of 1 microM Na2MoO4 or V2O5. Introduction of the same mutations into the nifHDK deletion strain CA11 resulted in strains that grew under diazotrophic conditions only in the presence of vanadium. The lack of nitrogenase 3 subunits in these mutant strains was demonstrated through two-dimensional gel analysis of protein extracts from cells derepressed for nitrogenase under Mo and V deficiency. These results indicate that anfH, anfD, and anfK encode structural proteins for nitrogenase 3.

  19. Examination of a Palatogenic Gene Program in Zebrafish

    PubMed Central

    Swartz, Mary E.; Sheehan-Rooney, Kelly; Dixon, Michael J.; Eberhart, Johann K.

    2011-01-01

    Human palatal clefting is debilitating and difficult to rectify surgically. Animal models enhance our understanding of palatogenesis and are essential in strategies designed to ameliorate palatal malformations in humans. Recent studies have shown that the zebrafish palate, or anterior neurocranium, is under similar genetic control to the amniote palatal skeleton. We extensively analyzed palatogenesis in zebrafish to determine the similarity of gene expression and function across vertebrates. By 36 hpf palatogenic cranial neural crest cells reside in homologous regions of the developing face compared to amniote species. Transcription factors and signaling molecules regulating mouse palatogenesis are expressed in similar domains during palatogenesis in zebrafish. Functional investigation of a subset of these genes, fgf10a, tgfb2, pax9 and smad5 revealed their necessity in zebrafish palatogenesis. Collectively, these results suggest that the gene regulatory networks regulating palatogenesis may be conserved across vertebrate species, demonstrating the utility of zebrafish as a model for palatogenesis. PMID:22016187

  20. An alternating treatment comparison of oral and total communications training programs with echolalic autistic children.

    PubMed

    Barrera, R D; Sulzer-Azaroff, B

    1983-01-01

    An alternating treatment comparison was conducted of the relative effectiveness of oral and total communication training models for teaching expressive labeling skills to three echolalic autistic children. The results of this comparison demonstrated that total communication proved to be the most successful approach with each of the subjects. In addition, the replication of these findings both within and across subjects suggest that total communication may be, in general, the most effective of these two training models for teaching basic vocal language skills to echolalic children. A number of hypotheses are presented that may provide a basis for the demonstrated effect.

  1. Advancing Translational Research Through the NHLBI Gene Therapy Resource Program (GTRP)

    PubMed Central

    Benson, Janet; Cornetta, Kenneth; Diggins, Margaret; Johnston, Julie C.; Sepelak, Susan; Wang, Gensheng; Wilson, James M.; Wright, J. Fraser; Skarlatos, Sonia I.

    2013-01-01

    Abstract Translational research is a lengthy, complex, and necessary endeavor in order to bring basic science discoveries to clinical fruition. The NIH offers several programs to support translational research including an important resource established specifically for gene therapy researchers—the National Heart, Lung, and Blood Institute (NHLBI) Gene Therapy Resource Program (GTRP). This paper reviews the core components of the GTRP and describes how the GTRP provides researchers with resources that are critical to advancing investigational gene therapy products into clinical testing. PMID:23692378

  2. Alternative Ultrasound Gel for a Sustainable Ultrasound Program: Application of Human Centered Design

    PubMed Central

    Bissinger, Alexa; Muller, Mundenga Mutendi; Gebreyesus, Alegnta; Geremew, Haimanot; Wendell, Sarah; Azaza, Aklilu; Salumu, Maurice; Benfield, Nerys

    2015-01-01

    This paper describes design of a low cost, ultrasound gel from local products applying aspects of Human Centered Design methodology. A multidisciplinary team worked with clinicians who use ultrasound where commercial gel is cost prohibitive and scarce. The team followed the format outlined in the Ideo Took Kit. Research began by defining the challenge "how to create locally available alternative ultrasound gel for a low-resourced environment? The "End-Users," were identified as clinicians who use ultrasound in Democratic Republic of the Congo and Ethiopia. An expert group was identified and queried for possible alternatives to commercial gel. Responses included shampoo, oils, water and cornstarch. Cornstarch, while a reasonable solution, was either not available or too expensive. We then sought deeper knowledge of locally sources materials from local experts, market vendors, to develop a similar product. Suggested solutions gleaned from these interviews were collected and used to create ultrasound gel accounting for cost, image quality, manufacturing capability. Initial prototypes used cassava root flour from Great Lakes Region (DRC, Rwanda, Uganda, Tanzania) and West Africa, and bula from Ethiopia. Prototypes were tested in the field and resulting images evaluated by our user group. A final prototype was then selected. Cassava and bula at a 32 part water, 8 part flour and 4 part salt, heated, mixed then cooled was the product design of choice. PMID:26252003

  3. Alternative Ultrasound Gel for a Sustainable Ultrasound Program: Application of Human Centered Design.

    PubMed

    Salmon, Margaret; Salmon, Christian; Bissinger, Alexa; Muller, Mundenga Mutendi; Gebreyesus, Alegnta; Geremew, Haimanot; Wendel, Sarah K; Wendell, Sarah; Azaza, Aklilu; Salumu, Maurice; Benfield, Nerys

    2015-01-01

    This paper describes design of a low cost, ultrasound gel from local products applying aspects of Human Centered Design methodology. A multidisciplinary team worked with clinicians who use ultrasound where commercial gel is cost prohibitive and scarce. The team followed the format outlined in the Ideo Took Kit. Research began by defining the challenge "how to create locally available alternative ultrasound gel for a low-resourced environment? The "End-Users," were identified as clinicians who use ultrasound in Democratic Republic of the Congo and Ethiopia. An expert group was identified and queried for possible alternatives to commercial gel. Responses included shampoo, oils, water and cornstarch. Cornstarch, while a reasonable solution, was either not available or too expensive. We then sought deeper knowledge of locally sources materials from local experts, market vendors, to develop a similar product. Suggested solutions gleaned from these interviews were collected and used to create ultrasound gel accounting for cost, image quality, manufacturing capability. Initial prototypes used cassava root flour from Great Lakes Region (DRC, Rwanda, Uganda, Tanzania) and West Africa, and bula from Ethiopia. Prototypes were tested in the field and resulting images evaluated by our user group. A final prototype was then selected. Cassava and bula at a 32 part water, 8 part flour and 4 part salt, heated, mixed then cooled was the product design of choice.

