WorldWideScience

Sample records for alternative gene programs

  1. An alternative nuclear program

    International Nuclear Information System (INIS)

    Goldemberg, J.

    1981-01-01

    An analysis of the development of nuclear energy in Brazil is made since its beginning, showing the fundamental policy changes introduced in the end of the 60's with the purchase of the Angra dos Reis I reactor. This decision discouraged the existing efforts of an autonomous development in nuclear energy. The reaction to this policy led to the Nuclear Deal with Germany, which although incorporating some positive aspects is nor capable to lead to nuclear independence. The presently existing options are discussed, as well as the transformation of the Nuclear Program in a R and D Program based only in the reactors I, II and III, located in Angra dos Reis. (Author) [pt

  2. Alternative Nuclear Program

    International Nuclear Information System (INIS)

    Goldemberg, J.

    1982-01-01

    An analysis of the development of nuclear energy in Brazil is made since its beginning, showing the fundamental policy changes introduced in the end of the 60's with the purchase of the Angra dos Reis I reactor. This decision discouraged the existing efforts of an autonomous development in nuclear energy. The reaction to this policy led to the Nuclear Deal with Germany, which although incorporating some positive aspects is not capable to lead to nuclear independence. The presently existing options are discussed, as well as the transformation of the Nuclear Program in a R and D Program based only in the reactors I, II and III, located in Angra dos Reis. (Author) [pt

  3. Alternatives for Revitalizing Student Services Programs.

    Science.gov (United States)

    Deegan, William L.

    1984-01-01

    Reviews alternatives for revitalizing the programs and management of community college student services. As program development models, considers Miami-Dade Community College's computer-based instructional management system; entrepreneurial fee-based services; and divestment of situational or special-interest services to student groups. In…

  4. 77 FR 31756 - Energy Conservation Program: Alternative Efficiency Determination Methods and Alternative Rating...

    Science.gov (United States)

    2012-05-30

    ...-AC46 Energy Conservation Program: Alternative Efficiency Determination Methods and Alternative Rating... regulations authorizing the use of alternative methods of determining energy efficiency or energy consumption... alternative methods of determining energy efficiency or energy consumption of various consumer products and...

  5. 78 FR 31535 - Assistive Technology Alternative Financing Program

    Science.gov (United States)

    2013-05-24

    ... DEPARTMENT OF EDUCATION Assistive Technology Alternative Financing Program AGENCY: Office of Special Education and Rehabilitative Services, Department of Education. ACTION: Notice. Catalog of Federal... developed for the Assistive Technology (AT) Alternative Financing Program (AFP) in fiscal year (FY) 2012 to...

  6. 76 FR 67287 - Alternative Fuel Transportation Program; Alternative Fueled Vehicle Credit Program (Subpart F...

    Science.gov (United States)

    2011-10-31

    ... additional credits for the use of biodiesel in blends of 20 percent biodiesel or greater and have provided an... discussion in Part II.A), the original program based upon AFV acquisitions and biodiesel use became known as... example, B20 (a 20 percent blend of biodiesel with 80 percent petroleum diesel) is not an alternative fuel...

  7. Resolving deconvolution ambiguity in gene alternative splicing

    Directory of Open Access Journals (Sweden)

    Hubbell Earl

    2009-08-01

    Full Text Available Abstract Background For many gene structures it is impossible to resolve intensity data uniquely to establish abundances of splice variants. This was empirically noted by Wang et al. in which it was called a "degeneracy problem". The ambiguity results from an ill-posed problem where additional information is needed in order to obtain an unique answer in splice variant deconvolution. Results In this paper, we analyze the situations under which the problem occurs and perform a rigorous mathematical study which gives necessary and sufficient conditions on how many and what type of constraints are needed to resolve all ambiguity. This analysis is generally applicable to matrix models of splice variants. We explore the proposal that probe sequence information may provide sufficient additional constraints to resolve real-world instances. However, probe behavior cannot be predicted with sufficient accuracy by any existing probe sequence model, and so we present a Bayesian framework for estimating variant abundances by incorporating the prediction uncertainty from the micro-model of probe responsiveness into the macro-model of probe intensities. Conclusion The matrix analysis of constraints provides a tool for detecting real-world instances in which additional constraints may be necessary to resolve splice variants. While purely mathematical constraints can be stated without error, real-world constraints may themselves be poorly resolved. Our Bayesian framework provides a generic solution to the problem of uniquely estimating transcript abundances given additional constraints that themselves may be uncertain, such as regression fit to probe sequence models. We demonstrate the efficacy of it by extensive simulations as well as various biological data.

  8. 7 CFR 58.141 - Alternate quality control program.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Alternate quality control program. 58.141 Section 58... Service 1 Quality Specifications for Raw Milk § 58.141 Alternate quality control program. When a plant has in operation an acceptable quality program, at the producer level, which is approved by the...

  9. 6 CFR 27.235 - Alternative security program.

    Science.gov (United States)

    2010-01-01

    ... 6 Domestic Security 1 2010-01-01 2010-01-01 false Alternative security program. 27.235 Section 27.235 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Chemical Facility Security Program § 27.235 Alternative security program. (a) Covered...

  10. 33 CFR 101.125 - Approved Alternative Security Programs.

    Science.gov (United States)

    2010-07-01

    ... 106 of this subchapter, as applicable: (a) American Gaming Association Alternative Security Program..., and Towboats and Barges, dated September 24, 2003. (c) Passenger Vessel Association Industry Standards...

  11. Insights into alternative splicing of sarcomeric genes in the heart

    NARCIS (Netherlands)

    Weeland, Cornelis J.; van den Hoogenhof, Maarten M.; Beqqali, Abdelaziz; Creemers, Esther E.

    2015-01-01

    Driven by rapidly evolving technologies in next-generation sequencing, alternative splicing has emerged as a crucial layer in gene expression, greatly expanding protein diversity and governing complex biological processes in the cardiomyocyte. At the core of cardiac contraction, the physical

  12. Alternative transportation fuels in the USA: government hydrogen vehicle programs

    International Nuclear Information System (INIS)

    Cannon, J.S.

    1993-01-01

    The linkage between natural gas-based transportation and hydrogen-based transportation strategies, two clean burning gaseous fuels, provides a strong policy rationale for increased government sponsorship of hydrogen vehicle research and demonstration programs. Existing federal and state government hydrogen vehicle projects are discussed in this paper: research at the NREL, alternate-fueled buses, Renewable Hydrogen for the State of Hawaii program, New York state alternative transportation fuels program, Colorado program. 9 refs

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

    Directory of Open Access Journals (Sweden)

    Zodwa Dlamini

    2015-11-01

    Full Text Available 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.

  14. 24 CFR 7.5 - EEO Alternative Dispute Resolution Program.

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false EEO Alternative Dispute Resolution... Provisions § 7.5 EEO Alternative Dispute Resolution Program. In accordance with the Secretary's Policy Statement regarding Alternative Dispute Resolution (ADR) located on the Department's website and 29 CFR 1614...

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

    Science.gov (United States)

    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)…

  16. Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing

    Directory of Open Access Journals (Sweden)

    Penny David

    2007-10-01

    Full Text Available Abstract Background Alternative splicing has been reported in various eukaryotic groups including plants, apicomplexans, diatoms, amoebae, animals and fungi. However, whether widespread alternative splicing has evolved independently in the different eukaryotic groups or was inherited from their last common ancestor, and may therefore predate multicellularity, is still unknown. To better understand the origin and evolution of alternative splicing and its usage in diverse organisms, we studied alternative splicing in 12 eukaryotic species, comparing rates of alternative splicing across genes of different functional classes, cellular locations, intron/exon structures and evolutionary origins. Results For each species, we find that genes from most functional categories are alternatively spliced. Ancient genes (shared between animals, fungi and plants show high levels of alternative splicing. Genes with products expressed in the nucleus or plasma membrane are generally more alternatively spliced while those expressed in extracellular location show less alternative splicing. We find a clear correspondence between incidence of alternative splicing and intron number per gene both within and between genomes. In general, we find several similarities in patterns of alternative splicing across these diverse eukaryotes. Conclusion Along with previous studies indicating intron-rich genes with weak intron boundary consensus and complex spliceosomes in ancestral organisms, our results suggest that at least a simple form of alternative splicing may already have been present in the unicellular ancestor of plants, fungi and animals. A role for alternative splicing in the evolution of multicellularity then would largely have arisen by co-opting the preexisting process.

  17. Deriving Trading Rules Using Gene Expression Programming

    Directory of Open Access Journals (Sweden)

    Adrian VISOIU

    2011-01-01

    Full Text Available This paper presents how buy and sell trading rules are generated using gene expression programming with special setup. Market concepts are presented and market analysis is discussed with emphasis on technical analysis and quantitative methods. The use of genetic algorithms in deriving trading rules is presented. Gene expression programming is applied in a form where multiple types of operators and operands are used. This gives birth to multiple gene contexts and references between genes in order to keep the linear structure of the gene expression programming chromosome. The setup of multiple gene contexts is presented. The case study shows how to use the proposed gene setup to derive trading rules encoded by Boolean expressions, using a dataset with the reference exchange rates between the Euro and the Romanian leu. The conclusions highlight the positive results obtained in deriving useful trading rules.

  18. Alternative Strategies for Funding a General Dentistry Residency Program.

    Science.gov (United States)

    Kralewski, John E.; Wiggins, Carla

    1987-01-01

    Three alternative program funding approaches used in other professions are examined: (1) the reorientation of selected dental schools toward graduate education, (2) emphasizing and marketing the service aspects of the programs, and (3) developing education programs as in-house training for large organizations. (MSE)

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. The Alternate Technology Program for Aluminum Research Reactor Spent Fuel

    International Nuclear Information System (INIS)

    Barlow, M.W.

    1998-01-01

    This paper describes the program for disposition of aluminum-based RRSNF, including the requirements for road-ready dry storage and repository disposal and the criteria to be considered in selecting among the alternative technologies

  1. Quality Alternative Certification Programs in Special Education Ensure High Retention

    Science.gov (United States)

    Karge, Belinda D.; McCabe, Marjorie

    2014-01-01

    Market driven alternative routes to teaching have evolved into a quality program option and not just an answer to the teacher shortage. Alternative certification is a viable means of recruiting, training, and certifying those who have a bachelor's degree and a strong desire to enter the field of teaching. California has been a leader in the…

  2. 24 CFR 7.26 - EEO Alternative Dispute Resolution Program.

    Science.gov (United States)

    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... chosen, the EEO Counselor shall advise the aggrieved person that if the dispute is resolved during the...

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

    Science.gov (United States)

    2011-09-06

    ... NUCLEAR REGULATORY COMMISSION [NRC-2011-0208] Implementation of the Alternative Dispute Resolution... stakeholders on its Alternative Dispute Resolution (ADR) Program in the Office of Enforcement (OE). The meeting... INFORMATION: I. Background Congress enacted the Administrative Dispute Resolution Act (Act) which requires...

  4. Alternative epigenetic chromatin states of polycomb target genes.

    Directory of Open Access Journals (Sweden)

    Yuri B Schwartz

    2010-01-01

    Full Text Available Polycomb (PcG regulation has been thought to produce stable long-term gene silencing. Genomic analyses in Drosophila and mammals, however, have shown that it targets many genes, which can switch state during development. Genetic evidence indicates that critical for the active state of PcG target genes are the histone methyltransferases Trithorax (TRX and ASH1. Here we analyze the repertoire of alternative states in which PcG target genes are found in different Drosophila cell lines and the role of PcG proteins TRX and ASH1 in controlling these states. Using extensive genome-wide chromatin immunoprecipitation analysis, RNAi knockdowns, and quantitative RT-PCR, we show that, in addition to the known repressed state, PcG targets can reside in a transcriptionally active state characterized by formation of an extended domain enriched in ASH1, the N-terminal, but not C-terminal moiety of TRX and H3K27ac. ASH1/TRX N-ter domains and transcription are not incompatible with repressive marks, sometimes resulting in a "balanced" state modulated by both repressors and activators. Often however, loss of PcG repression results instead in a "void" state, lacking transcription, H3K27ac, or binding of TRX or ASH1. We conclude that PcG repression is dynamic, not static, and that the propensity of a target gene to switch states depends on relative levels of PcG, TRX, and activators. N-ter TRX plays a remarkable role that antagonizes PcG repression and preempts H3K27 methylation by acetylation. This role is distinct from that usually attributed to TRX/MLL proteins at the promoter. These results have important implications for Polycomb gene regulation, the "bivalent" chromatin state of embryonic stem cells, and gene expression in development.

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  7. Evaluating the Effectiveness of Traditional and Alternative Principal Preparation Programs

    Science.gov (United States)

    Pannell, Summer; Peltier-Glaze, Bernnell M.; Haynes, Ingrid; Davis, Delilah; Skelton, Carrie

    2015-01-01

    This study sought to determine the effectiveness on increasing student achievement of principals trained in a traditional principal preparation program and those trained in an alternate route principal preparation program within the same Mississippi university. Sixty-six Mississippi principals and assistant principals participated in the study. Of…

  8. Discussion paper: direction for Canada's alternate fuels program

    Energy Technology Data Exchange (ETDEWEB)

    1982-09-01

    There is a growing need to accelerate the consideration of alternate fuels for use in Canadian vehicle transportation. At the present time various governments and corporations are initiating alternate fuel programs involving ethanol, methanol, CNG, propane, etc. There is a bewildering array of perspectives as to which fuel or fuels will best serve Canada's needs in the future. In response to the 'Discussion Paper on Liquid Fuels Options, 1980', by the Federal Dept. of Energy, Mines and Resources, Ford of Canada has prepared this perspective on each of the alternate fuels from the company's vantage point as a vehicle manufacturer.

  9. The Evolution of Discipline: Alternative to Suspension Programs.

    Science.gov (United States)

    Streva, Michael A.

    Historically, the chosen method of discipline in United States schools has gone from corporal punishment to an emphasis on suspension. Recently, as principals have become less certain about the extent of their authority to suspend students, many inschool programs have been developed as alternatives to suspension. Among the advantages of such…

  10. 76 FR 77716 - Alternate Passenger Rail Service Pilot Program

    Science.gov (United States)

    2011-12-14

    ...-0108; Notice No. 2] RIN 2130-AC19 Alternate Passenger Rail Service Pilot Program AGENCY: Federal... rule is in response to a statutory mandate that FRA complete a rulemaking proceeding to develop a pilot... enactment of the Passenger Rail Investment and Improvement Act of 2008. The final rule develops this pilot...

  11. Alternative Administrative Certification: Socializing Factors Influencing Program Choice

    Science.gov (United States)

    Bickmore, Dana L.; Bickmore, Steven T.; Raines, Sarah

    2013-01-01

    This study used an organizational socialization lens to examine factors influencing participants' decision to pursue the principalship and choice to engage in an alternate administration certification program. Through an analysis of participant focus groups and interviews, factors emerged from the codes that were compared with dimensions of…

  12. 76 FR 11310 - Alternatives Analysis Program Discretionary Funding Allocations

    Science.gov (United States)

    2011-03-01

    ... information on the Alternatives Analysis Program, contact Kenneth Cervenka, Office of Planning and Environment... Island, and Vermont. Mexico and Texas. Brigid Hynes-Cherin, Regional Mokhtee Ahmad, Regional............ City of Minneapolis...... Nicollet-Central Urban 900,000 Circulator. MN D2010-ALTA-09005...

  13. Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing

    DEFF Research Database (Denmark)

    Irimia, Manuel; Rukov, Jakob Lewin; Penny, David

    2007-01-01

    , and may therefore predate multicellularity, is still unknown. To better understand the origin and evolution of alternative splicing and its usage in diverse organisms, we studied alternative splicing in 12 eukaryotic species, comparing rates of alternative splicing across genes of different functional......, we find several similarities in patterns of alternative splicing across these diverse eukaryotes. CONCLUSION: Along with previous studies indicating intron-rich genes with weak intron boundary consensus and complex spliceosomes in ancestral organisms, our results suggest that at least a simple form...... of alternative splicing may already have been present in the unicellular ancestor of plants, fungi and animals. A role for alternative splicing in the evolution of multicellularity then would largely have arisen by co-opting the preexisting process....

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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…

  16. EM-31 Alternative and Enhanced Chemical Cleaning Program

    International Nuclear Information System (INIS)

    King, Bill

    2010-01-01

    King's introduction to his presentation made 5 important points: (1) Numerous SRS tanks scheduled for closure (contract commitments); (2) Cannot remove all sludge by mechanical means due to obstructions; (3) Chemical removal technology needed (likely oxalic acid); (4) Post - dissolution neutralization required prior to transfer to compliant tanks; (5) Sodium oxalate salts precipitate on neutralization and have negative downstream impacts. There were three SRS chemical cleaning programs in 2010: Baseline: 8wt percent OA batch contact, ECC: 1-3 wt. percent OA with oxalate destruction, and the Alternative/Enhanced Chemical Cleaning (EM-31). This talk is on the EM-31 program.

  17. Fast rate of evolution in alternatively spliced coding regions of mammalian genes

    Directory of Open Access Journals (Sweden)

    Nurtdinov Ramil N

    2006-04-01

    Full Text Available Abstract Background At least half of mammalian genes are alternatively spliced. Alternative isoforms are often genome-specific and it has been suggested that alternative splicing is one of the major mechanisms for generating protein diversity in the course of evolution. Another way of looking at alternative splicing is to consider sequence evolution of constitutive and alternative regions of protein-coding genes. Indeed, it turns out that constitutive and alternative regions evolve in different ways. Results A set of 3029 orthologous pairs of human and mouse alternatively spliced genes was considered. The rate of nonsynonymous substitutions (dN, the rate of synonymous substitutions (dS, and their ratio (ω = dN/dS appear to be significantly higher in alternatively spliced coding regions compared to constitutive regions. When N-terminal, internal and C-terminal alternatives are analysed separately, C-terminal alternatives appear to make the main contribution to the observed difference. The effects become even more pronounced in a subset of fast evolving genes. Conclusion These results provide evidence of weaker purifying selection and/or stronger positive selection in alternative regions and thus one more confirmation of accelerated evolution in alternative regions. This study corroborates the theory that alternative splicing serves as a testing ground for molecular evolution.

  18. Methanol supply issues for alternative fuels demonstration programs

    International Nuclear Information System (INIS)

    Teague, J.M.; Koyama, K.K.

    1995-01-01

    This paper surveys issues affecting the supply of fuel-grade methanol for the California Energy Commission's alternative fuels demonstration programs and operations by other public agencies such as transit and school districts. Establishing stable and reasonably priced sources of methanol (in particular) and of alternative fuels generally is essential to their demonstration and commercialization. Development both of vehicle technologies and of fuel supply and distribution are complementary and must proceed in parallel. However, the sequence of scaling up supply and distribution is not necessarily smooth; achievement of volume thresholds in demand and through-put of alternative fuels are marked by different kinds of challenges. Four basic conditions should be met in establishing a fuel supply: (1) it must be price competitive with petroleum-based fuels, at least when accounting for environmental and performance benefits; (2) bulk supply must meet volumes required at each phase; necessitating resilience among suppliers and a means of designating priority for high value users; (3) distribution systems must be reliable, comporting with end users' operational schedules; (4) volatility in prices to the end user for the fuel must be minimal. Current and projected fuel volumes appear to be insufficient to induce necessary economies of scale in production and distribution for fuel use. Despite their benefits, existing programs will suffer absent measures to secure economical fuel supplies. One solution is to develop sources that are dedicated to fuel markets and located within the end-use region

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

    Energy Technology Data Exchange (ETDEWEB)

    Lowell, Jon [ISO New England, Holyoke, MA (United States); Yoshimura, Henry [ISO New England, Holyoke, MA (United States)

    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.

  20. Automated discovery of functional generality of human gene expression programs.

    Directory of Open Access Journals (Sweden)

    Georg K Gerber

    2007-08-01

    Full Text Available An important research problem in computational biology is the identification of expression programs, sets of co-expressed genes orchestrating normal or pathological processes, and the characterization of the functional breadth of these programs. The use of human expression data compendia for discovery of such programs presents several challenges including cellular inhomogeneity within samples, genetic and environmental variation across samples, uncertainty in the numbers of programs and sample populations, and temporal behavior. We developed GeneProgram, a new unsupervised computational framework based on Hierarchical Dirichlet Processes that addresses each of the above challenges. GeneProgram uses expression data to simultaneously organize tissues into groups and genes into overlapping programs with consistent temporal behavior, to produce maps of expression programs, which are sorted by generality scores that exploit the automatically learned groupings. Using synthetic and real gene expression data, we showed that GeneProgram outperformed several popular expression analysis methods. We applied GeneProgram to a compendium of 62 short time-series gene expression datasets exploring the responses of human cells to infectious agents and immune-modulating molecules. GeneProgram produced a map of 104 expression programs, a substantial number of which were significantly enriched for genes involved in key signaling pathways and/or bound by NF-kappaB transcription factors in genome-wide experiments. Further, GeneProgram discovered expression programs that appear to implicate surprising signaling pathways or receptor types in the response to infection, including Wnt signaling and neurotransmitter receptors. We believe the discovered map of expression programs involved in the response to infection will be useful for guiding future biological experiments; genes from programs with low generality scores might serve as new drug targets that exhibit minimal

  1. Comparison of University-Based Teacher Certification Programs and Alternative Certification Programs

    Science.gov (United States)

    Roberts, Keonna

    2016-01-01

    The purpose of this qualitative study was to understand further similarities and differences between traditionally certified teachers and alternatively certified teachers specifically in the areas of teacher self-efficacy, classroom management, and teacher perceptions of their preparation program. The following research questions guided this…

  2. Two alternating motor programs drive navigation in Drosophila larva.

    Directory of Open Access Journals (Sweden)

    Subhaneil Lahiri

    Full Text Available 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.

  3. Peak flood estimation using gene expression programming

    Science.gov (United States)

    Zorn, Conrad R.; Shamseldin, Asaad Y.

    2015-12-01

    As a case study for the Auckland Region of New Zealand, this paper investigates the potential use of gene-expression programming (GEP) in predicting specific return period events in comparison to the established and widely used Regional Flood Estimation (RFE) method. Initially calibrated to 14 gauged sites, the GEP derived model was further validated to 10 and 100 year flood events with a relative errors of 29% and 18%, respectively. This is compared to the RFE method providing 48% and 44% errors for the same flood events. While the effectiveness of GEP in predicting specific return period events is made apparent, it is argued that the derived equations should be used in conjunction with those existing methodologies rather than as a replacement.

  4. Alternative splice variants of the human PD-1 gene

    DEFF Research Database (Denmark)

    Nielsen, Christian; Ohm-Laursen, Line; Barington, Torben

    2005-01-01

    PD-1 is an immunoregulatory receptor expressed on the surface of activated T cells, B cells, and monocytes. We describe four alternatively spliced PD-1 mRNA transcripts (PD-1Deltaex2, PD-1Deltaex3, PD-1Deltaex2,3, and PD-1Deltaex2,3,4) in addition to the full length isoform. PD-1Deltaex2 and PD-1...... and flPD-1 upon activation suggests an important interplay between the putative soluble PD-1 and flPD-1 possibly involved in maintenance of peripheral self-tolerance and prevention of autoimmunity....

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

    Science.gov (United States)

    2010-01-01

    ... 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 parties...

  6. Alternatives Analysis for the Resumption of Transient Testing Program

    Energy Technology Data Exchange (ETDEWEB)

    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

  7. Alternative mapping of probes to genes for Affymetrix chips

    DEFF Research Database (Denmark)

    Gautier, Laurent; Møller, M.; Friis-Hansen, L.

    2004-01-01

    transcripts: the NCBI RefSeq database. We also built mappings and used them in place of the original probe to genes associations provided by the manufacturer of the arrays. Results: In a large number of cases, 36%, the probes matching a reference sequence were consistent with the grouping of probes...... by the manufacturer of the chips. For the remaining cases there were discrepancies and we show how that can affect the analysis of data. Conclusions: While the probes on Affymetrix arrays remain the same for several years, the biological knowledge concerning the genomic sequences evolves rapidly. Using up...

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  9. School District Program Cost Accounting: An Alternative Approach

    Science.gov (United States)

    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)

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

    International Nuclear Information System (INIS)

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

    1990-01-01

    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

  11. Early Site Permit Demonstration Program: Station design alternatives report

    International Nuclear Information System (INIS)

    1993-03-01

    This report provides the results of investigating the basis for including Station Design Alternatives (SDAs) in the regulatory guidance given for nuclear plant environmental reports (ERs), explains approaches or processes for evaluating SDAs at the early site permit (ESP) stage, and applies one of the processes to each of the ten systems or subsystems considered as SDAS. The key objective o this report s to demonstrate an adequate examination of alternatives can be performed without the extensive development f design data. The report discusses the Composite Suitability Approach and the Established Cutoff Approach in evaluating station design alternatives and selects one of these approaches to evaluate alternatives for each of the plant or station that were considered. Four types of ALWRs have been considered due to the availability of extensive plant data: System 80+, AP600, Advanced Boiling Reactor (ABWR), and Simplified Boiling Water Reactor (SBWR). This report demonstrates the feasibility of evaluating station design alternatives when reactor design detail has not been determined, quantitatively compares the potential ental impacts of alternatives, and focuses the ultimate selection of a alternative on cost and applicant-specific factors. The range of alternatives system is deliberately limited to a reasonable number to demonstrate the or to the three most commonly used at operating plants

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  13. Misregulation of Gene Expression and Sterility in Interspecies Hybrids: Causal Links and Alternative Hypotheses.

    Science.gov (United States)

    Civetta, Alberto

    2016-05-01

    Understanding the origin of species is of interest to biologist in general and evolutionary biologist in particular. Hybrid male sterility (HMS) has been a focus in studies of speciation because sterility imposes a barrier to free gene flow between organisms, thus effectively isolating them as distinct species. In this review, I focus on the role of differential gene expression in HMS and speciation. Microarray and qPCR assays have established associations between misregulation of gene expression and sterility in hybrids between closely related species. These studies originally proposed disrupted expression of spermatogenesis genes as a causative of sterility. Alternatively, rapid genetic divergence of regulatory elements, particularly as they relate to the male sex (fast-male evolution), can drive the misregulation of sperm developmental genes in the absence of sterility. The use of fertile hybrids (both backcross and F1 progeny) as controls has lent support to this alternative explanation. Differences in gene expression between fertile and sterile hybrids can also be influenced by a pattern of faster evolution of the sex chromosome (fast-X evolution) than autosomes. In particular, it would be desirable to establish whether known X-chromosome sterility factors can act as trans-regulatory drivers of genome-wide patterns of misregulation. Genome-wide expression studies coupled with assays of proxies of sterility in F1 and BC progeny have identified candidate HMS genes but functional assays, and a better phenotypic characterization of sterility phenotypes, are needed to rigorously test how these genes might contribute to HMS.

  14. 75 FR 30100 - FY 2010 Discretionary Livability Funding Opportunity: Alternatives Analysis Program

    Science.gov (United States)

    2010-05-28

    ... to support a limited number of alternatives analyses, or technical work conducted as part of on-going... limited number of alternatives analyses, or technical work conducted as part of proposed or on-going... Projects Alternatives analyses must be documented in the Unified Planning Work Program of the metropolitan...

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

    Science.gov (United States)

    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…

  16. 46 CFR 71.50-31 - Continued participation in the Alternative Hull Examination (AHE) program.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 3 2010-10-01 2010-10-01 false Continued participation in the Alternative Hull... the Alternative Hull Examination (AHE) program. (a) To continue to participate in the AHE Program, vessel operators must conduct an annual hull condition assessment. At a minimum, vessel operators must...

  17. 46 CFR 176.630 - The Alternative Hull Examination (AHE) Program application.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false The Alternative Hull Examination (AHE) Program... PASSENGER VESSELS (UNDER 100 GROSS TONS) INSPECTION AND CERTIFICATION Hull and Tailshaft Examinations § 176.630 The Alternative Hull Examination (AHE) Program application. If your vessel meets the eligibility...

  18. 46 CFR 176.650 - Alternative Hull Examination Program options: Divers or underwater ROV.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Alternative Hull Examination Program options: Divers or...) SMALL PASSENGER VESSELS (UNDER 100 GROSS TONS) INSPECTION AND CERTIFICATION Hull and Tailshaft Examinations § 176.650 Alternative Hull Examination Program options: Divers or underwater ROV. To complete the...

  19. 46 CFR 71.50-19 - The Alternative Hull Examination (AHE) Program application.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 3 2010-10-01 2010-10-01 false The Alternative Hull Examination (AHE) Program...) PASSENGER VESSELS INSPECTION AND CERTIFICATION Drydocking § 71.50-19 The Alternative Hull Examination (AHE... apply to the AHE Program. You must submit an application at least 90 days before the requested hull...

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

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Alternative Hull Examination (AHE) Program options... MORE THAN 49 PASSENGERS INSPECTION AND CERTIFICATION Hull and Tailshaft Examinations § 115.650 Alternative Hull Examination (AHE) Program options: Divers or underwater ROV. To complete your underwater...

  1. DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

    Science.gov (United States)

    Wehe, André; Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver

    2008-07-01

    DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

  2. Progress in Tissue Specimens Alternative for the Driver Genes Testing of Non-small Cell Lung Cancer

    Directory of Open Access Journals (Sweden)

    Yan SUN

    2015-06-01

    Full Text Available Target treatment based on driver genes in advanced non-small cell lung cancer is very important currently. Tumor tissues is the gold standard for driver genes testing. However, most of patients could not get the gene information for lack of enough tissues. To explore the tissue specimens alternatives is a hot spot in clinical work. This report reviews the tissue specimen alternatives of driver gene testing in non-small cell lung cancer.

  3. Super gene alternation of magnetite and pyrite and the role of their alternation products in the fixation of uranium from the circulating media. Vol. 3

    Energy Technology Data Exchange (ETDEWEB)

    El-Gemmizi, M A [Nuclear Materials Authority, Cairo, (Egypt)

    1996-03-01

    In most of the Egyptian altered radioactive granites, highly magnetic heavy particles were found to be radioactive. They are a mixture of several iron oxide minerals which are products of super gene alternation of the preexisting hypo gene iron-bearing minerals especially magnetite and pyrite. The end products of this super gene alternation are mainly hydrated iron oxide minerals limonite and/or goethite. During the alternation, deformation and defects in the mineral structure took place, thereby promoting diffusion of the substitutional and interstitial ions (uranium) towards these sites. The mechanism of the alternation of the hypo gene iron-bearing minerals, magnetite and pyrite to form the secondary mineral hematite, limonite and goethite; and the role of these secondary minerals in fixing uranium from the circulating media, and as indicators to the radioactivity of the host rocks are discussed. 2 figs.

  4. Super gene alternation of magnetite and pyrite and the role of their alternation products in the fixation of uranium from the circulating media. Vol. 3

    International Nuclear Information System (INIS)

    El-Gemmizi, M.A.

    1996-01-01

    In most of the Egyptian altered radioactive granites, highly magnetic heavy particles were found to be radioactive. They are a mixture of several iron oxide minerals which are products of super gene alternation of the preexisting hypo gene iron-bearing minerals especially magnetite and pyrite. The end products of this super gene alternation are mainly hydrated iron oxide minerals limonite and/or goethite. During the alternation, deformation and defects in the mineral structure took place, thereby promoting diffusion of the substitutional and interstitial ions (uranium) towards these sites. The mechanism of the alternation of the hypo gene iron-bearing minerals, magnetite and pyrite to form the secondary mineral hematite, limonite and goethite; and the role of these secondary minerals in fixing uranium from the circulating media, and as indicators to the radioactivity of the host rocks are discussed. 2 figs

  5. Center for Alternative Fuels Research Program | College of Engineering &

    Science.gov (United States)

    Electrical Engineering Instructional Laboratories Student Resources Industrial & Manufacturing Engineering Industrial & Manufacturing Engineering Academic Programs Industrial & Manufacturing Engineering Major Industrial & Manufacturing Engineering Minor Industrial & Manufacturing Engineering

  6. 76 FR 55335 - Alternate Passenger Rail Service Pilot Program

    Science.gov (United States)

    2011-09-07

    ... provides that the proposed pilot program would not be made available to more than two Amtrak intercity... operation; provisions for accommodating the traveling public, including proposed arrangements for stations... program developed by this part will not be made available to more than two Amtrak intercity passenger rail...

  7. Colorado's Alternative School Calendar Program and the Four Day Week.

    Science.gov (United States)

    Brubacher, Roy G.; Stiverson, C. L.

    Taking advantage of legislation permitting modified school calendars, the four-day work week has been implemented by 23 small, rural Colorado school districts representing 5,200 children. Thirteen districts implemented the four-day program in the 1980-81 school year. Ten additional districts applied as first year pilot programs in the 1981-82…

  8. Human sex hormone-binding globulin gene expression- multiple promoters and complex alternative splicing

    Directory of Open Access Journals (Sweden)

    Rosner William

    2009-05-01

    Full Text Available Abstract Background Human sex hormone-binding globulin (SHBG regulates free sex steroid concentrations in plasma and modulates rapid, membrane based steroid signaling. SHBG is encoded by an eight exon-long transcript whose expression is regulated by a downstream promoter (PL. The SHBG gene was previously shown to express a second major transcript of unknown function, derived from an upstream promoter (PT, and two minor transcripts. Results We report that transcriptional expression of the human SHBG gene is far more complex than previously described. PL and PT direct the expression of at least six independent transcripts each, resulting from alternative splicing of exons 4, 5, 6, and/or 7. We mapped two transcriptional start sites downstream of PL and PT, and present evidence for a third SHBG gene promoter (PN within the neighboring FXR2 gene; PN regulates the expression of at least seven independent SHBG gene transcripts, each possessing a novel, 164-nt first exon (1N. Transcriptional expression patterns were generated for human prostate, breast, testis, liver, and brain, and the LNCaP, MCF-7, and HepG2 cell lines. Each expresses the SHBG transcript, albeit in varying abundance. Alternative splicing was more pronounced in the cancer cell lines. PL- PT- and PN-derived transcripts were most abundant in liver, testis, and prostate, respectively. Initial findings reveal the existence of a smaller immunoreactive SHBG species in LNCaP, MCF-7, and HepG2 cells. Conclusion These results extend our understanding of human SHBG gene transcription, and raise new and important questions regarding the role of novel alternatively spliced transcripts, their function in hormonally responsive tissues including the breast and prostate, and the role that aberrant SHBG gene expression may play in cancer.

  9. Gene expression programming for power system static security ...

    African Journals Online (AJOL)

    user

    Keywords: static security, gene expression programming, probabilistic neural network ... Hence digital computers are usually installed in operations control centers to gather ...... power system protection, and applications of AI in power systems.

  10. Multiobjective optimization in Gene Expression Programming for Dew Point

    OpenAIRE

    Shroff, Siddharth; Dabhi, Vipul

    2013-01-01

    The processes occurring in climatic change evolution and their variations play a major role in environmental engineering. Different techniques are used to model the relationship between temperatures, dew point and relative humidity. Gene expression programming is capable of modelling complex realities with great accuracy, allowing, at the same time, the extraction of knowledge from the evolved models compared to other learning algorithms. This research aims to use Gene Expression Programming ...

  11. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

    Directory of Open Access Journals (Sweden)

    Sugnet Charles

    2006-12-01

    Full Text Available Abstract Background Alternative splicing is a mechanism for increasing protein diversity by excluding or including exons during post-transcriptional processing. Alternatively spliced proteins are particularly relevant in oncology since they may contribute to the etiology of cancer, provide selective drug targets, or serve as a marker set for cancer diagnosis. While conventional identification of splice variants generally targets individual genes, we present here a new exon-centric array (GeneChip Human Exon 1.0 ST that allows genome-wide identification of differential splice variation, and concurrently provides a flexible and inclusive analysis of gene expression. Results We analyzed 20 paired tumor-normal colon cancer samples using a microarray designed to detect over one million putative exons that can be virtually assembled into potential gene-level transcripts according to various levels of prior supporting evidence. Analysis of high confidence (empirically supported transcripts identified 160 differentially expressed genes, with 42 genes occupying a network impacting cell proliferation and another twenty nine genes with unknown functions. A more speculative analysis, including transcripts based solely on computational prediction, produced another 160 differentially expressed genes, three-fourths of which have no previous annotation. We also present a comparison of gene signal estimations from the Exon 1.0 ST and the U133 Plus 2.0 arrays. Novel splicing events were predicted by experimental algorithms that compare the relative contribution of each exon to the cognate transcript intensity in each tissue. The resulting candidate splice variants were validated with RT-PCR. We found nine genes that were differentially spliced between colon tumors and normal colon tissues, several of which have not been previously implicated in cancer. Top scoring candidates from our analysis were also found to substantially overlap with EST-based bioinformatic

  12. Genomic organization and the tissue distribution of alternatively spliced isoforms of the mouse Spatial gene

    Directory of Open Access Journals (Sweden)

    Mattei Marie-Geneviève

    2004-07-01

    Full Text Available Abstract Background The stromal component of the thymic microenvironment is critical for T lymphocyte generation. Thymocyte differentiation involves a cascade of coordinated stromal genes controlling thymocyte survival, lineage commitment and selection. The "Stromal Protein Associated with Thymii And Lymph-node" (Spatial gene encodes a putative transcription factor which may be involved in T-cell development. In the testis, the Spatial gene is also expressed by round spermatids during spermatogenesis. Results The Spatial gene maps to the B3-B4 region of murine chromosome 10 corresponding to the human syntenic region 10q22.1. The mouse Spatial genomic DNA is organised into 10 exons and is alternatively spliced to generate two short isoforms (Spatial-α and -γ and two other long isoforms (Spatial-δ and -ε comprising 5 additional exons on the 3' site. Here, we report the cloning of a new short isoform, Spatial-β, which differs from other isoforms by an additional alternative exon of 69 bases. This new exon encodes an interesting proline-rich signature that could confer to the 34 kDa Spatial-β protein a particular function. By quantitative TaqMan RT-PCR, we have shown that the short isoforms are highly expressed in the thymus while the long isoforms are highly expressed in the testis. We further examined the inter-species conservation of Spatial between several mammals and identified that the protein which is rich in proline and positive amino acids, is highly conserved. Conclusions The Spatial gene generates at least five alternative spliced variants: three short isoforms (Spatial-α, -β and -γ highly expressed in the thymus and two long isoforms (Spatial-δ and -ε highly expressed in the testis. These alternative spliced variants could have a tissue specific function.

  13. Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis.

    Science.gov (United States)

    Kwon, Young-Ju; Park, Mi-Jeong; Kim, Sang-Gyu; Baldwin, Ian T; Park, Chung-Mo

    2014-05-19

    The circadian clock enables living organisms to anticipate recurring daily and seasonal fluctuations in their growth habitats and synchronize their biology to the environmental cycle. The plant circadian clock consists of multiple transcription-translation feedback loops that are entrained by environmental signals, such as light and temperature. In recent years, alternative splicing emerges as an important molecular mechanism that modulates the clock function in plants. Several clock genes are known to undergo alternative splicing in response to changes in environmental conditions, suggesting that the clock function is intimately associated with environmental responses via the alternative splicing of the clock genes. However, the alternative splicing events of the clock genes have not been studied at the molecular level. We systematically examined whether major clock genes undergo alternative splicing under various environmental conditions in Arabidopsis. We also investigated the fates of the RNA splice variants of the clock genes. It was found that the clock genes, including EARLY FLOWERING 3 (ELF3) and ZEITLUPE (ZTL) that have not been studied in terms of alternative splicing, undergo extensive alternative splicing through diverse modes of splicing events, such as intron retention, exon skipping, and selection of alternative 5' splice site. Their alternative splicing patterns were differentially influenced by changes in photoperiod, temperature extremes, and salt stress. Notably, the RNA splice variants of TIMING OF CAB EXPRESSION 1 (TOC1) and ELF3 were degraded through the nonsense-mediated decay (NMD) pathway, whereas those of other clock genes were insensitive to NMD. Taken together, our observations demonstrate that the major clock genes examined undergo extensive alternative splicing under various environmental conditions, suggesting that alternative splicing is a molecular scheme that underlies the linkage between the clock and environmental stress

  14. Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis

    Science.gov (United States)

    2014-01-01

    Background The circadian clock enables living organisms to anticipate recurring daily and seasonal fluctuations in their growth habitats and synchronize their biology to the environmental cycle. The plant circadian clock consists of multiple transcription-translation feedback loops that are entrained by environmental signals, such as light and temperature. In recent years, alternative splicing emerges as an important molecular mechanism that modulates the clock function in plants. Several clock genes are known to undergo alternative splicing in response to changes in environmental conditions, suggesting that the clock function is intimately associated with environmental responses via the alternative splicing of the clock genes. However, the alternative splicing events of the clock genes have not been studied at the molecular level. Results We systematically examined whether major clock genes undergo alternative splicing under various environmental conditions in Arabidopsis. We also investigated the fates of the RNA splice variants of the clock genes. It was found that the clock genes, including EARLY FLOWERING 3 (ELF3) and ZEITLUPE (ZTL) that have not been studied in terms of alternative splicing, undergo extensive alternative splicing through diverse modes of splicing events, such as intron retention, exon skipping, and selection of alternative 5′ splice site. Their alternative splicing patterns were differentially influenced by changes in photoperiod, temperature extremes, and salt stress. Notably, the RNA splice variants of TIMING OF CAB EXPRESSION 1 (TOC1) and ELF3 were degraded through the nonsense-mediated decay (NMD) pathway, whereas those of other clock genes were insensitive to NMD. Conclusion Taken together, our observations demonstrate that the major clock genes examined undergo extensive alternative splicing under various environmental conditions, suggesting that alternative splicing is a molecular scheme that underlies the linkage between the clock

  15. A MICROCOMPUTER LINEAR PROGRAMMING PACKAGE: AN ALTERNATIVE TO MAINFRAMES

    OpenAIRE

    Laughlin, David H.

    1984-01-01

    This paper presents the capabilities and limitations of a microcomputer linear programming package. The solution algorithm is a version of the revised simplex. Rapid problem entry, user ease of operation, sensitivity analyses on objective function and right hand sides are advantages. A problem size of 150 activities and 64 constraints can be solved in present form. Due to problem size, limitations and lack of parametric and integer programming routines, this package is thought to have the mos...

  16. 78 FR 45253 - National Toxicology Program Scientific Advisory Committee on Alternative Toxicological Methods...

    Science.gov (United States)

    2013-07-26

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Toxicology Program... Alternative Methods (ICCVAM), the National Toxicology Program (NTP) Interagency Center for the Evaluation of... Director, National Toxicology Program. [FR Doc. 2013-17919 Filed 7-25-13; 8:45 am] BILLING CODE 4140-01-P ...

  17. Gene selection for the reconstruction of stem cell differentiation trees: a linear programming approach.

    Science.gov (United States)

    Ghadie, Mohamed A; Japkowicz, Nathalie; Perkins, Theodore J

    2015-08-15

    Stem cell differentiation is largely guided by master transcriptional regulators, but it also depends on the expression of other types of genes, such as cell cycle genes, signaling genes, metabolic genes, trafficking genes, etc. Traditional approaches to understanding gene expression patterns across multiple conditions, such as principal components analysis or K-means clustering, can group cell types based on gene expression, but they do so without knowledge of the differentiation hierarchy. Hierarchical clustering can organize cell types into a tree, but in general this tree is different from the differentiation hierarchy itself. Given the differentiation hierarchy and gene expression data at each node, we construct a weighted Euclidean distance metric such that the minimum spanning tree with respect to that metric is precisely the given differentiation hierarchy. We provide a set of linear constraints that are provably sufficient for the desired construction and a linear programming approach to identify sparse sets of weights, effectively identifying genes that are most relevant for discriminating different parts of the tree. We apply our method to microarray gene expression data describing 38 cell types in the hematopoiesis hierarchy, constructing a weighted Euclidean metric that uses just 175 genes. However, we find that there are many alternative sets of weights that satisfy the linear constraints. Thus, in the style of random-forest training, we also construct metrics based on random subsets of the genes and compare them to the metric of 175 genes. We then report on the selected genes and their biological functions. Our approach offers a new way to identify genes that may have important roles in stem cell differentiation. tperkins@ohri.ca Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. The role of alternative Polyadenylation in regulation of rhythmic gene expression.

    Science.gov (United States)

    Ptitsyna, Natalia; Boughorbel, Sabri; El Anbari, Mohammed; Ptitsyn, Andrey

    2017-08-04

    Alternative transcription is common in eukaryotic cells and plays important role in regulation of cellular processes. Alternative polyadenylation results from ambiguous PolyA signals in 3' untranslated region (UTR) of a gene. Such alternative transcripts share the same coding part, but differ by a stretch of UTR that may contain important functional sites. The methodoogy of this study is based on mathematical modeling, analytical solution, and subsequent validation by datamining in multiple independent experimental data from previously published studies. In this study we propose a mathematical model that describes the population dynamics of alternatively polyadenylated transcripts in conjunction with rhythmic expression such as transcription oscillation driven by circadian or metabolic oscillators. Analysis of the model shows that alternative transcripts with different turnover rates acquire a phase shift if the transcript decay rate is different. Difference in decay rate is one of the consequences of alternative polyadenylation. Phase shift can reach values equal to half the period of oscillation, which makes alternative transcripts oscillate in abundance in counter-phase to each other. Since counter-phased transcripts share the coding part, the rate of translation becomes constant. We have analyzed a few data sets collected in circadian timeline for the occurrence of transcript behavior that fits the mathematical model. Alternative transcripts with different turnover rate create the effect of rectifier. This "molecular diode" moderates or completely eliminates oscillation of individual transcripts and stabilizes overall protein production rate. In our observation this phenomenon is very common in different tissues in plants, mice, and humans. The occurrence of counter-phased alternative transcripts is also tissue-specific and affects functions of multiple biological pathways. Accounting for this mechanism is important for understanding the natural and engineering

  19. LPS challenge regulates gene expression and tissue localization of a Ciona intestinalis gene through an alternative polyadenylation mechanism.

    Directory of Open Access Journals (Sweden)

    Aiti Vizzini

    Full Text Available A subtractive hybridization strategy for the identification of differentially expressed genes was performed between LPS-challenged and naive Ciona intestinalis. This strategy allowed the characterization of two transcripts (Ci8short and Ci8long generated by the use of two Alternative Polyadenylation sites. The Ci8long transcript contains a protein domain with relevant homology to several components of the Receptor Transporting Protein (RTP family not present in the Ci8short mRNA. By means of Real Time PCR and Northern Blot, the Ci8short and Ci8long transcripts showed a different pattern of gene expression with the Ci8short mRNA being strongly activated after LPS injection in the pharynx. In situ hybridization analysis demonstrated that the activation of the APA site also influenced the tissue localization of the Ci8short transcript. This analysis showed that the Ci8long mRNA was expressed in hemocytes meanwhile the Ci8short mRNA was highly transcribed also in vessel endothelial cells and in the epithelium of pharynx. These findings demonstrated that regulation of gene expression based on different polyadenylation sites is an ancestral powerful strategy influencing both the level of expression and tissue distribution of alternative transcripts.

  20. Acute hypoxia stress induced abundant differential expression genes and alternative splicing events in heart of tilapia.

    Science.gov (United States)

    Xia, Jun Hong; Li, Hong Lian; Li, Bi Jun; Gu, Xiao Hui; Lin, Hao Ran

    2018-01-10

    Hypoxia is one of the critical environmental stressors for fish in aquatic environments. Although accumulating evidences indicate that gene expression is regulated by hypoxia stress in fish, how genes undergoing differential gene expression and/or alternative splicing (AS) in response to hypoxia stress in heart are not well understood. Using RNA-seq, we surveyed and detected 289 differential expressed genes (DEG) and 103 genes that undergo differential usage of exons and splice junctions events (DUES) in heart of a hypoxia tolerant fish, Nile tilapia, Oreochromis niloticus following 12h hypoxic treatment. The spatio-temporal expression analysis validated the significant association of differential exon usages in two randomly selected DUES genes (fam162a and ndrg2) in 5 tissues (heart, liver, brain, gill and spleen) sampled at three time points (6h, 12h, and 24h) under acute hypoxia treatment. Functional analysis significantly associated the differential expressed genes with the categories related to energy conservation, protein synthesis and immune response. Different enrichment categories were found between the DEG and DUES dataset. The Isomerase activity, Oxidoreductase activity, Glycolysis and Oxidative stress process were significantly enriched for the DEG gene dataset, but the Structural constituent of ribosome and Structural molecule activity, Ribosomal protein and RNA binding protein were significantly enriched only for the DUES genes. Our comparative transcriptomic analysis reveals abundant stress responsive genes and their differential regulation function in the heart tissues of Nile tilapia under acute hypoxia stress. Our findings will facilitate future investigation on transcriptome complexity and AS regulation during hypoxia stress in fish. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Gene program-specific regulation of PGC-1{alpha} activity

    DEFF Research Database (Denmark)

    Schmidt, Søren F; Mandrup, Susanne

    2011-01-01

    Peroxisome proliferator-activated receptor γ (PPARγ) coactivator 1 α (PGC-1α) activation coordinates induction of the hepatic fasting response through coactivation of numerous transcription factors and gene programs. In the June 15, 2011, issue of Genes & Development, Lustig and colleagues (pp....... 1232-1244) demonstrated that phosphorylation of PGC-1α by the p70 ribosomal protein S6 kinase 1 (S6K1) specifically interfered with the interaction between PGC-1α and HNF4α in liver and blocked the coactivation of the gluconeogenic target genes. This demonstrates how independent fine-tuning of gene...

  2. Alternative Teacher Preparation Programs. Title II News You Can Use

    Science.gov (United States)

    Office of Postsecondary Education, US Department of Education, 2015

    2015-01-01

    Title II of the "Higher Education Act of 1965" ("HEA"), as amended in 2008 by the "Higher Education Opportunity Act," requires states to report annually on key elements of their teacher preparation programs and requirements for initial teacher credentialing, kindergarten through 12th grade. "Title II News You Can…

  3. An Alternative Avenue to Teacher Certification: A Cost Analysis of the Pathways to Teaching Careers Program.

    Science.gov (United States)

    Rice, Jennifer King; Brent, Brian O.

    2002-01-01

    Analyzes cost effectiveness of the Pathways to Teaching Careers, a program that supports an alternative route to university-based teacher certification primarily for noncertified teachers, paraprofessionals, and Peace Corps volunteers. (PKP)

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

    Science.gov (United States)

    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...

  5. Business Case Analysis of the Joint Strike Fighter's Alternate Engine Program

    National Research Council Canada - National Science Library

    Shick, BethAnn

    2007-01-01

    .... The JSF will serve the Air Force, Navy and Marine Corps, as well as many of our key international allies In 1998, the DoD initiated the JSF alternate engine program in an effort to achieve cost...

  6. Ethanol Research : Alternative Fuels & Life-Cycle Engineering Program : November 29, 2006 to November 28, 2011

    Science.gov (United States)

    2011-12-20

    This report presents the results of the successful ethanol fuel demonstration program conducted from September 2007 to September 2010. This project was a part of the U.S. Department of Transportation (DOT) Alternative Fuels and Life Cycle Engineering...

  7. Wellness-Based Group Counseling with Elementary Students in Disciplinary Alternative Education Programs

    Science.gov (United States)

    Perepiczka, Michelle

    2009-01-01

    Students in Disciplinary Alternative Education Programs (DAEPs) have a variety of behavior problems. School counselors in DAEPs have the opportunity to address emotional, academic, social, and behavioral concerns of these students. Counselors may use the strengths-based wellness paradigm as an alternative method of addressing students' holistic…

  8. 46 CFR 115.660 - Continued participation in the Alternative Hull Examination (AHE) Program.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Continued participation in the Alternative Hull... MORE THAN 49 PASSENGERS INSPECTION AND CERTIFICATION Hull and Tailshaft Examinations § 115.660 Continued participation in the Alternative Hull Examination (AHE) Program. (a) To continue to participate in...

  9. 46 CFR 176.660 - Continued participation in the Alternative Hull Examination (AHE) Program.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Continued participation in the Alternative Hull... (CONTINUED) SMALL PASSENGER VESSELS (UNDER 100 GROSS TONS) INSPECTION AND CERTIFICATION Hull and Tailshaft Examinations § 176.660 Continued participation in the Alternative Hull Examination (AHE) Program. (a) To...

  10. 46 CFR 115.630 - The Alternative Hull Examination (AHE) Program application.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false The Alternative Hull Examination (AHE) Program... PASSENGERS INSPECTION AND CERTIFICATION Hull and Tailshaft Examinations § 115.630 The Alternative Hull... hull examination date to the Officer in Charge, Marine Inspection (OCMI) who will oversee the survey...

  11. Linking linear programming and spatial simulation models to predict landscape effects of forest management alternatives

    Science.gov (United States)

    Eric J. Gustafson; L. Jay Roberts; Larry A. Leefers

    2006-01-01

    Forest management planners require analytical tools to assess the effects of alternative strategies on the sometimes disparate benefits from forests such as timber production and wildlife habitat. We assessed the spatial patterns of alternative management strategies by linking two models that were developed for different purposes. We used a linear programming model (...

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

    International Nuclear Information System (INIS)

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

    2008-01-01

    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 + 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. 46 CFR 71.50-15 - Description of the Alternative Hull Examination (AHE) Program for certain passenger vessels.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 3 2010-10-01 2010-10-01 false Description of the Alternative Hull Examination (AHE... Description of the Alternative Hull Examination (AHE) Program for certain passenger vessels. The Alternative Hull Examination (AHE) Program provides you with an alternative to a drydock examination by allowing...

  14. Molecular analysis of alternative transcripts of equine AXL receptor tyrosine kinase gene

    Directory of Open Access Journals (Sweden)

    Jeong-Woong Park

    2017-10-01

    Full Text Available Objective Since athletic performance is a most importance trait in horses, most research focused on physiological and physical studies of horse athletic abilities. In contrast, the molecular analysis as well as the regulatory pathway studies remain insufficient for evaluation and prediction of horse athletic abilities. In our previous study, we identified AXL receptor tyrosine kinase (AXL gene which was expressed as alternative spliced isoforms in skeletal muscle during exercise. In the present study, we validated two AXL alternative splicing transcripts (named as AXLa for long form and AXLb for short form in equine skeletal muscle to gain insight(s into the role of each alternative transcript during exercise. Methods We validated two isoforms of AXL transcripts in horse tissues by reverse transcriptase polymerase chain reaction (RT-PCR, and then cloned the transcripts to confirm the alternative locus and its sequences. Additionally, we examined the expression patterns of AXLa and AXLb transcripts in horse tissues by quantitative RT-PCR (qRT-PCR. Results Both of AXLa and AXLb transcripts were expressed in horse skeletal muscle and the expression levels were significantly increased after exercise. The sequencing analysis showed that there was an alternative splicing event at exon 11 between AXLa and AXLb transcripts. 3-dimentional (3D prediction of the alternative protein structures revealed that the structural distance of the connective region between fibronectin type 3 (FN3 and immunoglobin (Ig domain was different between two alternative isoforms. Conclusion It is assumed that the expression patterns of AXLa and AXLb transcripts would be involved in regulation of exercise-induced stress in horse muscle possibly through an NF-κB signaling pathway. Further study is necessary to uncover biological function(s and significance of the alternative splicing isoforms in race horse skeletal muscle.

  15. Molecular analysis of alternative transcripts of equine AXL receptor tyrosine kinase gene.

    Science.gov (United States)

    Park, Jeong-Woong; Song, Ki-Duk; Kim, Nam Young; Choi, Jae-Young; Hong, Seul A; Oh, Jin Hyeog; Kim, Si Won; Lee, Jeong Hyo; Park, Tae Sub; Kim, Jin-Kyoo; Kim, Jong Geun; Cho, Byung-Wook

    2017-10-01

    Since athletic performance is a most importance trait in horses, most research focused on physiological and physical studies of horse athletic abilities. In contrast, the molecular analysis as well as the regulatory pathway studies remain insufficient for evaluation and prediction of horse athletic abilities. In our previous study, we identified AXL receptor tyrosine kinase ( AXL ) gene which was expressed as alternative spliced isoforms in skeletal muscle during exercise. In the present study, we validated two AXL alternative splicing transcripts (named as AXLa for long form and AXLb for short form) in equine skeletal muscle to gain insight(s) into the role of each alternative transcript during exercise. We validated two isoforms of AXL transcripts in horse tissues by reverse transcriptase polymerase chain reaction (RT-PCR), and then cloned the transcripts to confirm the alternative locus and its sequences. Additionally, we examined the expression patterns of AXLa and AXLb transcripts in horse tissues by quantitative RT-PCR (qRT-PCR). Both of AXLa and AXLb transcripts were expressed in horse skeletal muscle and the expression levels were significantly increased after exercise. The sequencing analysis showed that there was an alternative splicing event at exon 11 between AXLa and AXLb transcripts. 3-dimentional (3D) prediction of the alternative protein structures revealed that the structural distance of the connective region between fibronectin type 3 (FN3) and immunoglobin (Ig) domain was different between two alternative isoforms. It is assumed that the expression patterns of AXLa and AXLb transcripts would be involved in regulation of exercise-induced stress in horse muscle possibly through an NF-κB signaling pathway. Further study is necessary to uncover biological function(s) and significance of the alternative splicing isoforms in race horse skeletal muscle.

  16. Differential HFE gene expression is regulated by alternative splicing in human tissues.

    Science.gov (United States)

    Martins, Rute; Silva, Bruno; Proença, Daniela; Faustino, Paula

    2011-03-03

    The pathophysiology of HFE-derived Hereditary Hemochromatosis and the function of HFE protein in iron homeostasis remain uncertain. Also, the role of alternative splicing in HFE gene expression regulation and the possible function of the corresponding protein isoforms are still unknown. The aim of this study was to gain insights into the physiological significance of these alternative HFE variants. Alternatively spliced HFE transcripts in diverse human tissues were identified by RT-PCR, cloning and sequencing. Total HFE transcripts, as well as two alternative splicing transcripts were quantified using a real-time PCR methodology. Intracellular localization, trafficking and protein association of GFP-tagged HFE protein variants were analysed in transiently transfected HepG2 cells by immunoprecipitation and immunofluorescence assays. Alternatively spliced HFE transcripts present both level- and tissue-specificity. Concerning the exon 2 skipping and intron 4 inclusion transcripts, the liver presents the lowest relative level, while duodenum presents one of the highest amounts. The protein resulting from exon 2 skipping transcript is unable to associate with β2M and TfR1 and reveals an ER retention. Conversely, the intron 4 inclusion transcript gives rise to a truncated, soluble protein (sHFE) that is mostly secreted by cells to the medium in association with β2M. HFE gene post-transcriptional regulation is clearly affected by a tissue-dependent alternative splicing mechanism. Among the corresponding proteins, a sHFE isoform stands out, which upon being secreted into the bloodstream, may act in remote tissues. It could be either an agonist or antagonist of the full length HFE, through hepcidin expression regulation in the liver or by controlling dietary iron absorption in the duodenum.

  17. Differential HFE gene expression is regulated by alternative splicing in human tissues.

    Directory of Open Access Journals (Sweden)

    Rute Martins

    Full Text Available BACKGROUND: The pathophysiology of HFE-derived Hereditary Hemochromatosis and the function of HFE protein in iron homeostasis remain uncertain. Also, the role of alternative splicing in HFE gene expression regulation and the possible function of the corresponding protein isoforms are still unknown. The aim of this study was to gain insights into the physiological significance of these alternative HFE variants. METHODOLOGY/PRINCIPAL FINDINGS: Alternatively spliced HFE transcripts in diverse human tissues were identified by RT-PCR, cloning and sequencing. Total HFE transcripts, as well as two alternative splicing transcripts were quantified using a real-time PCR methodology. Intracellular localization, trafficking and protein association of GFP-tagged HFE protein variants were analysed in transiently transfected HepG2 cells by immunoprecipitation and immunofluorescence assays. Alternatively spliced HFE transcripts present both level- and tissue-specificity. Concerning the exon 2 skipping and intron 4 inclusion transcripts, the liver presents the lowest relative level, while duodenum presents one of the highest amounts. The protein resulting from exon 2 skipping transcript is unable to associate with β2M and TfR1 and reveals an ER retention. Conversely, the intron 4 inclusion transcript gives rise to a truncated, soluble protein (sHFE that is mostly secreted by cells to the medium in association with β2M. CONCLUSIONS/SIGNIFICANCE: HFE gene post-transcriptional regulation is clearly affected by a tissue-dependent alternative splicing mechanism. Among the corresponding proteins, a sHFE isoform stands out, which upon being secreted into the bloodstream, may act in remote tissues. It could be either an agonist or antagonist of the full length HFE, through hepcidin expression regulation in the liver or by controlling dietary iron absorption in the duodenum.

  18. Expression pattern of the AHP gene family from Arabidopsis thaliana and organ specific alternative splicing in the AHP5 gene

    Czech Academy of Sciences Publication Activity Database

    Hradilová, Jana; Brzobohatý, Břetislav

    2007-01-01

    Roč. 51, č. 2 (2007), s. 257-267 ISSN 0006-3134 Grant - others:GA MŠk(CZ) LN00A081; GA AV ČR(CZ) IAA600040612 Program:LN; IA Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : Arabidopsis two component systems * gene expression analysis * real time RT-PCR Subject RIV: BO - Biophysics Impact factor: 1.259, year: 2007

  19. Hanford grout disposal program - an environmentally sound alternative

    International Nuclear Information System (INIS)

    Bergman, T.B.; Allison, J.M.

    1987-01-01

    The Hanford Grout Disposal Program (HGDP) is a comprehensive, integrated program to develop technology and facilities for the disposal of ∼ 3.0 x 10 5 m 3 (80 million gal) of the low-level fraction of liquid radioactive tank wastes at the Hanford site in southeastern Washington state. Environmentally sound disposal via long-term protection of the public and the environment is the principal goal of the HGDP. To accomplish this goal, several criteria have been established that guide technology and facility development activities. The key criteria are discussed. To meet the challenges posed by disposal of these wastes, the HGDP is developing a waste form using grout-forming materials, such as blast furnace slag, fly ash, clays, and Portland cement for solidification and immobilization of both the radioactive and hazardous chemical constituents. In addition to development of a final waste form, the HGDP is also developing a unique disposal system to assure long-term protection of the public and the environment. Disposal of a low-level nonhazardous waste will be initiated, as a demonstration of the disposal system concept, in June 1988. Disposal of higher activity hazardous wastes is scheduled to begin in October 1989

  20. ALTERNATIVES TO IMPROVE HYBRIDIZATION EFFICIENCY IN Eucalyptus BREEDING PROGRAMS

    Directory of Open Access Journals (Sweden)

    Roselaine Cristina Pereira

    2002-01-01

    Full Text Available Simple and quick hybridization procedures and ways to keep pollen grains viable for long periods are sought in plant breeding programs to provide greater work flexibility. The presentstudy was carried out to assess the efficiency of pollinations made shortly after flower emasculationand the viability of stored pollen from Eucalyptus camaldulensis and Eucalyptus urophylla clones cultivated in Northwestern Minas Gerais State. Controlled pollinations were carried out at zero, one,three, five and seven days after emasculation. Hybridization efficiency was assessed by thepercentage of viable fruits, number of seeds produced per fruit, percentage of viable seeds and also bycytological observation of the pollen development along the style. Flower buds from clones of the twospecies were collected close to anthesis to assess the viability of pollen grain storage. Pollen was thencollected and stored in a freezer (-18oC for 1, 2 and 3 months. Pollen assessed was carried out by invitro and in vivo germination tests. The efficiency of the pollinations varied with their delay and alsobetween species. The greatest pollination efficiency was obtained when they were carried out on thethird and fifth day after emasculation, but those performed simultaneously with emasculationproduced enough seeds to allow this practice in breeding programs. The decrease in pollen viabilitywith storage was not sufficiently significant to preclude the use of this procedure in artificialhybridization.

  1. Functions, structure, and read-through alternative splicing of feline APOBEC3 genes

    Science.gov (United States)

    Münk, Carsten; Beck, Thomas; Zielonka, Jörg; Hotz-Wagenblatt, Agnes; Chareza, Sarah; Battenberg, Marion; Thielebein, Jens; Cichutek, Klaus; Bravo, Ignacio G; O'Brien, Stephen J; Lochelt, Martin; Yuhki, Naoya

    2008-01-01

    Background Over the past years a variety of host restriction genes have been identified in human and mammals that modulate retrovirus infectivity, replication, assembly, and/or cross-species transmission. Among these host-encoded restriction factors, the APOBEC3 (A3; apolipoprotein B mRNA-editing catalytic polypeptide 3) proteins are potent inhibitors of retroviruses and retrotransposons. While primates encode seven of these genes (A3A to A3H), rodents carry only a single A3 gene. Results Here we identified and characterized several A3 genes in the genome of domestic cat (Felis catus) by analyzing the genomic A3 locus. The cat genome presents one A3H gene and three very similar A3C genes (a-c), probably generated after two consecutive gene duplications. In addition to these four one-domain A3 proteins, a fifth A3, designated A3CH, is expressed by read-through alternative splicing. Specific feline A3 proteins selectively inactivated only defined genera of feline retroviruses: Bet-deficient feline foamy virus was mainly inactivated by feA3Ca, feA3Cb, and feA3Cc, while feA3H and feA3CH were only weakly active. The infectivity of Vif-deficient feline immunodeficiency virus and feline leukemia virus was reduced only by feA3H and feA3CH, but not by any of the feA3Cs. Within Felidae, A3C sequences show significant adaptive selection, but unexpectedly, the A3H sequences present more sites that are under purifying selection. Conclusion Our data support a complex evolutionary history of expansion, divergence, selection and individual extinction of antiviral A3 genes that parallels the early evolution of Placentalia, becoming more intricate in taxa in which the arms race between host and retroviruses is harsher. PMID:18315870

  2. Daemen Alternative Energy/Geothermal Technologies Demonstration Program, Erie County

    Energy Technology Data Exchange (ETDEWEB)

    Beiswanger, Robert C. [Daemen College, Amherst, NY (United States)

    2013-02-28

    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 that are 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

  3. IMPLEMENTING INFORMATION TECHNOLOGY: AN ALTERNATIVE FOR URBAN RESETTLEMENT PROGRAM

    Directory of Open Access Journals (Sweden)

    Bauni Hamid

    2001-01-01

    Full Text Available Revitalizing slum-area has been recognized as one of the most complicated parts in urban resettlement program. With such a context we need a particular mode of communication to initiate and generate the project based on people's own aspiration. There are problem characteristics here, which are usually executed by Information Technology (IT. It is a potential to overcome the problem by using IT based on its ability to manage abundant information with various variables. At least there are three prospective opportunities in applying IT in this area. Firstly, it is the role of visualization, where computer can execute several visual features of the projects, which will be more representative than the previous ones. Secondly, it is the role of IT in generating the customization process to everyone involved in the projects. The last is the role of IT as executing tool for project's database management.

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

    Science.gov (United States)

    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…

  5. 75 FR 57027 - National Toxicology Program (NTP); NTP Interagency Center for the Evaluation of Alternative...

    Science.gov (United States)

    2010-09-17

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Toxicology Program (NTP); NTP Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM); Availability of Interagency..., Associate Director, National Toxicology Program. [FR Doc. 2010-23262 Filed 9-16-10; 8:45 am] BILLING CODE...

  6. 75 FR 32942 - National Toxicology Program (NTP); NTP Interagency Center for the Evaluation of Alternative...

    Science.gov (United States)

    2010-06-10

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Toxicology Program (NTP); NTP Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM): Availability of the Biennial... Toxicology Program. [FR Doc. 2010-13952 Filed 6-9-10; 8:45 am] BILLING CODE 4140-01-P ...

  7. 75 FR 25867 - National Toxicology Program (NTP) Interagency Center for the Evaluation of Alternative...

    Science.gov (United States)

    2010-05-10

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Toxicology Program (NTP) Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM.... Bucher, Associate Director, National Toxicology Program. [FR Doc. 2010-10958 Filed 5-7-10; 8:45 am...

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

    Science.gov (United States)

    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…

  9. 78 FR 42159 - Medicaid and Children's Health Insurance Programs: Essential Health Benefits in Alternative...

    Science.gov (United States)

    2013-07-15

    ... and 156 Medicaid and Children's Health Insurance Programs: Essential Health Benefits in Alternative... Secretary 45 CFR Parts 155 and 156 [CMS-2334-F] RIN 0938-AR04 Medicaid and Children's Health Insurance... Medicaid and the Children's Health Insurance Program (CHIP) eligibility notices, delegation of appeals, and...

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

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Alternate quality control programs for dairy products... for dairy products. (a) When a plant has in operation an acceptable quality control program which is... (CONTINUED) REGULATIONS AND STANDARDS UNDER THE AGRICULTURAL MARKETING ACT OF 1946 AND THE EGG PRODUCTS...

  11. Benchmarking of gene prediction programs for metagenomic data.

    Science.gov (United States)

    Yok, Non; Rosen, Gail

    2010-01-01

    This manuscript presents the most rigorous benchmarking of gene annotation algorithms for metagenomic datasets to date. We compare three different programs: GeneMark, MetaGeneAnnotator (MGA) and Orphelia. The comparisons are based on their performances over simulated fragments from one hundred species of diverse lineages. We defined four different types of fragments; two types come from the inter- and intra-coding regions and the other types are from the gene edges. Hoff et al. used only 12 species in their comparison; therefore, their sample is too small to represent an environmental sample. Also, no predecessors has separately examined fragments that contain gene edges as opposed to intra-coding regions. General observations in our results are that performances of all these programs improve as we increase the length of the fragment. On the other hand, intra-coding fragments of our data show low annotation error in all of the programs if compared to the gene edge fragments. Overall, we found an upper-bound performance by combining all the methods.

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

    Science.gov (United States)

    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.

  13. Can Thrifty Gene(s or Predictive Fetal Programming for Thriftiness Lead to Obesity?

    Directory of Open Access Journals (Sweden)

    Ulfat Baig

    2011-01-01

    Full Text Available Obesity and related disorders are thought to have their roots in metabolic “thriftiness” that evolved to combat periodic starvation. The association of low birth weight with obesity in later life caused a shift in the concept from thrifty gene to thrifty phenotype or anticipatory fetal programming. The assumption of thriftiness is implicit in obesity research. We examine here, with the help of a mathematical model, the conditions for evolution of thrifty genes or fetal programming for thriftiness. The model suggests that a thrifty gene cannot exist in a stable polymorphic state in a population. The conditions for evolution of thrifty fetal programming are restricted if the correlation between intrauterine and lifetime conditions is poor. Such a correlation is not observed in natural courses of famine. If there is fetal programming for thriftiness, it could have evolved in anticipation of social factors affecting nutrition that can result in a positive correlation.

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

    Science.gov (United States)

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

    2016-01-01

    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

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

    International Nuclear Information System (INIS)

    Kristofferson, K.

    1995-01-01

    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

  16. Alternative Polyadenylation of Tumor Suppressor Genes in Small Intestinal Neuroendocrine Tumors

    OpenAIRE

    Rehfeld, Anders; Plass, Mireya; Døssing, Kristina; Knigge, Ulrich; Kjær, Andreas; Krogh, Anders; Friis-Hansen, Lennart

    2014-01-01

    The tumorigenesis of small intestinal neuroendocrine tumors (SI-NETs) is poorly understood. Recent studies have associated alternative polyadenylation (APA) with proliferation, cell transformation, and cancer. Polyadenylation is the process in which the pre-messenger RNA is cleaved at a polyA site and a polyA tail is added. Genes with two or more polyA sites can undergo APA. This produces two or more distinct mRNA isoforms with different 3′ untranslated regions. Additionally, APA can also pro...

  17. Alternative Polyadenylation Patterns for Novel Gene Discovery and Classification in Cancer

    Directory of Open Access Journals (Sweden)

    Oguzhan Begik

    2017-07-01

    Full Text Available Certain aspects of diagnosis, prognosis, and treatment of cancer patients are still important challenges to be addressed. Therefore, we propose a pipeline to uncover patterns of alternative polyadenylation (APA, a hidden complexity in cancer transcriptomes, to further accelerate efforts to discover novel cancer genes and pathways. Here, we analyzed expression data for 1045 cancer patients and found a significant shift in usage of poly(A signals in common tumor types (breast, colon, lung, prostate, gastric, and ovarian compared to normal tissues. Using machine-learning techniques, we further defined specific subsets of APA events to efficiently classify cancer types. Furthermore, APA patterns were associated with altered protein levels in patients, revealed by antibody-based profiling data, suggesting functional significance. Overall, our study offers a computational approach for use of APA in novel gene discovery and classification in common tumor types, with important implications in basic research, biomarker discovery, and precision medicine approaches.

  18. Transfer of toxin genes to alternate bacterial hosts for mosquito control

    Directory of Open Access Journals (Sweden)

    Sergio Orduz

    1995-02-01

    Full Text Available Mosquitoes are vector of serious human and animal diseases, such as malaria, dengue, yellow fever, among others. The use of biological control agents has provide an environmentally safe and highly specific alternative to the use of chemical insecticides in the control of vector borne diseases. Bacillus thuringiensis and B. sphaericus produce toxic proteins to mosquito larvae. Great progress has been made on the biochemical and molecular characterization of such proteins and the genes encoding them. Nevertheless, the low residuality of these biological insecticides is one of the major drawbacks. This article present some interesting aspects of the mosquito larvae feeding habits and review the attempts that have been made to genetically engineer microorganisms that while are used by mosquito larvae as a food source should express the Bacillus toxin genes in order to improve the residuality and stability in the mosquito breeding ponds.

  19. Alternative polyadenylation of tumor suppressor genes in small intestinal neuroendocrine tumors

    DEFF Research Database (Denmark)

    Rehfeld, Anders Aagaard; Plass, Mireya; Døssing, Kristina

    2014-01-01

    The tumorigenesis of small intestinal neuroendocrine tumors (SI-NETs) is poorly understood. Recent studies have associated alternative polyadenylation (APA) with proliferation, cell transformation, and cancer. Polyadenylation is the process in which the pre-messenger RNA is cleaved at a polyA site...... and a polyA tail is added. Genes with two or more polyA sites can undergo APA. This produces two or more distinct mRNA isoforms with different 3' untranslated regions. Additionally, APA can also produce mRNAs containing different 3'-terminal coding regions. Therefore, APA alters both the repertoire...... and the expression level of proteins. Here, we used high-throughput sequencing data to map polyA sites and characterize polyadenylation genome-wide in three SI-NETs and a reference sample. In the tumors, 16 genes showed significant changes of APA pattern, which lead to either the 3' truncation of mRNA coding regions...