  4. Alternative Ultrasound Gel for a Sustainable Ultrasound Program: Application of Human Centered Design.

    PubMed

    Salmon, Margaret; Salmon, Christian; Bissinger, Alexa; Muller, Mundenga Mutendi; Gebreyesus, Alegnta; Geremew, Haimanot; Wendel, Sarah K; Wendell, Sarah; Azaza, Aklilu; Salumu, Maurice; Benfield, Nerys

    2015-01-01

    This paper describes design of a low cost, ultrasound gel from local products applying aspects of Human Centered Design methodology. A multidisciplinary team worked with clinicians who use ultrasound where commercial gel is cost prohibitive and scarce. The team followed the format outlined in the Ideo Took Kit. Research began by defining the challenge "how to create locally available alternative ultrasound gel for a low-resourced environment? The "End-Users," were identified as clinicians who use ultrasound in Democratic Republic of the Congo and Ethiopia. An expert group was identified and queried for possible alternatives to commercial gel. Responses included shampoo, oils, water and cornstarch. Cornstarch, while a reasonable solution, was either not available or too expensive. We then sought deeper knowledge of locally sources materials from local experts, market vendors, to develop a similar product. Suggested solutions gleaned from these interviews were collected and used to create ultrasound gel accounting for cost, image quality, manufacturing capability. Initial prototypes used cassava root flour from Great Lakes Region (DRC, Rwanda, Uganda, Tanzania) and West Africa, and bula from Ethiopia. Prototypes were tested in the field and resulting images evaluated by our user group. A final prototype was then selected. Cassava and bula at a 32 part water, 8 part flour and 4 part salt, heated, mixed then cooled was the product design of choice. PMID:26252003

  5. Offer of rapid testing and alternative biological samples as practical tools to implement HIV screening programs.

    PubMed

    Parisi, Maria Rita; Soldini, Laura; Di Perri, Giovanni; Tiberi, Simon; Lazzarin, Adriano; Lillo, Flavia B

    2009-10-01

    Implementation of HIV testing has the objective to increase screening, identify and counsel persons with infection, link them to clinical services and reduce transmission. Rapid tests and/or alternative biological samples (like oral fluid) give the option for a better general consent in approaching screening, immediate referral of HIV positives to medical treatment and partner notification. We tested the performance characteristics of an oral fluid-based rapid HIV test (Rapidtest HIV lateral flow-Healthchem diag. LLC) in comparison with routinely utilized methods in a selected population of known positive (N = 121) or negative (N = 754) subjects. The sensitivity of the rapid test was 99.1% (one false negative sample) and the specificity 98.8%. Five negatives showed a faint reactivity, 3 of these were reactive also in the reference test, one with a p24 only reaction in Western blot. If these 3 samples were excluded from the analysis the specificity increases to 99.2%. Results from our study confirm that, although a continuous improvement of the test performance is still needed to minimize false negative and positive results, rapid test and alternative biological samples may contribute to HIV prevention strategies by reaching a larger population particularly when and where regular screening procedures are difficult to obtain. PMID:20128446

  6. Analyses of Alternatively Processed Genes in Ciliates Provide Insights into the Origins of Scrambled Genomes and May Provide a Mechanism for Speciation

    PubMed Central

    Gao, Feng; Roy, Scott W.

    2015-01-01

    ABSTRACT  Chromosome rearrangements occur in a variety of eukaryotic life cycles, including during the development of the somatic macronuclear genome in ciliates. Previous work on the phyllopharyngean ciliate Chilodonella uncinata revealed that macronuclear β-tubulin and protein kinase gene families share alternatively processed germ line segments nested within divergent regions. To study genome evolution in this ciliate further, we characterized two additional alternatively processed gene families from two cryptic species of the ciliate morphospecies C. uncinata: those encoding histidine acid phosphatase protein (Hap) and leishmanolysin family protein (Lei). Analyses of the macronuclear Hap and Lei sequences reveal that each gene family consists of three members in the macronucleus that are marked by identical regions nested among highly divergent regions. Investigation of the micronuclear Hap sequences revealed a complex pattern in which the three macronuclear sequences are derived either from a single micronuclear region or from a combination of this shared region recombined with additional duplicate micronuclear copies of Hap. We propose a model whereby gene scrambling evolves by gene duplication followed by partial and reciprocal degradation of the duplicate sequences. In this model, alternative processing represents an intermediate step in the evolution of scrambled genes. Finally, we speculate on the possible role of genome architecture in speciation in ciliates by describing what might happen if changes in alternatively processed loci occur in subdivided populations. PMID:25650397

  7. Comparison of Teaching Attitudes, Teacher Efficacy, and Teacher Performance of First Year Teachers Prepared by Alternative and Traditional Teacher Education Programs.

    ERIC Educational Resources Information Center

    Guyton, Edith; And Others

    1991-01-01

    The findings from this study of Georgia teachers generally support the contention that condensed pedagogical preparation and a supervised internship are a reasonable alternative to traditional teacher preparation programs for persons with degrees in the subject they will teach. (IAH)

  8. Fighting High School Senior Slump: The Spread of an Alternative Senior Program.

    ERIC Educational Resources Information Center

    Wade, Taron

    1999-01-01

    At several New York State high schools, seniors hold internships in architectural firms, Planned Parenthood, dentists' offices, and television and radio stations. Some make documentaries or pursue independent study in various subjects. These opportunities arise through a program (WISE) allowing second-semester seniors to design and complete their…

  9. An Alternative Approach for MBA Mentor Programs: Empower the Protégé

    ERIC Educational Resources Information Center

    Artis, Andrew B.

    2013-01-01

    A new approach is proposed to maximize the benefits of mentor relationships between master of business administration (MBA) students and executives by empowering students to select and recruit their own mentors, and then be responsible for managing those relationships. This mentor program is designed to be short but intensive. First-year MBA…

  10. Analysis of Student Misbehavior Patterns: Corrective Guidelines for Administrators and Teachers in Alternative Education Programs.

    ERIC Educational Resources Information Center

    Dix, Jerry Edward; Karr-Kidwell, PJ

    This paper presents an analysis of adolescent violent behavior in schools. The paper offers an overview that includes student violence and discipline issues, school law, special services for at-risk students, and programs to enhance the opportunities for successful interventions. The paper is also a vehicle for a new discipline-management…

  11. Alternate Perspectives for Program Development and Research in Teacher Education. R&D Report No. 9019.

    ERIC Educational Resources Information Center

    Griffin, Gary, Ed.; Hukill, Hobart, Ed.