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

    International Nuclear Information System (INIS)

    Smirnova, Anna S.; Morgun, Andrey; Shulzhenko, Natalia; Silva, Ismael D.C.G.; Gerbase-DeLima, Maria

    2005-01-01

    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

  1. Alternative polyadenylation of tumor suppressor genes in small intestinal neuroendocrine tumors.

    Science.gov (United States)

    Rehfeld, Anders; Plass, Mireya; Døssing, Kristina; Knigge, Ulrich; Kjær, Andreas; Krogh, Anders; Friis-Hansen, Lennart

    2014-01-01

    The tumorigenesis of small intestinal neuroendocrine tumors (SI-NETs) is poorly understood. Recent studies have associated alternative polyadenylation (APA) with proliferation, cell transformation, and cancer. Polyadenylation is the process in which the pre-messenger RNA is cleaved at a polyA site and a polyA tail is added. Genes with two or more polyA sites can undergo APA. This produces two or more distinct mRNA isoforms with different 3' untranslated regions. Additionally, APA can also produce mRNAs containing different 3'-terminal coding regions. Therefore, APA alters both the repertoire and the expression level of proteins. Here, we used high-throughput sequencing data to map polyA sites and characterize polyadenylation genome-wide in three SI-NETs and a reference sample. In the tumors, 16 genes showed significant changes of APA pattern, which lead to either the 3' truncation of mRNA coding regions or 3' untranslated regions. Among these, 11 genes had been previously associated with cancer, with 4 genes being known tumor suppressors: DCC, PDZD2, MAGI1, and DACT2. We validated the APA in three out of three cases with quantitative real-time-PCR. Our findings suggest that changes of APA pattern in these 16 genes could be involved in the tumorigenesis of SI-NETs. Furthermore, they also point to APA as a new target for both diagnostic and treatment of SI-NETs. The identified genes with APA specific to the SI-NETs could be further tested as diagnostic markers and drug targets for disease prevention and treatment.

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

    Directory of Open Access Journals (Sweden)

    Lukasz F Sobala

    2016-05-01

    Full Text Available 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.

  3. Epigenetic Machinery Regulates Alternative Splicing of Androgen Receptor (AR) Gene in Castration Resistant Prostate Cancer

    Science.gov (United States)

    2017-09-01

    resistant prostate cancer PRINCIPAL INVESTIGATOR: Zhi-Ping Liu CONTRACTING ORGANIZATION: UT Southwestern Medical Center Dallas, TX 75390 REPORT DATE...NUMBER gene in castration-resistant prostate cancer 5b. GRANT NUMBER W81XWH-16-1-0531 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Zhi-Ping Liu 5d...NOTES 14. ABSTRACT Androgen deprivation therapy (ADT) is the primary treatment for metastatic prostate cancer (PCa) since PCa depends on androgen for

  4. 46 CFR 176.620 - Description of the Alternative Hull Examination (AHE) Program for certain passenger vessels.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Description of the Alternative Hull Examination (AHE... Hull and Tailshaft Examinations § 176.620 Description of the Alternative Hull Examination (AHE) Program for certain passenger vessels. The Alternative Hull Examination (AHE) Program provides you with an...

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

  6. GPAW optimized for Blue Gene/P using hybrid programming

    DEFF Research Database (Denmark)

    Kristensen, Mads Ruben Burgdorff; Happe, Hans Henrik; Vinter, Brian

    2009-01-01

    In this work we present optimizations of a Grid-based projector-augmented wave method software, GPAW for the Blue Gene/P architecture. The improvements are achieved by exploring the advantage of shared and distributed memory programming also known as hybrid programming. The work focuses on optimi......In this work we present optimizations of a Grid-based projector-augmented wave method software, GPAW for the Blue Gene/P architecture. The improvements are achieved by exploring the advantage of shared and distributed memory programming also known as hybrid programming. The work focuses...... on optimizing a very time consuming operation in GPAW, the finite-different stencil operation, and different hybrid programming approaches are evaluated. The work succeeds in demonstrating a hybrid programming model which is clearly beneficial compared to the original flat programming model. In total...... an improvement of 1.94 compared to the original implementation is obtained. The results we demonstrate here are reasonably general and may be applied to other finite difference codes....

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

    International Nuclear Information System (INIS)

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

    2011-01-01

    Highlights: → Novel role for poliovirus 2A protease as splicing modulator. → Poliovirus 2A protease inhibits the alternative splicing of pre-mRNAs. → 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 pro modulating the alternative splicing of pre-mRNAs. Expression of 2A pro potently inhibits splicing of reporter genes in HeLa cells. Low amounts of 2A 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 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 pro on splicing is to selectively block the second catalytic step.

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

    Energy Technology Data Exchange (ETDEWEB)

    Alvarez, Enrique, E-mail: ealvarez@cbm.uam.es [Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera, 1 Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); Castello, Alfredo; Carrasco, Luis; Izquierdo, Jose M. [Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera, 1 Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain)

    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.

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

    Directory of Open Access Journals (Sweden)

    Junyu Zhang

    Full Text Available 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

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

    Science.gov (United States)

    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.

  12. The selector gene Pax7 dictates alternate pituitary cell fates through its pioneer action on chromatin remodeling

    NARCIS (Netherlands)

    Budry, L.; Balsalobre, A.; Gauthier, Y.; Khetchoumian, K.; L'Honore, A.; Vallette-Kasic, S.; Brue, T; Figarella-Branger, D.; Meij, B.P.; Drouin, J.

    2012-01-01

    Genes Dev. 2012 Oct 15;26(20):2299-310. doi: 10.1101/gad.200436.112. The selector gene Pax7 dictates alternate pituitary cell fates through its pioneer action on chromatin remodeling. Budry L, Balsalobre A, Gauthier Y, Khetchoumian K, L'honoré A, Vallette S, Brue T, Figarella-Branger D, Meij B,

  13. Plutonium-bearing materials feed report for the DOE Fissile Materials Disposition Program alternatives

    International Nuclear Information System (INIS)

    Brough, W.G.; Boerigter, S.T.

    1995-01-01

    This report has identified all plutonium currently excess to DOE Defense Programs under current planning assumptions. A number of material categories win clearly fan within the scope of the MD (Materials Disposition) program, but the fate of the other categories are unknown at the present time. MD planning requires that estimates be made of those materials likely to be considered for disposition actions so that bounding cases for the PEIS (Programmatic Environmental Impact Statement) can be determined and so that processing which may be required can be identified in considering the various alternatives. A systematic analysis of the various alternatives in reachmg the preferred alternative requires an understanding of the possible range of values which may be taken by the various categories of feed materials. One table identifies the current total inventories excess to Defense Program planning needs and represents the bounding total of Pu which may become part of the MD disposition effort for all materials, except site return weapons. The other categories, principally irradiated fuel, rich scrap, and lean scrap, are discussed. Another table summarizes the ranges and expected quantities of Pu which could become the responsibility of the MD program. These values are to be used for assessing the impact of the various alternatives and for scaling operations to assess PEIS impact. Determination of the actual materials to be included in the disposition program will be done later

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

    Directory of Open Access Journals (Sweden)

    Rosanna Aversa

    2016-01-01

    Full Text Available 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.

  15. Bureaucratic discretion and alternative teacher certification: understanding program variation in Missouri.

    Directory of Open Access Journals (Sweden)

    Ethan B. Heinen

    2007-06-01

    Full Text Available Alternative teacher certification literature has contributed significantly to our understanding of this approach to teacher preparation. However, this literature has more often than not treated alternative teacher certification programs (ATCPs as a black box, thus ignoring program heterogeneity. The present study examines how and why five ATCPs in Missouri have evolved in different ways. To understand this variation and its potential significance for researchers and practitioners, we use political science literature on bureaucratic discretion to understand programs' varied responses within the same state policy context. Using a multiple case study design, we present two key findings. First, external factors such as the state's regulatory approach, programs' relationships with school districts, and programs' relationship with external partners shape program coordinators' perceptions of their discretionary authority. Second, within an environment of limited regulation, programs responded to these external factors in ways that shaped programs in dramatically different ways. These approaches ranged from formal partnerships with large urban school districts and philanthropic funders to alternative certification programs that were at least partially blended with existing undergraduate and post baccalaureate teacher preparation programs. In our discussion, we explore how state attempts to widen the discretionary space between the rules may have allowed external interests (e.g., school districts, and external funders to backfill that space in ways that limit the potential for programs to provide high quality preparation experiences. This study explores these consequences and trade offs in order to inform policy makers and practitioners who are concerned with fostering innovative and creative ways to prepare high quality teachers.

  16. Programs and Practices for Special Education Students in Alternative Education Settings. Research to Practice Brief. Volume 6, Issue 1

    Science.gov (United States)

    Unruh, Deanne; Bullis, Michael; Todis, Bonnie; Waintrup, Miriam; Atkins, Trent

    2007-01-01

    This brief presents a review of alternative education programs targeting students with disabilities. Because there is no clear picture of how alternative education programs operate, specifically regarding youth with disabilities, the U.S. Department of Education's Office of Special Education Programs (OSEP) funded three grants to develop a…

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

    Science.gov (United States)

    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.

  18. The restructured fusion program and the role of alternative fusion concepts

    International Nuclear Information System (INIS)

    Perkins, L.J.

    1996-01-01

    This testimony to the subcommittee on Energy and the Environment of the U.S. House of Representatives's Committee on Science pushes for about 25% of the fusion budget to go to alternative fusion concepts. These concepts are: low density magnetic confinement, inertial confinement fusion, high density magnetic confinement, and non- thermonuclear and miscellaneous programs. Various aspects of each of these concepts are outlined

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

    Science.gov (United States)

    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…

  20. 76 FR 72493 - ITS Joint Program Office Webinar on Alternative Organizational Structures for a Certificate...

    Science.gov (United States)

    2011-11-23

    ... organizational structures for a certificate management entity (CME) to support a trusted and secure connected... DEPARTMENT OF TRANSPORTATION ITS Joint Program Office Webinar on Alternative Organizational... Adam Hopps at (202) 680-0091. The ITS JPO will present results from an early analysis of organizational...

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

    Science.gov (United States)

    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…

  2. Alternative Transportation Program, P.L. 94-142. 1985-86 Evaluation Report.

    Science.gov (United States)

    Case, Elizabeth J.; Bouchard, Donald

    Overall effectiveness and impact were evaluated for the Alternative Transportation Program (ATP) of the Albuquerque (New Mexico) Public Schools, funded under Public Law 94-142, the Education for All Handicapped Children Act. Two specialists implemented the ATP, which developed and presented curricula and assemblies tailored to handicapped students…

  3. Two Reading Assessments for Youth in Alternative Basic Skills and Livelihood Skills Training Programs

    Science.gov (United States)

    Comings, John P.; Strucker, John; Bell, Brenda

    2017-01-01

    This article describes two assessment tools that have been used to assess the reading skills of youth participating in alternative basic skills and livelihood skills training programs. The Rapid Assessment of Reading Skills (RARS) was developed to identify potential participants who needed to improve their reading skills before beginning training…

  4. Conceptions of Teaching Science Held by Novice Teachers in an Alternative Certification Program

    Science.gov (United States)

    Koballa, Thomas R.; Glynn, Shawn M.; Upson, Leslie

    2005-01-01

    Case studies to investigate the conceptions of teaching science held by three novice teachers participating in an alternative secondary science teacher certification program were conducted, along with the relationships between their conceptions of science teaching and their science teaching practice. Data used to build the cases included the…

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

    Science.gov (United States)

    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.

  6. Secondary Mathematics Teacher Differences: Teacher Quality and Preparation in a New York City Alternative Certification Program

    Science.gov (United States)

    Evans, Brian R.

    2011-01-01

    Providing students in urban settings with quality teachers is important for student achievement. This study examined the differences in content knowledge, attitudes toward mathematics, and teacher efficacy among several different types of alternatively certified teachers in a sample from the New York City Teaching Fellows program in order to…

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

  9. Exchange program. Alternative options for purchase of environmentally friendly vehicles in Stockholm

    Energy Technology Data Exchange (ETDEWEB)

    Rader Olsson, Amy [Inregia AB, Stockholm (Sweden); Elam, N. [Atrax Energi AB, Goeteborg (Sweden)

    1999-11-01

    The city of Stockholm has decided to exchange 300 of its gasoline-driven vehicles for vehicles which emit fewer hazardous pollutants. A vehicle exchange program is being developed based on analyses which describe the driving patterns of Stockholm's vehicles, alternative fuel technology status, and financing alternatives. This report comprises the first two analyses, that of Stockholm's fleet driving patterns and alternative fuel technology options. The report has four major sections: * a technical analysis of the status of certain fuels and vehicles, including prognoses of availability in Sweden and the future development potential of each. (electric, biogas, ethanol, RME), * a driving study, which identifies those vehicles currently in Stockholm's fleet which could be exchanged for alternatively-fueled vehicles, * an analysis of five purchase package alternatives, and * a location analysis, which describes the accessibility of vehicles in each alternative to alternative fuel refueling facilities in Stockholm. Given current prices and availability of the alternative fuels and vehicles studied, we recommend a high share of electric and biogas vehicles for purchases during 1997. The cost-effectiveness of different vehicle types in their reduction of various hazardous pollutants, may however change dramatically as prices and availability of vehicles changes and the market for alternative fuels develops. Accessibility to alternative fuel refueling facilities is adequate in Stockholm, though not always ideal. To improve the accessibility of biogas vehicles further, we suggest a third biogas refueling facility in the city's northeastern area (Ropsten, Vaertahamnen). If MFO chooses to purchase a significant number of diesel passenger vehicles to be driven on RME; we propose that a facility in the northeastern area would improve accessibility more than another facility in southern Stockholm.

  10. Protein targeting in the analysis of learning and memory: a potential alternative to gene targeting.

    Science.gov (United States)

    Gerlai, R; Williams, S P; Cairns, B; Van Bruggen, N; Moran, P; Shih, A; Caras, I; Sauer, H; Phillips, H S; Winslow, J W

    1998-11-01

    Gene targeting using homologous recombination in embryonic stem (ES) cells offers unprecedented precision with which one may manipulate single genes and investigate the in vivo effects of defined mutations in the mouse. Geneticists argue that this technique abrogates the lack of highly specific pharmacological tools in the study of brain function and behavior. However, by now it has become clear that gene targeting has some limitations too. One problem is spatial and temporal specificity of the generated mutation, which may appear in multiple brain regions or even in other organs and may also be present throughout development, giving rise to complex, secondary phenotypical alterations. This may be a disadvantage in the functional analysis of a number of genes associated with learning and memory processes. For example, several proteins, including neurotrophins--cell-adhesion molecules--and protein kinases, that play a significant developmental role have recently been suggested to be also involved in neural and behavioral plasticity. Knocking out genes of such proteins may lead to developmental alterations or even embryonic lethality in the mouse, making it difficult to study their function in neural plasticity, learning, and memory. Therefore, alternative strategies to gene targeting may be needed. Here, we suggest a potentially useful in vivo strategy based on systemic application of immunoadhesins, genetically engineered fusion proteins possessing the Fc portion of the human IgG molecule and, for example, a binding domain of a receptor of interest. These proteins are stable in vivo and exhibit high binding specificity and affinity for the endogenous ligand of the receptor, but lack the ability to signal. Thus, if delivered to the brain, immunoadhesins may specifically block signalling of the receptor of interest. Using osmotic minipumps, the protein can be infused in a localized region of the brain for a specified period of time (days or weeks). Thus, the location

  11. Isoflurane is a suitable alternative to ether for anesthetizing rats prior to euthanasia for gene expression analysis.

    Science.gov (United States)

    Nakatsu, Noriyuki; Igarashi, Yoshinobu; Aoshi, Taiki; Hamaguchi, Isao; Saito, Masumichi; Mizukami, Takuo; Momose, Haruka; Ishii, Ken J; Yamada, Hiroshi

    2017-01-01

    Diethyl ether (ether) had been widely used in Japan for anesthesia, despite its explosive properties and toxicity to both humans and animals. We also had used ether as an anesthetic for euthanizing rats for research in the Toxicogenomics Project (TGP). Because the use of ether for these purposes will likely cease, it is required to select an alternative anesthetic which is validated for consistency with existing TGP data acquired under ether anesthesia. We therefore compared two alternative anesthetic candidates, isoflurane and pentobarbital, with ether in terms of hematological findings, serum biochemical parameters, and gene expressions. As a result, few differences among the three agents were observed. In hematological and serum biochemistry analysis, no significant changes were found. In gene expression analysis, four known genes were extracted as differentially expressed genes in the liver of rats anesthetized with ether, isoflurane, or pentobarbital. However, no significant relationships were detected using gene ontology, pathway, or gene enrichment analyses by DAVID and TargetMine. Surprisingly, although it was expected that the lung would be affected by administration via inhalation, only one differentially expressed gene was extracted in the lung. Taken together, our data indicate that there are no significant differences among ether, isoflurane, and pentobarbital with respect to effects on hematological parameters, serum biochemistry parameters, and gene expression. Based on its smallest affect to existing data and its safety profile for humans and animals, we suggest isoflurane as a suitable alternative anesthetic for use in rat euthanasia in toxicogenomics analysis.

  12. [HER2 gene amplification assay: is CISH an alternative to FISH?].

    Science.gov (United States)

    Denoux, Yves; Arnould, Laurent; Fiche, Maryse; Lannes, B; Couturier, Jérôme; Vincent-Salomon, Anne; Penault-Llorca, Frédérique; Antoine, M; Balaton, A; Baranzelli, M C; Becette, V; Bellocq, J P; Bibeau, F; Ettore, F; Fridman, V; Gnassia, J P; Jacquemier, J; MacGrogan, G; Mathieu, M C; Migeon, C; Rigaud, C; Roger, P; Sigal-Zafrani, B; Simony-Lafontaine, J; Trassard, M; Treilleux, I; Verriele, V; Voigt, J J

    2003-12-01

    The HER2 proto-oncogene encodes a transmembrane protein, which is considered to function as a growth factor receptor. Overexpression of this protein found by immunohistochemistry in about 20% of infiltrating breast carcinomas, has a predictive value of response to treatment by trastuzumab, an anti-HER2 humanized monoclonal antibody. Search for HER2 gene amplification is necessary to adapt the immunohistochemical technique quality and also in the cases of delicate analysis or weak overexpression. It is usually carried out by Fluorescence In Situ Hybridization (FISH). A more recent hybridization technique, named CISH because of its chromogenic revelation is an alternative method, which gives highly correlated results with FISH. We present details of this technique, which may be more familiar for the pathologists than FISH, because reading analysis is similar to that of immunohistochemical staining.

  13. A dual-specificity isoform of the protein kinase inhibitor PKI produced by alternate gene splicing.

    Science.gov (United States)

    Kumar, Priyadarsini; Walsh, Donal A

    2002-03-15

    We have previously shown that the protein kinase inhibitor beta (PKIbeta) form of the cAMP-dependent protein kinase inhibitor exists in multiple isoforms, some of which are specific inhibitors of the cAMP-dependent protein kinase, whereas others also inhibit the cGMP-dependent enzyme [Kumar, Van Patten and Walsh (1997), J. Biol. Chem. 272, 20011-20020]. We have now demonstrated that the switch from a cAMP-dependent protein kinase (PKA)-specific inhibitor to one with dual specificity arises as a consequence of alternate gene splicing. We have confirmed using bacterially produced pure protein that a single inhibitor species has dual specificity for both PKA and cGMP-dependent protein kinase (PKG), inhibiting each with very high and closely similar inhibitory potencies. The gene splicing converted a protein with 70 amino acids into one of 109 amino acids, and did not change the inhibitory potency to PKA, but changed it from a protein that had no detectable PKG inhibitory activity to one that now inhibited PKG in the nanomolar range.

  14. [Alternating hemiplegia of childhood: ATP1A3 gene analysis in 16 patients].

    Science.gov (United States)

    Ulate-Campos, Adriana; Fons, Carmen; Campistol, Jaume; Martorell, Loreto; Cancho-Candela, Ramón; Eiris, Jesús; López-Laso, Eduardo; Pineda, Mercedes; Sans, Anna; Velázquez, Ramón

    2014-07-07

    Alternating hemiplegia in childhood (AHC) is a disease characterized by recurrent episodes of hemiplegia, tonic or dystonic crisis and abnormal ocular movements. Recently, mutations in the ATP1A3 gene have been identified as the causal mechanism of AHC. The objective is to describe a series of 16 patients with clinical and genetic diagnosis of AHC. It is a descriptive, retrospective, multicenter study of 16 patients with clinical diagnosis of AHC in whom mutations in ATP1A3 were identified. Six heterozygous, de novo mutations were found in the ATP1A3 gene. The most frequent mutation was G2401A in 8 patients (50%) followed by G2443A in 3 patients (18.75%), G2893A in 2 patients (12.50%) and C2781G, G2893C and C2411T in one patient, respectively (6.25% each). In the studied population with AHC, de novo mutations were detected in 100% of patients. The most frequent mutations were D801N y la E815K, as reported in other series. Copyright © 2013 Elsevier España, S.L. All rights reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

    Du, Kejun; Chen, Yaoming; Dai, Zongming; Bi, Yuan; Cai, Tongjian [Department of Occupational and Environmental Health, Fourth Military Medical University, Xi' an 710032, Shaanxi Province (China); Hou, Lichao [Department of Anesthesiology, Xijing Hospital, Fourth Military Medical University, Xi' an 710032, Shaanxi Province (China); Chai, Yubo; Song, Qinghe; Chen, Sumin [Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi' an 710032, Shaanxi Province (China); Luo, Wenjing, E-mail: luowenj@fmmu.edu.cn [Department of Occupational and Environmental Health, Fourth Military Medical University, Xi' an 710032, Shaanxi Province (China); Chen, Jingyuan, E-mail: jy_chen@fmmu.edu.cn [Department of Occupational and Environmental Health, Fourth Military Medical University, Xi' an 710032, Shaanxi Province (China)

    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.

  16. Evaluation Policy Alternatives for the Reengineering of the Department of Defense Personal Property Shipment and Storage Program - A Stakeholder Approach

    National Research Council Canada - National Science Library

    Lepson, Michael

    1999-01-01

    ...) to evaluate the personal property pilot programs as part of Management Reform Memorandum # 6. This thesis evaluates the policy alternatives for reengineering the DOD personal property program using a stakeholder approach...

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

    Science.gov (United States)

    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. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  18. A Preventive Intervention Program for Urban African American Youth Attending an Alternative Education Program: Background, Implementation, and Feasibility.

    Science.gov (United States)

    Carswell, Steven B; Hanlon, Thomas E; O'Grady, Kevin E; Watts, Amy M; Pothong, Pattarapan

    2009-01-01

    This paper presents background, implementation, and feasibility findings associated with planning and conducting an after-school intervention program in an alternative education setting designed to prevent the initiation and escalation of violence and substance abuse among urban African American youth at high risk for life-long problem behaviors. Evolving from earlier preventive interventions implemented in clinic and school settings, the program, entitled The Village Model of Care, consisted of structured group mentoring, parental support, and community outreach services administered to alternative education students and their primary caregiver(s) during the school year. Over a two-year intake period, 109 youth participated in the present process evaluation study. Findings from the study not only provided relevant demographic information on the characteristics of youth likely to be included in such programs but also indicated the importance of including the family in the rehabilitation effort and the need for school administrative system support for the underlying alternative education approach. The information presented in this report has a direct bearing on the planning of future prevention efforts conducted in similar settings that are aimed at reducing problem behaviors and promoting positive lifestyles among high-risk youth.

  19. Alternative Renewable Biomass Tracking Program Document under the Renewable Fuel Standard Program

    Science.gov (United States)

    The approval letters that EPA approves a company's biomass tracking program meeting all the requirements outlined in 40 CFR part 80.1454, including elements determined necessary to achieve the level of quality assurance required under the regulation list.

  20. 46 CFR 115.620 - Description of the Alternative Hull Examination (AHE) Program for certain passenger vessels.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Description of the Alternative Hull Examination (AHE... ACCOMMODATIONS FOR MORE THAN 49 PASSENGERS INSPECTION AND CERTIFICATION Hull and Tailshaft Examinations § 115.620 Description of the Alternative Hull Examination (AHE) Program for certain passenger vessels. The Alternative...

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

    Science.gov (United States)

    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. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  2. 46 CFR 71.50-27 - Alternative Hull Examination (AHE) program options: Divers or underwater remotely operated...

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 3 2010-10-01 2010-10-01 false Alternative Hull Examination (AHE) program options...-27 Alternative Hull Examination (AHE) program options: Divers or underwater remotely operated vehicle... operations; (2) Provide permanent hull markings, a temporary grid system of wires or cables spaced not more...

  3. Gene expression programming for prediction of scour depth downstream of sills

    Science.gov (United States)

    Azamathulla, H. Md.

    2012-08-01

    SummaryLocal scour is crucial in the degradation of river bed and the stability of grade control structures, stilling basins, aprons, ski-jump bucket spillways, bed sills, weirs, check dams, etc. This short communication presents gene-expression programming (GEP), which is an extension to genetic programming (GP), as an alternative approach to predict scour depth downstream of sills. Published data were compiled from the literature for the scour depth downstream of sills. The proposed GEP approach gives satisfactory results (R2 = 0.967 and RMSE = 0.088) compared to the existing predictors (Chinnarasri and Kositgittiwong, 2008) with R2 = 0.87 and RMSE = 2.452 for relative scour depth.

  4. Report on the Concept Review Committee recommendations for proof-of-principle alternate concept programs

    International Nuclear Information System (INIS)

    1979-03-01

    The report is organized as follows: Section II contains a discussion of the meeting procedures used on October 16--18, 1978, and the rules employed for technical consultants and advisors to the CRC. Section III contains a discussion of the CRC recommendations and some of the factors taken into consideration by the Committee. Section IV briefly discusses where do we go from here in DOE's alternate concepts program

  5. Transcriptome analyses and differential gene expression in a non-model fish species with alternative mating tactics.

    Science.gov (United States)

    Schunter, Celia; Vollmer, Steven V; Macpherson, Enrique; Pascual, Marta

    2014-02-28

    Social dominance is important for the reproductive success of males in many species. In the black-faced blenny (Tripterygion delaisi) during the reproductive season, some males change color and invest in nest making and defending a territory, whereas others do not change color and 'sneak' reproductions when females lay their eggs. Using RNAseq, we profiled differential gene expression between the brains of territorial males, sneaker males, and females to study the molecular signatures of male dimorphism. We found that more genes were differentially expressed between the two male phenotypes than between males and females, suggesting that during the reproductive period phenotypic plasticity is a more important factor in differential gene expression than sexual dimorphism. The territorial male overexpresses genes related to synaptic plasticity and the sneaker male overexpresses genes involved in differentiation and development. Previously suggested candidate genes for social dominance in the context of alternative mating strategies seem to be predominantly species-specific. We present a list of novel genes which are differentially expressed in Tripterygion delaisi. This is the first genome-wide study for a molecular non-model species in the context of alternative mating strategies and provides essential information for further studies investigating the molecular basis of social dominance.

  6. XRCC1 suppresses somatic hypermutation and promotes alternative nonhomologous end joining in Igh genes.

    Science.gov (United States)

    Saribasak, Huseyin; Maul, Robert W; Cao, Zheng; McClure, Rhonda L; Yang, William; McNeill, Daniel R; Wilson, David M; Gearhart, Patricia J

    2011-10-24

    Activation-induced deaminase (AID) deaminates cytosine to uracil in immunoglobulin genes. Uracils in DNA can be recognized by uracil DNA glycosylase and abasic endonuclease to produce single-strand breaks. The breaks are repaired either faithfully by DNA base excision repair (BER) or mutagenically to produce somatic hypermutation (SHM) and class switch recombination (CSR). To unravel the interplay between repair and mutagenesis, we decreased the level of x-ray cross-complementing 1 (XRCC1), a scaffold protein involved in BER. Mice heterozygous for XRCC1 showed a significant increase in the frequencies of SHM in Igh variable regions in Peyer's patch cells, and of double-strand breaks in the switch regions during CSR. Although the frequency of CSR was normal in Xrcc1(+/-) splenic B cells, the length of microhomology at the switch junctions decreased, suggesting that XRCC1 also participates in alternative nonhomologous end joining. Furthermore, Xrcc1(+/-) B cells had reduced Igh/c-myc translocations during CSR, supporting a role for XRCC1 in microhomology-mediated joining. Our results imply that AID-induced single-strand breaks in Igh variable and switch regions become substrates simultaneously for BER and mutagenesis pathways.

  7. Alternative bio-based fuels for aviation: the clean airports program

    International Nuclear Information System (INIS)

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

    1997-01-01

    The Renewable Aviation Fuels Development Center at Baylor University in Waco, Texas, has been designated as the national coordinator of the Clean Airports Program. The U.S. Dept. of Energy (US DOE) conferred this designation in March 1996. This program, a spin-off of the Clean Cities Program, was initiated to increase the use of alternative fuels in aviation. The two major fuels used in aviation are 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 U.S. today. Turbine engine fuel (jet fuel) produces two major environmental impacts: a local one, in the vicinity of the airports, and a global impact on climate change. The Clean Airports Program was established to achieve and maintain clean air at and in the vicinity of airports, through the use of alternative fuel-powered air and ground transportation vehicles. (author)

  8. Abnormalities in alternative splicing of angiogenesis-related genes and their role in HIV-related cancers

    Directory of Open Access Journals (Sweden)

    Mthembu NN

    2017-03-01

    Full Text Available Nonkululeko N Mthembu,1 Zukile Mbita,2 Rodney Hull,1 Zodwa Dlamini1 1Research, Innovation and Engagements, Mangosuthu University of Technology, Durban, 2Department of Biochemistry, Microbiology and Biotechnology, University of Limpopo, Sovenga, South Africa Abstract: Alternative splicing of mRNA leads to an increase in proteome biodiversity by allowing the generation of multiple mRNAs, coding for multiple protein isoforms of various structural and functional properties from a single primary pre-mRNA transcript. The protein isoforms produced are tightly regulated in normal development but are mostly deregulated in various cancers. In HIV-infected individuals with AIDS, there is an increase in aberrant alternative splicing, resulting in an increase in HIV/AIDS-related cancers, such as Kaposi’s sarcoma, non-Hodgkin’s lymphoma, and cervical cancer. This aberrant splicing leads to abnormal production of protein and is caused by mutations in cis-acting elements or trans-acting factors in angiogenesis-related genes. Restoring the normal regulation of alternative splicing of angiogenic genes would alter the expression of protein isoforms and may confer normal cell physiology in patients with these cancers. This review highlights the abnormalities in alternative splicing of angiogenesis-related genes and their implication in HIV/AIDS-related cancers. This allows us to gain an insight into the pathogenesis of HIV/AIDS-related cancer and in turn elucidate the therapeutic potential of alternatively spliced genes in HIV/AIDS-related malignancies. Keywords: vascular endothelial growth factor, oncogenic viruses, hypoxia induced factor 1, Kaposi’s sarcoma, non-Hodgkin’s lymphoma, therapies targeting alternative splicing

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

    International Nuclear Information System (INIS)

    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)

  10. Nuclear proliferation and civilian nuclear power: report of the Nonproliferation Alternative Systems Assessment Program. Volume 1. Program summary

    Energy Technology Data Exchange (ETDEWEB)

    1979-12-01

    This report summarizes the Nonproliferation Alternative Systems Assessment Program (NASAP): its background, its studies, and its results. This introductory chapter traces the growth of the issue of nuclear weapons proliferation and the organization and objectives of NASAP. Chapter 2 summarizes the program's assessments, findings and recommendations. Each of Volumes II-VII reports on an individual assessment (Volume II: Proliferation Resistance; Volume III: Resources and Fuel Cycle Facilities; Volume IV: Commercial Potential; Volume V: Economics and Systems Analysis; Volume VI: Safety and Environmental Considerations for Licensing; Volume VII: International Perspectives). Volume VIII (Advanced Concepts) presents a combined assessment of several less fully developed concepts, and Volume IX (Reactor and Fuel Cycle Descriptions) provides detailed descriptions of the reactor and fuel-cycle systems studied by NASAP.

  11. Nuclear proliferation and civilian nuclear power: report of the Nonproliferation Alternative Systems Assessment Program. Volume 1. Program summary

    International Nuclear Information System (INIS)

    1979-12-01

    This report summarizes the Nonproliferation Alternative Systems Assessment Program (NASAP): its background, its studies, and its results. This introductory chapter traces the growth of the issue of nuclear weapons proliferation and the organization and objectives of NASAP. Chapter 2 summarizes the program's assessments, findings and recommendations. Each of Volumes II-VII reports on an individual assessment (Volume II: Proliferation Resistance; Volume III: Resources and Fuel Cycle Facilities; Volume IV: Commercial Potential; Volume V: Economics and Systems Analysis; Volume VI: Safety and Environmental Considerations for Licensing; Volume VII: International Perspectives). Volume VIII (Advanced Concepts) presents a combined assessment of several less fully developed concepts, and Volume IX (Reactor and Fuel Cycle Descriptions) provides detailed descriptions of the reactor and fuel-cycle systems studied by NASAP

  12. Nuclear proliferation and civilian nuclear power. Report of the Nonproliferation Alternative Systems Assessment Program. Volume I. Program summary

    International Nuclear Information System (INIS)

    1980-06-01

    This report summarizes the Nonproliferation Alternative Systems Assessment Program (NASAP): its background, its studies, and its results. The introductory chapter traces the growth of the issue of nuclear weapons proliferation and the organization and objectives of NASAP. Chapter 2 summarizes the program's assessments, findings, and recommendations. Each of Volumes II-VII reports on an individual assessment (Volumn II: Proliferation Resistance; Volume III: Resources and Fuel Cycle Facilities; Volume IV: Commercial Potential; Volume V: Economics and Systems Analysis; Volume VI: Safety and Environmental Considerations for Licensing; Volume VII: International Perspectives). Volume VIII (Advanced Concepts) presents a combined assessment of several less fully developed concepts, and Volume IX (Reactor and Fuel Cycle Descriptions) provides detailed descriptions of the reactor and fuel-cycle systems studied by NASAP

  13. 4β-Hydroxywithanolide E Modulates Alternative Splicing of Apoptotic Genes in Human Hepatocellular Carcinoma Huh-7 Cells.

    Science.gov (United States)

    Lee, Chien-Chin; Chang, Wen-Hsin; Chang, Ya-Sian; Liu, Ting-Yuan; Chen, Yu-Chia; Wu, Yang-Chang; Chang, Jan-Gowth

    2017-08-04

    Alternative splicing is a mechanism for increasing protein diversity from a limited number of genes. Studies have demonstrated that aberrant regulation in the alternative splicing of apoptotic gene transcripts may contribute to the development of cancer. In this study, we isolated 4β-Hydroxywithanolide E (4bHWE) from the traditional herb Physalis peruviana and investigated its biological effect in cancer cells. The results demonstrated that 4bHWE modulates the alternative splicing of various apoptotic genes, including HIPK3, SMAC/DIABLO, and SURVIVIN. We also discovered that the levels of SRSF1 phospho-isoform were decreased and the levels of H3K36me3 were increased in 4bHWE treatment. Knockdown experiments revealed that the splicing site selection of SMAC/DIABLO could be mediated by changes in the level of H3K36me3 in 4bHWE-treated cells. Furthermore, we extended our study to apoptosis-associated molecules, and detected increased levels of poly ADP-ribose polymerase cleavage and the active form of CASPASE-3 in 4bHWE-induced apoptosis. In vivo experiments indicated that the treatment of tumor-bearing mice with 4bHWE resulted in a marked decrease in tumor size. This study is the first to demonstrate that 4bHWE affects alternative splicing by modulating splicing factors and histone modifications, and provides a novel view of the antitumor mechanism of 4bHWE.

  14. Determining true HER2 gene status in breast cancers with polysomy by using alternative chromosome 17 reference genes: implications for anti-HER2 targeted therapy.

    Science.gov (United States)

    Tse, Chun Hing; Hwang, Harry C; Goldstein, Lynn C; Kandalaft, Patricia L; Wiley, Jesse C; Kussick, Steven J; Gown, Allen M

    2011-11-01

    The ratio of human epidermal growth factor receptor 2 (HER2) to CEP17 by fluorescent in situ hybridization (FISH) with the centromeric probe CEP17 is used to determine HER2 gene status in breast cancer. Increases in CEP17 copy number have been interpreted as representing polysomy 17. However, pangenomic studies have demonstrated that polysomy 17 is rare. This study tests the hypothesis that the use of alternative chromosome 17 reference genes might more accurately assess true HER2 gene status. In all, 171 patients with breast cancer who had HER2 FISH that had increased mean CEP17 copy numbers (> 2.6) were selected for additional chromosome 17 studies that used probes for Smith-Magenis syndrome (SMS), retinoic acid receptor alpha (RARA), and tumor protein p53 (TP53) genes. A eusomic copy number exhibited in one or more of these loci was used to calculate a revised HER2-to-chromosome-17 ratio by using the eusomic gene locus as the reference. Of 132 cases classified as nonamplified on the basis of their HER2:CEP17 ratios, 58 (43.9%) were scored as amplified by using alternative chromosome 17 reference gene probes, and 13 (92.9%) of 14 cases scored as equivocal were reclassified as amplified. Among the cases with mean HER2 copy number of 4 to 6, 41 (47.7%) of 86 had their HER2 gene status upgraded from nonamplified to amplified, and four (4.7%) of 86 were upgraded from equivocal to amplified. Our results support the findings of recent pangenomic studies that true polysomy 17 is uncommon. Additional FISH studies that use probes to the SMS, RARA, and TP53 genes are an effective way to determine the true HER2 amplification status in patients with polysomy 17 and they have important potential implications for guiding HER2-targeted therapy in breast cancer.

  15. 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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    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.

  18. StrateGene: object-oriented programming in molecular biology.

    Science.gov (United States)

    Carhart, R E; Cash, H D; Moore, J F

    1988-03-01

    This paper describes some of the ways that object-oriented programming methodologies have been used to represent and manipulate biological information in a working application. When running on a Xerox 1100 series computer, StrateGene functions as a genetic engineering workstation for the management of information about cloning experiments. It represents biological molecules, enzymes, fragments, and methods as classes, subclasses, and members in a hierarchy of objects. These objects may have various attributes, which themselves can be defined and classified. The attributes and their values can be passed from the classes of objects down to the subclasses and members. The user can modify the objects and their attributes while using them. New knowledge and changes to the system can be incorporated relatively easily. The operations on the biological objects are associated with the objects themselves. This makes it easier to invoke them correctly and allows generic operations to be customized for the particular object.

  19. Myeloid translocation genes differentially regulate colorectal cancer programs

    Science.gov (United States)

    Parang, Bobak; Bradley, Amber M.; Mittal, Mukul K.; Short, Sarah P.; Thompson, Joshua J.; Barrett, Caitlyn W.; Naik, Rishi D.; Bilotta, Anthony J.; Washington, Mary K.; Revetta, Frank L.; Smith, Jesse J.; Chen, Xi; Wilson, Keith T.; Hiebert, Scott W.; Williams, Christopher S.

    2016-01-01

    Myeloid translocation genes (MTGs), originally identified as chromosomal translocations in acute myelogenous leukemia, are transcriptional corepressors that regulate hematopoietic stem cell programs. Analysis of The Cancer Genome Atlas (TCGA) database revealed that MTGs were mutated in epithelial malignancy and suggested that loss of function might promote tumorigenesis. Genetic deletion of MTGR1 and MTG16 in the mouse has revealed unexpected and unique roles within the intestinal epithelium. Mtgr1−/− mice have progressive depletion of all intestinal secretory cells, and Mtg16−/− mice have a decrease in goblet cells. Furthermore, both Mtgr1−/− and Mtg16−/− mice have increased intestinal epithelial cell proliferation. We thus hypothesized that loss of MTGR1 or MTG16 would modify Apc1638/+-dependent intestinal tumorigenesis. Mtgr1−/− mice, but not Mtg16−/− mice, had a 10-fold increase in tumor multiplicity. This was associated with more advanced dysplasia, including progression to invasive adenocarcinoma, and augmented intratumoral proliferation. Analysis of ChIP-seq datasets for MTGR1 and MTG16 targets indicated that MTGR1 can regulate Wnt and Notch signaling. In support of this, immunohistochemistry and gene expression analysis revealed that both Wnt and Notch signaling pathways were hyperactive in Mtgr1−/− tumors. Furthermore, in human colorectal cancer (CRC) samples MTGR1 was downregulated at both the transcript and protein level. Overall our data indicates that MTGR1 has a context dependent effect on intestinal tumorigenesis. PMID:27270437

  20. Alternative response technology program for the Deepwater Horizon in the Gulf of Mexico - an overview

    International Nuclear Information System (INIS)

    Cortez, Michael J.; Rowe, Hunter G.

    2011-01-01

    The innovative approach utilized by the Alternative Response Technology (ART) Program for the MC252 Deepwater Horizon response in the Gulf of Mexico during 2010 was presented in this paper. The ART program is authorized by the Unified Area Command. This paper focuses on the spill response technologies that were implemented offshore, near shore and on-shore, and covers technologies related to booming, skimming, separation, sand cleaning, surveillance and detection. A process was designed and implemented for capturing ideas real time, which leveraged the public's ingenuity and entrepreneurial spirit. About 120,000 individual ideas were submitted by the public globally from more than 100 countries. About 40,000 of these ideas were related to addressing the spill response. There are about 100 new technologies related to spill response that were formally evaluated and/or field tested, and approximately 25 of those tested were successfully implemented across the spill response area.

  1. Alternative response technology program for the Deepwater Horizon in the Gulf of Mexico - an overview

    Energy Technology Data Exchange (ETDEWEB)

    Cortez, Michael J.; Rowe, Hunter G. [BP - Gulf Coast Restoration (United States)], email: michael.cortez@bp.com

    2011-07-01

    The innovative approach utilized by the Alternative Response Technology (ART) Program for the MC252 Deepwater Horizon response in the Gulf of Mexico during 2010 was presented in this paper. The ART program is authorized by the Unified Area Command. This paper focuses on the spill response technologies that were implemented offshore, near shore and on-shore, and covers technologies related to booming, skimming, separation, sand cleaning, surveillance and detection. A process was designed and implemented for capturing ideas real time, which leveraged the public's ingenuity and entrepreneurial spirit. About 120,000 individual ideas were submitted by the public globally from more than 100 countries. About 40,000 of these ideas were related to addressing the spill response. There are about 100 new technologies related to spill response that were formally evaluated and/or field tested, and approximately 25 of those tested were successfully implemented across the spill response area.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Djian-Caporalino, Caroline; Palloix, Alain; Fazari, Ariane; Marteu, Nathalie; Barbary, Arnaud; Abad, Pierre; Sage-Palloix, Anne-Marie; Mateille, Thierry; Risso, Sabine; Lanza, Roger; Taussig, Catherine; Castagnone-Sereno, Philippe

    2014-02-22

    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. 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. 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.

  4. 46 CFR 115.625 - Eligibility requirements for the Alternative Hull Examination (AHE) Program for certain passenger...

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Eligibility requirements for the Alternative Hull... OVERNIGHT ACCOMMODATIONS FOR MORE THAN 49 PASSENGERS INSPECTION AND CERTIFICATION Hull and Tailshaft Examinations § 115.625 Eligibility requirements for the Alternative Hull Examination (AHE) Program for certain...

  5. 46 CFR 71.50-17 - Eligibility requirements for the Alternative Hull Examination (AHE) Program for certain passenger...

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 3 2010-10-01 2010-10-01 false Eligibility requirements for the Alternative Hull...-17 Eligibility requirements for the Alternative Hull Examination (AHE) Program for certain passenger... aluminum; (2) It has an effective hull protection system; (3) It has operated exclusively in fresh water...

  6. Environmental restoration program pollution prevention checklist guide for the evaluation of alternatives project phase

    International Nuclear Information System (INIS)

    1993-09-01

    Evaluation of alternative studies determine what decontamination and decommissioning (D ampersand D) alternatives are presented to regulators for facility and site cleanup. A key consideration in this process is the waste to be generated. Minimizing the volume and toxicity of this waste will ultimately contribute to the selection of the best clean-up option. The purpose of this checklist guide is to assist the user with incorporating pollution prevention/waste minimization (PP/WM) in all Evaluation of Alternatives (EV) phase projects of the Environmental Restoration (ER) Program. This guide will assist users with documenting PP/WM activities for technology transfer and reporting requirements. Automated computer screens will be created from the checklist data to help users implement and evaluate waste reduction. Users can then establish numerical performance measures to measure progress in planning, training, self-assessments, field implementation, documentation, and technology transfer. Cost savings result as users train and assess themselves, eliminating expensive process waste assessments and audit teams

  7. Actualizing culture change: The Promoting Excellent Alternatives in Kansas Nursing Homes (PEAK 2.0) program.

    Science.gov (United States)

    Doll, Gayle A; Cornelison, Laci J; Rath, Heath; Syme, Maggie L

    2017-08-01

    Nursing homes have been challenged in their attempts to achieve deep, organizational change (i.e., culture change) aimed at providing quality of care and quality of life for nursing home residents through person-centered care. To attain deep change, 2 well-defined components must be in place: a shared understanding of (a) the what, or content goals, and (b) the how, or process of change. However, there are few examples of this at a macro or micro level in long-term care. In an effort to enact true culture change in nursing homes statewide, the Kansas Department for Aging and Disability Services implemented the Promoting Excellent Alternatives in Kansas Nursing Homes program. This program is a Medicaid, pay-for-performance program that formalizes the content and process of achieving culture change through person-centered care principles. This article aims to detail the content (what) and process (how) of a model macro-level program of culture change throughout the State of Kansas. Applications to the micro level (individual homes) are presented, and implications for psychologists' roles in facilitating culture change are discussed. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  8. Production Data - Captive Broodstock Gene Rescue Program for Odd Year Class Elwha River Pink Salmon

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Conduct captive brood stock gene rescue program for Elwha River odd-year class pink salmon. Information on the number of smolts received into the program is...

  9. Prodrug encapsulated albumin nanoparticles as an alternative approach to manifest anti-proliferative effects of suicide gene therapy

    International Nuclear Information System (INIS)

    Tirkey, Bulbul; Bhushan, Bharat; Uday Kumar, S.; Gopinath, P.

    2017-01-01

    Conventional anticancer agents are associated with limited therapeutic efficacy and substantial nonspecific cytotoxicity. Thus, there is an imminent need for an alternative approach that can specifically annihilate the cancer cells with minimal side effects. Among such alternative approaches, CD::UPRT (cytosine deaminase uracil phosphoribosyl transferase) suicide gene therapy has tremendous potential due to its high efficacy. Prodrug 5-Fluorocytosine (5-FC) used in combination with CD::UPRT suicide gene suffers from limited solubility which subsequently leads to decline in therapeutic efficacy. In order to overcome this, 5-FC encapsulated bovine serum albumin nanoparticles (BSA-5-FC NPs) were prepared in this work by desolvation method. Physico-chemical characterizations studies revealed amorphous nature of BSA-5-FC NPs with uniform spherical morphology. Apart from increase in solubility, encapsulated 5-FC followed slow and sustained release profile. Suicide gene expressing stable clone of L-132 cells were adapted for investigating therapeutic potential of BSA-5-FC NPs. These nanoparticles were readily taken up by the cells in a concentration dependent manner and subsequently manifested apoptosis, which was further confirmed by morphological examination and gene expression analysis. These findings clearly illustrate that CD::UPRT suicide gene therapy can be efficiently utilized in combination with this nanosystem for improved suicide gene therapy and tumor eradication. - Highlights: • In this work, BSA-5-FC NPs has been prepared to achieve its sustained release and also facilitate its uptake by cells. • A protein based system has been realized for the first time to deliver prodrug for cancer therapy. • Physico-chemical characterizations further validate the formation of spherical, monodispersed and stable nanoparticles. • The therapeutic efficacy of BSA-5-FC NPs has been validated against CD::UPRT expressing stable cells.

  10. Prodrug encapsulated albumin nanoparticles as an alternative approach to manifest anti-proliferative effects of suicide gene therapy

    Energy Technology Data Exchange (ETDEWEB)

    Tirkey, Bulbul [Nanobiotechnology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667 (India); Bhushan, Bharat; Uday Kumar, S. [Nanobiotechnology Laboratory, Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667 (India); Gopinath, P., E-mail: pgopifnt@iitr.ernet.in [Nanobiotechnology Laboratory, Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667 (India); Nanobiotechnology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667 (India)

    2017-04-01

    Conventional anticancer agents are associated with limited therapeutic efficacy and substantial nonspecific cytotoxicity. Thus, there is an imminent need for an alternative approach that can specifically annihilate the cancer cells with minimal side effects. Among such alternative approaches, CD::UPRT (cytosine deaminase uracil phosphoribosyl transferase) suicide gene therapy has tremendous potential due to its high efficacy. Prodrug 5-Fluorocytosine (5-FC) used in combination with CD::UPRT suicide gene suffers from limited solubility which subsequently leads to decline in therapeutic efficacy. In order to overcome this, 5-FC encapsulated bovine serum albumin nanoparticles (BSA-5-FC NPs) were prepared in this work by desolvation method. Physico-chemical characterizations studies revealed amorphous nature of BSA-5-FC NPs with uniform spherical morphology. Apart from increase in solubility, encapsulated 5-FC followed slow and sustained release profile. Suicide gene expressing stable clone of L-132 cells were adapted for investigating therapeutic potential of BSA-5-FC NPs. These nanoparticles were readily taken up by the cells in a concentration dependent manner and subsequently manifested apoptosis, which was further confirmed by morphological examination and gene expression analysis. These findings clearly illustrate that CD::UPRT suicide gene therapy can be efficiently utilized in combination with this nanosystem for improved suicide gene therapy and tumor eradication. - Highlights: • In this work, BSA-5-FC NPs has been prepared to achieve its sustained release and also facilitate its uptake by cells. • A protein based system has been realized for the first time to deliver prodrug for cancer therapy. • Physico-chemical characterizations further validate the formation of spherical, monodispersed and stable nanoparticles. • The therapeutic efficacy of BSA-5-FC NPs has been validated against CD::UPRT expressing stable cells.

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

    Science.gov (United States)

    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…

  12. The building of the kitchen table : In search of an alternative model for in-company leadership development programs

    NARCIS (Netherlands)

    Sigaloff, C.L.; Nabben, E.H. (Iselien); Bergsma, E.

    2007-01-01

    The purpose of this paper is to provide an alternative model of a leadership-development program. Design/methodology/approach: A leadership-development program based on a "closure-type description" instead of an "input-type description" (Varela) was designed and executed for an organization. The

  13. Multicriteria decision methodology for selecting technical alternatives in the Mixed Waste Integrated Program

    International Nuclear Information System (INIS)

    Ferrada, J.J.; Berry, J.B.

    1993-11-01

    The US Department of Energy (DOE) Mixed Waste Integrated Program (MWIP) has as one of its tasks the identification of a decision methodology and key decision criteria for the selection methodology. The aim of a multicriteria analysis is to provide an instrument for a systematic evaluation of distinct alternative projects. Determination of this methodology will clarify (1) the factors used to evaluate these alternatives, (2) the evaluator's view of the importance of the factors, and (3) the relative value of each alternative. The selected methodology must consider the Comprehensive Environmental Response Compensation and Liability Act (CERCLA) decision-making criteria for application to the analysis technology subsystems developed by the DOE Office of Technology Development. This report contains a compilation of several decision methodologies developed in various national laboratories, institutions, and universities. The purpose of these methodologies may vary, but the core of the decision attributes are very similar. Six approaches were briefly analyzed; from these six, in addition to recommendations made by the MWIP technical support group leaders and CERCLA, the final decision methodology was extracted. Slight variations are observed in the many methodologies developed by different groups, but most of the analyzed methodologies address similar aspects for the most part. These common aspects were the core of the methodology suggested in this report for use within MWIP for the selection of technologies. The set of criteria compiled and developed for this report have been grouped in five categories: (1) process effectiveness, (2) developmental status, (3) life-cycle cost, (4) implementability, and (5) regulatory compliance

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

    Science.gov (United States)

    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.

  15. Organization and alternative splicing of the Caenorhabditis elegans cAMP-dependent protein kinase catalytic-subunit gene (kin-1).

    Science.gov (United States)

    Tabish, M; Clegg, R A; Rees, H H; Fisher, M J

    1999-04-01

    The cAMP-dependent protein kinase (protein kinase A, PK-A) is multifunctional in nature, with key roles in the control of diverse aspects of eukaryotic cellular activity. In the case of the free-living nematode, Caenorhabditis elegans, a gene encoding the PK-A catalytic subunit has been identified and two isoforms of this subunit, arising from a C-terminal alternative-splicing event, have been characterized [Gross, Bagchi, Lu and Rubin (1990) J. Biol. Chem. 265, 6896-6907]. Here we report the occurrence of N-terminal alternative-splicing events that, in addition to generating a multiplicity of non-myristoylatable isoforms, also generate the myristoylated variant(s) of the catalytic subunit that we have recently characterized [Aspbury, Fisher, Rees and Clegg (1997) Biochem. Biophys. Res. Commun. 238, 523-527]. The gene spans more than 36 kb and is divided into a total of 13 exons. Each of the mature transcripts contains only 7 exons. In addition to the already characterized exon 1, the 5'-untranslated region and first intron actually contain 5 other exons, any one of which may be alternatively spliced on to exon 2 at the 5' end of the pre-mRNA. This N-terminal alternative splicing occurs in combination with either of the already characterized C-terminal alternative exons. Thus, C. elegans expresses at least 12 different isoforms of the catalytic subunit of PK-A. The significance of this unprecedented structural diversity in the family of PK-A catalytic subunits is discussed.

  16. Comprehensive gene expression analysis of rice aleurone cells: probing the existence of an alternative gibberellin receptor.

    Science.gov (United States)

    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. © 2015 American Society of Plant Biologists. All Rights Reserved.

  17. Comparison of CpG island methylator phenotype (CIMP frequency in colon cancer using different probe- and gene-specific scoring alternatives on recommended multi-gene panels.

    Directory of Open Access Journals (Sweden)

    Marianne Berg

    Full Text Available BACKGROUND: In colorectal cancer a distinct subgroup of tumours demonstrate the CpG island methylator phenotype (CIMP. However, a consensus of how to score CIMP is not reached, and variation in definition may influence the reported CIMP prevalence in tumours. Thus, we sought to compare currently suggested definitions and cut-offs for methylation markers and how they influence CIMP classification in colon cancer. METHODS: Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA, with subsequent fragment analysis, was used to investigate methylation of tumour samples. In total, 31 CpG sites, located in 8 different genes (RUNX3, MLH1, NEUROG1, CDKN2A, IGF2, CRABP1, SOCS1 and CACNA1G were investigated in 64 distinct colon cancers and 2 colon cancer cell lines. The Ogino gene panel includes all 8 genes, in addition to the Weisenberger panel of which only 5 of the 8 genes included were investigated. In total, 18 alternative combinations of scoring of CIMP positivity on probe-, gene-, and panel-level were analysed and compared. RESULTS: For 47 samples (71%, the CIMP status was constant and independent of criteria used for scoring; 34 samples were constantly scored as CIMP negative, and 13 (20% consistently scored as CIMP positive. Only four of 31 probes (13% investigated showed no difference in the numbers of positive samples using the different cut-offs. Within the panels a trend was observed that increasing the gene-level stringency resulted in a larger difference in CIMP positive samples than increasing the probe-level stringency. A significant difference between positive samples using 'the most stringent' as compared to 'the least stringent' criteria (20% vs 46%, respectively; p<0.005 was demonstrated. CONCLUSIONS: A statistical significant variation in the frequency of CIMP depending on the cut-offs and genes included in a panel was found, with twice as many positives samples by least compared to most stringent definition

  18. Comparison of CpG island methylator phenotype (CIMP) frequency in colon cancer using different probe- and gene-specific scoring alternatives on recommended multi-gene panels.

    Science.gov (United States)

    Berg, Marianne; Hagland, Hanne R; Søreide, Kjetil

    2014-01-01

    In colorectal cancer a distinct subgroup of tumours demonstrate the CpG island methylator phenotype (CIMP). However, a consensus of how to score CIMP is not reached, and variation in definition may influence the reported CIMP prevalence in tumours. Thus, we sought to compare currently suggested definitions and cut-offs for methylation markers and how they influence CIMP classification in colon cancer. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), with subsequent fragment analysis, was used to investigate methylation of tumour samples. In total, 31 CpG sites, located in 8 different genes (RUNX3, MLH1, NEUROG1, CDKN2A, IGF2, CRABP1, SOCS1 and CACNA1G) were investigated in 64 distinct colon cancers and 2 colon cancer cell lines. The Ogino gene panel includes all 8 genes, in addition to the Weisenberger panel of which only 5 of the 8 genes included were investigated. In total, 18 alternative combinations of scoring of CIMP positivity on probe-, gene-, and panel-level were analysed and compared. For 47 samples (71%), the CIMP status was constant and independent of criteria used for scoring; 34 samples were constantly scored as CIMP negative, and 13 (20%) consistently scored as CIMP positive. Only four of 31 probes (13%) investigated showed no difference in the numbers of positive samples using the different cut-offs. Within the panels a trend was observed that increasing the gene-level stringency resulted in a larger difference in CIMP positive samples than increasing the probe-level stringency. A significant difference between positive samples using 'the most stringent' as compared to 'the least stringent' criteria (20% vs 46%, respectively; pCIMP depending on the cut-offs and genes included in a panel was found, with twice as many positives samples by least compared to most stringent definition used.

  19. Tissue-specific alternative splicing and expression of ATP1B2 gene

    African Journals Online (AJOL)

    user6

    2012-05-15

    May 15, 2012 ... retention; these isoforms were found in liver, kidney, muscle and breast tissues. ... lower levels than the complete ATP1B2 gene transcript in all the ... temperature. ... growth, differentiation, and disease (Zhou et al., 2002;.

  20. Cloning and characterization of the mouse Mcoln1 gene reveals an alternatively spliced transcript not seen in humans

    Directory of Open Access Journals (Sweden)

    Stahl Stefanie

    2002-02-01

    Full Text Available Abstract Background Mucolipidosis type IV (MLIV is an autosomal recessive lysosomal storage disorder characterized by severe neurologic and ophthalmologic abnormalities. Recently the MLIV gene, MCOLN1, has been identified as a new member of the transient receptor potential (TRP cation channel superfamily. Here we report the cloning and characterization of the mouse homologue, Mcoln1, and report a novel splice variant that is not seen in humans. Results The human and mouse genes display a high degree of synteny. Mcoln1 shows 91% amino acid and 86% nucleotide identity to MCOLN1. Also, Mcoln1 maps to chromosome 8 and contains an open reading frame of 580 amino acids, with a transcript length of approximately 2 kb encoded by 14 exons, similar to its human counterpart. The transcript that results from murine specific alternative splicing encodes a 611 amino acid protein that differs at the c-terminus. Conclusions Mcoln1 is highly similar to MCOLN1, especially in the transmembrane domains and ion pore region. Also, the late endosomal/lysosomal targeting signal is conserved, supporting the hypothesis that the protein is localized to these vesicle membranes. To date, there are very few reports describing species-specific splice variants. While identification of Mcoln1 is crucial to the development of mouse models for MLIV, the fact that there are two transcripts in mice suggests an additional or alternate function of the gene that may complicate phenotypic assessment.

  1. DNAM-1 Expression Marks an Alternative Program of NK Cell Maturation

    Directory of Open Access Journals (Sweden)

    Ludovic Martinet

    2015-04-01

    Full Text Available Natural killer (NK cells comprise a heterogeneous population of cells important for pathogen defense and cancer surveillance. However, the functional significance of this diversity is not fully understood. Here, we demonstrate through transcriptional profiling and functional studies that the activating receptor DNAM-1 (CD226 identifies two distinct NK cell functional subsets: DNAM-1+ and DNAM-1− NK cells. DNAM-1+ NK cells produce high levels of inflammatory cytokines, have enhanced interleukin 15 signaling, and proliferate vigorously. By contrast, DNAM-1− NK cells that differentiate from DNAM-1+ NK cells have greater expression of NK-cell-receptor-related genes and are higher producers of MIP1 chemokines. Collectively, our data reveal the existence of a functional program of NK cell maturation marked by DNAM-1 expression.

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

    Science.gov (United States)

    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.

  3. Nuclear proliferation and civilian nuclear power: report of the Nonproliferation Alternative Systems Assessment Program. Volume V. Economics and systems analysis

    International Nuclear Information System (INIS)

    1979-12-01

    This assessment considers the economics of alternative nuclear reactor and fuel-cycle systems in the light of possible patterns of uranium supply and energy demand, as well as the economic implications of improving the proliferation resistance of the various systems. The assessment focuses on the costs of alternative nuclear technologies and the possible timing of their implementation, based on their economic attractiveness. The objectives of this assessment are to identify when economic incentives to deploy advanced nuclear power systems might exist, to estimate the costs of using technologies that would reduce the risk of proliferation, to assess the impact of major economic uncertainties on the transition to new technologies, and to compare the investments required for alternative systems. This information can then be used to assess the potential economic benefits of alternative research, development, and demonstration programs and the timing of those programs

  4. Nuclear proliferation and civilian nuclear power: report of the Nonproliferation Alternative Systems Assessment Program. Volume V. Economics and systems analysis

    Energy Technology Data Exchange (ETDEWEB)

    None

    1979-12-01

    This assessment considers the economics of alternative nuclear reactor and fuel-cycle systems in the light of possible patterns of uranium supply and energy demand, as well as the economic implications of improving the proliferation resistance of the various systems. The assessment focuses on the costs of alternative nuclear technologies and the possible timing of their implementation, based on their economic attractiveness. The objectives of this assessment are to identify when economic incentives to deploy advanced nuclear power systems might exist, to estimate the costs of using technologies that would reduce the risk of proliferation, to assess the impact of major economic uncertainties on the transition to new technologies, and to compare the investments required for alternative systems. This information can then be used to assess the potential economic benefits of alternative research, development, and demonstration programs and the timing of those programs.

  5. Alternation of apoptotic and implanting genes expression of mouse embryos after re-vitrification

    Directory of Open Access Journals (Sweden)

    Nasrin Majidi Gharenaz

    2016-08-01

    Full Text Available 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

  6. Alternation of apoptotic and implanting genes expression of mouse embryos after re-vitrification

    Science.gov (United States)

    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

  7. Alternate bearing in citrus: changes in the expression of flowering control genes and in global gene expression in ON- versus OFF-crop trees.

    Science.gov (United States)

    Shalom, Liron; Samuels, Sivan; Zur, Naftali; Shlizerman, Lyudmila; Zemach, Hanita; Weissberg, Mira; Ophir, Ron; Blumwald, Eduardo; Sadka, Avi

    2012-01-01

    Alternate bearing (AB) is the process in fruit trees by which cycles of heavy yield (ON crop) one year are followed by a light yield (OFF crop) the next. Heavy yield usually reduces flowering intensity the following year. Despite its agricultural importance, how the developing crop influences the following year's return bloom and yield is not fully understood. It might be assumed that an 'AB signal' is generated in the fruit, or in another organ that senses fruit presence, and moves into the bud to determine its fate-flowering or vegetative growth. The bud then responds to fruit presence by altering regulatory and metabolic pathways. Determining these pathways, and when they are altered, might indicate the nature of this putative AB signal. We studied bud morphology, the expression of flowering control genes, and global gene expression in ON- and OFF-crop buds. In May, shortly after flowering and fruit set, OFF-crop buds were already significantly longer than ON-crop buds. The number of differentially expressed genes was higher in May than at the other tested time points. Processes differentially expressed between ON- and OFF-crop trees included key metabolic and regulatory pathways, such as photosynthesis and secondary metabolism. The expression of genes of trehalose metabolism and flavonoid metabolism was validated by nCounter technology, and the latter was confirmed by metabolomic analysis. Among genes induced in OFF-crop trees was one homologous to SQUAMOSA PROMOTER BINDING-LIKE (SPL), which controls juvenile-to-adult and annual phase transitions, regulated by miR156. The expression pattern of SPL-like, miR156 and other flowering control genes suggested that fruit load affects bud fate, and therefore development and metabolism, a relatively long time before the flowering induction period. Results shed light on some of the metabolic and regulatory processes that are altered in ON and OFF buds.

  8. Species trees for the tree swallows (Genus Tachycineta): an alternative phylogenetic hypothesis to the mitochondrial gene tree.

    Science.gov (United States)

    Dor, Roi; Carling, Matthew D; Lovette, Irby J; Sheldon, Frederick H; Winkler, David W

    2012-10-01

    The New World swallow genus Tachycineta comprises nine species that collectively have a wide geographic distribution and remarkable variation both within- and among-species in ecologically important traits. Existing phylogenetic hypotheses for Tachycineta are based on mitochondrial DNA sequences, thus they provide estimates of a single gene tree. In this study we sequenced multiple individuals from each species at 16 nuclear intron loci. We used gene concatenated approaches (Bayesian and maximum likelihood) as well as coalescent-based species tree inference to reconstruct phylogenetic relationships of the genus. We examined the concordance and conflict between the nuclear and mitochondrial trees and between concatenated and coalescent-based inferences. Our results provide an alternative phylogenetic hypothesis to the existing mitochondrial DNA estimate of phylogeny. This new hypothesis provides a more accurate framework in which to explore trait evolution and examine the evolution of the mitochondrial genome in this group. Copyright © 2012 Elsevier Inc. All rights reserved.

  9. Allelic variation, alternative splicing and expression analysis of Psy1 gene in Hordeum chilense Roem. et Schult.

    Directory of Open Access Journals (Sweden)

    Cristina Rodríguez-Suárez

    Full Text Available BACKGROUND: The wild barley Hordeum chilense Roem. et Schult. is a valuable source of genes for increasing carotenoid content in wheat. Tritordeums, the amphiploids derived from durum or common wheat and H. chilense, systematically show higher values of yellow pigment colour and carotenoid content than durum wheat. Phytoene synthase 1 gene (Psy1 is considered a key step limiting the carotenoid biosynthesis, and the correlation of Psy1 transcripts accumulation and endosperm carotenoid content has been demonstrated in the main grass species. METHODOLOGY/PRINCIPAL FINDINGS: We analyze the variability of Psy1 alleles in three lines of H. chilense (H1, H7 and H16 representing the three ecotypes described in this species. Moreover, we analyze Psy1 expression in leaves and in two seed developing stages of H1 and H7, showing mRNA accumulation patterns similar to those of wheat. Finally, we identify thirty-six different transcripts forms originated by alternative splicing of the 5' UTR and/or exons 1 to 5 of Psy1 gene. Transcripts function is tested in a heterologous complementation assay, revealing that from the sixteen different predicted proteins only four types (those of 432, 370, 364 and 271 amino acids, are functional in the bacterial system. CONCLUSIONS/SIGNIFICANCE: The large number of transcripts originated by alternative splicing of Psy1, and the coexistence of functional and non functional forms, suggest a fine regulation of PSY activity in H. chilense. This work is the first analysis of H. chilense Psy1 gene and the results reported here are the bases for its potential use in carotenoid enhancement in durum wheat.

  10. Alternative transcription of sodium/bicarbonate transporter SLC4A7 gene enhanced by single nucleotide polymorphisms.

    Science.gov (United States)

    Park, Hae Jeong; Lee, Soojung; Ju, Eunji; Jones, Jayre A; Choi, Inyeong

    2017-03-01

    Genome-wide association studies have identified the single nucleotide polymorphism (SNP) rs3278 in the human SLC4A7 gene as one of the marker loci for addiction vulnerability. This marker is located in an intron of the gene, and its genomic role has been unknown. In this study, we examined rs3278 and three adjacent SNPs prevalent in alcoholics for their effects on an alternative promoter that would lead to the production of the NH 2 -terminally truncated protein NBCn1ΔN450, missing the first 450 amino acids. Analysis of the transcription start site database and a promoter prediction algorithm identified a cluster of three promoters in intron 7 and two short CpG-rich sites in intron 6. The promoter closest to rs3278 showed strong transcription activity in luciferase reporter gene assays. Major-to-minor allele substitution at rs3278 resulted in increased transcription activity. Equivalent substitutions at adjacent rs3772723 (intron 7) and rs13077400 (exon 8) had negligible effect; however, the substitution at nonsynonymous rs3755652 (exon 8) increased the activity by more than twofold. The concomitant substitution at rs3278/rs3755652 produced an additive effect. The rs3755652 had more profound effects on the promoter than the upstream regulatory CpG sites. The amino acid change E326K caused by rs3755652 had negligible effect on transporter function. In HEK 293 cells, NBCn1ΔN450 was expressed in plasma membranes, but at significantly lower levels than the nontruncated NBCn1-E. The pH change mediated by NBCn1ΔN450 was also low. We conclude that rs3278 and rs3755652 stimulate an alternative transcription of the SLC4A7 gene, increasing the production of a defective transporter. Copyright © 2017 the American Physiological Society.

  11. Tissue-specific alternative splicing and expression of ATP1B2 gene ...

    African Journals Online (AJOL)

    After heat-stress, the expression levels of the different transcripts were lower in different tissues; however, the expression of the ATP1B2-complete transcript increased in heart and lung tissues. The results of this research provide some useful information for further studies into the function of the bovine ATP1B2 gene.

  12. Epigenetic Machinery Regulates Alternative Splicing of Androgen Receptor (AR) Gene in Castration-Resistant Prostate Cancer (CRPC)

    Science.gov (United States)

    2017-09-01

    Splicing of Androgen Receptor (AR) Gene in Castration-Resistant Prostate Cancer (CRPC) 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Jer...Epigenetic regulation of androgen receptor signaling in prostate cancer . Epigenetics. 5, 100-104. 2. Duan LL, Rai G , Roggero C, Zhang Q-J, Wei Q... Prostate Cancer (CRPC) PRINCIPAL INVESTIGATOR: Hsieh, Jer-Tsong CONTRACTING ORGANIZATION: University of Texas Southwestern Medical Center

  13. 77 FR 14587 - FY 2012 Discretionary Livability Funding Opportunity: Alternatives Analysis Program

    Science.gov (United States)

    2012-03-12

    ... alternatives analysis or to support additional technical tasks in an on-going alternatives analysis that will.... FTA will consider proposals for all areas of technical work that can better develop information about... analysis, or for work performed after the Locally Preferred Alternative (LPA) has been selected. There is...

  14. Intragenic deletions affecting two alternative transcripts of the IMMP2L gene in patients with Tourette syndrome

    Science.gov (United States)

    Bertelsen, Birgitte; Melchior, Linea; Jensen, Lars R; Groth, Camilla; Glenthøj, Birte; Rizzo, Renata; Debes, Nanette Mol; Skov, Liselotte; Brøndum-Nielsen, Karen; Paschou, Peristera; Silahtaroglu, Asli; Tümer, Zeynep

    2014-01-01

    Tourette syndrome is a neurodevelopmental disorder characterized by multiple motor and vocal tics, and the disorder is often accompanied by comorbidities such as attention-deficit hyperactivity-disorder and obsessive compulsive disorder. Tourette syndrome has a complex etiology, but the underlying environmental and genetic factors are largely unknown. IMMP2L (inner mitochondrial membrane peptidase, subunit 2) located on chromosome 7q31 is one of the genes suggested as a susceptibility factor in disease pathogenesis. Through screening of a Danish cohort comprising 188 unrelated Tourette syndrome patients for copy number variations, we identified seven patients with intragenic IMMP2L deletions (3.7%), and this frequency was significantly higher (P=0.0447) compared with a Danish control cohort (0.9%). Four of the seven deletions identified did not include any known exons of IMMP2L, but were within intron 3. These deletions were found to affect a shorter IMMP2L mRNA species with two alternative 5′-exons (one including the ATG start codon). We showed that both transcripts (long and short) were expressed in several brain regions, with a particularly high expression in cerebellum and hippocampus. The current findings give further evidence for the role of IMMP2L as a susceptibility factor in Tourette syndrome and suggest that intronic changes in disease susceptibility genes should be investigated further for presence of alternatively spliced exons. PMID:24549057

  15. Development of dose calculation program (DBADOSE) incorporating alternative source term due to design basis accident

    International Nuclear Information System (INIS)

    Bae, Young Jig; Nam, Ki Mun; Lee, Yu Jong; Chung, Chan Young

    2003-01-01

    Source terms presented in TID-14844 and Regulatory Guide 1.4 have been used for radiological analysis of design basis accidents for licensing existing pressurized water reactor (PWR). However, more realistic and physically-based source term based on results of study and experiments for about 30 years after the publication of TID-14844 was developed and presented in NUREG-1465 published by U.S NRC in 1995. In addition, ICRP has revised dose concepts and criteria through the publication of ICRP-9, 26, 60 and recommended effective dose concepts rather than critical organ concept since the publication of ICRP-26. Accordingly, multipurpose computer program called DBADOSE incorporating alternative source terms in NUREG-1465 and effective dose concepts in ICRP-60 was developed. Comparison of results of DBADOSE with those of POSTDBA and STARDOSE was performed and verified and no significant difference and inaccuracy were found. DBADOSE will be used to evaluate accidental doses for licensing application according to the domestic laws that are expected to be revised in the near future

  16. EM-21 Alternative Enhanced Chemical Cleaning Program For Sludge Heel Removal

    International Nuclear Information System (INIS)

    Hay, M.; King, W.; Martino, C.

    2009-01-01

    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.

  17. Linear programming: an alternative approach for developing formulations for emergency food products.

    Science.gov (United States)

    Sheibani, Ershad; Dabbagh Moghaddam, Arasb; Sharifan, Anousheh; Afshari, Zahra

    2018-03-01

    To minimize the mortality rates of individuals affected by disasters, providing high-quality food relief during the initial stages of an emergency is crucial. The goal of this study was to develop a formulation for a high-energy, nutrient-dense prototype using linear programming (LP) model as a novel method for developing formulations for food products. The model consisted of the objective function and the decision variables, which were the formulation costs and weights of the selected commodities, respectively. The LP constraints were the Institute of Medicine and the World Health Organization specifications of the content of nutrients in the product. Other constraints related to the product's sensory properties were also introduced to the model. Nonlinear constraints for energy ratios of nutrients were linearized to allow their use in the LP. Three focus group studies were conducted to evaluate the palatability and other aspects of the optimized formulation. New constraints were introduced to the LP model based on the focus group evaluations to improve the formulation. LP is an appropriate tool for designing formulations of food products to meet a set of nutritional requirements. This method is an excellent alternative to the traditional 'trial and error' method in designing formulations. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  18. Targeted gene panels and microbiota analysis provide insight into the effects of effects of alternative production diet formulations on channel catfish nutritional physiology

    Science.gov (United States)

    The present research evaluated targeted gene panels and microbiota analysis to provide greater insight into the effects of alternatively-sourced dietary ingredients on production indices, gut health, changes in the gut microbiota and genes involved in the regulation of appetite, growth, metabolism, ...