    This document presents four symposium papers on the theme of what might happen in teacher education program research and development if educational psychology were replaced by other bodies of theory, proposition, and research findings. Maxine Green's views, presented in "What the Known Demands," center around the necessity of considering teaching…

  12. Value-Added Models for Teacher Preparation Programs: Validity and Reliability Threats, and a Manageable Alternative

    ERIC Educational Resources Information Center

    Brady, Michael P.; Heiser, Lawrence A.; McCormick, Jazarae K.; Forgan, James

    2016-01-01

    High-stakes standardized student assessments are increasingly used in value-added evaluation models to connect teacher performance to P-12 student learning. These assessments are also being used to evaluate teacher preparation programs, despite validity and reliability threats. A more rational model linking student performance to candidates who…

  13. A Peer-Led AIDS Prevention Program for Students in an Alternative School.

    ERIC Educational Resources Information Center

    O'Hara, Peggy; Messick, Barbara J.; Parris, Don; Fichtner, Ronald R.

    1998-01-01

    Describes a peer-led sexually transmitted disease (STD)/human immunodeficiency virus (HIV) intervention for students in a dropout prevention program. Trained peer counselors/educators led schoolwide activities and classroom sessions. Teachers and students rated peer counselors' effectiveness. Pre- and postintervention surveys indicated an increase…

  14. Criteria for Evaluating Alternative Network and Link Layer Protocols for the NASA Constellation Program Communication Architecture

    NASA Technical Reports Server (NTRS)

    Benbenek, Daniel; Soloff, Jason; Lieb, Erica

    2010-01-01

    Selecting a communications and network architecture for future manned space flight requires an evaluation of the varying goals and objectives of the program, development of communications and network architecture evaluation criteria, and assessment of critical architecture trades. This paper uses Cx Program proposed exploration activities as a guideline; lunar sortie, outpost, Mars, and flexible path options are described. A set of proposed communications network architecture criteria are proposed and described. They include: interoperability, security, reliability, and ease of automating topology changes. Finally a key set of architecture options are traded including (1) multiplexing data at a common network layer vs. at the data link layer, (2) implementing multiple network layers vs. a single network layer, and (3) the use of a particular network layer protocol, primarily IPv6 vs. Delay Tolerant Networking (DTN). In summary, the protocol options are evaluated against the proposed exploration activities and their relative performance with respect to the criteria are assessed. An architectural approach which includes (a) the capability of multiplexing at both the network layer and the data link layer and (b) a single network layer for operations at each program phase, as these solutions are best suited to respond to the widest array of program needs and meet each of the evaluation criteria.

  15. 75 FR 25913 - Alternative Transportation in Parks and Public Lands Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-10

    ... Lands (ATPPL)) program, authorized by Section 3021 of the Safe, Accountable, Flexible, Efficient... systems in parks and public lands. Federal land management agencies and State, tribal and local governments acting with the consent of a Federal land management agency are eligible recipients. FOR...

  16. 78 FR 22026 - Alternative Transportation in Parks and Public Lands Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-12

    ... authorized by Section 3021 of the Safe, Accountable, Flexible, Efficient Transportation Equity Act--A Legacy... lands. Federal land management agencies and State, tribal and local governments acting with the consent of a federal land management agency are eligible recipients. This program was not re-authorized...

  17. An Exploratory Inquiry of the Outcomes of Adults Who Participated in a Virginia Alternative Education Program: Making Sense of Their Experience

    ERIC Educational Resources Information Center

    Hackney, Melody D.

    2012-01-01

    The purpose of this retrospective study was to develop an understanding of how one group of adults who graduated from a Virginia regional alternative program made sense of their experience in an alternative education setting. Specifically, this study sought to determine if adult participants, several years later, perceived participation in the…

  18. Income and Employment Generation in Rural Areas in Relation to Alternative Farm Programs (with Special Emphasis on the North Central Region).

    ERIC Educational Resources Information Center

    Heady, Earl O.; Sonka, Steven T.

    Four alternative government farm policies were analyzed to determine their effect upon farm income and employment generation in rural areas and agriculturally related industries. A linear programming model of interregional competition was used to determine the impact of alternative farm policies on the quantity of major commodities produced, the…

  19. Simulation of alternatives for the Dutch Johne's disease certification-and-monitoring program.

    PubMed

    Weber, Maarten F; Groenendaal, Huybert; van Roermund, Herman J W; Nielen, Mirjam

    2004-01-30

    To identify optimal method(s) for certification and subsequent monitoring of Mycobacterium avium subsp. paratuberculosis (Map)-unsuspected herds, certification-and-monitoring schemes were studied using a stochastic simulation model ("JohneSSim"). JohneSSim simulated the within-herd transmission and economic aspects of Map in closed Dutch dairy herds. The model was validated with field observations on Map-unsuspected herds. The current Dutch certification-and-monitoring schemes were compared with 11 alternative schemes in which individual and pooled fecal culture, ELISA, Johnin-intradermal test and gamma-IFN ELISA were used, varying the test frequency, tested age group and number of tested animals. On reaching the 'Map-free' status with the standard certification scheme, 11% of the simulated herds were not truly Map-free. Therefore, the designation 'Map-free' should be changed into, for instance, 'low-risk Map'. In the most-attractive alternative certification scheme, the 'Map-free' status was reached after four herd examinations (at 2-year intervals) consisting of serial testing of all cattle > or = 2 years of age with a pooled fecal culture and individual fecal culture of positive pools. This scheme resulted in lower total and annual discounted costs and a lower animal-level prevalence at reaching the 'Map-free' status compared to the standard scheme, assuming that there was no new introduction of the infection. Schemes to monitor the 'Map-free' status were compared, assuming that this status was reached with the standard certification scheme. In comparison to the standard monitoring scheme, none of the alternative monitoring schemes resulted in both a lower animal-level prevalence of undetected pre-existing Map infections in closed herds, and lower median annual discounted costs. Results of the model were very sensitive to the assumed sensitivity of the fecal culture test and to management measures that prevent within-herd transmission of Map. If these preventive

  20. Riboswitch Control of Gene Expression in Plants by Splicing and Alternative 3′ End Processing of mRNAs[W][OA

    PubMed Central

    Wachter, Andreas; Tunc-Ozdemir, Meral; Grove, Beth C.; Green, Pamela J.; Shintani, David K.; Breaker, Ronald R.