  19. Alternative splicing, gene localization, and binding of SH2-B to the insulin receptor kinase domain

    OpenAIRE

    Nelms, Keats; O'Neill, Thomas J.; Li, Shiqing; Hubbard, Stevan R.; Gustafson, Thomas A.; Paul, William E.

    1999-01-01

    . The SH2-B protein is an SH2-domain-containing molecule that interacts with a number of phosphorylated kinase and receptor molecules including the insulin receptor. Two isoforms of the SH2-B have been identified and have been proposed to arise through alternate splicing. Here we have identified a third isoform of the SH2-B protein, SH2-Bγ, that interacts specifically with the insulin receptor. This interaction required phosphorylation of residue Y1146 in the triple tyrosine motif within the ...

  20. Educators' Perceptions of the Effects of School Uniforms on School Climate in a Selected Metropolitan Disciplinary Alternative Education Program

    Science.gov (United States)

    Chime, Emmanuel Onoh

    2010-01-01

    The purpose of this study was to examine educators' perceptions regarding the effects of school uniforms on school climate in a selected metropolitan disciplinary alternative education program. More specifically, this study investigated the influence of the variables group status, gender, ethnicity, age and years of experience on the perceptions…

  1. When There Is No Blueprint: The Provision of Mental Health Services in Alternative School Programs for Suspended and Expelled Youth

    Science.gov (United States)

    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…

  2. An Analysis of the Efficacy Beliefs of Special Education Teachers Completing the Alternative versus the Traditional Certification Programs

    Science.gov (United States)

    Beasley, Thomas Hunter

    2012-01-01

    This study investigated the efficacy beliefs of two groups of special education teachers who had completed certification requirements in mild/moderate disabilities. The first group included 26 special education teachers who had completed an alternative certification program at a midsize public university in Louisiana between 2003 and 2008. The…

  3. An Interactive Microcomputer Program for Teaching the Impacts of Alternative Policy Sets in the Market for a Single Commodity.

    Science.gov (United States)

    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)

  4. Capacity Building Special Alternatives Program Community School District 3. Final Evaluation Report, 1993-94. OER Report.

    Science.gov (United States)

    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,…

  5. Glucocorticoid effects on the programming of AT1b angiotensin receptor gene methylation and expression in the rat.

    Directory of Open Access Journals (Sweden)

    Irina Bogdarina

    2010-02-01

    Full Text Available Adverse events in pregnancy may 'programme' offspring for the later development of cardiovascular disease and hypertension. Previously, using a rodent model of programmed hypertension we have demonstrated the role of the renin-angiotensin system in this process. More recently we showed that a maternal low protein diet resulted in undermethylation of the At1b angiotensin receptor promoter and the early overexpression of this gene in the adrenal of offspring. Here, we investigate the hypothesis that maternal glucocorticoid modulates this effect on fetal DNA methylation and gene expression. We investigated whether treatment of rat dams with the 11beta-hydroxylase inhibitor metyrapone, could prevent the epigenetic and gene expression changes we observed. Offspring of mothers subjected to a low protein diet in pregnancy showed reduced adrenal Agtr1b methylation and increased adrenal gene expression as we observed previously. Treatment of mothers with metyrapone for the first 14 days of pregnancy reversed these changes and prevented the appearance of hypertension in the offspring at 4 weeks of age. As a control for non-specific effects of programmed hypertension we studied offspring of mothers treated with dexamethasone from day 15 of pregnancy and showed that, whilst they had raised blood pressure, they failed to show any evidence of Agtr1b methylation or increase in gene expression. We conclude that maternal glucocorticoid in early pregnancy may induce changes in methylation and expression of the Agtr1b gene as these are clearly reversed by an 11 beta-hydroxylase inhibitor. However in later pregnancy a converse effect with dexamethasone could not be demonstrated and this may reflect either an alternative mechanism of this glucocorticoid or a stage-specific influence.

  6. [The teaching and application of alternative medicine in medical education programs].

    Science.gov (United States)

    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.

  7. Assessment of ptxD gene as an alternative selectable marker for Agrobacterium-mediated maize transformation.

    Science.gov (United States)

    Nahampun, Hartinio N; López-Arredondo, Damar; Xu, Xing; Herrera-Estrella, Luis; Wang, Kan

    2016-05-01

    Bacterial phosphite oxidoreductase gene and chemical phosphite can be used as a selection system for Agrobacterium -mediated maize transformation. Application of phosphite (Phi) on plants can interfere the plant metabolic system leading to stunted growth and lethality. On the other hand, ectopic expression of the ptxD gene in tobacco and Arabidopsis allowed plants to grow in media with Phi as the sole phosphorous source. The phosphite oxidoreductase (PTXD) enzyme catalyzes the conversion of Phi into phosphate (Pi) that can then be metabolized by plants and utilized as their essential phosphorous source. Here we assess an alternative selectable marker based on a bacterial ptxD gene for Agrobacterium-mediated maize transformation. We compared the transformation frequencies of maize using either the ptxD/Phi selection system or a standard herbicide bar/bialaphos selection system. Two maize genotypes, a transformation amenable hybrid Hi II and an inbred B104, were tested. Transgene presence, insertion copy numbers, and ptxD transcript levels were analyzed and compared. This work demonstrates that the ptxD/Phi selection system can be used for Agrobacterium-mediated maize transformation of both type I and type II callus culture and achieve a comparable frequency as that of the herbicide bar/bialaphos selection system.

  8. Single Nucleotide Polymorphisms Can Create Alternative Polyadenylation Signals and Affect Gene Expression through Loss of MicroRNA-Regulation

    Science.gov (United States)

    Thomas, Laurent F.; Sætrom, Pål

    2012-01-01

    Alternative polyadenylation (APA) can for example occur when a protein-coding gene has several polyadenylation (polyA) signals in its last exon, resulting in messenger RNAs (mRNAs) with different 3′ untranslated region (UTR) lengths. Different 3′UTR lengths can give different microRNA (miRNA) regulation such that shortened transcripts have increased expression. The APA process is part of human cells' natural regulatory processes, but APA also seems to play an important role in many human diseases. Although altered APA in disease can have many causes, we reasoned that mutations in DNA elements that are important for the polyA process, such as the polyA signal and the downstream GU-rich region, can be one important mechanism. To test this hypothesis, we identified single nucleotide polymorphisms (SNPs) that can create or disrupt APA signals (APA-SNPs). By using a data-integrative approach, we show that APA-SNPs can affect 3′UTR length, miRNA regulation, and mRNA expression—both between homozygote individuals and within heterozygote individuals. Furthermore, we show that a significant fraction of the alleles that cause APA are strongly and positively linked with alleles found by genome-wide studies to be associated with disease. Our results confirm that APA-SNPs can give altered gene regulation and that APA alleles that give shortened transcripts and increased gene expression can be important hereditary causes for disease. PMID:22915998

  9. Biosynthesis of actinorhodin and related antibiotics: discovery of alternative routes for quinone formation encoded in the act gene cluster.

    Science.gov (United States)

    Okamoto, Susumu; Taguchi, Takaaki; Ochi, Kozo; Ichinose, Koji

    2009-02-27

    All known benzoisochromanequinone (BIQ) biosynthetic gene clusters carry a set of genes encoding a two-component monooxygenase homologous to the ActVA-ORF5/ActVB system for actinorhodin biosynthesis in Streptomyces coelicolor A3(2). Here, we conducted molecular genetic and biochemical studies of this enzyme system. Inactivation of actVA-ORF5 yielded a shunt product, actinoperylone (ACPL), apparently derived from 6-deoxy-dihydrokalafungin. Similarly, deletion of actVB resulted in accumulation of ACPL, indicating a critical role for the monooxygenase system in C-6 oxygenation, a biosynthetic step common to all BIQ biosyntheses. Furthermore, in vitro, we showed a quinone-forming activity of the ActVA-ORF5/ActVB system in addition to that of a known C-6 monooxygenase, ActVA-ORF6, by using emodinanthrone as a model substrate. Our results demonstrate that the act gene cluster encodes two alternative routes for quinone formation by C-6 oxygenation in BIQ biosynthesis.

  10. Alternative Splicing Profile and Sex-Preferential Gene Expression in the Female and Male Pacific Abalone Haliotis discus hannai.

    Science.gov (United States)

    Kim, Mi Ae; Rhee, Jae-Sung; Kim, Tae Ha; Lee, Jung Sick; Choi, Ah-Young; Choi, Beom-Soon; Choi, Ik-Young; Sohn, Young Chang

    2017-03-09

    In order to characterize the female or male transcriptome of the Pacific abalone and further increase genomic resources, we sequenced the mRNA of full-length complementary DNA (cDNA) libraries derived from pooled tissues of female and male Haliotis discus hannai by employing the Iso-Seq protocol of the PacBio RSII platform. We successfully assembled whole full-length cDNA sequences and constructed a transcriptome database that included isoform information. After clustering, a total of 15,110 and 12,145 genes that coded for proteins were identified in female and male abalones, respectively. A total of 13,057 putative orthologs were retained from each transcriptome in abalones. Overall Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyzed in each database showed a similar composition between sexes. In addition, a total of 519 and 391 isoforms were genome-widely identified with at least two isoforms from female and male transcriptome databases. We found that the number of isoforms and their alternatively spliced patterns are variable and sex-dependent. This information represents the first significant contribution to sex-preferential genomic resources of the Pacific abalone. The availability of whole female and male transcriptome database and their isoform information will be useful to improve our understanding of molecular responses and also for the analysis of population dynamics in the Pacific abalone.

  11. Alternative Splicing Profile and Sex-Preferential Gene Expression in the Female and Male Pacific Abalone Haliotis discus hannai

    Directory of Open Access Journals (Sweden)

    Mi Ae Kim

    2017-03-01

    Full Text Available In order to characterize the female or male transcriptome of the Pacific abalone and further increase genomic resources, we sequenced the mRNA of full-length complementary DNA (cDNA libraries derived from pooled tissues of female and male Haliotis discus hannai by employing the Iso-Seq protocol of the PacBio RSII platform. We successfully assembled whole full-length cDNA sequences and constructed a transcriptome database that included isoform information. After clustering, a total of 15,110 and 12,145 genes that coded for proteins were identified in female and male abalones, respectively. A total of 13,057 putative orthologs were retained from each transcriptome in abalones. Overall Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG pathways analyzed in each database showed a similar composition between sexes. In addition, a total of 519 and 391 isoforms were genome-widely identified with at least two isoforms from female and male transcriptome databases. We found that the number of isoforms and their alternatively spliced patterns are variable and sex-dependent. This information represents the first significant contribution to sex-preferential genomic resources of the Pacific abalone. The availability of whole female and male transcriptome database and their isoform information will be useful to improve our understanding of molecular responses and also for the analysis of population dynamics in the Pacific abalone.

  12. Broodyear Data - Captive Broodstock Gene Rescue Program for Odd Year Class Elwha River Pink Salmon

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Conduct captive brood stock gene rescue program for Elwha River odd-year class pink salmon. Data is collected by broodyear on % survival to adult, % maturity as two...

  13. Fish Health Data - Captive Broodstock Gene Rescue Program for Odd Year Class Elwha River Pink Salmon

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Conduct captive brood stock gene rescue program for Elwha River odd-year class pink salmon. All fresh mortalities larger than 100 mm are sent to Fish Health for...

  14. Growth Data - Captive Broodstock Gene Rescue Program for Odd Year Class Elwha River Pink Salmon

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Conduct captive brood stock gene rescue program for Elwha River odd-year class pink salmon. The fork length to the nearest mm and weight to the nearest gram of a...

  15. Fish Culture Data - Captive Broodstock Gene Rescue Program for Odd Year Class Elwha River Pink Salmon

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Conduct captive brood stock gene rescue program for Elwha River odd-year class pink salmon. Raw data on rearing density, loading density, water temperature, ration,...

  16. TUMOR-SPECIFIC EXPRESSION AND ALTERNATIVE SPLICING OF THE COL6A3 GENE IN PANCREATIC CANCER

    Science.gov (United States)

    Arafat, Hwyda; Lazar, Melissa; Salem, Khalifa; Chipitsyna, Galina; Gong, Qiaoke; Pan, Te-Cheng; Zhang, Rui-Zhu; Yeo, Charles J.; Chu, Mon-Li

    2011-01-01

    Introduction Pancreatic ductal adenocarcinoma (PDA) is a highly lethal disease in which a prominent desmoplastic reaction is a defining characteristic. Fibrillar collagens, such as collagen I and to a lesser extent, collagen III and V comprise the majority of this stromal fibrosis. Type VI collagen (COL6) forms a microfibrillar network associated with type I collagen fibrils. The expression of COL6 has been linked to inflammation and survival. Importantly, tumor-specific alternative splicing in COL6A3 has been identified in several cancers by genome exon arrays. We evaluated the expression and localization of COL6A3 in PDA and premalignant lesions and explored the presence of alternative splicing events. Methods We analyzed paired PDA-normal (n=18), IPMN (n=5), pancreatic cystadenoma (n=5), and eight PDA cell lines with RT-PCR, using unique primers that identify total COL6A3 gene and alternative splicing sites in several of its exons. Western blot analysis and immunohistochemistry were used to analyze the expression levels and localization of COL6A3 protein in the different lesions, and in two animal models of PDA. Results COL6A3 protein levels were significantly upregulated in 77% of the paired PDA-adjacent tissue examined. COL6A3 was mainly present in the desmoplastic stroma of PDA, with high deposition around the malignant ducts and in between the sites of stromal fatty infiltration. Analysis of the COL6A3 splice variants showed tumor-specific consistent inclusion of exons 3 and 6 in 17 of the 18 (94%) paired PDA-adjacent tissues. Inclusion of exon 4 was exclusively tumor-specific, with barely detectable expression in the adjacent tissues. IPMN and pancreatic cystadenomas showed no expression of any of the examined exons. Total COL6A3 mRNA and exon 6 were identified in six PDA cell lines, but only two cell lines (MIA PACA-2 and ASPC-1) expressed exons 3 and 4. In both the xenograft and transgenic models of PDA, COL6A3 immunoreactivity was present in the stroma

  17. Examination of a Palatogenic Gene Program in Zebrafish

    Science.gov (United States)

    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

  18. Revised genomic structure of the human ghrelin gene and identification of novel exons, alternative splice variants and natural antisense transcripts

    Directory of Open Access Journals (Sweden)

    Herington Adrian C

    2007-08-01

    Full Text Available Abstract Background Ghrelin is a multifunctional peptide hormone expressed in a range of normal tissues and pathologies. It has been reported that the human ghrelin gene consists of five exons which span 5 kb of genomic DNA on chromosome 3 and includes a 20 bp non-coding first exon (20 bp exon 0. The availability of bioinformatic tools enabling comparative analysis and the finalisation of the human genome prompted us to re-examine the genomic structure of the ghrelin locus. Results We have demonstrated the presence of an additional novel exon (exon -1 and 5' extensions to exon 0 and 1 using comparative in silico analysis and have demonstrated their existence experimentally using RT-PCR and 5' RACE. A revised exon-intron structure demonstrates that the human ghrelin gene spans 7.2 kb and consists of six rather than five exons. Several ghrelin gene-derived splice forms were detected in a range of human tissues and cell lines. We have demonstrated ghrelin gene-derived mRNA transcripts that do not code for ghrelin, but instead may encode the C-terminal region of full-length preproghrelin (C-ghrelin, which contains the coding region for obestatin and a transcript encoding obestatin-only. Splice variants that differed in their 5' untranslated regions were also found, suggesting a role of these regions in the post-transcriptional regulation of preproghrelin translation. Finally, several natural antisense transcripts, termed ghrelinOS (ghrelin opposite strand transcripts, were demonstrated via orientation-specific RT-PCR, 5' RACE and in silico analysis of ESTs and cloned amplicons. Conclusion The sense and antisense alternative transcripts demonstrated in this study may function as non-coding regulatory RNA, or code for novel protein isoforms. This is the first demonstration of putative obestatin and C-ghrelin specific transcripts and these findings suggest that these ghrelin gene-derived peptides may also be produced independently of preproghrelin

  19. Serving a Higher Power: The Influence of Alternative Break Programs on Students' Religiousness

    Science.gov (United States)

    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. Non-proliferation, safeguards, and security for the fissile materials disposition program immobilization alternatives

    Energy Technology Data Exchange (ETDEWEB)

    Duggan, R.A.; Jaeger, C.D.; Tolk, K.M. [Sandia National Labs., Albuquerque, NM (United States); Moore, L.R. [Lawrence Livermore National Lab., CA (United States)

    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.

  1. Chromosome structures: reduction of certain problems with unequal gene content and gene paralogs to integer linear programming.

    Science.gov (United States)

    Lyubetsky, Vassily; Gershgorin, Roman; Gorbunov, Konstantin

    2017-12-06

    Chromosome structure is a very limited model of the genome including the information about its chromosomes such as their linear or circular organization, the order of genes on them, and the DNA strand encoding a gene. Gene lengths, nucleotide composition, and intergenic regions are ignored. Although highly incomplete, such structure can be used in many cases, e.g., to reconstruct phylogeny and evolutionary events, to identify gene synteny, regulatory elements and promoters (considering highly conserved elements), etc. Three problems are considered; all assume unequal gene content and the presence of gene paralogs. The distance problem is to determine the minimum number of operations required to transform one chromosome structure into another and the corresponding transformation itself including the identification of paralogs in two structures. We use the DCJ model which is one of the most studied combinatorial rearrangement models. Double-, sesqui-, and single-operations as well as deletion and insertion of a chromosome region are considered in the model; the single ones comprise cut and join. In the reconstruction problem, a phylogenetic tree with chromosome structures in the leaves is given. It is necessary to assign the structures to inner nodes of the tree to minimize the sum of distances between terminal structures of each edge and to identify the mutual paralogs in a fairly large set of structures. A linear algorithm is known for the distance problem without paralogs, while the presence of paralogs makes it NP-hard. If paralogs are allowed but the insertion and deletion operations are missing (and special constraints are imposed), the reduction of the distance problem to integer linear programming is known. Apparently, the reconstruction problem is NP-hard even in the absence of paralogs. The problem of contigs is to find the optimal arrangements for each given set of contigs, which also includes the mutual identification of paralogs. We proved that these

  2. Alternative splicing of DENND1A, a PCOS candidate gene, generates variant 2.

    Science.gov (United States)

    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. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  3. Global identification of the full-length transcripts and alternative splicing related to phenolic acid biosynthetic genes in Salvia miltiorrhiza

    Directory of Open Access Journals (Sweden)

    Zhichao eXu

    2016-02-01

    Full Text Available Salvianolic acids are among the main bioactive components in Salvia miltiorrhiza, and their biosynthesis has attracted widespread interest. However, previous studies on the biosynthesis of phenolic acids using next-generation sequencing platforms are limited with regard to the assembly of full-length transcripts. Based on hybrid-seq (next-generation and single molecular real-time sequencing of the S. miltiorrhiza root transcriptome, we experimentally identified 15 full-length transcripts and 4 alternative splicing events of enzyme-coding genes involved in the biosynthesis of rosmarinic acid. Moreover, we herein demonstrate that lithospermic acid B accumulates in the phloem and xylem of roots, in agreement with the expression patterns of the identified key genes related to rosmarinic acid biosynthesis. According to co-expression patterns, we predicted that 6 candidate cytochrome P450s and 5 candidate laccases participate in the salvianolic acid pathway. Our results provide a valuable resource for further investigation into the synthetic biology of phenolic acids in S. miltiorrhiza.

  4. Alternative splicing: a novel mechanism of regulation identified in the chorismate mutase gene of the potato cyst nematode Globodera rostochiensis.

    Science.gov (United States)

    Lu, Shun-Wen; Tian, Duanhua; Borchardt-Wier, Harmony B; Wang, Xiaohong

    2008-11-01

    Chorismate mutase (CM) secreted from the stylet of plant-parasitic nematodes plays an important role in plant parasitism. We isolated and characterized a new nematode CM gene (Gr-cm-1) from the potato cyst nematode, Globodera rostochiensis. The Gr-cm-1 gene was found to exist in the nematode genome as a single-copy gene that has two different alleles, Gr-cm-1A and Gr-cm-1B, both of which could give rise to two different mRNA transcripts of Gr-cm-1 and Gr-cm-1-IRII. In situ mRNA hybridization showed that the Gr-cm-1 gene was exclusively expressed within the subventral oesophageal gland cells of the nematode. Gr-cm-1 was demonstrated to encode a functional CM (GR-CM-1) potentially having a dimeric structure as the secreted bacterial *AroQ CMs. Gr-cm-1-IRII, generated by retention of intron 2 of the Gr-cm-1 pre-mRNA through alternative splicing (AS), would encode a truncated protein (GR-CM-1t) lacking the CM domain with no CM activity. The quantitative real-time reverse transcription-PCR assay revealed that splicing of the Gr-cm-1 gene was developmentally regulated; Gr-cm-1 was up-regulated whereas Gr-cm-1-IRII was down-regulated in early nematode parasitic stages compared to the preparasitic juvenile stage. Low-temperature SDS-PAGE analysis revealed that GR-CM-1 could form homodimers when expressed in Escherichia coli and the dimerization domain was retained in the truncated GR-CM-1t protein. The specific interaction between the two proteins was demonstrated in yeast. Our data suggested that the novel splice variant might function as a dominant negative isoform through heterodimerization with the full-length GR-CM-1 protein and that AS may represent an important mechanism for regulating CM activity during nematode parasitism.

  5. The National Shipbuilding Research Program: Producibility Cost Reductions through Alternative Materials and Processes

    National Research Council Canada - National Science Library

    Horsmon, Jr., Albert W; Johnson, Karl; Gans-Devney, Barbara

    1999-01-01

    This report describes research into the use of alternative materials and processes to reduce material and labor costs while also looking at the influence of these choices on the life cycle costs of the vessel...

  6. Synthesis of the project leadership staffing needs for successful development of alternative delivery programs.

    Science.gov (United States)

    2017-08-01

    This research provides a synthesis of practices in organizational structuring and professional staffing of the innovative delivery units in several state DOTs across the nation that are actively utilizing alternative project delivery. Several major c...

  7. Alternative Schools and Programs for Public School Students at Risk of Educational Failure: 2007-08. First Look. NCES 2010-026

    Science.gov (United States)

    Carver, Priscilla Rouse; Lewis, Laurie; Tice, Peter

    2010-01-01

    This report provides national estimates on the availability of alternative schools and programs for students at risk of educational failure in public school districts during the 2007-08 school year. The National Center for Education Statistics (NCES) previously reported results from a similar survey of alternative schools and programs conducted…

  8. 77 FR 22321 - National Toxicology Program (NTP) Interagency Center for the Evaluation of Alternative...

    Science.gov (United States)

    2012-04-13

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Toxicology Program (NTP) Interagency Center for... (HTS) Assays for the Tox21 Initiative AGENCY: Division of the National Toxicology Program (DNTP...: April 5, 2012. John R. Bucher, Associate Director, National Toxicology Program. [FR Doc. 2012-8942 Filed...

  9. Lifeline electric rates and alternative approaches to the problems of low-income ratepayers. Ten case studies of implemented programs

    Energy Technology Data Exchange (ETDEWEB)

    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)

  10. Nuclear proliferation and civilian nuclear power. Report of the Nonproliferation Alternative Systems Assessment Program. Volume IV. Commercial potential

    Energy Technology Data Exchange (ETDEWEB)

    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.

  11. Nuclear proliferation and civilian nuclear power. Report of the Nonproliferation Alternative Systems Assessment Program. Volume IV. Commercial potential

    International Nuclear Information System (INIS)

    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

  12. Translational read-through as an alternative approach for ocular gene therapy of retinal dystrophies caused by in-frame nonsense mutations.

    Science.gov (United States)

    Nagel-Wolfrum, Kerstin; Möller, Fabian; Penner, Inessa; Wolfrum, Uwe

    2014-09-01

    The eye has become an excellent target for gene therapy, and gene augmentation therapy of inherited retinal disorders has made major progress in recent years. Nevertheless, a recent study indicated that gene augmentation intervention might not stop the progression of retinal degeneration in patients. In addition, for many genes, viral-mediated gene augmentation is currently not feasible due to gene size and limited packaging capacity of viral vectors as well as expression of various heterogeneous isoforms of the target gene. Thus, alternative gene-based strategies to stop or delay the retinal degeneration are necessary. This review focuses on an alternative pharmacologic treatment strategy based on the usage of translational read-through inducing drugs (TRIDs) such as PTC124, aminoglycoside antibiotics, and designer aminoglycosides for overreading in-frame nonsense mutations. This strategy has emerged as an option for up to 30-50% of all cases of recessive hereditary retinal dystrophies. In-frame nonsense mutations are single-nucleotide alterations within the gene coding sequence resulting in a premature stop codon. Consequently, translation of such mutated genes leads to the synthesis of truncated proteins, which are unable to fulfill their physiologic functions. In this context, application of TRIDs facilitates the recoding of the premature termination codon into a sense codon, thus restoring syntheses of full-length proteins. So far, clinical trials for non-ocular diseases have been initiated for diverse TRIDs. Although the clinical outcome is not analyzed in detail, an excellent safety profile, namely for PTC124, was clearly demonstrated. Moreover, recent data demonstrated sustained read-through efficacies of nonsense mutations causing retinal degeneration, as manifested in the human Usher syndrome. In addition, a strong retinal biocompatibility for PTC124 and designer aminoglycosides has been demonstrated. In conclusion, recent progress emphasizes the

  13. Array data extractor (ADE): a LabVIEW program to extract and merge gene array data.

    Science.gov (United States)

    Kurtenbach, Stefan; Kurtenbach, Sarah; Zoidl, Georg

    2013-12-01

    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. 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. 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.

  14. Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming

    Energy Technology Data Exchange (ETDEWEB)

    Song, Hyun-Seob; Goldberg, Noam; Mahajan, Ashutosh; Ramkrishna, Doraiswami

    2017-03-27

    Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of relevant EMs needs to be known, for which optimization-based sequential computation is a useful alternative. Most of the currently available methods along this line are based on the iterative use of mixed integer linear programming (MILP), the effectiveness of which significantly deteriorates as the number of iterations builds up. To alleviate the computational burden associated with the MILP implementation, we here present a novel optimization algorithm termed alternate integer linear programming (AILP). Results: Our algorithm was designed to iteratively solve a pair of integer programming (IP) and linear programming (LP) to compute EMs in a sequential manner. In each step, the IP identifies a minimal subset of reactions, the deletion of which disables all previously identified EMs. Thus, a subsequent LP solution subject to this reaction deletion constraint becomes a distinct EM. In cases where no feasible LP solution is available, IP-derived reaction deletion sets represent minimal cut sets (MCSs). Despite the additional computation of MCSs, AILP achieved significant time reduction in computing EMs by orders of magnitude. The proposed AILP algorithm not only offers a computational advantage in the EM analysis of genome-scale networks, but also improves the understanding of the linkage between EMs and MCSs.

  15. Two alternatively spliced GPR39 transcripts in seabream: molecular cloning, genomic organization, and regulation of gene expression by metabolic signals.

    Science.gov (United States)

    Zhang, Yong; Liu, Yun; Huang, Xigui; Liu, Xiaochun; Jiao, Baowei; Meng, Zining; Zhu, Pei; Li, Shuisheng; Lin, Haoran; Cheng, Christopher H K

    2008-12-01

    Two GPR39 transcripts, designated as sbGPR39-1a and sbGPR39-1b, were identified in black seabream (Acanthopagrus schlegeli). The deduced amino acid (aa) sequence of sbGPR39-1a contains 423 residues with seven putative transmembrane (TM) domains. On the other hand, sbGPR39-1b contains 284 aa residues with only five putative TM domains. Northern blot analysis confirmed the presence of two GPR39 transcripts in the seabream intestine, stomach, and liver. Apart from seabream, the presence of two GPR39 transcripts was also found to exist in a number of teleosts (zebrafish and pufferfish) and mammals (human and mouse). Analysis of the GPR39 gene structure in different species suggests that the two GPR39 transcripts are generated by alternative splicing. When the seabream receptors were expressed in cultured HEK293 cells, Zn(2)(+) could trigger sbGPR39-1a signaling through the serum response element pathway, but no such functionality could be detected for the sbGPR39-1b receptor. The two receptors were found to be differentially expressed in seabream tissues. sbGPR39-1a is predominantly expressed in the gastrointestinal tract. On the other hand, sbGPR39-1b is widely expressed in most central and peripheral tissues except muscle and ovary. The expression of sbGPR39-1a in the intestine and the expression of sbGPR39-1b in the hypothalamus were decreased significantly during food deprivation in seabream. On the contrary, the expression of the GH secretagogue receptors (sbGHSR-1a and sbGHSR-1b) was significantly increased in the hypothalamus of the food-deprived seabream. The reciprocal regulatory patterns of expression of these two genes suggest that both of them are involved in controlling the physiological response of the organism during starvation.

  16. Turkish Student Teachers' Attitudes toward Teaching in University-Based and Alternative Certification Programs in Turkey

    Science.gov (United States)

    Aksoy, Erdem

    2017-01-01

    The objective of this study is to comparatively analyze the university-based and alternative teacher certification systems in Turkey in terms of the attitudes of trainee teachers toward the teaching profession, explore the reasons of choosing teaching as a career as well as analyze attitudes by gender, department, and graduating faculty type in…

  17. Alternative Pathways into University: Are Tertiary Preparation Programs a Viable Option?

    Science.gov (United States)

    Chesters, Jenny; Rutter, Kerry; Nelson, Karen; Watson, Louis

    2018-01-01

    During the past three decades, the student populations of Australian universities have become more heterogeneous as the higher education sector expanded and new alternative entry pathways were established. Broadening access to university study and, therefore, to professional and semi-professional occupations, provides avenues for social mobility.…

  18. 78 FR 14843 - Temporary Scope Expansion of the Post-Investigation Alternative Dispute Resolution Program

    Science.gov (United States)

    2013-03-07

    ... dialogues that can be used to assist parties in resolving disputes and potential conflicts. These techniques..., and improved relationships between the agency and the other party. On August 14, 1992 (57 FR 36678... enforcement action. In SECY-12-0161, ``Status Update, Tasks Related to Alternative Dispute Resolution in the...

  19. Harvesting Alternative Credit Transfer Students: Redefining Selectivity in Your Online Learning Program Enrollment Leads

    Science.gov (United States)

    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…

  20. Low Emissions Alternative Power (LEAP) Project Office Business Team of the Aeropropulsion Research Program Office (ARPO) Org. 0140

    Science.gov (United States)

    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

  1. A rapid pathway toward a superb gene delivery system: programming structural and functional diversity into a supramolecular nanoparticle library.

    Science.gov (United States)

    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.

  2. IT0: Discrete Math and Programming Logic Topics as a Hybrid Alternative to CS0

    Science.gov (United States)

    Martin, Nancy L.

    2015-01-01

    This paper describes the development of a hybrid introductory course for students in their first or second year of an information systems technologies degree program at a large Midwestern university. The course combines topics from discrete mathematics and programming logic and design, a unique twist on most introductory courses. The objective of…

  3. An Alternating Direction Method for Convex Quadratic Second-Order Cone Programming with Bounded Constraints

    Directory of Open Access Journals (Sweden)

    Xuewen Mu

    2015-01-01

    quadratic programming over second-order cones and a bounded set. At each iteration, we only need to compute the metric projection onto the second-order cones and the projection onto the bound set. The result of convergence is given. Numerical results demonstrate that our method is efficient for the convex quadratic second-order cone programming problems with bounded constraints.

  4. 19 CFR 101.9 - Test programs or procedures; alternate requirements.

    Science.gov (United States)

    2010-04-01

    ... basis for selecting participants. (b) NCAP testing. For purposes of conducting an approved test program or procedure designed to evaluate planned components of the National Customs Automation Program (NCAP... publication requirement. For tests affecting the NCAP, notice shall be published in the Federal Register not...

  5. An alternate property tax program requiring a forest management plan and scheduled harvesting

    Science.gov (United States)

    D.F. Dennis; P.E. Sendak

    1991-01-01

    Vermont's Use Value Appraisal property tax program, designed to address problems such as tax inequity and forced development caused by taxing agricultural and forest land based on speculative values, requires a forest management plan and scheduled harvests. A probit analysis of enrollment provides evidence of the program's success in attracting large parcels...

  6. An Evaluation of an Alternative Teacher Certification Program: A Matter of Trust

    Science.gov (United States)

    Grubbs, Scott T.

    2009-01-01

    For the internal evaluator, the issue of trust can be one of the more difficult ethical matters to manage. An organization might choose to conduct an internal program evaluation for a variety of reasons, including capitalizing on the abilities of invested stakeholders to assess aspects of a program, building an institutional culture oriented…

  7. Employee assistance programs: an alternative resource for mental health service delivery.

    Science.gov (United States)

    Santa-Barbara, J

    1984-09-01

    The purpose of this article is to provide a very brief introduction to employee assistance programs (EAPs) and their role in the mental health delivery system. In addition, some consideration will be given to the opportunity these programs offer for making a significant impact on both the mental health of Canadians and the productivity of Canadian business.

  8. Effects of a pain education program in Complementary and Alternative Medicine treatment utilization at a VA medical center.

    Science.gov (United States)

    Cosio, David; Lin, Erica H

    2015-06-01

    Past studies have shown that U.S. Veterans are consumers of CAM. However, more than 75% of Veteran non-users report they would utilize these treatment options if made available. Thus, Veterans may not be fully aware of the CAM options currently available to them in the current U.S. VA health care system. The current study tested the hypothesis that Veterans would report an increase in CAM utilization after completing a formal pain education program in a VA medical center. The study used a quasi-experimental, one-group, pre/post-test design. Midwestern, U.S. VA Medical Center. The responses from 103 Veterans who elected to participate in the program and the assessment measures were included in the outcome analyses. "Pain Education School" is a 12-week, educational program that is open to all Veterans and their families. It is a comprehensive program that introduces patients to 23 different disciplines at the VA Medical Center that deal with chronic, non-cancer pain. An adaptation of the Complementary and Alternative Medicine Questionnaire(©), SECTION A: Use of Alternative Health Care Providers. There was a significant difference found in overall utilization of CAM after completing the pain education program. The most utilized CAM modality was the chiropractor; the least utilized were hypnosis and aromatherapy. Not all health care systems or providers may have access to an education-focused, professionally driven program as an amenity. However, lessons can be learned from this study in terms of what pain providers may be able to accomplish in their practice. Published by Elsevier Ltd.

  9. Detection of mecA Gene Associated with Methicillin Resistant Staphylococcus aureus and its Alternatives using Nanoparticles and Chia Seeds

    Directory of Open Access Journals (Sweden)

    M. Rajamani

    2017-11-01

    Full Text Available Staphylococcus aureus, a member of the family Micrococcaceae, is a Gram-positive coccus whose cells tend to occur either singly or if dividing cells do not separate, form pairs, tetrads and distinctive irregular “grape-like” structures, which is resistant to few antibiotics like Methicillin which is termed as Methicillin resistant Staphylococcus aureus. MRSA was isolated from the pus sample. Confirmation of MRSA was done by using Kirby Bauer disk method. Followed by sub culturing in Luria bertani broth and DNA isolation was performed by phenol chloroform method and confirmed by AGE (Agarose gel electrophoresis. The amplification of mecA gene thermocycler-PCR was done. Restriction fragmented linked polymorphism was done for knowing how much restriction sites are available for organism. To calculate the molecular weight of the protein SDS-PAGE (Sodium dodecyl sulphate - Polyacrylamide gel electrophoresis was performed. Followed by alternative measures was done, by using Silver nanoparticles at different concentrations and Chia seeds against MRSA.

  10. Conserved alternative and antisense transcripts at the programmed cell death 2 locus

    Czech Academy of Sciences Publication Activity Database

    Mihola, Ondřej; Forejt, Jiří; Trachtulec, Zdeněk

    2007-01-01

    Roč. 8, - (2007), s. 20 ISSN 1471-2164 R&D Projects: GA ČR(CZ) GA204/01/0997; GA ČR GA301/05/0738; GA AV ČR IAA5052406; GA MŠk(CZ) 1M0520 Institutional research plan: CEZ:AV0Z50520514 Keywords : Pdcd2 * antisense * alternative transcript * imprinting Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.180, year: 2007

  11. Transcriptomic insights into the alternative splicing-mediated adaptation of the entomopathogenic fungus Beauveria bassiana to host niches: autophagy-related gene 8 as an example.

    Science.gov (United States)

    Dong, Wei-Xia; Ding, Jin-Li; Gao, Yang; Peng, Yue-Jin; Feng, Ming-Guang; Ying, Sheng-Hua

    2017-10-01

    Alternative splicing (AS) regulates various biological processes in fungi by extending the cellular proteome. However, comprehensive studies investigating AS in entomopathogenic fungi are lacking. Based on transcriptome data obtained via dual RNA-seq, the first overview of AS events was developed for Beauveria bassiana growing in an insect haemocoel. The AS was demonstrated for 556 of 8840 expressed genes, accounting for 5.4% of the total genes in B. bassiana. Intron retention was the most abundant type of AS, accounting for 87.1% of all splicing events and exon skipping events were rare, only accounting for 2.0% of all events. Functional distribution analysis indicated an association between alternatively spliced genes and several physiological processes. Notably, B. bassiana autophagy-related gene 8 (BbATG8), an indispensable gene for autophagy, was spliced at an alternative 5' splice site to generate two transcripts (BbATG8-α and BbATG8-β). The BbATG8-α transcript was necessary for fungal autophagy and oxidation tolerance, while the BbATG8-β transcript was not. These two transcripts differentially contributed to the formation of conidia or blastospores as well as fungal virulence. Thus, AS acts as a powerful post-transcriptional regulatory strategy in insect mycopathogens and significantly mediates fungal transcriptional adaption to host niches. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  12. Alternative Aviation Jet Fuel Sustainability Evaluation Report Task 1 : Report Evaluating Existing Sustainability Evaluation Programs

    Science.gov (United States)

    2011-10-25

    This report describes how existing biofuel sustainability evaluation programs meet requirements that are under consideration or are in early phases of adoption and implementation in various US and international contexts. Biofuel sustainability evalua...

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

    OpenAIRE

    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. INTERVENTION...

  14. Converging and Diverging Service Delivery Systems in Alternative Education Programs for Disabled and Non-Disabled Youth Involved in the Juvenile Justice System

    Science.gov (United States)

    Atkins, Trent; Bullis, Michael; Todis, Bonnie

    2005-01-01

    This study is part of a directed research project funded by the Office of Special Education Programs. Using qualitative research methods, consisting of interviews and participant observations, the policies and procedures of three alternative education programs in various settings were investigated. These programs served youth with and without…

  15. Global transcriptome analysis reveals extensive gene remodeling, alternative splicing and differential transcription profiles in non-seed vascular plant Selaginella moellendorffii.

    Science.gov (United States)

    Zhu, Yan; Chen, Longxian; Zhang, Chengjun; Hao, Pei; Jing, Xinyun; Li, Xuan

    2017-01-25

    Selaginella moellendorffii, a lycophyte, is a model plant to study the early evolution and development of vascular plants. As the first and only sequenced lycophyte to date, the genome of S. moellendorffii revealed many conserved genes and pathways, as well as specialized genes different from flowering plants. Despite the progress made, little is known about long noncoding RNAs (lncRNA) and the alternative splicing (AS) of coding genes in S. moellendorffii. Its coding gene models have not been fully validated with transcriptome data. Furthermore, it remains important to understand whether the regulatory mechanisms similar to flowering plants are used, and how they operate in a non-seed primitive vascular plant. RNA-sequencing (RNA-seq) was performed for three S. moellendorffii tissues, root, stem, and leaf, by constructing strand-specific RNA-seq libraries from RNA purified using RiboMinus isolation protocol. A total of 176 million reads (44 Gbp) were obtained from three tissue types, and were mapped to S. moellendorffii genome. By comparing with 22,285 existing gene models of S. moellendorffii, we identified 7930 high-confidence novel coding genes (a 35.6% increase), and for the first time reported 4422 lncRNAs in a lycophyte. Further, we refined 2461 (11.0%) of existing gene models, and identified 11,030 AS events (for 5957 coding genes) revealed for the first time for lycophytes. Tissue-specific gene expression with functional implication was analyzed, and 1031, 554, and 269 coding genes, and 174, 39, and 17 lncRNAs were identified in root, stem, and leaf tissues, respectively. The expression of critical genes for vascular development stages, i.e. formation of provascular cells, xylem specification and differentiation, and phloem specification and differentiation, was compared in S. moellendorffii tissues, indicating a less complex regulatory mechanism in lycophytes than in flowering plants. The results were further strengthened by the evolutionary trend of

  16. Integrated neuroscience program: an alternative approach to teaching neurosciences to chiropractic students.

    Science.gov (United States)

    He, Xiaohua; La Rose, James; Zhang, Niu

    2009-01-01

    Most chiropractic colleges do not offer independent neuroscience courses because of an already crowded curriculum. The Palmer College of Chiropractic Florida has developed and implemented an integrated neuroscience program that incorporates neurosciences into different courses. The goals of the program have been to bring neurosciences to students, excite students about the interrelationship of neuroscience and chiropractic, improve students' understanding of neuroscience, and help the students understand the mechanisms underpinning the chiropractic practice. This study provides a descriptive analysis on how the integrated neuroscience program is taught via students' attitudes toward neuroscience and the comparison of students' perceptions of neuroscience content knowledge at different points in the program. A questionnaire consisting of 58 questions regarding the neuroscience courses was conducted among 339 students. The questionnaire was developed by faculty members who were involved in teaching neuroscience and administered in the classroom by faculty members who were not involved in the study. Student perceptions of their neuroscience knowledge, self-confidence, learning strategies, and knowledge application increased considerably through the quarters, especially among the 2nd-year students. The integrated neuroscience program achieved several of its goals, including an increase in students' confidence, positive attitude, ability to learn, and perception of neuroscience content knowledge. The authors believe that such gains can expand student ability to interpret clinical cases and inspire students to become excited about chiropractic research. The survey provides valuable information for teaching faculty to make the course content more relevant to chiropractic students.

  17. Stunned Silence: Gene Expression Programs in Human Cells Infected with Monkeypox or Vaccinia Virus

    Science.gov (United States)

    Rubins, Kathleen H.; Hensley, Lisa E.; Relman, David A.; Brown, Patrick O.

    2011-01-01

    Poxviruses use an arsenal of molecular weapons to evade detection and disarm host immune responses. We used DNA microarrays to investigate the gene expression responses to infection by monkeypox virus (MPV), an emerging human pathogen, and Vaccinia virus (VAC), a widely used model and vaccine organism, in primary human macrophages, primary human fibroblasts and HeLa cells. Even as the overwhelmingly infected cells approached their demise, with extensive cytopathic changes, their gene expression programs appeared almost oblivious to poxvirus infection. Although killed (gamma-irradiated) MPV potently induced a transcriptional program characteristic of the interferon response, no such response was observed during infection with either live MPV or VAC. Moreover, while the gene expression response of infected cells to stimulation with ionomycin plus phorbol 12-myristate 13-acetate (PMA), or poly (I-C) was largely unimpaired by infection with MPV, a cluster of pro-inflammatory genes were a notable exception. Poly(I-C) induction of genes involved in alerting the innate immune system to the infectious threat, including TNF-alpha, IL-1 alpha and beta, CCL5 and IL-6, were suppressed by infection with live MPV. Thus, MPV selectively inhibits expression of genes with critical roles in cell-signaling pathways that activate innate immune responses, as part of its strategy for stealthy infection. PMID:21267444

  18. Stunned silence: gene expression programs in human cells infected with monkeypox or vaccinia virus.

    Directory of Open Access Journals (Sweden)

    Kathleen H Rubins

    2011-01-01

    Full Text Available Poxviruses use an arsenal of molecular weapons to evade detection and disarm host immune responses. We used DNA microarrays to investigate the gene expression responses to infection by monkeypox virus (MPV, an emerging human pathogen, and Vaccinia virus (VAC, a widely used model and vaccine organism, in primary human macrophages, primary human fibroblasts and HeLa cells. Even as the overwhelmingly infected cells approached their demise, with extensive cytopathic changes, their gene expression programs appeared almost oblivious to poxvirus infection. Although killed (gamma-irradiated MPV potently induced a transcriptional program characteristic of the interferon response, no such response was observed during infection with either live MPV or VAC. Moreover, while the gene expression response of infected cells to stimulation with ionomycin plus phorbol 12-myristate 13-acetate (PMA, or poly (I-C was largely unimpaired by infection with MPV, a cluster of pro-inflammatory genes were a notable exception. Poly(I-C induction of genes involved in alerting the innate immune system to the infectious threat, including TNF-alpha, IL-1 alpha and beta, CCL5 and IL-6, were suppressed by infection with live MPV. Thus, MPV selectively inhibits expression of genes with critical roles in cell-signaling pathways that activate innate immune responses, as part of its strategy for stealthy infection.

  19. The implementation limitations of and alternative policy solutions for Indonesia's REDD+ program concerning peatland restoration

    Directory of Open Access Journals (Sweden)

    Sarah Guzick

    2013-07-01

    Full Text Available Recent increases in global demand for palm oil have resulted in rapid, widespread deforestation in Indonesia, making Indonesia the third largest emitter of greenhouse gases in the world. Although the Indonesian government has sought to pursue progressive environmental policies to curb deforestation, such as through REDD+, implementation has been hampered by legal loopholes, corruption and weak rule of law. This paper will examine two alternative carbon sequestration policies to REDD+: a drying up of the palm oil market and a buy-out of palm oil plantations.

  20. Towards ABET accreditation for a SWE program: alternative student assessment techniques

    International Nuclear Information System (INIS)

    Alghamdi, A.; Nasir, M.; Alnafjan, K.

    2011-01-01

    This paper describes assessment techniques utilized for assessing undergraduate students studying in a software engineering program. The purpose behind this work is to get the program accredited by the Accreditation Board of Engineering and Technology (ABET). Therefore, a number of applied direct and indirect assessment techniques are described. These techniques are implemented towards the end of the semester to assess the extent to which the student and course outcomes are satisfied. Consequently, results are obtained and analyzed and various learning issues are eventually identified. Finally, the paper provides suggestions for improvement in course delivery as well as learning mechanism. (author)

  1. Alternative Ultrasound Gel for a Sustainable Ultrasound Program: Application of Human Centered Design.

    Directory of Open Access Journals (Sweden)

    Margaret Salmon

    Full Text Available 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.

  2. Alternative Ultrasound Gel for a Sustainable Ultrasound Program: Application of Human Centered Design.

    Science.gov (United States)

    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.

  3. WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data.

    Science.gov (United States)

    Boyer, Frédéric; Besson, Bruno; Baptist, Guillaume; Izard, Jérôme; Pinel, Corinne; Ropers, Delphine; Geiselmann, Johannes; de Jong, Hidde

    2010-05-01

    Fluorescent and luminescent reporter gene systems in combination with automated microplate readers allow real-time monitoring of gene expression on the population level at high precision and sampling density. This generates large amounts of data for the analysis of which computer tools are missing to date. We have developed WellReader, a MATLAB program for the analysis of fluorescent and luminescent reporter gene data. WellReader allows the user to load the output files of microplate readers, remove outliers, correct for background effects and smooth and fit the data. Moreover, it computes biologically relevant quantities from the measured signals, notably promoter activities and protein concentrations, and compares the resulting expression profiles of different genes under different conditions. WellReader is available under a LGPL licence at http://prabi1.inrialpes.fr/trac/wellreader.

  4. Analysis of Student Misbehavior Patterns: Corrective Guidelines for Administrators and Teachers in Alternative Education Programs.

    Science.gov (United States)

    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…

  5. Feasibility of Using Alternate Fuels in the U.S. Antarctic Program: Initial Assessment

    Science.gov (United States)

    2017-09-01

    Polar Programs. Morris, A. 2015a. Email communication. 21 April. Centennial , CO: Antarctic Support Contractor. ———. 2015b. Personal...communication. 19 May. Centennial , CO: Antarctic Support Contractor. ———. 2014. Email communication. 24 November. Centennial , CO: Antarctic Support

  6. 77 FR 47375 - Applications for New Awards; Assistive Technology Alternative Financing Program

    Science.gov (United States)

    2012-08-08

    ... (AT) they need. In addition, programs such as Medicaid, Medicare, and vocational rehabilitation cannot... sources. Competitive Preference Priorities: Within this absolute priority, we give competitive preference... comment on the proposed absolute and competitive preference priorities under section 437(d)(1)of GEPA. The...

  7. Criteria for Evaluating Alternative Network and Link Layer Protocols for the NASA Constellation Program Communication Architecture

    Science.gov (United States)

    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.

  8. 75 FR 62845 - National Toxicology Program (NTP) Interagency Center for the Evaluation of Alternative...

    Science.gov (United States)

    2010-10-13

    ..., respectively. These one-day workshops will help participants gain a practical understanding of the theory and... have an opportunity to apply knowledge gained from the program using case studies in breakout group... Induced Eye Injuries (January 19, 2011) Welcome, Introduction, and Public Health Impact of Chemically...

  9. Madison Park Alternative Education Program: Sweet Street Academy. Final Evaluation Report.

    Science.gov (United States)

    Walizer, Michael H.; And Others

    The Sweet Street Academy is a school within a school. Most of its 26 students are below grade level in reading and mathematics and have histories of behavioral difficulties or adjustment problems. The objectives of the program are to build meaningful personal relationships with each student and to develop student reading and mathematics…

  10. An Alternative Approach for MBA Mentor Programs: Empower the Protégé

    Science.gov (United States)

    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…

  11. Value-Added Models for Teacher Preparation Programs: Validity and Reliability Threats, and a Manageable Alternative

    Science.gov (United States)

    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…

  12. The Enforcer Aircraft Program: A Lower-Cost Alternative Weapon System.

    Science.gov (United States)

    1984-03-01

    armoured striking forces. NATO’s air forces then, sns 1.select the optimum aircraft(s) to maximize the damage to the enemy while minimizing the cost to...the reascns Congress kept the Enforcer program alive was their inclination to support the underdog , an underdog with persuasiveness and tenacity. To

  13. 78 FR 52116 - Request for Public Comment on a Review Level Alternative Dispute Resolution Program

    Science.gov (United States)

    2013-08-22

    .... Department of Labor's Occupational Safety and Health Administration (``OSHA'') at the trial level before an... and voluntary procedures to promote case settlement. Under the program, an administrative law judge acts as a settlement judge and oversees the ADR process. If a case does not settle, an administrative...

  14. Dissecting an alternative splicing analysis workflow for GeneChip® Exon 1.0 ST Affymetrix arrays

    Directory of Open Access Journals (Sweden)

    Calogero Raffaele A

    2008-11-01

    Full Text Available Abstract Background A new microarray platform (GeneChip® Exon 1.0 ST has recently been developed by Affymetrix http://www.affymetrix.com. This microarray platform changes the conventional view of transcript analysis since it allows the evaluation of the expression level of a transcript by querying each exon component. The Exon 1.0 ST platform does however raise some issues regarding the approaches to be used in identifying genome-wide alternative splicing events (ASEs. In this study an exon-level data analysis workflow is dissected in order to detect limit and strength of each step, thus modifying the overall workflow and thereby optimizing the detection of ASEs. Results This study was carried out using a semi-synthetic exon-skipping benchmark experiment embedding a total of 268 exon skipping events. Our results point out that summarization methods (RMA, PLIER do not affect the efficacy of statistical tools in detecting ASEs. However, data pre-filtering is mandatory if the detected number of false ASEs are to be reduced. MiDAS and Rank Product methods efficiently detect true ASEs but they suffer from the lack of multiple test error correction. The intersection of MiDAS and Rank Product results efficiently moderates the detection of false ASEs. Conclusion To optimize the detection of ASEs we propose the following workflow: i data pre-filtering, ii statistical selection of ASEs using both MiDAS and Rank Product, iii intersection of results derived from the two statistical analyses in order to moderate family-wise errors (FWER.

  15. Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing

    DEFF Research Database (Denmark)

    Pang, Chi; Tay, Aidan; Aya, Carlos

    2014-01-01

    contigs, along with RNA-seq reads. This is done in the Integrated Genome Viewer (IGV). A Results Analyzer reports the precise base position where LC-MS/MS-derived peptides cover genes or gene isoforms, on the chromosomes or contigs where this occurs. In prokaryotes, the PG Nexus pipeline facilitates...... the validation of genes, where annotation or gene prediction is available, or the discovery of genes using a "virtual protein"-based unbiased approach. We illustrate this with a comprehensive proteogenomics analysis of two strains of Campylobacter concisus . For higher eukaryotes, the PG Nexus facilitates gene...

  16. Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming.

    Science.gov (United States)

    Song, Hyun-Seob; Goldberg, Noam; Mahajan, Ashutosh; Ramkrishna, Doraiswami

    2017-08-01

    Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of relevant EMs needs to be known, for which optimization-based sequential computation is a useful alternative. Most of the currently available methods along this line are based on the iterative use of mixed integer linear programming (MILP), the effectiveness of which significantly deteriorates as the number of iterations builds up. To alleviate the computational burden associated with the MILP implementation, we here present a novel optimization algorithm termed alternate integer linear programming (AILP). Our algorithm was designed to iteratively solve a pair of integer programming (IP) and linear programming (LP) to compute EMs in a sequential manner. In each step, the IP identifies a minimal subset of reactions, the deletion of which disables all previously identified EMs. Thus, a subsequent LP solution subject to this reaction deletion constraint becomes a distinct EM. In cases where no feasible LP solution is available, IP-derived reaction deletion sets represent minimal cut sets (MCSs). Despite the additional computation of MCSs, AILP achieved significant time reduction in computing EMs by orders of magnitude. The proposed AILP algorithm not only offers a computational advantage in the EM analysis of genome-scale networks, but also improves the understanding of the linkage between EMs and MCSs. The software is implemented in Matlab, and is provided as supplementary information . hyunseob.song@pnnl.gov. Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2017. This work is written by US Government employees and are in the public domain in the US.

  17. Tanks Focus Area Alternative Salt Processing Research and Development Program Plan

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. Tanks Focus Area Alternative Salt Processing Research and Development Program Plan

    Energy Technology Data Exchange (ETDEWEB)

    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.

  19. Pro-socially shareable entertainment television programmes: a programming alternative in developing countries?

    Science.gov (United States)

    Singhal, A; Svenkerud, P J

    1994-12-01

    Over the period 1975-82, the Mexican television network created and aired seven entertainment soap operas promoting educational-development themes like adult literacy, smaller family size norms, and an higher social status for women. These emissions earned high ratings in Mexico and in other Latin American countries where they were subsequently broadcast. Evidence suggests that many of the social objectives of the soaps were met. In light of such success, the authors investigated the potential of pro-socially shareable entertainment television programs in developing countries. These programs use entertaining media formats to carry pro-social messages to a wide, yet culturally-proximate audience group. Entertainment television genres such as melodramatic soap operas offer certain advantages for carrying pro-socially shareable messages to audiences. The possibility of using other television genres and media channels, however, also needs to be seriously considered. Pro-socially shareable entertainment programs do have their limitations and problems, with a certain degree of message dilution invariably accompanying the quest for shareability. Targeting specific problems in specific audience groups is difficult and the identity of a relatively small homogeneous group can be threatened in a larger culturally proximate group. The value-laden nature of pro-social content can also be problematic.

  20. From Punishment to Treatment: The “Clinical Alternative to Punitive Segregation” (CAPS Program in New York City Jails

    Directory of Open Access Journals (Sweden)

    Sarah Glowa-Kollisch

    2016-02-01

    Full Text Available 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.

  1. Alternative splicing studies of the reactive oxygen species gene network in Populus reveal two isoforms of high-isoelectric-point superoxide dismutase.

    Science.gov (United States)

    Srivastava, Vaibhav; Srivastava, Manoj Kumar; Chibani, Kamel; Nilsson, Robert; Rouhier, Nicolas; Melzer, Michael; Wingsle, Gunnar

    2009-04-01

    Recent evidence has shown that alternative splicing (AS) is widely involved in the regulation of gene expression, substantially extending the diversity of numerous proteins. In this study, a subset of expressed sequence tags representing members of the reactive oxygen species gene network was selected from the PopulusDB database to investigate AS mechanisms in Populus. Examples of all known types of AS were detected, but intron retention was the most common. Interestingly, the closest Arabidopsis (Arabidopsis thaliana) homologs of half of the AS genes identified in Populus are not reportedly alternatively spliced. Two genes encoding the protein of most interest in our study (high-isoelectric-point superoxide dismutase [hipI-SOD]) have been found in black cottonwood (Populus trichocarpa), designated PthipI-SODC1 and PthipI-SODC2. Analysis of the expressed sequence tag libraries has indicated the presence of two transcripts of PthipI-SODC1 (hipI-SODC1b and hipI-SODC1s). Alignment of these sequences with the PthipI-SODC1 gene showed that hipI-SODC1b was 69 bp longer than hipI-SODC1s due to an AS event involving the use of an alternative donor splice site in the sixth intron. Transcript analysis showed that the splice variant hipI-SODC1b was differentially expressed, being clearly expressed in cambial and xylem, but not phloem, regions. In addition, immunolocalization and mass spectrometric data confirmed the presence of hipI-SOD proteins in vascular tissue. The functionalities of the spliced gene products were assessed by expressing recombinant hipI-SOD proteins and in vitro SOD activity assays.

  2. Alternative Splicing Studies of the Reactive Oxygen Species Gene Network in Populus Reveal Two Isoforms of High-Isoelectric-Point Superoxide Dismutase1[C][W

    Science.gov (United States)

    Srivastava, Vaibhav; Srivastava, Manoj Kumar; Chibani, Kamel; Nilsson, Robert; Rouhier, Nicolas; Melzer, Michael; Wingsle, Gunnar

    2009-01-01

    Recent evidence has shown that alternative splicing (AS) is widely involved in the regulation of gene expression, substantially extending the diversity of numerous proteins. In this study, a subset of expressed sequence tags representing members of the reactive oxygen species gene network was selected from the PopulusDB database to investigate AS mechanisms in Populus. Examples of all known types of AS were detected, but intron retention was the most common. Interestingly, the closest Arabidopsis (Arabidopsis thaliana) homologs of half of the AS genes identified in Populus are not reportedly alternatively spliced. Two genes encoding the protein of most interest in our study (high-isoelectric-point superoxide dismutase [hipI-SOD]) have been found in black cottonwood (Populus trichocarpa), designated PthipI-SODC1 and PthipI-SODC2. Analysis of the expressed sequence tag libraries has indicated the presence of two transcripts of PthipI-SODC1 (hipI-SODC1b and hipI-SODC1s). Alignment of these sequences with the PthipI-SODC1 gene showed that hipI-SODC1b was 69 bp longer than hipI-SODC1s due to an AS event involving the use of an alternative donor splice site in the sixth intron. Transcript analysis showed that the splice variant hipI-SODC1b was differentially expressed, being clearly expressed in cambial and xylem, but not phloem, regions. In addition, immunolocalization and mass spectrometric data confirmed the presence of hipI-SOD proteins in vascular tissue. The functionalities of the spliced gene products were assessed by expressing recombinant hipI-SOD proteins and in vitro SOD activity assays. PMID:19176719

  3. Evaluating bacterial gene-finding HMM structures as probabilistic logic programs.

    Science.gov (United States)

    Mørk, Søren; Holmes, Ian

    2012-03-01

    Probabilistic logic programming offers a powerful way to describe and evaluate structured statistical models. To investigate the practicality of probabilistic logic programming for structure learning in bioinformatics, we undertook a simplified bacterial gene-finding benchmark in PRISM, a probabilistic dialect of Prolog. We evaluate Hidden Markov Model structures for bacterial protein-coding gene potential, including a simple null model structure, three structures based on existing bacterial gene finders and two novel model structures. We test standard versions as well as ADPH length modeling and three-state versions of the five model structures. The models are all represented as probabilistic logic programs and evaluated using the PRISM machine learning system in terms of statistical information criteria and gene-finding prediction accuracy, in two bacterial genomes. Neither of our implementations of the two currently most used model structures are best performing in terms of statistical information criteria or prediction performances, suggesting that better-fitting models might be achievable. The source code of all PRISM models, data and additional scripts are freely available for download at: http://github.com/somork/codonhmm. Supplementary data are available at Bioinformatics online.

  4. Abundance and distribution of antibiotic resistance genes in a full-scale anaerobic-aerobic system alternately treating ribostamycin, spiramycin and paromomycin production wastewater.

    Science.gov (United States)

    Tang, Mei; Dou, Xiaomin; Wang, Chunyan; Tian, Zhe; Yang, Min; Zhang, Yu

    2017-12-01

    The occurrence of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs) has been intensively investigated for wastewater treatment systems treating single class of antibiotic in recent years. However, the impacts of alternately occurring antibiotics in antibiotic production wastewater on the behavior of ARGs in biological treatment systems were not well understood yet. Herein, techniques including high-capacity quantitative PCR and quantitative PCR (qPCR) were used to investigate the behavior of ARGs in an anaerobic-aerobic full-scale system. The system alternately treated three kinds of antibiotic production wastewater including ribostamycin, spiramycin and paromomycin, which referred to stages 1, 2 and 3. The aminoglycoside ARGs (52.1-79.3%) determined using high-capacity quantitative PCR were the most abundant species in all sludge samples of the three stages. The total relative abundances of macrolide-lincosamide-streptogramin (MLS) resistance genes and aminoglycoside resistance genes measured using qPCR were significantly higher (P  0.05) in both aerobic and anaerobic sludge samples. In aerobic sludge, one acetyltransferase gene (aacA4) and the other three nucleotidyltransferase genes (aadB, aadA and aadE) exhibited positive correlations with intI1 (r 2  = 0.83-0.94; P < 0.05), implying the significance of horizontal transfer in their proliferation. These results and facts will be helpful to understand the abundance and distribution of ARGs from antibiotic production wastewater treatment systems.

  5. Early experiences mediate distinct adult gene expression and reproductive programs in Caenorhabditis elegans

    Science.gov (United States)

    Ow, Maria C.; Nichitean, Alexandra M.; Dorus, Steve; Hall, Sarah E.

    2018-01-01

    Environmental stress during early development in animals can have profound effects on adult phenotypes via programmed changes in gene expression. Using the nematode C. elegans, we demonstrated previously that adults retain a cellular memory of their developmental experience that is manifested by differences in gene expression and life history traits; however, the sophistication of this system in response to different environmental stresses, and how it dictates phenotypic plasticity in adults that contribute to increased fitness in response to distinct environmental challenges, was unknown. Using transcriptional profiling, we show here that C. elegans adults indeed retain distinct cellular memories of different environmental conditions. We identified approximately 500 genes in adults that entered dauer due to starvation that exhibit significant opposite (“seesaw”) transcriptional phenotypes compared to adults that entered dauer due to crowding, and are distinct from animals that bypassed dauer. Moreover, we show that two-thirds of the genes in the genome experience a 2-fold or greater seesaw trend in gene expression, and based upon the direction of change, are enriched in large, tightly linked regions on different chromosomes. Importantly, these transcriptional programs correspond to significant changes in brood size depending on the experienced stress. In addition, we demonstrate that while the observed seesaw gene expression changes occur in both somatic and germline tissue, only starvation-induced changes require a functional GLP-4 protein necessary for germline development, and both programs require the Argonaute CSR-1. Thus, our results suggest that signaling between the soma and the germ line can generate phenotypic plasticity as a result of early environmental experience, and likely contribute to increased fitness in adverse conditions and the evolution of the C. elegans genome. PMID:29447162

  6. Early experiences mediate distinct adult gene expression and reproductive programs in Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Maria C Ow

    2018-02-01

    Full Text Available Environmental stress during early development in animals can have profound effects on adult phenotypes via programmed changes in gene expression. Using the nematode C. elegans, we demonstrated previously that adults retain a cellular memory of their developmental experience that is manifested by differences in gene expression and life history traits; however, the sophistication of this system in response to different environmental stresses, and how it dictates phenotypic plasticity in adults that contribute to increased fitness in response to distinct environmental challenges, was unknown. Using transcriptional profiling, we show here that C. elegans adults indeed retain distinct cellular memories of different environmental conditions. We identified approximately 500 genes in adults that entered dauer due to starvation that exhibit significant opposite ("seesaw" transcriptional phenotypes compared to adults that entered dauer due to crowding, and are distinct from animals that bypassed dauer. Moreover, we show that two-thirds of the genes in the genome experience a 2-fold or greater seesaw trend in gene expression, and based upon the direction of change, are enriched in large, tightly linked regions on different chromosomes. Importantly, these transcriptional programs correspond to significant changes in brood size depending on the experienced stress. In addition, we demonstrate that while the observed seesaw gene expression changes occur in both somatic and germline tissue, only starvation-induced changes require a functional GLP-4 protein necessary for germline development, and both programs require the Argonaute CSR-1. Thus, our results suggest that signaling between the soma and the germ line can generate phenotypic plasticity as a result of early environmental experience, and likely contribute to increased fitness in adverse conditions and the evolution of the C. elegans genome.

  7. Transitional orientation: a cost-effective alternative to traditional RN residency programs.

    Science.gov (United States)

    Guthrie, Kimberly; Tyrna, Jaime; Giannuzzi, Donna

    2013-01-01

    Recruitment, orientation, and development costs, particularly for inexperienced RNs, challenge hospitals to find cost-effective methods to assure patients receive competent nursing care. Nurse leaders at the Lee Memorial Health System (LMHS) initiated a multifaceted development methodology called the Transitional Orientation Program, designed to develop and retain competent RNs. To assist in the intensive development needs required by the transitional unit interns and for other inexperienced RNs assigned initially to their unit of hire, LMHS established new clinical educator positions called intern development specialists (IDS). Results of this initiative showed a significant decrease in total orientation times and costs, and a dramatic increase in retention rates of inexperienced RNs.

  8. Mapping goal alignment of deployment programs for alternative fuel technologies: An analysis of wide-scope grant programs in the United States

    International Nuclear Information System (INIS)

    Sobin, Nathaniel; Molenaar, Keith; Cahill, Eric

    2012-01-01

    Governments have attempted to advance alternative fuels (AFs) in the on-road transportation sector with the goal of addressing multiple environmental, energy security, economic growth, and technology transition objectives. However there is little agreement, at all governmental levels, on how to prioritize goals and how to measure progress towards goals. Literature suggests that a consistent, aligned, and prioritized approach will increase the effectiveness of deployment efforts. While literature states that goal alignment and prioritization should occur, there are few studies suggesting how to measure the alignment of deployment programs. This paper presents a methodology for measuring goal alignment by applying the theories of goal ambiguity. It then demonstrates this methodology within the context of fuel- and project-neutral (wide-scope) grant programs directed toward AF deployment. This paper analyzes forty-seven (47) wide-scope federal, state, and regional grant programs in the United States, active between 2006 and 2011. On the whole, governments most use deployment grant programs to address environmental concerns and are highly aligned in doing so between agency levels. In contrast, there is much less consensus (and therefore goal alignment) on whether or how governments should address other priorities such as energy security, economic growth, and technology transition. - Highlights: ► Grants that deploy AFs most often address environmental goals and are highly aligned in doing so. ► Economic growth goals are most often addressed by federal AF deployment grant programs. ► Energy security goals are most often addressed by state and regional AF deployment grant programs. ► Technology transition goals are the least aligned when considering alignment across agencies.

  9. Impacts of alternative allowance allocation methods under a cap-and-trade program in power sector

    International Nuclear Information System (INIS)

    Liu Beibei; He Pan; Zhang Bing; Bi Jun

    2012-01-01

    Emission trading is considered to be a cost-effective environmental economic instrument for pollution control. However, the policy design of an emission trading program has a decisive impact on its performance. Allowance allocation is one of the most important policy design issues in emission trading, not only for equity but also for policy performance. In this research, an artificial market for sulfur dioxide (SO 2 ) emission trading was constructed by applying an agent-based model. The performance of the Jiangsu SO 2 emission trading market was examined under different allowance allocation methods and transaction costs. The results showed that the market efficiency of emission trading would be affected by the allocation methods when the transaction costs are positive. The auction allowance allocation method was more efficient and had the lowest total emission control costs than the other three allocation methods examined. However, the use of this method will require that power plants pay for all of their allowance, and doing so will increase the production costs of power plants. On the other hand, output-based allowance allocation is the second best method. - Highlights: ► The impact of allowance allocation methods is examined for a cap-and-trade program. ► The market efficiency would be distinct when the transaction costs are positive. ► The auction method would have lowest total emission control costs.

  10. Experimental alternatives for evaluation of progenies and clones in eucalyptus breeding programs

    Directory of Open Access Journals (Sweden)

    Souza Elaine Aparecida de

    2003-01-01

    Full Text Available The feasibility of using augmented block designs and spatial analysis methods for early stage selection in eucalyptus breeding programs was tested. A total of 113 half-sib progenies of Eucalyptus urophylla and eight clones were evaluated in an 11 x 11 triple lattice experiment at two locations: Posto da Mata (Bahia, Brazil and São Mateus (Minas Gerais, Brazil. Four checks were randomly allocated within each block. Plots consisted of 15 m long rows containing 6 plants spaced 3 m apart. The girth at breast height (cm/plant was evaluated at 19 and 26 months of age. Variance analyses were performed according to the following methods: lattice design, randomized complete block design, augmented block design, Papadakis method, moving means method, and check plots. Comparisons among different methods were based on the magnitude of experimental errors and precision of the estimates of genetic and phenotypic parameters. General results indicated that augmented block design is useful to evaluate progenies and clones in early selection in eucalyptus breeding programs using moderate and low selection intensities. However, this design is not suitable for estimating genetic and phenotypic parameters due to its low precision. Check plots, nearest neighbour, Papadakis (1937, and moving means methods were efficient in removing the heterogeneity within blocks. These efficiencies were compared to that in lattice analysis for estimation of genetic and phenotypic parameters.

  11. Capturing the Alternative Cleavage and Polyadenylation Sites of 14 NAC Genes in Populus Using a Combination of 3′-RACE and High-Throughput Sequencing

    Directory of Open Access Journals (Sweden)

    Haoran Wang

    2018-03-01

    Full Text Available Detection of complex splice sites (SSs and polyadenylation sites (PASs of eukaryotic genes is essential for the elucidation of gene regulatory mechanisms. Transcriptome-wide studies using high-throughput sequencing (HTS have revealed prevalent alternative splicing (AS and alternative polyadenylation (APA in plants. However, small-scale and high-depth HTS aimed at detecting genes or gene families are very few and limited. We explored a convenient and flexible method for profiling SSs and PASs, which combines rapid amplification of 3′-cDNA ends (3′-RACE and HTS. Fourteen NAC (NAM, ATAF1/2, CUC2 transcription factor genes of Populus trichocarpa were analyzed by 3′-RACE-seq. Based on experimental reproducibility, boundary sequence analysis and reverse transcription PCR (RT-PCR verification, only canonical SSs were considered to be authentic. Based on stringent criteria, candidate PASs without any internal priming features were chosen as authentic PASs and assumed to be PAS-rich markers. Thirty-four novel canonical SSs, six intronic/internal exons and thirty 3′-UTR PAS-rich markers were revealed by 3′-RACE-seq. Using 3′-RACE and real-time PCR, we confirmed that three APA transcripts ending in/around PAS-rich markers were differentially regulated in response to plant hormones. Our results indicate that 3′-RACE-seq is a robust and cost-effective method to discover SSs and label active regions subjected to APA for genes or gene families. The method is suitable for small-scale AS and APA research in the initial stage.

  12. Mixed Waste Focus Area alternative oxidation technologies development and demonstration program

    International Nuclear Information System (INIS)

    Borduin, L.C.; Fewell, T.; Gombert, D.; Priebe, S.

    1998-01-01

    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

  13. Valuation of selected environmental impacts associated with Bonneville Power Administration Resource Program alternatives

    International Nuclear Information System (INIS)

    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

  14. Low-Budget Computer Programming in Your School (An Alternative to the Cost of Large Computers). Illinois Series on Educational Applications of Computers. No. 14.

    Science.gov (United States)

    Dennis, J. Richard; Thomson, David

    This paper is concerned with a low cost alternative for providing computer experience to secondary school students. The brief discussion covers the programmable calculator and its relevance for teaching the concepts and the rudiments of computer programming and for computer problem solving. A list of twenty-five programming activities related to…

  15. The Post-Secondary Student Support Program: An Examination of Alternative Delivery Mechanisms. A Report to the Indian and Northern Affairs Canada

    Science.gov (United States)

    Usher, Alex

    2009-01-01

    The purpose of this document is to examine the Department of Indian and Northern Affairs Canada (INAC)'s Post-Secondary Student Support Program (PSSSP) and analyse the advantages and disadvantages of both the existing system of program delivery and a trio of alternative delivery mechanisms. It does not issue any recommendation with respect to a…

  16. Programmed improvements of the alternating gradient synchrotron complex at Brookhaven National Laboratory, Upton, New York. Environmental assessment

    International Nuclear Information System (INIS)

    1994-03-01

    The purpose and need for DOE to undertake the actions described in this document are to improve the efficiency of the Alternating Gradient Synchrotron (AGS) complex. Benefits would include optimization of the AGS scientific program, increased high-energy and nuclear physics experimentation, improved health and safety conditions for workers and users, reduced impact on the environment and the general public, energy conservation, decreased generation of hazardous and radioactive wastes, and completion of actions required to permit the AGS to be the injector to the Relativistic Heavy Ion Collider (RHIC)., Improved efficiency is defined as increasing the AGS's capabilities to capture and accelerate the proton intensity transferred to the AGS from the AGS booster. Improved capture of beam intensity would reduce the beam losses which equate to lost scientific opportunity for study and increased potential for radiation doses to workers and the general public. The action would also refurbish magnets used in the transfer tunnel which connects the AGS complex to RHIC to permit smooth injection of beam into the RHIC accelerator. These magnets were previously used to direct beam to fixed targets for high energy physics studies but have hot received proper maintenance to be reliable as injectors to RHIC. The document describes alternative actions, the affected environment, and environmental impacts

  17. Comparative transcriptional profiling of the axolotl limb identifies a tripartite regeneration-specific gene program.