    2007-01-01

    The most widespread riboswitch class, found in organisms from all three domains of life, is responsive to the vitamin B1 derivative thiamin pyrophosphate (TPP). We have established that a TPP-sensing riboswitch is present in the 3′ untranslated region (UTR) of the thiamin biosynthetic gene THIC of all plant species examined. The THIC TPP riboswitch controls the formation of transcripts with alternative 3′ UTR lengths, which affect mRNA accumulation and protein production. We demonstrate that riboswitch-mediated regulation of alternative 3′ end processing is critical for TPP-dependent feedback control of THIC expression. Our data reveal a mechanism whereby metabolite-dependent alteration of RNA folding controls splicing and alternative 3′ end processing of mRNAs. These findings highlight the importance of metabolite sensing by riboswitches in plants and further reveal the significance of alternative 3′ end processing as a mechanism of gene control in eukaryotes. PMID:17993623

  1. Alternative splicing of DENND1A, a PCOS candidate gene, generates variant 2.

    PubMed

    Tee, Meng Kian; Speek, Mart; Legeza, Balázs; Modi, Bhavi; Teves, Maria Eugenia; McAllister, Janette M; Strauss, Jerome F; Miller, Walter L

    2016-10-15

    Polycystic ovary syndrome (PCOS) is a common endocrinopathy characterized by hyperandrogenism and metabolic disorders. The excess androgens may be of both ovarian and adrenal origin. PCOS has a strong genetic component, and genome-wide association studies have identified several candidate genes, notably DENND1A, which encodes connecdenn 1, involved in trafficking of endosomes. DENND1A encodes two principal variants, V1 (1009 amino acids) and V2 (559 amino acids). The androgen-producing ovarian theca cells of PCOS women over-express V2. Knockdown of V2 in these cells reduces androgen production, and overexpression of V2 in normal theca cells confers upon them a PCOS phenotype of increased androgen synthesis. We report that human adrenal NCI-H295A cells express V1 and V2 mRNA and that the V2 isoform is produced by exonization of sequences in intron 20, which generates a unique exon 20A, encoding the C-terminus of V2. As in human theca cells from normal women, forced expression of V2 in NCI-H295A cells resulted in increased abundance of CYP17A1 and CYP11A1 mRNAs. We also found genetic variation in the intronic region 330 bp upstream from exon 20A, which could have the potential to drive the selective expression of V2. There was no clear association with these variants with PCOS when we analyzed genomc DNA from normal women and women with PCOS. Using minigene expression vectors in NCI-H295A cells, this variable region did not consistently favor splicing of the V2 transcript. These findings suggest increased V2 expression in PCOS theca cells is not the result of genomic sequence variation in intron 20. PMID:27297658

  2. The expression of the human steroid sulfatase-encoding gene is driven by alternative first exons.

    PubMed

    Dalla Valle, Luisa; Toffolo, Vania; Nardi, Alessia; Fiore, Cristina; Armanini, Decio; Belvedere, Paola; Colombo, Lorenzo

    2007-10-01

    We have analyzed steroid sulfatase (STS) gene transcription in 10 human tissues: ovary, adrenal cortex, uterus, thyroid, liver, pancreas, colon, mammary gland, dermal papilla of the hair follicle, and peripheral mononuclear leukocytes. Overall, six different promoters were found to drive STS expression, giving rise to transcripts with unique first exons that were labeled 0a, 0b, 0c, 1a, 1c, and 1d, of which the last two and 0c are newly reported. All of them, except exon 1d, vary in length owing to the occurrence of multiple transcriptional start sites. While placental exon 1a is partially coding, the other five first exons are all untranslated. Three of these (0a, 0b, and 0c) are spliced to the common partially coding exon 1b, whereas the other two (1c and 1d) are spliced to the coding exon 2, which occurs in all transcripts. Whatever the ATG actually used, the differences are restricted to the signal peptide which is post-transcriptionally cleaved. Transcripts with exons 0a and 0b have the broadest tissue distribution, occurring, in 6 out of the 12 tissues so far investigated, while the other first exons are restricted to one or two tissues. The proximal promoter of each first exon was devoid of TATA box or initiator element and lacked consensus elements for transcription factors related to steroidogenesis, suggesting that regulatory sequences are probably placed at greater distance. In conclusion, the regulation of STS transcription appears to be more complex than previously thought, suggesting that this enzyme plays a substantial role in intercellular integration. PMID:17601726

  3. Alternative splicing of DENND1A, a PCOS candidate gene, generates variant 2.

    PubMed

    Tee, Meng Kian; Speek, Mart; Legeza, Balázs; Modi, Bhavi; Teves, Maria Eugenia; McAllister, Janette M; Strauss, Jerome F; Miller, Walter L

    2016-10-15

    Polycystic ovary syndrome (PCOS) is a common endocrinopathy characterized by hyperandrogenism and metabolic disorders. The excess androgens may be of both ovarian and adrenal origin. PCOS has a strong genetic component, and genome-wide association studies have identified several candidate genes, notably DENND1A, which encodes connecdenn 1, involved in trafficking of endosomes. DENND1A encodes two principal variants, V1 (1009 amino acids) and V2 (559 amino acids). The androgen-producing ovarian theca cells of PCOS women over-express V2. Knockdown of V2 in these cells reduces androgen production, and overexpression of V2 in normal theca cells confers upon them a PCOS phenotype of increased androgen synthesis. We report that human adrenal NCI-H295A cells express V1 and V2 mRNA and that the V2 isoform is produced by exonization of sequences in intron 20, which generates a unique exon 20A, encoding the C-terminus of V2. As in human theca cells from normal women, forced expression of V2 in NCI-H295A cells resulted in increased abundance of CYP17A1 and CYP11A1 mRNAs. We also found genetic variation in the intronic region 330 bp upstream from exon 20A, which could have the potential to drive the selective expression of V2. There was no clear association with these variants with PCOS when we analyzed genomc DNA from normal women and women with PCOS. Using minigene expression vectors in NCI-H295A cells, this variable region did not consistently favor splicing of the V2 transcript. These findings suggest increased V2 expression in PCOS theca cells is not the result of genomic sequence variation in intron 20.

  4. Alternative Oxidase Gene Family in Hypericum perforatum L.: Characterization and Expression at the Post-germinative Phase.