    Directory of Open Access Journals (Sweden)

    Dunja Knapp

    Full Text Available Understanding how the limb blastema is established after the initial wound healing response is an important aspect of regeneration research. Here we performed parallel expression profile time courses of healing lateral wounds versus amputated limbs in axolotl. This comparison between wound healing and regeneration allowed us to identify amputation-specific genes. By clustering the expression profiles of these samples, we could detect three distinguishable phases of gene expression - early wound healing followed by a transition-phase leading to establishment of the limb development program, which correspond to the three phases of limb regeneration that had been defined by morphological criteria. By focusing on the transition-phase, we identified 93 strictly amputation-associated genes many of which are implicated in oxidative-stress response, chromatin modification, epithelial development or limb development. We further classified the genes based on whether they were or were not significantly expressed in the developing limb bud. The specific localization of 53 selected candidates within the blastema was investigated by in situ hybridization. In summary, we identified a set of genes that are expressed specifically during regeneration and are therefore, likely candidates for the regulation of blastema formation.

  18. Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1.

    Directory of Open Access Journals (Sweden)

    Christopher Terranova

    Full Text Available Genetic studies have placed the Fgfr1 gene at the top of major ontogenic pathways that enable gastrulation, tissue development and organogenesis. Using genome-wide sequencing and loss and gain of function experiments the present investigation reveals a mechanism that underlies global and direct gene regulation by the nuclear form of FGFR1, ensuring that pluripotent Embryonic Stem Cells differentiate into Neuronal Cells in response to Retinoic Acid. Nuclear FGFR1, both alone and with its partner nuclear receptors RXR and Nur77, targets thousands of active genes and controls the expression of pluripotency, homeobox, neuronal and mesodermal genes. Nuclear FGFR1 targets genes in developmental pathways represented by Wnt/β-catenin, CREB, BMP, the cell cycle and cancer-related TP53 pathway, neuroectodermal and mesodermal programing networks, axonal growth and synaptic plasticity pathways. Nuclear FGFR1 targets the consensus sequences of transcription factors known to engage CREB-binding protein, a common coregulator of transcription and established binding partner of nuclear FGFR1. This investigation reveals the role of nuclear FGFR1 as a global genomic programmer of cell, neural and muscle development.

  19. Comprehensive Gene Expression Analysis of Rice Aleurone Cells: Probing the Existence of an Alternative Gibberellin Receptor1

    Science.gov (United States)

    Yano, Kenji; Aya, Koichiro; Hirano, Ko; Ordonio, Reynante Lacsamana; Ueguchi-Tanaka, Miyako; Matsuoka, Makoto

    2015-01-01

    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. PMID:25511432

  20. Fine mapping of the latency-related gene of herpes simplex virus type 1: alternative splicing produces distinct latency-related RNAs containing open reading frames

    International Nuclear Information System (INIS)

    Wechsler, S.L.; Nesburn, A.B.; Watson, R.; Slanina, S.M.; Ghiasi, H.

    1988-01-01

    The latency-related (LR) gene of herpes simplex virus type 1 (HSV-1) is transcriptionally active during HSV-1 latency, producing at least two LR-RNAs. The LR gene partially overlaps the immediate-early gene ICP0 and is transcribed in the opposite direction from ICP0, producing LR-RNAs that are complementary (antisense) to ICP0 mRNA. The LR gene is thought to be involved in HSV-1 latency. The authors report here the time mapping and partial sequence analysis of this HSV-1 LR gene. 32 P-labeled genomic DNA restriction fragments and synthetic oligonucleotides were used as probes for in situ hybridizations and Northern (RNA) blot hybridizations of RNA from trigeminal ganglia of rabbits latently infected with HSV-1. The two most abundant LR-RNAs appeared to share their 5' and 3' ends and to be produced by alternative splicing. These LR-RNAs were approximately 2 and 1.3 to 1.5 kilobases in length and were designated LR-RNA 1 and LF-RNA 2, respectively. LR-RNA 1 appeared to have at least one intron removed, while LR-RNA 2 appeared to have at least two introns removed. The LR-RNAs contained two potential long open reading frames, suggesting the possibility that one or more of the LR-RNAs may be a functional mRNA

  1. Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing.

    Science.gov (United States)

    Pang, Chi Nam Ignatius; Tay, Aidan P; Aya, Carlos; Twine, Natalie A; Harkness, Linda; Hart-Smith, Gene; Chia, Samantha Z; Chen, Zhiliang; Deshpande, Nandan P; Kaakoush, Nadeem O; Mitchell, Hazel M; Kassem, Moustapha; Wilkins, Marc R

    2014-01-03

    Direct links between proteomic and genomic/transcriptomic data are not frequently made, partly because of lack of appropriate bioinformatics tools. To help address this, we have developed the PG Nexus pipeline. The PG Nexus allows users to covisualize peptides in the context of genomes or genomic contigs, along with RNA-seq reads. This is done in the Integrated Genome Viewer (IGV). A Results Analyzer reports the precise base position where LC-MS/MS-derived peptides cover genes or gene isoforms, on the chromosomes or contigs where this occurs. In prokaryotes, the PG Nexus pipeline facilitates the validation of genes, where annotation or gene prediction is available, or the discovery of genes using a "virtual protein"-based unbiased approach. We illustrate this with a comprehensive proteogenomics analysis of two strains of Campylobacter concisus . For higher eukaryotes, the PG Nexus facilitates gene validation and supports the identification of mRNA splice junction boundaries and splice variants that are protein-coding. This is illustrated with an analysis of splice junctions covered by human phosphopeptides, and other examples of relevance to the Chromosome-Centric Human Proteome Project. The PG Nexus is open-source and available from https://github.com/IntersectAustralia/ap11_Samifier. It has been integrated into Galaxy and made available in the Galaxy tool shed.

  2. Rapid gene expression changes in peripheral blood lymphocytes upon practice of a comprehensive yoga program.

    Directory of Open Access Journals (Sweden)

    Su Qu

    Full Text Available One of the most common integrative medicine (IM modalities is yoga and related practices. Previous work has shown that yoga may improve wellness in healthy people and have benefits for patients. However, the mechanisms of how yoga may positively affect the mind-body system are largely unknown. Here we have assessed possible rapid changes in global gene expression profiles in the peripheral blood mononuclear cells (PBMCs in healthy people that practiced either a comprehensive yoga program or a control regimen. The experimental sessions included gentle yoga postures, breathing exercises, and meditation (Sudarshan Kriya and Related Practices--SK&P compared with a control regimen of a nature walk and listening to relaxing music. We show that the SK&P program has a rapid and significantly greater effect on gene expression in PBMCs compared with the control regimen. These data suggest that yoga and related practices result in rapid gene expression alterations which may be the basis for their longer term cell biological and higher level health effects.

  3. Early results of sarcomeric gene screening from the Egyptian National BA-HCM Program.

    Science.gov (United States)

    Kassem, Heba Sh; Azer, Remon S; Saber-Ayad, Maha; Ayad, Maha S; Moharem-Elgamal, Sarah; Magdy, Gehan; Elguindy, Ahmed; Cecchi, Franco; Olivotto, Iacopo; Yacoub, Magdi H

    2013-02-01

    The present study comprised sarcomeric genotyping of the three most commonly involved sarcomeric genes: MYBPC3, MYH7, and TNNT2 in 192 unrelated Egyptian hypertrophic cardiomyopathy (HCM) index patients. Mutations were detected in 40 % of cases. Presence of positive family history was significantly (p=0.002) associated with a higher genetic positive yield (49/78, 62.8 %). The majority of the detected mutations in the three sarcomeric genes were novel (40/62, 65 %) and mostly private (47/62, 77 %). Single nucleotide substitution was the most frequently detected mutation type (51/62, 82 %). Over three quarters of these substitutions (21/27, 78 %) involved CpG dinucleotide sites and resulted from C>T or G>A transition in the three analyzed genes, highlighting the significance of CpG high mutability within the sarcomeric genes examined. This study could aid in global comparative studies in different ethnic populations and constitutes an important step in the evolution of the integrated clinical, translational, and basic science HCM program.

  4. Automatic Design of Synthetic Gene Circuits through Mixed Integer Non-linear Programming

    Science.gov (United States)

    Huynh, Linh; Kececioglu, John; Köppe, Matthias; Tagkopoulos, Ilias

    2012-01-01

    Automatic design of synthetic gene circuits poses a significant challenge to synthetic biology, primarily due to the complexity of biological systems, and the lack of rigorous optimization methods that can cope with the combinatorial explosion as the number of biological parts increases. Current optimization methods for synthetic gene design rely on heuristic algorithms that are usually not deterministic, deliver sub-optimal solutions, and provide no guaranties on convergence or error bounds. Here, we introduce an optimization framework for the problem of part selection in synthetic gene circuits that is based on mixed integer non-linear programming (MINLP), which is a deterministic method that finds the globally optimal solution and guarantees convergence in finite time. Given a synthetic gene circuit, a library of characterized parts, and user-defined constraints, our method can find the optimal selection of parts that satisfy the constraints and best approximates the objective function given by the user. We evaluated the proposed method in the design of three synthetic circuits (a toggle switch, a transcriptional cascade, and a band detector), with both experimentally constructed and synthetic promoter libraries. Scalability and robustness analysis shows that the proposed framework scales well with the library size and the solution space. The work described here is a step towards a unifying, realistic framework for the automated design of biological circuits. PMID:22536398

  5. {sup 3}He Replacement for Nuclear Safeguards Applications- an integrated test program to compare alternative neutron detectors

    Energy Technology Data Exchange (ETDEWEB)

    Menlove, H. O.; Henzlova, D.; Evans, L. G.; Swinhoe, M. T.; Marlow, J. B. [Los Alamos National Laboratory, Safeguards Science and Technology Group, Los Alamos, (United States)

    2011-12-15

    During the past several years, the demand for {sup 3}He gas has far exceeded the gas supply. This shortage of {sup 3}He gas is projected to continue into the foreseeable future. There is a need for alternative neutron detectors that do not require {sup 3}He gas. For more than four decades, neutron detection has played a fundamental role in the safeguarding and control of nuclear materials at production facilities, fabrication plants and storage sites worldwide. Neutron measurements for safeguards applications have requirements that are unique to the quantitative assay of special nuclear materials. These neutron systems measure the neutron multiplicity distributions from each spontaneous fission and/or induced fission event. The neutron time correlation counting requires that two or more neutrons from a single fission event be detected. The doubles and triples neutron counting rate depends on the detector efficiency to the 2nd and 3rd power, respectively, so low efficiency systems will not work for the coincidence measurements, and any detector instabilities are greatly amplified. In the current test program, we will measure the alternative detector properties including efficiency, die-away time, multiplicity precision, gamma sensitivity, dead-time, and we will also consider the detector properties that would allow commercial production to safeguards scale assay systems. This last step needs to be accomplished before the proposed technologies can reduce the demand on {sup 3}He gas in the safeguards world. This paper will present the methodology that includes MCNPX simulations for comparing divergent detector types such as {sup 10}B lined proportional counters with {sup 3}He gas based systems where the performance metrics focus on safeguards applications.

  6. Loop-mediated isothermal amplification (LAMP) as an alternative to PCR: A rapid on-site detection of gene doping.

    Science.gov (United States)

    Salamin, Olivier; Kuuranne, Tiia; Saugy, Martial; Leuenberger, Nicolas

    2017-11-01

    Innovation in medical research has been diverted at multiple occasions to enhance human performance. The predicted great progress in gene therapy has raised some concerns regarding its misuse in the world of sports (gene doping) for several years now. Even though there is no evidence that gene doping has ever been used in sports, the continuous improvement of gene therapy techniques increases the likelihood of abuse. Therefore, since 2004, efforts have been invested by the anti-doping community and WADA for the development of detection methods. Several nested PCR and qPCR-based strategies exploiting the absence of introns in the transgenic DNA have been proposed for the long-term detection of transgene in blood. Despite their great sensitivity, those protocols are hampered by limitations of the techniques that can be cumbersome and costly. The purpose of this perspective is to describe a new approach based on loop-mediated isothermal amplification (LAMP) for the detection of gene doping. This protocol enables a rapid and simple method to amplify nucleic acids with a high sensitivity and specificity and with a simple visual detection of the results. LAMP is already being used in clinical application for the detection of viruses or mutations. Therefore, this technique has the potential to be further developed for the detection of foreign genetic material in elite athletes. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  7. Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean.

    Science.gov (United States)

    Syed, Naeem H; Prince, Silvas J; Mutava, Raymond N; Patil, Gunvant; Li, Song; Chen, Wei; Babu, Valliyodan; Joshi, Trupti; Khan, Saad; Nguyen, Henry T

    2015-12-01

    Circadian clocks are a great evolutionary innovation and provide competitive advantage during the day/night cycle and under changing environmental conditions. The circadian clock mediates expression of a large proportion of genes in plants, achieving a harmonious relationship between energy metabolism, photosynthesis, and biotic and abiotic stress responses. Here it is shown that multiple paralogues of clock genes are present in soybean (Glycine max) and mediate flooding and drought responses. Differential expression of many clock and SUB1 genes was found under flooding and drought conditions. Furthermore, natural variation in the amplitude and phase shifts in PRR7 and TOC1 genes was also discovered under drought and flooding conditions, respectively. PRR3 exhibited flooding- and drought-specific splicing patterns and may work in concert with PRR7 and TOC1 to achieve energy homeostasis under flooding and drought conditions. Higher expression of TOC1 also coincides with elevated levels of abscisic acid (ABA) and variation in glucose levels in the morning and afternoon, indicating that this response to abiotic stress is mediated by ABA, endogenous sugar levels, and the circadian clock to fine-tune photosynthesis and energy utilization under stress conditions. It is proposed that the presence of multiple clock gene paralogues with variation in DNA sequence, phase, and period could be used to screen exotic germplasm to find sources for drought and flooding tolerance. Furthermore, fine tuning of multiple clock gene paralogues (via a genetic engineering approach) should also facilitate the development of flooding- and drought-tolerant soybean varieties. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  8. Multi-gene genetic programming based predictive models for municipal solid waste gasification in a fluidized bed gasifier.

    Science.gov (United States)

    Pandey, Daya Shankar; Pan, Indranil; Das, Saptarshi; Leahy, James J; Kwapinski, Witold

    2015-03-01

    A multi-gene genetic programming technique is proposed as a new method to predict syngas yield production and the lower heating value for municipal solid waste gasification in a fluidized bed gasifier. The study shows that the predicted outputs of the municipal solid waste gasification process are in good agreement with the experimental dataset and also generalise well to validation (untrained) data. Published experimental datasets are used for model training and validation purposes. The results show the effectiveness of the genetic programming technique for solving complex nonlinear regression problems. The multi-gene genetic programming are also compared with a single-gene genetic programming model to show the relative merits and demerits of the technique. This study demonstrates that the genetic programming based data-driven modelling strategy can be a good candidate for developing models for other types of fuels as well. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. BLENDED LEARNING (BL AS PEDAGOGICAL ALTERNATIVE TO TEACH BUSINESS COMMUNICATION COURSE: Case Study of UUM Executive Diploma Program

    Directory of Open Access Journals (Sweden)

    Hisham DZAKIRIA

    2012-07-01

    Full Text Available Globally, blended learning (BL technologies have been increasingly applied in a variety of fields, both public and private sectors. In recent years, universities, public and private businesses and organizations are among those employing blended learning methods and technologies in training and re-training of professionals in the workforce. In Malaysia, the increasing use of blended learning to enhance learning and enriching of soft skills among professionals and individuals in the work place is evident. The advancement of technology is an onset to many new avenues and tool for learning and teaching, and it is the coalescing of these various technologies with particular pedagogy or andragogy has helped to popularize BL. However, when an institution makes the critical choice of delivery methods, it is pertinent that the university needs to consider various success factors. One in particular is student-centered approach that entails the need to understand the students as the beneficiary of learning, and the support system they need to help them learn. This qualitative study reports in detail the experience of a small group of students undertaking Executive Diplomas at Executive Development Centre (EDC, Universiti Utara Malaysia as they progress through their Executive program. This paper looks at learning experiences as described by the learners- it is their story, their experience, and their perspective. This study suggests that BL offered a comfortable middle ground, and has lots of potential in higher education in Malaysia. It is a pedagogical alternative that could play a significant role not only for teaching Business Communication, but has the potential to promote lifelong learning initiatives in Malaysia in a much meaningful and inviting way. Although this study shows that BL contributed a significant and meaningful learning particularly for adult learners, it needs more definitive studies. Such information can be used to guide policy makers

  10. Alternative Oxidase Transcription Factors AOD2 and AOD5 of Neurospora crassa Control the Expression of Genes Involved in Energy Production and Metabolism.

    Science.gov (United States)

    Qi, Zhigang; Smith, Kristina M; Bredeweg, Erin L; Bosnjak, Natasa; Freitag, Michael; Nargang, Frank E

    2017-02-09

    In Neurospora crassa , blocking the function of the standard mitochondrial electron transport chain results in the induction of an alternative oxidase (AOX). AOX transfers electrons directly from ubiquinol to molecular oxygen. AOX serves as a model of retrograde regulation since it is encoded by a nuclear gene that is regulated in response to signals from mitochondria. The N. crassa transcription factors AOD2 and AOD5 are necessary for the expression of the AOX gene. To gain insight into the mechanism by which these factors function, and to determine if they have roles in the expression of additional genes in N. crassa , we constructed strains expressing only tagged versions of the proteins. Cell fractionation experiments showed that both proteins are localized to the nucleus under both AOX inducing and noninducing conditions. Furthermore, chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) analysis revealed that the proteins are bound to the promoter region of the AOX gene under both conditions. ChIP-seq also showed that the transcription factors bind to the upstream regions of a number of genes that are involved in energy production and metabolism. Dependence on AOD2 and AOD5 for the expression of several of these genes was verified by quantitative PCR. The majority of ChIP-seq peaks observed were enriched for both AOD2 and AOD5. However, we also observed occasional sites where one factor appeared to bind preferentially. The most striking of these was a conserved sequence that bound large amounts of AOD2 but little AOD5. This sequence was found within a 310 bp repeat unit that occurs at several locations in the genome. Copyright © 2017 Qi et al.

  11. The ipdC, hisC1 and hisC2 genes involved in indole-3-acetic production used as alternative phylogenetic markers in Azospirillum brasilense.

    Science.gov (United States)

    Jijón-Moreno, Saúl; Marcos-Jiménez, Cynthia; Pedraza, Raúl O; Ramírez-Mata, Alberto; de Salamone, I García; Fernández-Scavino, Ana; Vásquez-Hernández, Claudia A; Soto-Urzúa, Lucia; Baca, Beatriz E

    2015-06-01

    Plant growth-promoting bacteria of the genus Azospirillum are present in the rhizosphere and as endophytes of many crops. In this research we studied 40 Azospirillum strains isolated from different plants and geographic regions. They were first characterized by 16S rDNA restriction analysis, and their phylogenetic position was established by sequencing the genes 16S rDNA, ipdC, hisC1, and hisC2. The latter three genes are involved in the indole-3-pyruvic acid (IPyA) biosynthesis pathway of indole-3-acetic acid (IAA). Furthermore, the suitability of the 16S-23S rDNA intergenic spacer sequence (IGS) for the differentiation of closely related Azospirillum taxa and development of PCR protocols allows for specific detection of strains. The IGS-RFLP analysis enabled intraspecies differentiation, particularly of Azospirillum brasilense and Azospirillum lipoferum strains. Results demonstrated that the ipdC, hisC1, and hisC2 genes are highly conserved in all the assessed A. brasilense isolates, suggesting that these genes can be used as an alternative phylogenetic marker. In addition, IAA production determined by HPLC ranged from 0.17 to 98.2 μg mg(-1) protein. Southern hybridization with the A. brasilense ipdC gene probe did not show, a hybridization signal with A. lipoferum, Azospirillum amazonense, Azospirillum halopreferans and Azospirillum irakense genomic DNA. This suggests that these species produce IAA by other pathways. Because IAA is mainly synthesized via the IPyA pathway in A. brasilense strains, a species that is used worldwide in agriculture, the identification of ipdC, hisC1, and hisC2 genes by PCR may be suitable for selecting exploitable strains.

  12. C-Speak Aphasia alternative communication program for people with severe aphasia: importance of executive functioning and semantic knowledge.

    Science.gov (United States)

    Nicholas, Marjorie; Sinotte, Michele P; Helm-Estabrooks, Nancy

    2011-06-01

    Learning how to use a computer-based communication system can be challenging for people with severe aphasia even if the system is not word-based. This study explored cognitive and linguistic factors relative to how they affected individual patients' ability to communicate expressively using C-Speak Aphasia (CSA), an alternative communication computer program that is primarily picture-based. Ten individuals with severe non-fluent aphasia received at least six months of training with CSA. To assess carryover of training, untrained functional communication tasks (i.e., answering autobiographical questions, describing pictures, making telephone calls, describing a short video, and two writing tasks) were repeatedly probed in two conditions: (1) using CSA in addition to natural forms of communication, and (2) using only natural forms of communication, e.g., speaking, writing, gesturing, drawing. Four of the 10 participants communicated more information on selected probe tasks using CSA than they did without the computer. Response to treatment was also examined in relation to baseline measures of non-linguistic executive function skills, pictorial semantic abilities, and auditory comprehension. Only nonlinguistic executive function skills were significantly correlated with treatment response.

  13. Program of rational energy use and alternative sources; Programa de uso racional de energia e fontes alternativas-PUREFA

    Energy Technology Data Exchange (ETDEWEB)

    Coelho, Suani Teixeira; Velazquez, Silvia Maria Stortini Gonzalez; Silva, Orlando Cristiano da; Varkulya Junior, Americo; Pecora, Vanessa [Universidade de Sao Paulo (USP), Sao Paulo, SP (Brazil). Inst. de Eletrotecnica e Energia. Centro Nacional de Referencia em Biomassa (CENBIO)

    2004-07-01

    The PUREFA (Program of Rational Energy Use and Alternative Sources), developed by USP - University of Sao Paulo and supported by FINEP - Financial of Studies and Projects, consists of 14 purposes and has three main objectives: to introduce measures of management and energy efficiency proceedings; to increase the distributed generation at USP, employing renewable and not conventional energy resources and to introduce permanent incentive polices of efficient and rational energy use. In this project, the CENBIO - Brazilian Reference Center on Biomass is responsible for purposes 11 and 12 that are related to the biogas use for electricity generation. The first one, the 11th has as main objectives to implant the generation system, to capture and to stock the biogas produced by the biodigestor located at the Technological Hydraulically Center (CTH - USP). The biodigestors type is a UASB (Upflow Anaerobic Sludge Blanket), whose outflow of the biogas produced is near to 4m{sup 3}/day and operates 24 hours per day, utilizing sewer from the residential buildings located at Sao Paulo University, inside the campus. Nowadays, this equipment is used for biogas treatment researches, the biogas emitted to the atmosphere. In order to use the biogas, it is necessary to identify its outflow, chemical composition and heat value, parameters that will determinate its real potential for generation and will show the necessity of a previous treatment, as H{sub 2}S removal. Finished this stage will be started the purpose 12, purpose that regards the biogas use as fuel for electricity generation. (author)

  14. C-Speak Aphasia Alternative Communication Program for People with Severe Aphasia: Importance of Executive Functioning and Semantic Knowledge

    Science.gov (United States)

    Nicholas, Marjorie; Sinotte, Michele P.; Helm-Estabrooks, Nancy

    2011-01-01

    Learning how to use a computer-based communication system can be challenging for people with severe aphasia even if the system is not word-based. This study explored cognitive and linguistic factors relative to how they affected individual patients’ ability to communicate expressively using C-Speak Aphasia, (CSA), an alternative communication computer program that is primarily picture-based. Ten individuals with severe non-fluent aphasia received at least six months of training with CSA. To assess carryover of training, untrained functional communication tasks (i.e., answering autobiographical questions, describing pictures, making telephone calls, describing a short video, and two writing tasks) were repeatedly probed in two conditions: 1) using CSA in addition to natural forms of communication, and 2) using only natural forms of communication, e.g., speaking, writing, gesturing, drawing. Four of the ten participants communicated more information on selected probe tasks using CSA than they did without the computer. Response to treatment also was examined in relation to baseline measures of non-linguistic executive function skills, pictorial semantic abilities, and auditory comprehension. Only nonlinguistic executive function skills were significantly correlated with treatment response. PMID:21506045

  15. Identification of MYCN gene amplification in neuroblastoma using chromogenic in situ hybridization (CISH): an alternative and practical method.

    Science.gov (United States)

    Bhargava, Rohit; Oppenheimer, Orit; Gerald, William; Jhanwar, Suresh C; Chen, Beiyun

    2005-06-01

    Chromogenic in situ hybridization (CISH) is a recently developed technique, which utilizes the general principles of in situ hybridization and a detection system similar to immunohistochemistry. To assess the utility of CISH for analysis of MYCN gene amplification, we compared this assay with established diagnostic assays such as Southern blot analysis (SB) and fluorescent in situ hybridization (FISH). CISH was performed on 67 cases of neuroblastoma using tissue microarray (65 cases) and whole tissue sections (2 cases). Unequivocal, high-level amplification (> or =10 gene copies per tumor nucleus) was identified in 19 of 67 (28.4%) tumors. Two (3%) tumors showed low-level amplification (6-9 gene copies per tumor nucleus). No amplification was seen in 46 of 67 (68.6%) tumors. SB data were available in 44 tumors. Forty-one of the 44 tumors (93%) showed concordant results between CISH and SB. Three tumors showed MYCN amplification by CISH but no amplification by SB, most likely due to dilution effect of nonneoplastic tissue in the test samples. Two of these three tumors also showed MYCN amplification by FISH, and the third tumor was not analyzed by FISH. FISH data were available in total of 30 tumors. All 30 tumors showed concordant results between CISH and FISH for classifying a tumor as MYCN amplified or not amplified. We conclude that CISH is an accurate method for determining MYCN gene amplification, with added advantages that make it a more practically useful method.

  16. Working Together in Urban Schools: How a University Teacher Education Program and Teach for America Partner to Support Alternatively Certified Teachers

    Science.gov (United States)

    Heineke, Amy J.; Carter, Heather; Desimone, Melissa; Cameron, Quanna

    2010-01-01

    The College of Teacher Education and Leadership (CTEL) at Arizona State University (ASU) embraced the opportunity to partner with Teach For America (TFA) to tailor existing teacher preparation programs to meet the unique needs of alternatively certified teachers in urban schools. Rather than harp on the distinctions between ideologies and…

  17. Assessing the Impact of Pilot School Snack Programs on Milk and Alternatives Intake in 2 Remote First Nation Communities in Northern Ontario, Canada

    Science.gov (United States)

    Gates, Michelle; Hanning, Rhona M.; Gates, Allison; McCarthy, Daniel D.; Tsuji, Leonard J. S.

    2013-01-01

    Background: Canadian Aboriginal youth have poorer diet quality and higher rates of overweight and obesity than the general population. This research aimed to assess the impact of simple food provision programs on the intakes of milk and alternatives among youth in Kashechewan and Attawapiskat First Nations (FNs), Ontario, Canada. Methods: A pilot…

  18. Induction of a program gene expression during osteoblast differentiation with strontium ranelate

    International Nuclear Information System (INIS)

    Zhu Lingling; Zaidi, Samir; Peng Yuanzhen; Zhou Hang; Moonga, Baljit S.; Blesius, Alexia; Dupin-Roger, Isabelle; Zaidi, Mone; Sun Li

    2007-01-01

    Strontium ranelate, a new agent for the treatment of osteoporosis, has been shown stimulate bone formation in various experimental models. This study examines the effect of strontium ranelate on gene expression in osteoblasts, as well as the formation of mineralized (von Kossa-positive) colony-forming unit-osteoblasts (CFU-obs). Bone marrow-derived stromal cells cultured for 21 days under differentiating conditions, when exposed to strontium ranelate, displayed a significant time- and concentration-dependent increase in the expression of the master gene, Runx2, as well as bone sialoprotein (BSP), but interestingly without effects on osteocalcin. This was associated with a significant increase in the formation of CFU-obs at day 21 of culture. In U-33 pre-osteoblastic cells, strontium ranelate significantly enhanced the expression of Runx2 and osteocalcin, but not BSP. Late, more mature osteoblastic OB-6 cells showed significant elevations in BSP and osteocalcin, but with only minimal effects on Runx2. In conclusion, strontium ranelate stimulates osteoblast differentiation, but the induction of the program of gene expression appears to be cell type-specific. The increased osteoblastic differentiation is the likely basis underlying the therapeutic bone-forming actions of strontium ranelate

  19. Artificial Neural Networks and Gene Expression Programing based age estimation using facial features

    Directory of Open Access Journals (Sweden)

    Baddrud Z. Laskar

    2015-10-01

    Full Text Available This work is about estimating human age automatically through analysis of facial images. It has got a lot of real-world applications. Due to prompt advances in the fields of machine vision, facial image processing, and computer graphics, automatic age estimation via faces in computer is one of the dominant topics these days. This is due to widespread real-world applications, in areas of biometrics, security, surveillance, control, forensic art, entertainment, online customer management and support, along with cosmetology. As it is difficult to estimate the exact age, this system is to estimate a certain range of ages. Four sets of classifications have been used to differentiate a person’s data into one of the different age groups. The uniqueness about this study is the usage of two technologies i.e., Artificial Neural Networks (ANN and Gene Expression Programing (GEP to estimate the age and then compare the results. New methodologies like Gene Expression Programing (GEP have been explored here and significant results were found. The dataset has been developed to provide more efficient results by superior preprocessing methods. This proposed approach has been developed, tested and trained using both the methods. A public data set was used to test the system, FG-NET. The quality of the proposed system for age estimation using facial features is shown by broad experiments on the available database of FG-NET.

  20. Temperature based daily incoming solar radiation modeling based on gene expression programming, neuro-fuzzy and neural network computing techniques.

    Science.gov (United States)

    Landeras, G.; López, J. J.; Kisi, O.; Shiri, J.

    2012-04-01

    The correct observation/estimation of surface incoming solar radiation (RS) is very important for many agricultural, meteorological and hydrological related applications. While most weather stations are provided with sensors for air temperature detection, the presence of sensors necessary for the detection of solar radiation is not so habitual and the data quality provided by them is sometimes poor. In these cases it is necessary to estimate this variable. Temperature based modeling procedures are reported in this study for estimating daily incoming solar radiation by using Gene Expression Programming (GEP) for the first time, and other artificial intelligence models such as Artificial Neural Networks (ANNs), and Adaptive Neuro-Fuzzy Inference System (ANFIS). Traditional temperature based solar radiation equations were also included in this study and compared with artificial intelligence based approaches. Root mean square error (RMSE), mean absolute error (MAE) RMSE-based skill score (SSRMSE), MAE-based skill score (SSMAE) and r2 criterion of Nash and Sutcliffe criteria were used to assess the models' performances. An ANN (a four-input multilayer perceptron with ten neurons in the hidden layer) presented the best performance among the studied models (2.93 MJ m-2 d-1 of RMSE). A four-input ANFIS model revealed as an interesting alternative to ANNs (3.14 MJ m-2 d-1 of RMSE). Very limited number of studies has been done on estimation of solar radiation based on ANFIS, and the present one demonstrated the ability of ANFIS to model solar radiation based on temperatures and extraterrestrial radiation. By the way this study demonstrated, for the first time, the ability of GEP models to model solar radiation based on daily atmospheric variables. Despite the accuracy of GEP models was slightly lower than the ANFIS and ANN models the genetic programming models (i.e., GEP) are superior to other artificial intelligence models in giving a simple explicit equation for the

  1. Influence of crop load on the expression patterns of starch metabolism genes in alternate-bearing Citrus trees.

    OpenAIRE

    González Nebauer, Sergio; Renau Morata, Begoña; Lluch Gomez, Yolanda Patricia; BAROJA FERNANDEZ, EDURNE; POZUETA-ROMERO, JAVIER; Molina Romero, Rosa Victoria

    2014-01-01

    [EN] The fruit is the main sink organ in Citrus and captures almost all available photoassimilates during its development. Consequently, carbohydrate partitioning and starch content depend on the crop load of Citrus trees. Nevertheless, little is known about the mechanisms controlling the starch metabolism at the tree level in relation to presence of fruit. The aim of this study was to find the relation between the seasonal variation of expression and activity of the genes involved in carbon...

  2. The U.S. Marine Corps Combined Action Program (CAP): A Proposed Alternative Strategy for the Vietnam War

    National Research Council Canada - National Science Library

    Williamson, Curtis

    2002-01-01

    .... The CAP offered a viable alternative to the strategy taken in Vietnam, challenging the sustaining infrastructure of the guerrilla, while providing security for the largely agrarian populace. Discussion...

  3. Alternative Splicing and Tissue-specific Elastin Misassembly Act as Biological Modifiers of Human Elastin Gene Frameshift Mutations Associated with Dominant Cutis Laxa*

    Science.gov (United States)

    Sugitani, Hideki; Hirano, Eiichi; Knutsen, Russell H.; Shifren, Adrian; Wagenseil, Jessica E.; Ciliberto, Christopher; Kozel, Beth A.; Urban, Zsolt; Davis, Elaine C.; Broekelmann, Thomas J.; Mecham, Robert P.

    2012-01-01

    Elastin is the extracellular matrix protein in vertebrates that provides elastic recoil to blood vessels, the lung, and skin. Because the elastin gene has undergone significant changes in the primate lineage, modeling elastin diseases in non-human animals can be problematic. To investigate the pathophysiology underlying a class of elastin gene mutations leading to autosomal dominant cutis laxa, we engineered a cutis laxa mutation (single base deletion) into the human elastin gene contained in a bacterial artificial chromosome. When expressed as a transgene in mice, mutant elastin was incorporated into elastic fibers in the skin and lung with adverse effects on tissue function. In contrast, only low levels of mutant protein incorporated into aortic elastin, which explains why the vasculature is relatively unaffected in this disease. RNA stability studies found that alternative exon splicing acts as a modifier of disease severity by influencing the spectrum of mutant transcripts that survive nonsense-mediated decay. Our results confirm the critical role of the C-terminal region of tropoelastin in elastic fiber assembly and suggest tissue-specific differences in the elastin assembly pathway. PMID:22573328

  4. Cellular Reprogramming, Genome Editing, and Alternative CRISPR Cas9 Technologies for Precise Gene Therapy of Duchenne Muscular Dystrophy

    Science.gov (United States)

    Xu, Huaigeng

    2017-01-01

    In the past decade, the development of two innovative technologies, namely, induced pluripotent stem cells (iPSCs) and the CRISPR Cas9 system, has enabled researchers to model diseases derived from patient cells and precisely edit DNA sequences of interest, respectively. In particular, Duchenne muscular dystrophy (DMD) has been an exemplary monogenic disease model for combining these technologies to demonstrate that genome editing can correct genetic mutations in DMD patient-derived iPSCs. DMD is an X-linked genetic disorder caused by mutations that disrupt the open reading frame of the dystrophin gene, which plays a critical role in stabilizing muscle cells during contraction and relaxation. The CRISPR Cas9 system has been shown to be capable of targeting the dystrophin gene and rescuing its expression in in vitro patient-derived iPSCs and in vivo DMD mouse models. In this review, we highlight recent advances made using the CRISPR Cas9 system to correct genetic mutations and discuss how emerging CRISPR technologies and iPSCs in a combined platform can play a role in bringing a therapy for DMD closer to the clinic. PMID:28607562

  5. Cellular Reprogramming, Genome Editing, and Alternative CRISPR Cas9 Technologies for Precise Gene Therapy of Duchenne Muscular Dystrophy

    Directory of Open Access Journals (Sweden)

    Peter Gee

    2017-01-01

    Full Text Available In the past decade, the development of two innovative technologies, namely, induced pluripotent stem cells (iPSCs and the CRISPR Cas9 system, has enabled researchers to model diseases derived from patient cells and precisely edit DNA sequences of interest, respectively. In particular, Duchenne muscular dystrophy (DMD has been an exemplary monogenic disease model for combining these technologies to demonstrate that genome editing can correct genetic mutations in DMD patient-derived iPSCs. DMD is an X-linked genetic disorder caused by mutations that disrupt the open reading frame of the dystrophin gene, which plays a critical role in stabilizing muscle cells during contraction and relaxation. The CRISPR Cas9 system has been shown to be capable of targeting the dystrophin gene and rescuing its expression in in vitro patient-derived iPSCs and in vivo DMD mouse models. In this review, we highlight recent advances made using the CRISPR Cas9 system to correct genetic mutations and discuss how emerging CRISPR technologies and iPSCs in a combined platform can play a role in bringing a therapy for DMD closer to the clinic.

  6. Nuclear proliferation and civilian nuclear power. Report of the Nonproliferation Alternative Systems Assessment Program. Volume V. Economics and systems analysis

    International Nuclear Information System (INIS)

    1980-06-01

    This NASAP assessment considers the economics of alternative nuclear reactor and fuel-cycle systems in the light of possible patterns of uranium supply and energy demand, as well as the economic implications of improvng the proliferation resistance of the various systems. The assessment focuses on the costs of alternative nuclear technologies and the possible timing of their implementation, based on their economic attractiveness

  7. 46 CFR 176.625 - Eligibility requirements for the Alternative Hull Examination (AHE) Program for certain passenger...

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Eligibility requirements for the Alternative Hull... CERTIFICATION Hull and Tailshaft Examinations § 176.625 Eligibility requirements for the Alternative Hull... if— (1) It is constructed of steel or aluminum; (2) It has an effective hull protection system; (3...