    PubMed

    Velada, Isabel; Cardoso, Hélia G; Ragonezi, Carla; Nogales, Amaia; Ferreira, Alexandre; Valadas, Vera; Arnholdt-Schmitt, Birgit

    2016-01-01

    Alternative oxidase (AOX) protein is located in the inner mitochondrial membrane and is encoded in the nuclear genome being involved in plant response upon a diversity of environmental stresses and also in normal plant growth and development. Here we report the characterization of the AOX gene family of Hypericum perforatum L. Two AOX genes were identified, both with a structure of four exons (HpAOX1, acc. KU674355 and HpAOX2, acc. KU674356). High variability was found at the N-terminal region of the protein coincident with the high variability identified at the mitochondrial transit peptide. In silico analysis of regulatory elements located at intronic regions identified putative sequences coding for miRNA precursors and trace elements of a transposon. Simple sequence repeats were also identified. Additionally, the mRNA levels for the HpAOX1 and HpAOX2, along with the ones for the HpGAPA (glyceraldehyde-3-phosphate dehydrogenase A subunit) and the HpCAT1 (catalase 1), were evaluated during the post-germinative development. Gene expression analysis was performed by RT-qPCR with accurate data normalization, pointing out HpHYP1 (chamba phenolic oxidative coupling protein 1) and HpH2A (histone 2A) as the most suitable reference genes (RGs) according to GeNorm algorithm. The HpAOX2 transcript demonstrated larger stability during the process with a slight down-regulation in its expression. Contrarily, HpAOX1 and HpGAPA (the corresponding protein is homolog to the chloroplast isoform involved in the photosynthetic carbon assimilation in other plant species) transcripts showed a marked increase, with a similar expression pattern between them, during the post-germinative development. On the other hand, the HpCAT1 (the corresponding protein is homolog to the major H2O2-scavenging enzyme in other plant species) transcripts showed an opposite behavior with a down-regulation during the process. In summary, our findings, although preliminary, highlight the importance to

  5. Evolutionary diversification and characterization of the eubacterial gene family encoding DXR type II, an alternative isoprenoid biosynthetic enzyme

    PubMed Central

    2013-01-01

    Background Isoprenoids constitute a vast family of natural compounds performing diverse and essential functions in all domains of life. In most eubacteria, isoprenoids are synthesized through the methylerythritol 4-phosphate (MEP) pathway. The production of MEP is usually catalyzed by deoxyxylulose 5-phosphate reductoisomerase (DXR-I) but a few organisms use an alternative DXR-like enzyme (DXR-II). Results Searches through 1498 bacterial complete proteomes detected 130 sequences with similarity to DXR-II. Phylogenetic analysis identified three well-resolved clades: the DXR-II family (clustering 53 sequences including eleven experimentally verified as functional enzymes able to produce MEP), and two previously uncharacterized NAD(P)-dependent oxidoreductase families (designated DLO1 and DLO2 for DXR-II-like oxidoreductases 1 and 2). Our analyses identified amino acid changes critical for the acquisition of DXR-II biochemical function through type-I functional divergence, two of them mapping onto key residues for DXR-II activity. DXR-II showed a markedly discontinuous distribution, which was verified at several levels: taxonomic (being predominantly found in Alphaproteobacteria and Firmicutes), metabolic (being mostly found in bacteria with complete functional MEP pathways with or without DXR-I), and phenotypic (as no biological/phenotypic property was found to be preferentially distributed among DXR-II-containing strains, apart from pathogenicity in animals). By performing a thorough comparative sequence analysis of GC content, 3:1 dinucleotide frequencies, codon usage and codon adaptation indexes (CAI) between DXR-II sequences and their corresponding genomes, we examined the role of horizontal gene transfer (HGT), as opposed to an scenario of massive gene loss, in the evolutionary origin and diversification of the DXR-II subfamily in bacteria. Conclusions Our analyses support a single origin of the DXR-II family through functional divergence, in which constitutes

  6. Alternative Oxidase Gene Family in Hypericum perforatum L.: Characterization and Expression at the Post-germinative Phase

    PubMed Central

    Velada, Isabel; Cardoso, Hélia G.; Ragonezi, Carla; Nogales, Amaia; Ferreira, Alexandre; Valadas, Vera; Arnholdt-Schmitt, Birgit

    2016-01-01

    Alternative oxidase (AOX) protein is located in the inner mitochondrial membrane and is encoded in the nuclear genome being involved in plant response upon a diversity of environmental stresses and also in normal plant growth and development. Here we report the characterization of the AOX gene family of Hypericum perforatum L. Two AOX genes were identified, both with a structure of four exons (HpAOX1, acc. KU674355 and HpAOX2, acc. KU674356). High variability was found at the N-terminal region of the protein coincident with the high variability identified at the mitochondrial transit peptide. In silico analysis of regulatory elements located at intronic regions identified putative sequences coding for miRNA precursors and trace elements of a transposon. Simple sequence repeats were also identified. Additionally, the mRNA levels for the HpAOX1 and HpAOX2, along with the ones for the HpGAPA (glyceraldehyde-3-phosphate dehydrogenase A subunit) and the HpCAT1 (catalase 1), were evaluated during the post-germinative development. Gene expression analysis was performed by RT-qPCR with accurate data normalization, pointing out HpHYP1 (chamba phenolic oxidative coupling protein 1) and HpH2A (histone 2A) as the most suitable reference genes (RGs) according to GeNorm algorithm. The HpAOX2 transcript demonstrated larger stability during the process with a slight down-regulation in its expression. Contrarily, HpAOX1 and HpGAPA (the corresponding protein is homolog to the chloroplast isoform involved in the photosynthetic carbon assimilation in other plant species) transcripts showed a marked increase, with a similar expression pattern between them, during the post-germinative development. On the other hand, the HpCAT1 (the corresponding protein is homolog to the major H2O2-scavenging enzyme in other plant species) transcripts showed an opposite behavior with a down-regulation during the process. In summary, our findings, although preliminary, highlight the importance to

  7. Tissue-specific expression of the bovine aromatase-encoding gene uses multiple transcriptional start sites and alternative first exons.

    PubMed

    Fürbass, R; Kalbe, C; Vanselow, J

    1997-07-01

    Here we report on the genomic structure of the bovine aromatase cytochrome P450-encoding gene (Cyp19) and its tissue-specific transcript variants. The gene comprises at least 14 exons (1.1, 1.2a, 1.2b, 1.3,1.4, and 2-10) spanning more than 56 kilobases of genomic DNA. The coding area is confined to exons 2-10. Transcriptional start sites of Cyp19 were examined in granulosa cells, placenta, testis, adrenal gland, and brain, employing 5'-RACE (rapid amplification of complementary DNA ends) and primer extension. The analysis of 5'-RACE clones revealed six Cyp19 transcript variants that were different within their 5'-untranslated regions (5'-UTR). Yet, the coding region was identical in all clones. Although two of these 5'-UTR (the first 152 nucleotides of exon 2 and exon 1.4) are conserved among different species, four others (exons 1.1, 1.2a, 1.2b, and 1.3) did not show sequence homology to any other species. Transcription from exons 1.1 and 2 starts at several adjacent sites. In granulosa cells and placenta, but not in brain, a fraction of transcripts starting with exon 1.2a contains an additional untranslated exon, 1.2b, due to alternative splicing. Transcript variants comprising exon 1.1, 1.2a, 1.2b, or 1.3 were mainly found in the placenta, those with the 5'-UTR of exon 2 were predominant in granulosa cells, and transcripts with exon 1.4 prevailed in the brain. Estimates of Cyp19 transcript concentrations in six different tissues revealed high levels in granulosa cells and placenta, intermediate levels in testis and brain, and low levels in adrenal gland and liver. Our experiments demonstrate that six transcript variants of the bovine Cyp19 gene, including 9-11 exons, are expressed with tissue-specific preferences. These transcripts are presumably generated using five different promoter regions and tissue-specific alternative splicing. PMID:9202222

  8. Tanks Focus Area Alternative Salt Processing Research and Development Program Plan

    SciTech Connect

    Harmon, Harry D.

    2000-11-30

    In March 2000, DOE-Headquarters (HQ) requested the Tanks Focus Area (TFA) to assume management responsibility for the Salt Processing Project technology development program at Savannah River Site. The TFA was requested to conduct several activities, including review and revision of the technology development roadmaps, development of down-selection criteria, and preparation of a comprehensive Research and Development (R&D) Program Plan for three candidate cesium removal technologies, as well as the Alpha and strontium removal processes that must also be carried out. The three cesium removal candidate technologies are Crystalline Silicotitanate (CST) Non-Elutable Ion Exchange, Caustic Side Solvent Extraction (CSSX), and Small Tank Tetraphenylborate Precipitation (STTP). This plan describes the technology development needs for each process that must be satisfied in order to reach a down-selection decision, as well as continuing technology development required to support conceptual design activities.

  9. Tanks Focus Area Alternative Salt Processing Research and Development Program Plan

    SciTech Connect

    Harmon, Harry D.

    2000-05-15

    In March 2000, DOE-Headquarters (HQ) requested the Tanks Focus Area (TFA)to assume management responsibility for the Salt Processing Project technology development program at Savannah River Site. The TFA was requested to conduct several activities, including review and revision of the technology development roadmaps, development of down-selection criteria, and preparation of a comprehensive Research and Development (R&D) Program Plan for three candidate cesium removal technologies, as well as the Alpha and strontium removal processes that must also be carried out. The three cesium removal candidate technologies are Crystalline Silicotitanate (CST) Non-Elutable Ion Exchange, Caustic Side Solvent Extraction (CSSX), and Small Tank Tetraphenylborate Precipitation (STTP). This plan describes the technology development needs for each process that must be satisfied in order to reach a down-selection decision, as well as continuing technology development required to support conceptual design activities.

  10. From Punishment to Treatment: The “Clinical Alternative to Punitive Segregation” (CAPS) Program in New York City Jails

    PubMed Central

    Glowa-Kollisch, Sarah; Kaba, Fatos; Waters, Anthony; Leung, Y. Jude; Ford, Elizabeth; Venters, Homer

    2016-01-01

    The proliferation of jails and prisons as places of institutionalization for persons with serious mental illness (SMI) has resulted in many of these patients receiving jail-based punishments, including solitary confinement. Starting in 2013, the New York City (NYC) jail system developed a new treatment unit for persons with SMI who were judged to have violated jail rules (and previously would have been punished with solitary confinement) called the Clinical Alternative to Punitive Segregation (CAPS) unit. CAPS is designed to offer a full range of therapeutic activities and interventions for these patients, including individual and group therapy, art therapy, medication counseling and community meetings. Each CAPS unit requires approximately $1.5 million more investment per year, largely in additional staff as compared to existing mental health units, and can house approximately 30 patients. Patients with less serious mental illness who received infractions were housed on units that combined solitary confinement with some clinical programming, called Restrictive Housing Units (RHU). Between 1 December 2013 and 31 March 2015, a total of 195 and 1433 patients passed through the CAPS and RHU units, respectively. A small cohort of patients experienced both CAPS and RHU (n = 90). For these patients, their rates of self-harm and injury were significantly lower while on the CAPS unit than when on the RHU units. Improvements in clinical outcomes are possible for incarcerated patients with mental illness with investment in new alternatives to solitary confinement. We have started to adapt the CAPS approach to existing mental health units as a means to promote better clinical outcomes and also help prevent jail-based infractions. The cost of these programs and the dramatic differences in length of stay for patients who earn these jail-based infractions highlight the need for alternatives to incarceration, some of which have recently been announced in NYC. PMID:26848667

  11. From Punishment to Treatment: The "Clinical Alternative to Punitive Segregation" (CAPS) Program in New York City Jails.

    PubMed

    Glowa-Kollisch, Sarah; Kaba, Fatos; Waters, Anthony; Leung, Y Jude; Ford, Elizabeth; Venters, Homer

    2016-02-02

    The proliferation of jails and prisons as places of institutionalization for persons with serious mental illness (SMI) has resulted in many of these patients receiving jail-based punishments, including solitary confinement. Starting in 2013, the New York City (NYC) jail system developed a new treatment unit for persons with SMI who were judged to have violated jail rules (and previously would have been punished with solitary confinement) called the Clinical Alternative to Punitive Segregation (CAPS) unit. CAPS is designed to offer a full range of therapeutic activities and interventions for these patients, including individual and group therapy, art therapy, medication counseling and community meetings. Each CAPS unit requires approximately $1.5 million more investment per year, largely in additional staff as compared to existing mental health units, and can house approximately 30 patients. Patients with less serious mental illness who received infractions were housed on units that combined solitary confinement with some clinical programming, called Restrictive Housing Units (RHU). Between 1 December 2013 and 31 March 2015, a total of 195 and 1433 patients passed through the CAPS and RHU units, respectively. A small cohort of patients experienced both CAPS and RHU (n = 90). For these patients, their rates of self-harm and injury were significantly lower while on the CAPS unit than when on the RHU units. Improvements in clinical outcomes are possible for incarcerated patients with mental illness with investment in new alternatives to solitary confinement. We have started to adapt the CAPS approach to existing mental health units as a means to promote better clinical outcomes and also help prevent jail-based infractions. The cost of these programs and the dramatic differences in length of stay for patients who earn these jail-based infractions highlight the need for alternatives to incarceration, some of which have recently been announced in NYC.

  12. From Punishment to Treatment: The "Clinical Alternative to Punitive Segregation" (CAPS) Program in New York City Jails.

    PubMed

    Glowa-Kollisch, Sarah; Kaba, Fatos; Waters, Anthony; Leung, Y Jude; Ford, Elizabeth; Venters, Homer

    2016-02-01

    The proliferation of jails and prisons as places of institutionalization for persons with serious mental illness (SMI) has resulted in many of these patients receiving jail-based punishments, including solitary confinement. Starting in 2013, the New York City (NYC) jail system developed a new treatment unit for persons with SMI who were judged to have violated jail rules (and previously would have been punished with solitary confinement) called the Clinical Alternative to Punitive Segregation (CAPS) unit. CAPS is designed to offer a full range of therapeutic activities and interventions for these patients, including individual and group therapy, art therapy, medication counseling and community meetings. Each CAPS unit requires approximately $1.5 million more investment per year, largely in additional staff as compared to existing mental health units, and can house approximately 30 patients. Patients with less serious mental illness who received infractions were housed on units that combined solitary confinement with some clinical programming, called Restrictive Housing Units (RHU). Between 1 December 2013 and 31 March 2015, a total of 195 and 1433 patients passed through the CAPS and RHU units, respectively. A small cohort of patients experienced both CAPS and RHU (n = 90). For these patients, their rates of self-harm and injury were significantly lower while on the CAPS unit than when on the RHU units. Improvements in clinical outcomes are possible for incarcerated patients with mental illness with investment in new alternatives to solitary confinement. We have started to adapt the CAPS approach to existing mental health units as a means to promote better clinical outcomes and also help prevent jail-based infractions. The cost of these programs and the dramatic differences in length of stay for patients who earn these jail-based infractions highlight the need for alternatives to incarceration, some of which have recently been announced in NYC. PMID:26848667

  13. Array data extractor (ADE): a LabVIEW program to extract and merge gene array data

    PubMed Central

    2013-01-01

    Background Large data sets from gene expression array studies are publicly available offering information highly valuable for research across many disciplines ranging from fundamental to clinical research. Highly advanced bioinformatics tools have been made available to researchers, but a demand for user-friendly software allowing researchers to quickly extract expression information for multiple genes from multiple studies persists. Findings Here, we present a user-friendly LabVIEW program to automatically extract gene expression data for a list of genes from multiple normalized microarray datasets. Functionality was tested for 288 class A G protein-coupled receptors (GPCRs) and expression data from 12 studies comparing normal and diseased human hearts. Results confirmed known regulation of a beta 1 adrenergic receptor and further indicate novel research targets. Conclusions Although existing software allows for complex data analyses, the LabVIEW based program presented here, “Array Data Extractor (ADE)”, provides users with a tool to retrieve meaningful information from multiple normalized gene expression datasets in a fast and easy way. Further, the graphical programming language used in LabVIEW allows applying changes to the program without the need of advanced programming knowledge. PMID:24289243

  14. Intronic DNA elements regulate Nrf-2 chemical responsiveness of the human microsomal epoxide hydrolase gene (EPHX1) through a far upstream alternative promoter

    PubMed Central

    Su, Shengzhong; Yang, Xi; Omiecinski, Curtis J.

    2014-01-01

    In humans, microsomal epoxide hydrolase (mEH) contributes important biological functions that underlie both detoxification and bioactivation fates arising from exposures to foreign chemicals. Previously, we discovered that human mEH gene transcription is initiated from alternative promoters. The respective transcripts are programmed with tissue specificity and the upstream E1b promoter contributes predominantly to mEH expression. The results presented demonstrate that exposures to the Nrf2 activators, sulforaphane (SFN) and tert-butylhydroquinone (tBHQ), markedly activate E1b transcription in human lung and liver cells. Genomic analyses identified two major DNase I hypersensitive regions (HS-1 and HS-2) within the ~15 kb intervening sequence separating E1b from the downstream E1 promoter. In BEAS-2B cells, the Nrf2 effectors, SFN and tBHQ, selectively activated the more distal HS-2 through an antioxidant-response element (ARE). An activator protein 1/12-O-tetradecanoylphorbol-13-acetate interaction was further identified within the HS-2 enhancer that functioned to additionally contribute to ARE-mediated induction responsiveness of the E1b promoter. The results demonstrate that ARE modulation, integrated with additional transcriptional complexes, regulates the tissue-specific expression of mEH and that these processes likely coordinate both the protective and bioactivation functions contributed by mEH activities in human tissues. PMID:24704207

  15. More than one way to produce protein diversity: duplication and limited alternative splicing of an adhesion molecule gene in basal arthropods.

    PubMed

    Brites, Daniela; Brena, Carlo; Ebert, Dieter; Du Pasquier, Louis

    2013-10-01

    Exon duplication and alternative splicing evolved multiple times in metazoa and are of overall importance in shaping genomes and allowing organisms to produce many fold more proteins than there are genes in the genome. No other example is as striking as the one of the Down syndrome cell adhesion molecule (Dscam) of insects and crustaceans (pancrustaceans) involved in the nervous system differentiation and in the immune system. To elucidate the evolutionary history of this extraordinary gene, we investigated Dscam homologs in two basal arthropods, the myriapod Strigamia maritima and the chelicerate Ixodes scapularis. In both, Dscam diversified extensively by whole gene duplications resulting in multigene expansions. Within some of the S. maritima genes, exons coding for one of the immunoglobulin domains (Ig7) duplicated and are mutually exclusively alternatively spliced. Our results suggest that Dscam diversification was selected independently in chelicerates, myriapods, and pancrustaceans and that the usage of Dscam diversity by immune cells evolved for the first time in basal arthropods. We propose an evolutionary scenario for the appearance of the highly variable Dscam gene of pancrustaceans, adding to the understanding of how alternative splicing, exon, and gene duplication contribute to create molecular diversity associated with potentially new cellular functions.

  16. Mixed Waste Focus Area alternative oxidation technologies development and demonstration program

    SciTech Connect

    Borduin, L.C.; Fewell, T.; Gombert, D.; Priebe, S.

    1998-07-01

    The Mixed Waste Focus Area (MWFA) is currently supporting the development and demonstration of several alternative oxidation technology (AOT) processes for treatment of combustible mixed low-level wastes. The impetus for this support derives from regulatory and political hurdles frequently encountered by traditional thermal techniques, primarily incinerators. AOTs have been defined as technologies that destroy organic material without using open-flame reactions. Whether thermal or nonthermal, the processes have the potential advantages of relatively low-volume gaseous emissions, generation of few or no dioxin/furan compounds, and operation at low enough temperatures that metals (except mercury) and most radionuclides are not volatilized. Technology development and demonstration are needed to confirm and realize the potential of AOTs and to compare them on an equal basis with their fully demonstrated thermal counterparts. AOTs include both thermal and nonthermal processes that oxidize organic wastes but operate under significantly different physical and chemical conditions than incinerators. Nonthermal processes currently being studied include Delphi DETOX and acid digestion at the Savannah River Site, and direct chemical oxidation at Lawrence Livermore National Laboratory. All three technologies are at advanced stages of development or are entering the demonstration phase. Nonflame thermal processes include catalytic chemical oxidation, which is being developed and deployed at Lawrence Berkeley National Laboratory, and team reforming, a commercial process being supported by Department of Energy. Related technologies include two low-flow, secondary oxidation processes (Phoenix and Thermatrix units) that have been tested at MSE, Inc., in Butte, Montana. Although testing is complete on some AOT technologies, most require additional support to complete some or all of the identified development objectives. Brief descriptions, status, and planned paths forward for each

  17. Development of a Student Mentored Research Program between a Complementary and Alternative Medicine University and a Traditional, Research Intensive University

    PubMed Central

    Sullivan, Barbara M.; Furner, Sylvia E.; Cramer, Gregory D.

    2014-01-01

    The global need to develop clinician-scientists capable of using research in clinical practice, translating research knowledge into practice, and carrying out research that affects the quality, efficacy, and efficiency of health care is well-documented. The complementary and alternative medicine (CAM) professions embrace the call to develop physician-researchers to carry out translational and applied research for CAM modalities. CAM universities face unique challenges when implementing research training compared to traditional, research intensive (TRI) universities and medical centers where the majority of medical research is carried out. The authors present the development and outcomes of a mentored research program (MRP) between a CAM and a TRI institution, the National University of Health Sciences and the University of Illinois at Chicago School of Public Health, between 2006 and 2012. CAM pre-doctoral students engaged in a full-immersion semester at the TRI, including didactic courses and active research with a TRI faculty research mentor. Half of the participating doctor of chiropractic (DC) students continued on to PhD programs and half established integrative medicine, primary care clinical careers. Establishing rigorous criteria for mentors and mentees, communicating expectations, developing solid relationships between the mentor, mentee, and home school advisor, responding quickly to impediments, and providing adequate support from CAM and TRI investigators were key to the MRP success. To sustain research opportunities, coordinated degree programs for the DC and master of public health (DC/MPH) and master of clinical and translational research (DC/MS CTS) were established. PMID:24988423

  18. Valuation of selected environmental impacts associated with Bonneville Power Administration Resource Program alternatives

    SciTech Connect

    Englin, J E; Gygi, K F

    1992-03-01

    This report documents work undertaken by the Pacific Northwest Laboratory (PNL) and its contractors to assist the Bonneville Power Administration (Bonneville) in assessing the potential environmental consequences of new power resources. A major purpose of this effort is to describe and evaluate the techniques available for economic valuation of environmental costs. Another is to provide estimates of the environmental costs associated with specific power resources called for under Bonneville's Resource Programs. Bonneville's efforts to extend valuation techniques to as many impacts as can be reliably assessed represents a substantial advance in the application of state-of-the-art economic techniques to environmental assessments. This economic analysis evaluates effects on human health, wildlife, crops, and visibility impacts associated with air pollution. This report also discusses river recreation (primarily fishing) which may be affected by fluctuations in water levels. 70 refs.

  19. A Case Study of the Approach to Teaching and to Technology of Three New Teachers in an Alternative Teacher Certification Program

    ERIC Educational Resources Information Center

    O'Connor, Eileen A.

    2007-01-01

    The Master of Arts in Teaching program at Empire State College, a new alternative teacher certification program focused on bringing career-changing adults to high-needs schools, provides a unique opportunity to understand the challenges facing new teachers, in their content area and in their use of technology. This article describes aspects of…

  20. A rapid pathway toward a superb gene delivery system: programming structural and functional diversity into a supramolecular nanoparticle library.

    PubMed

    Wang, Hao; Liu, Kan; Chen, Kuan-Ju; Lu, Yujie; Wang, Shutao; Lin, Wei-Yu; Guo, Feng; Kamei, Ken-ichiro; Chen, Yi-Chun; Ohashi, Minori; Wang, Mingwei; Garcia, Mitch André; Zhao, Xing-Zhong; Shen, Clifton K-F; Tseng, Hsian-Rong

    2010-10-26

    Nanoparticles are regarded as promising transfection reagents for effective and safe delivery of nucleic acids into a specific type of cells or tissues providing an alternative manipulation/therapy strategy to viral gene delivery. However, the current process of searching novel delivery materials is limited due to conventional low-throughput and time-consuming multistep synthetic approaches. Additionally, conventional approaches are frequently accompanied with unpredictability and continual optimization refinements, impeding flexible generation of material diversity creating a major obstacle to achieving high transfection performance. Here we have demonstrated a rapid developmental pathway toward highly efficient gene delivery systems by leveraging the powers of a supramolecular synthetic approach and a custom-designed digital microreactor. Using the digital microreactor, broad structural/functional diversity can be programmed into a library of DNA-encapsulated supramolecular nanoparticles (DNA⊂SNPs) by systematically altering the mixing ratios of molecular building blocks and a DNA plasmid. In vitro transfection studies with DNA⊂SNPs library identified the DNA⊂SNPs with the highest gene transfection efficiency, which can be attributed to cooperative effects of structures and surface chemistry of DNA⊂SNPs. We envision such a rapid developmental pathway can be adopted for generating nanoparticle-based vectors for delivery of a variety of loads.