  8. Nuclear proliferation and civilian nuclear power. Report of the Nonproliferation Alternative Systems Assessment Program. Volume VI. Safety and environmental considerations for licensing

    International Nuclear Information System (INIS)

    1980-06-01

    This volume of the Nonproliferation Alternative Systems Assessment Program report addresses safety and environmental considerations in licensing the principal alternative nuclear reactors and fuel cycles in the United States for large-scale commercial nuclear power plants. In addition, this volume examines the safety and environmental considerations for licensing fuel service centers. These centers, which have been proposed for controlling sensitive fuel-cycle facilities and special nuclear materials, would contain a combination of such facilities as reprocessing plants, fabrication plants, and reactors. For this analysis, two fuel service center concepts were selected - one with power - generating capability and one without

  9. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  10. Verification of predicted alternatively spliced Wnt genes reveals two new splice variants (CTNNB1 and LRP5 and altered Axin-1 expression during tumour progression

    Directory of Open Access Journals (Sweden)

    Reich Jens G

    2006-06-01

    Full Text Available Abstract Background Splicing processes might play a major role in carcinogenesis and tumour progression. The Wnt pathway is of crucial relevance for cancer progression. Therefore we focussed on the Wnt/β-catenin signalling pathway in order to validate the expression of sequences predicted as alternatively spliced by bioinformatic methods. Splice variants of its key molecules were selected, which may be critical components for the understanding of colorectal tumour progression and may have the potential to act as biological markers. For some of the Wnt pathway genes the existence of splice variants was either proposed (e.g. β-Catenin and CTNNB1 or described only in non-colon tissues (e.g. GSK3β or hitherto not published (e.g. LRP5. Results Both splice variants – normal and alternative form – of all selected Wnt pathway components were found to be expressed in cell lines as well as in samples derived from tumour, normal and healthy tissues. All splice positions corresponded totally with the bioinformatical prediction as shown by sequencing. Two hitherto not described alternative splice forms (CTNNB1 and LRP5 were detected. Although the underlying EST data used for the bioinformatic analysis suggested a tumour-specific expression neither a qualitative nor a significant quantitative difference between the expression in tumour and healthy tissues was detected. Axin-1 expression was reduced in later stages and in samples from carcinomas forming distant metastases. Conclusion We were first to describe that splice forms of crucial genes of the Wnt-pathway are expressed in human colorectal tissue. Newly described splicefoms were found for β-Catenin, LRP5, GSK3β, Axin-1 and CtBP1. However, the predicted cancer specificity suggested by the origin of the underlying ESTs was neither qualitatively nor significant quantitatively confirmed. That let us to conclude that EST sequence data can give adequate hints for the existence of alternative splicing

  11. Influence of crop load on the expression patterns of starch metabolism genes in alternate-bearing citrus trees.

    Science.gov (United States)

    Nebauer, Sergio G; Renau-Morata, Begoña; Lluch, Yolanda; Baroja-Fernández, Edurne; Pozueta-Romero, Javier; Molina, Rosa-Victoria

    2014-07-01

    The fruit is the main sink organ in Citrus and captures almost all available photoassimilates during its development. Consequently, carbohydrate partitioning and starch content depend on the crop load of Citrus trees. Nevertheless, little is known about the mechanisms controlling the starch metabolism at the tree level in relation to presence of fruit. The aim of this study was to find the relation between the seasonal variation of expression and activity of the genes involved in carbon metabolism and the partition and allocation of carbohydrates in 'Salustiana' sweet orange trees with different crop loads. Metabolisable carbohydrates, and the expression and activity of the enzymes involved in sucrose and starch metabolism, including sucrose transport, were determined during the year in the roots and leaves of 40-year-old trees bearing heavy crop loads ('on' trees) and trees with almost no fruits ('off' trees). Fruit altered photoassimilate partitioning in trees. Sucrose content tended to be constant in roots and leaves, and surplus fixed carbon is channeled to starch production. Differences between 'on' and 'off' trees in starch content can be explained by differences in ADP-glucose pyrophosphorylase (AGPP) expression/activity and α-amylase activity which varies depending on crop load. The observed relation of AGPP and UGPP (UDP-glucose pyrophosphorylase) is noteworthy and indicates a direct link between sucrose and starch synthesis. Furthermore, different roles for sucrose transporter SUT1 and SUT2 have been proposed. Variation in soluble sugars content cannot explain the differences in gene expression between the 'on' and 'off' trees. A still unknown signal from fruit should be responsible for this control. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  12. Epilepsy caused by an abnormal alternative splicing with dosage effect of the SV2A gene in a chicken model.

    Directory of Open Access Journals (Sweden)

    Marine Douaud

    Full Text Available Photosensitive reflex epilepsy is caused by the combination of an individual's enhanced sensitivity with relevant light stimuli, such as stroboscopic lights or video games. This is the most common reflex epilepsy in humans; it is characterized by the photoparoxysmal response, which is an abnormal electroencephalographic reaction, and seizures triggered by intermittent light stimulation. Here, by using genetic mapping, sequencing and functional analyses, we report that a mutation in the acceptor site of the second intron of SV2A (the gene encoding synaptic vesicle glycoprotein 2A is causing photosensitive reflex epilepsy in a unique vertebrate model, the Fepi chicken strain, a spontaneous model where the neurological disorder is inherited as an autosomal recessive mutation. This mutation causes an aberrant splicing event and significantly reduces the level of SV2A mRNA in homozygous carriers. Levetiracetam, a second generation antiepileptic drug, is known to bind SV2A, and SV2A knock-out mice develop seizures soon after birth and usually die within three weeks. The Fepi chicken survives to adulthood and responds to levetiracetam, suggesting that the low-level expression of SV2A in these animals is sufficient to allow survival, but does not protect against seizures. Thus, the Fepi chicken model shows that the role of the SV2A pathway in the brain is conserved between birds and mammals, in spite of a large phylogenetic distance. The Fepi model appears particularly useful for further studies of physiopathology of reflex epilepsy, in comparison with induced models of epilepsy in rodents. Consequently, SV2A is a very attractive candidate gene for analysis in the context of both mono- and polygenic generalized epilepsies in humans.

  13. Maternal programming of defensive responses through sustained effects on gene expression.

    Science.gov (United States)

    Zhang, Tie-Yuan; Bagot, Rose; Parent, Carine; Nesbitt, Cathy; Bredy, Timothy W; Caldji, Christian; Fish, Eric; Anisman, Hymie; Szyf, Moshe; Meaney, Michael J

    2006-07-01

    There are profound maternal effects on individual differences in defensive responses and reproductive strategies in species ranging literally from plants to insects to birds. Maternal effects commonly reflect the quality of the environment and are most likely mediated by the quality of the maternal provision (egg, propagule, etc.), which in turn determines growth rates and adult phenotype. In this paper we review data from the rat that suggest comparable forms of maternal effects on defensive responses stress, which are mediated by the effects of variations in maternal behavior on gene expression. Under conditions of environmental adversity maternal effects enhance the capacity for defensive responses in the offspring. In mammals, these effects appear to 'program' emotional, cognitive and endocrine systems towards increased sensitivity to adversity. In environments with an increased level of adversity, such effects can be considered adaptive, enhancing the probability of offspring survival to sexual maturity; the cost is that of an increased risk for multiple forms of pathology in later life.

  14. Use of Gene Expression Programming in regionalization of flow duration curve

    Science.gov (United States)

    Hashmi, Muhammad Z.; Shamseldin, Asaad Y.

    2014-06-01

    In this paper, a recently introduced artificial intelligence technique known as Gene Expression Programming (GEP) has been employed to perform symbolic regression for developing a parametric scheme of flow duration curve (FDC) regionalization, to relate selected FDC characteristics to catchment characteristics. Stream flow records of selected catchments located in the Auckland Region of New Zealand were used. FDCs of the selected catchments were normalised by dividing the ordinates by their median value. Input for the symbolic regression analysis using GEP was (a) selected characteristics of normalised FDCs; and (b) 26 catchment characteristics related to climate, morphology, soil properties and land cover properties obtained using the observed data and GIS analysis. Our study showed that application of this artificial intelligence technique expedites the selection of a set of the most relevant independent variables out of a large set, because these are automatically selected through the GEP process. Values of the FDC characteristics obtained from the developed relationships have high correlations with the observed values.

  15. Unpredictable Variable Prenatal Stress Programs Expression of Genes Involved in Appetite Control and Energy Expenditure

    Science.gov (United States)

    Moyer, E. L.; Al-Shayeb, B.; Baer, L. A.; Ronca, A. E.

    2016-01-01

    Exposure to stress in the womb shapes neurobiological and physiological outcomes of offspring in later life, including body weight regulation and metabolic profiles. Our previous work utilizing a centrifugation-induced hyper-gravity demonstrated significantly increased (8-15%) body mass in male, but not female, rats exposed throughout gestation to chronic 2-g from conception to birth. We reported a similar outcome in adult offspring exposed throughout gestation to Unpredictable Variable Prenatal Stress (UVPS). Here we examine gene expression changes and the plasma of animals treated with our UVPS model to identify a potential role for prenatal stress in this hypergravity programming effect. Specifically we focused on appetite control and energy expenditure pathways in prenatally stressed adult (90-day-old) male Sprague-Dawley rats.

  16. Parallelizing Gene Expression Programming Algorithm in Enabling Large-Scale Classification

    Directory of Open Access Journals (Sweden)

    Lixiong Xu

    2017-01-01

    Full Text Available As one of the most effective function mining algorithms, Gene Expression Programming (GEP algorithm has been widely used in classification, pattern recognition, prediction, and other research fields. Based on the self-evolution, GEP is able to mine an optimal function for dealing with further complicated tasks. However, in big data researches, GEP encounters low efficiency issue due to its long time mining processes. To improve the efficiency of GEP in big data researches especially for processing large-scale classification tasks, this paper presents a parallelized GEP algorithm using MapReduce computing model. The experimental results show that the presented algorithm is scalable and efficient for processing large-scale classification tasks.

  17. Incentive policies for promoting wind power production in Brazil: Scenarios for the Alternative Energy Sources Incentive Program (PROINFA) under the New Brazilian electric power sector regulation

    International Nuclear Information System (INIS)

    Dutra, Ricardo Marques; Szklo, Alexandre Salem

    2008-01-01

    The Alternative Energy Sources Incentive Program (PROINFA) was designed in 2002 to stimulate the electricity generation from three energy sources (wind, biomass and small-scale hydro) in Brazil. The Program was divided into two phases. The first one uses feed-in tariffs for promoting the development of 3300 MW. The second one that was originally based on feed-in tariffs was modified in 2003, in order to be based on biddings for renewables. These biddings are capped to limit their impact on the final electricity tariff. Due to this bound, the highest-cost power option promoted by PROINFA (wind power generation) might have development problems. Simulating different scenarios for the biddings, it was verified that the only way to reach the original goal set by PROINFA (10% of the annual electricity consumption provided by alternative sources up to 2020) and, simultaneously, not overcome the bidding bound is to promote biomass-fired power generation alone, during the Program's second phase. However, this action contradicts one of the targets of the Program, which is to diversify the energy matrix. An alternative option could be biddings for renewables according to specific criteria (complementarities, industrial and technological development and cost), based not only on their cost-effectiveness. (author)

  18. Gene expression program of regeneration in Eisenia fetida: a transcriptomics study

    Directory of Open Access Journals (Sweden)

    Aksheev Bhambri

    2017-10-01

    Full Text Available Annelids form a connecting link between segmented and non-segmented organisms.  In other words, phylogenetically, the segmented body pattern starts from Annelida, a phylum that consists of thousands of species, including marine worms, freshwater leeches and earthworms that inhabit deep layers of soil to environmental niches in forests and cultivated land. We are using Eisenia fetida (Indian isolate a top dwelling, vermicomposting worm due to its ability to regenerate its posterior after damage, injury or complete removal. On average, Eisenia fetida has 100-110 segments. We separated the anterior (upto 55-60th segment and posterior of the worm, and allowed it to regenerate.  In this model, only the posterior could be regenerated after injury.  We isolated RNA from the regenerated tissue and the immediate adjacent old tissue at 15 days, 20 days and 30 days during regeneration. We carried out transcriptome sequencing and analysis. With the aim of identifying specific factors which promote nerve regeneration, we have annotated the differentially expressed genes. In all organisms which possess a segmented body, the expression pattern of the Hox cluster is conserved. Hox gene expression, a conserved developmental phenomenon in establishment of body plan has been studied by comparative genomics of other annelids like the marine worm Capitella telleta, the leech Helobdella robusta.  We have used a combination of high-throughput sequencing based techniques and validation through cell and molecular biology to identify key aspects of the gene expression program of regeneration in this worm. Besides the transcriptome, we have also done whole genome sequencing, miRnome and metagenome sequencing of this terrestrial annelid.

  19. Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients

    DEFF Research Database (Denmark)

    Rapin, Nicolas; Bagger, Frederik Otzen; Jendholm, Johan

    2014-01-01

    Gene expression profiling has been used extensively to characterize cancer, identify novel subtypes, and improve patient stratification. However, it has largely failed to identify transcriptional programs that differ between cancer and corresponding normal cells and has not been efficient in iden......-karyotype AML, which allowed for the generation of a highly prognostic survival signature. Collectively, our CvN method holds great potential as a tool for the analysis of gene expression profiles of cancer patients....

  20. A double base change in alternate base pairs induced by ultraviolet irradiation in a glycine transfer RNA gene

    International Nuclear Information System (INIS)

    Coleman, R.D.; Dunst, R.W.; Hill, C.W.; Pennsylvania State Univ., Hershey

    1980-01-01

    The glyUsusub(AGA) mutation affects Escherichia coli tRNAsup(Gly)sub(GGG), changing it to an AGA missense suppressor tRNA. Sequence studies have shown that the mutation involves a double base substitution at the first and third positions of the tRNA anticodon, the result being a change in the anticodon from CCC to UCU. A system has been developed to facilitate the detection of this novel mutation, and we have shown that ultraviolet irradiation and N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) are effective in causing the double base change. A single observation of the mutation occuring spontaneously has been made also. The frequency of MNNG-induced glyUsusub(AGA) mutations is compatible with their being caused by two separate mutagenic events. The frequency of UV-induced glyUsusub(AGA) mutations, however, strongly suggests that the occurence of one base substitution strongly enhances the chance of finding the second substitution at the alternate position. In addition to the double change in the anticodon, the glyUsusub(AGA) tRNA differs from tRNAsup(gly)sub(GGG) in that it bears a modification of the A adjacent to the 3' position of the anticodon. Most likely, this modified base is N-[9-(β-D-ribofuranosyl)-purin-6-ylcarbamoyl] threonine. (orig.) 891 AJ/orig. 892 BRE [de

  1. Comparison of Gene Expression Programming with neuro-fuzzy and neural network computing techniques in estimating daily incoming solar radiation in the Basque Country (Northern Spain)

    International Nuclear Information System (INIS)

    Landeras, Gorka; López, José Javier; Kisi, Ozgur; Shiri, Jalal

    2012-01-01

    Highlights: ► Solar radiation estimation based on Gene Expression Programming is unexplored. ► This approach is evaluated for the first time in this study. ► Other artificial intelligence models (ANN and ANFIS) are also included in the study. ► New alternatives for solar radiation estimation based on temperatures are provided. - Abstract: Surface incoming solar radiation is a key variable for many agricultural, meteorological and solar energy conversion related applications. In absence of the required meteorological sensors for the detection of global solar radiation it is necessary to estimate this variable. Temperature based modeling procedures are reported in this study for estimating daily incoming solar radiation by using Gene Expression Programming (GEP) for the first time, and other artificial intelligence models such as Artificial Neural Networks (ANNs), and Adaptive Neuro-Fuzzy Inference System (ANFIS). A comparison was also made among these techniques and traditional temperature based global solar radiation estimation equations. Root mean square error (RMSE), mean absolute error (MAE) RMSE-based skill score (SS RMSE ), MAE-based skill score (SS MAE ) and r 2 criterion of Nash and Sutcliffe criteria were used to assess the models’ performances. An ANN (a four-input multilayer perceptron with 10 neurons in the hidden layer) presented the best performance among the studied models (2.93 MJ m −2 d −1 of RMSE). The ability of GEP approach to model global solar radiation based on daily atmospheric variables was found to be satisfactory.

  2. Hepatitis C Virus Frameshift/Alternate Reading Frame Protein Suppresses Interferon Responses Mediated by Pattern Recognition Receptor Retinoic-Acid-Inducible Gene-I.

    Directory of Open Access Journals (Sweden)

    Seung Bum Park

    Full Text Available Hepatitis C virus (HCV actively evades host interferon (IFN responses but the mechanisms of how it does so are not completely understood. In this study, we present evidence for an HCV factor that contributes to the suppression of retinoic-acid-inducible gene-I (RIG-I-mediated IFN induction. Expression of frameshift/alternate reading frame protein (F/ARFP from HCV -2/+1 frame in Huh7 hepatoma cells suppressed type I IFN responses stimulated by HCV RNA pathogen-associated molecular pattern (PAMP and poly(IC. The suppression occurred independently of other HCV factors; and activation of interferon stimulated genes, TNFα, IFN-λ1, and IFN-λ2/3 was likewise suppressed by HCV F/ARFP. Point mutations in the full-length HCV sequence (JFH1 genotype 2a strain were made to introduce premature termination codons in the -2/+1 reading frame coding for F/ARFP while preserving the original reading frame, which enhanced IFNα and IFNβ induction by HCV. The potentiation of IFN response by the F/ARFP mutations was diminished in Huh7.5 cells, which already have a defective RIG-I, and by decreasing RIG-I expression in Huh7 cells. Furthermore, adding F/ARFP back via trans-complementation suppressed IFN induction in the F/ARFP mutant. The F/ARFP mutants, on the other hand, were not resistant to exogenous IFNα. Finally, HCV-infected human liver samples showed significant F/ARFP antibody reactivity, compared to HCV-uninfected control livers. Therefore, HCV F/ARFP likely cooperates with other viral factors to suppress type I and III IFN induction occurring through the RIG-I signaling pathway. This study identifies a novel mechanism of pattern recognition receptor modulation by HCV and suggests a biological function of the HCV alternate reading frame in the modulation of host innate immunity.

  3. Clean air program : design guidelines for bus transit systems using electric and hybrid electric propulsion as an alternative fuel

    Science.gov (United States)

    2003-03-01

    The use of alternative fuels to power transit buses is steadily increasing. Several fuels, including : Compressed Natural Gas (CNG), Liquefied Natural Gas (LNG), Liquefied Petroleum Gas (LPG), and : Methanol/Ethanol, are already being used. At presen...

  4. Nuclear proliferation and civilian nuclear power: report of the Nonproliferation Alternative Systems Assessment Program. Volume VI. Safety and environmental considerations for licensing

    International Nuclear Information System (INIS)

    1979-12-01

    Volume 6 of the Nonproliferation Alternative Systems Assessment Program report addresses safety and environmental considerations in licensing the principal alternative nuclear reactors and fuel cycles in the United States for large-scale commercial nuclear power plants. In addition, this volume examines the safety and environmental considerations for licensing fuel service centers. These centers, which have been proposed for controlling sensitive fuel-cycle facilities and special nuclear materials, would contain a combination of such facilities as reprocessing plants, fabrication plants, and reactors. For this analysis, two fuel service center concepts were selected - one with power-generating capability and one without. This volume also provides estimates of the time required for development of large-scale commercial reactor systems to reach the construction permit application stage and for fuel-cycle facilities to reach the operating license application stage, which is a measure of the relative technical status of alternative nuclear systems

  5. Genetic disruption of the alternative splicing of drebrin gene impairs context-dependent fear learning in adulthood.

    Science.gov (United States)

    Kojima, N; Hanamura, K; Yamazaki, H; Ikeda, T; Itohara, S; Shirao, T

    2010-01-13

    Dendritic spines are postsynaptic structures at excitatory synapses that play important roles in synaptic transmission and plasticity. Dendritic spine morphology and function are regulated by an actin-based cytoskeletal network. Drebrin A, an adult form of drebrin, is an actin-binding protein in dendritic spines, and its decrease is purportedly concerned with synaptic dysfunction in Alzheimer's disease. Rapid conversion of drebrin E, an embryonic form of drebrin, to drebrin A occurs in parallel with synaptic maturation. To understand the physiological role of drebrin isoform conversion in vivo, we generated knockout mice in which a drebrin A-specific exon was deleted from the drebrin gene. Drebrin A-specific knockout (DAKO) mice expressed drebrin E, which substituted for drebrin A. Subcellular fractionation experiment indicated that cytosolic form of drebrin was increased in the brains of DAKO mice. Furthermore, drebrin accumulation in synaptosomes of DAKO mice was much higher than that of wild-type (WT) mice. DAKO mice were viable and showed no apparent abnormalities in their gross brain morphology and general behaviors. However, DAKO mice were impaired in a context-dependent freezing after fear conditioning. These data indicate that drebrin A plays an indispensable role in some processes of generating fear learning and memory.

  6. 9-genes reinforce the phylogeny of holometabola and yield alternate views on the phylogenetic placement of Strepsiptera.

    Directory of Open Access Journals (Sweden)

    Duane D McKenna

    2010-07-01

    Full Text Available The extraordinary morphology, reproductive and developmental biology, and behavioral ecology of twisted wing parasites (order Strepsiptera have puzzled biologists for centuries. Even today, the phylogenetic position of these enigmatic "insects from outer space" [1] remains uncertain and contentious. Recent authors have argued for the placement of Strepsiptera within or as a close relative of beetles (order Coleoptera, as sister group of flies (order Diptera, or even outside of Holometabola.Here, we combine data from several recent studies with new data (for a total of 9 nuclear genes and approximately 13 kb of aligned data for 34 taxa, to help clarify the phylogenetic placement of Strepsiptera. Our results unequivocally support the monophyly of Neuropteroidea (=Neuropterida+Coleoptera+Strepsiptera, but recover Strepsiptera either derived from within polyphagan beetles (order Coleoptera, or in a position sister to Neuropterida. All other supra-ordinal- and ordinal-level relationships recovered with strong nodal support were consistent with most other recent studies.These results, coupled with the recent proposed placement of Strepsiptera sister to Coleoptera, suggest that while the phylogenetic neighborhood of Strepsiptera has been identified, unequivocal placement to a specific branch within Neuropteroidea will require additional study.

  7. Alternative Approaches for Educating Future Global Marketing Professionals: A Comparison of Foreign Study and Research-Intensive Marketing Programs

    Science.gov (United States)

    Kaufman, Peter A.; Melton, Horace L.; Varner, Iris I.; Hoelscher, Mark; Schmidt, Klaus; Spaulding, Aslihan D.

    2011-01-01

    Using an experiential learning model as a conceptual background, this article discusses characteristics and learning objectives for well-known foreign study programs such as study tours, study abroad, and internships and compares them with a less common overseas program called the "Global Marketing Program" (GMP). GMP involves…

  8. Oligophrenin-1 (OPHN1, a gene involved in X-linked intellectual disability, undergoes RNA editing and alternative splicing during human brain development.

    Directory of Open Access Journals (Sweden)

    Sabina Barresi

    Full Text Available Oligophrenin-1 (OPHN1 encodes for a Rho-GTPase-activating protein, important for dendritic morphogenesis and synaptic function. Mutations in this gene have been identified in patients with X-linked intellectual disability associated with cerebellar hypoplasia. ADAR enzymes are responsible for A-to-I RNA editing, an essential post-transcriptional RNA modification contributing to transcriptome and proteome diversification. Specifically, ADAR2 activity is essential for brain development and function. Herein, we show that the OPHN1 transcript undergoes post-transcriptional modifications such as A-to-I RNA editing and alternative splicing in human brain and other tissues. We found that OPHN1 editing is detectable already at the 18th week of gestation in human brain with a boost of editing at weeks 20 to 33, concomitantly with OPHN1 expression increase and the appearance of a novel OPHN1 splicing isoform. Our results demonstrate that multiple post-transcriptional events occur on OPHN1, a gene playing an important role in brain function and development.

  9. MeCP2 regulates Tet1-catalyzed demethylation, CTCF binding, and learning-dependent alternative splicing of the BDNF gene in Turtle

    Science.gov (United States)

    Zheng, Zhaoqing; Ambigapathy, Ganesh; Keifer, Joyce

    2017-01-01

    MECP2 mutations underlying Rett syndrome cause widespread misregulation of gene expression. Functions for MeCP2 other than transcriptional are not well understood. In an ex vivo brain preparation from the pond turtle Trachemys scripta elegans, an intraexonic splicing event in the brain-derived neurotrophic factor (BDNF) gene generates a truncated mRNA transcript in naïve brain that is suppressed upon classical conditioning. MeCP2 and its partners, splicing factor Y-box binding protein 1 (YB-1) and methylcytosine dioxygenase 1 (Tet1), bind to BDNF chromatin in naïve but dissociate during conditioning; the dissociation correlating with decreased DNA methylation. Surprisingly, conditioning results in new occupancy of BDNF chromatin by DNA insulator protein CCCTC-binding factor (CTCF), which is associated with suppression of splicing in conditioning. Knockdown of MeCP2 shows it is instrumental for splicing and inhibits Tet1 and CTCF binding thereby negatively impacting DNA methylation and conditioning-dependent splicing regulation. Thus, mutations in MECP2 can have secondary effects on DNA methylation and alternative splicing. DOI: http://dx.doi.org/10.7554/eLife.25384.001 PMID:28594324

  10. [Alternation of proteins in brain of Parkinson's disease model rats after the transplantation of TH-NTN gene modified bone marrow mesenchymal stem cells].

    Science.gov (United States)

    Huang, Yue; Chang, Cheng; Zhang, Jie-wen; Gao, Xiao-qun

    2012-09-04

    To explore the effects of tyrosine hydroxylase-neurturin (TH-NTN) gene modified bone marrow mesenchymal stem cell (BMSC) transplantation in Parkinson's disease (PD) model rats and the alternations of correlated proteins. The PD rat model was established by the 2-point injection of 6-hydroxydopamine (6-OHDA) into unilateral (right) striatum. Successful modeling rats were separated into PD, BMSC and TH-NTN-BMSC groups. BMSC and TH-NTN-BMSC groups were transplanted into BMSCs and TH-NTN gene modified BMSC cells separately into right striatum. After transplantation, ethology detection in all groups was made with an intraperitoneal injection of apomorphine (APO). Dopamine (DA) and Dihydroxyphenylacetic Acid (DOPAC) in striatum were detected by high performance liquid electrochemical analysis. TH and NTN proteins in right striatum were also analyzed by immunohistochemistry and Western blot. Finally the density of dopamine receptors in post synaptic density of dopaminergic synapses of corpus striatum were compared between each group by post-embedding immunogold electron microscopy. After an injection of APO, rotation frequency decreased in TH-NTN-BMSC group, i.e. (5.7 ± 1.3) circles/min versus (10.8 ± 2.2), (9.9 ± 1.2) circles/min in PD and BMSC groups (P TH-NTN-BMSC group versus (923 ± 132)/µm(2) in PD and (860 ± 116)/µm(2) in BMSC groups was also found. The combined therapy of TH and NTN genes increases the synthesis of DA and also protects the dopaminergic neurons to achieve double therapeutic effects. It may provide potential innovations of PD genetic therapy.

  11. Nuclear proliferation and civilian nuclear power: report of the nonproliferation alternative systems assessment program. Volume V. Economics and systems analysis

    International Nuclear Information System (INIS)

    1979-12-01

    This NASAP assessment considers the economics of alternative nuclear reactor and fuel-cycle systems in the light of possible patterns of uranium supply and energy demand, as well as the economic implications of improving the proliferation resistance of the various systems. The assessment focuses on the costs of alternative nuclear technologies and the possible timing of their implementation, based on their economic attractiveness. The objectives of this assessment are to identify when economic incentives to deploy advanced nuclear power systems might exist, to estimate the costs of using technologies that would reduce the risk of proliferation, to assess the impact of major economic uncertainties on the transition to new technologies, and to compare the investments required for alternative systems

  12. Maternal obesity programs mitochondrial and lipid metabolism gene expression in infant umbilical vein endothelial cells.

    Science.gov (United States)

    Costa, S M R; Isganaitis, E; Matthews, T J; Hughes, K; Daher, G; Dreyfuss, J M; da Silva, G A P; Patti, M-E

    2016-11-01

    Maternal obesity increases risk for childhood obesity, but molecular mechanisms are not well understood. We hypothesized that primary umbilical vein endothelial cells (HUVEC) from infants of overweight and obese mothers would harbor transcriptional patterns reflecting offspring obesity risk. In this observational cohort study, we recruited 13 lean (pre-pregnancy body mass index (BMI) obese ('ov-ob', BMI⩾25.0 kg m -2 ) women. We isolated primary HUVEC, and analyzed both gene expression (Primeview, Affymetrix) and cord blood levels of hormones and adipokines. A total of 142 transcripts were differentially expressed in HUVEC from infants of overweight-obese mothers (false discovery rate, FDRmaternal BMI (FDRmaternal obesity, we analyzed the cord blood lipidome and noted significant increases in the levels of total free fatty acids (lean: 95.5±37.1 μg ml -1 , ov-ob: 124.1±46.0 μg ml -1 , P=0.049), palmitate (lean: 34.5±12.7 μg ml -1 , ov-ob: 46.3±18.4 μg ml -1 , P=0.03) and stearate (lean: 20.8±8.2 μg ml -1 , ov-ob: 29.7±17.2 μg ml -1 , P=0.04), in infants of overweight-obese mothers. Prenatal exposure to maternal obesity alters HUVEC expression of genes involved in mitochondrial and lipid metabolism, potentially reflecting developmentally programmed differences in oxidative and lipid metabolism.

  13. The gene expression program of prostate fibroblast senescence modulates neoplastic epithelial cell proliferation through paracrine mechanisms.

    Science.gov (United States)

    Bavik, Claes; Coleman, Ilsa; Dean, James P; Knudsen, Beatrice; Plymate, Steven; Nelson, Peter S

    2006-01-15

    The greatest risk factor for developing carcinoma of the prostate is advanced age. Potential molecular and physiologic contributors to the frequency of cancer occurrence in older individuals include the accumulation of somatic mutations through defects in genome maintenance, epigenetic gene silencing, oxidative stress, loss of immune surveillance, telomere dysfunction, chronic inflammation, and alterations in tissue microenvironment. In this context, the process of prostate carcinogenesis can be influenced through interactions between intrinsic cellular alterations and the extrinsic microenvironment and macroenvironment, both of which change substantially as a consequence of aging. In this study, we sought to characterize the molecular alterations that occur during the process of prostate fibroblast senescence to identify factors in the aged tissue microenvironment capable of promoting the proliferation and potentially the neoplastic progression of prostate epithelium. We evaluated three mechanisms leading to cell senescence: oxidative stress, DNA damage, and replicative exhaustion. We identified a consistent program of gene expression that includes a subset of paracrine factors capable of influencing adjacent prostate epithelial growth. Both direct coculture and conditioned medium from senescent prostate fibroblasts stimulated epithelial cell proliferation, 3-fold and 2-fold, respectively. The paracrine-acting proteins fibroblast growth factor 7, hepatocyte growth factor, and amphiregulin (AREG) were elevated in the extracellular environment of senescent prostate fibroblasts. Exogenous AREG alone stimulated prostate epithelial cell growth, and neutralizing antibodies and small interfering RNA targeting AREG attenuated, but did not completely abrogate the growth-promoting effects of senescent fibroblast conditioned medium. These results support the concept that aging-related changes in the prostate microenvironment may contribute to the progression of prostate

  14. trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags.

    Science.gov (United States)

    Renaud, Gabriel; LaFave, Matthew C; Liang, Jin; Wolfsberg, Tyra G; Burgess, Shawn M

    2014-10-13

    Quantification of a transcriptional profile is a useful way to evaluate the activity of a cell at a given point in time. Although RNA-Seq has revolutionized transcriptional profiling, the costs of RNA-Seq are still significantly higher than microarrays, and often the depth of data delivered from RNA-Seq is in excess of what is needed for simple transcript quantification. Digital Gene Expression (DGE) is a cost-effective, sequence-based approach for simple transcript quantification: by sequencing one read per molecule of RNA, this technique can be used to efficiently count transcripts while obviating the need for transcript-length normalization and reducing the total numbers of reads necessary for accurate quantification. Here, we present trieFinder, a program specifically designed to rapidly map, parse, and annotate DGE tags of various lengths against cDNA and/or genomic sequence databases. The trieFinder algorithm maps DGE tags in a two-step process. First, it scans FASTA files of RefSeq, UniGene, and genomic DNA sequences to create a database of all tags that can be derived from a predefined restriction site. Next, it compares the experimental DGE tags to this tag database, taking advantage of the fact that the tags are stored as a prefix tree, or "trie", which allows for linear-time searches for exact matches. DGE tags with mismatches are analyzed by recursive calls in the data structure. We find that, in terms of alignment speed, the mapping functionality of trieFinder compares favorably with Bowtie. trieFinder can quickly provide the user an annotation of the DGE tags from three sources simultaneously, simplifying transcript quantification and novel transcript detection, delivering the data in a simple parsed format, obviating the need to post-process the alignment results. trieFinder is available at http://research.nhgri.nih.gov/software/trieFinder/.

  15. The Temporal Program of Peripheral Blood Gene Expression in the Response of Nonhuman Primates to Ebola Hemorrhagic Fever

    Science.gov (United States)

    2007-08-28

    the family Filoviridae. The EBOV genus consists of four distinct species: Ivory Coast Ebola virus, Reston Ebola virus, Sudan Ebola virus, and Zaire...S, Liu CL, Belcher CE, Botstein D, Staudt LM, Brown PO, Relman DA: Stereotyped and specific gene expression programs in human innate immune responses

  16. Muscle-specific splicing factors ASD-2 and SUP-12 cooperatively switch alternative pre-mRNA processing patterns of the ADF/cofilin gene in Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Genta Ohno

    Full Text Available Pre-mRNAs are often processed in complex patterns in tissue-specific manners to produce a variety of protein isoforms from single genes. However, mechanisms orchestrating the processing of the entire transcript are not well understood. Muscle-specific alternative pre-mRNA processing of the unc-60 gene in Caenorhabditis elegans, encoding two tissue-specific isoforms of ADF/cofilin with distinct biochemical properties in regulating actin organization, provides an excellent in vivo model of complex and tissue-specific pre-mRNA processing; it consists of a single first exon and two separate series of downstream exons. Here we visualize the complex muscle-specific processing pattern of the unc-60 pre-mRNA with asymmetric fluorescence reporter minigenes. By disrupting juxtaposed CUAAC repeats and UGUGUG stretch in intron 1A, we demonstrate that these elements are required for retaining intron 1A, as well as for switching the processing patterns of the entire pre-mRNA from non-muscle-type to muscle-type. Mutations in genes encoding muscle-specific RNA-binding proteins ASD-2 and SUP-12 turned the colour of the unc-60 reporter worms. ASD-2 and SUP-12 proteins specifically and cooperatively bind to CUAAC repeats and UGUGUG stretch in intron 1A, respectively, to form a ternary complex in vitro. Immunohistochemical staining and RT-PCR analyses demonstrate that ASD-2 and SUP-12 are also required for switching the processing patterns of the endogenous unc-60 pre-mRNA from UNC-60A to UNC-60B in muscles. Furthermore, systematic analyses of partially spliced RNAs reveal the actual orders of intron removal for distinct mRNA isoforms. Taken together, our results demonstrate that muscle-specific splicing factors ASD-2 and SUP-12 cooperatively promote muscle-specific processing of the unc-60 gene, and provide insight into the mechanisms of complex pre-mRNA processing; combinatorial regulation of a single splice site by two tissue-specific splicing regulators

  17. Alcohol, Tobacco, and Other Drug Misuse Prevention and Cessation Programming for Alternative High School Youth: A Review

    Science.gov (United States)

    Sussman, Steve; Arriaza, Bridget; Grigsby, Timothy J.

    2014-01-01

    Background: Relative to youth in regular high schools, alternative high school (AHS) youth are at high risk for alcohol, tobacco, and other drug (ATOD) misuse. Prevention and cessation efforts are needed for this population. Methods: A systematic, exhaustive literature search was completed to identify ATOD misuse prevention and cessation research…

  18. Community Alternatives for Love and Limits (CALL: A community-based family strengthening multi-family intervention program to respond to adolescents at risk

    Directory of Open Access Journals (Sweden)

    David Wilkerson

    2005-12-01

    Full Text Available Family strengthening has become a source of growing interest, research, and program design in the fields of prevention and treatment for problems of youth delinquency, school failure, alcohol, tobacco and other drug abuse (ATOD. Despite many studies that illustrate the positive outcomes of family strengthening programs and family-focused interventions, their use in communities has not advanced commensurate with their promise. This article offers a rationale for why programming efforts should continue to be directed towards family strengthening efforts as opposed to youth-focused only interventions. In addition, a community-based, family-strengthening alternative is described that addresses issues of youth delinquency while reducing barriers associated with availability, accessibility, and cost.

  19. EXONSAMPLER: a computer program for genome-wide and candidate gene exon sampling for targeted next-generation sequencing.

    Science.gov (United States)

    Cosart, Ted; Beja-Pereira, Albano; Luikart, Gordon

    2014-11-01

    The computer program EXONSAMPLER automates the sampling of thousands of exon sequences from publicly available reference genome sequences and gene annotation databases. It was designed to provide exon sequences for the efficient, next-generation gene sequencing method called exon capture. The exon sequences can be sampled by a list of gene name abbreviations (e.g. IFNG, TLR1), or by sampling exons from genes spaced evenly across chromosomes. It provides a list of genomic coordinates (a bed file), as well as a set of sequences in fasta format. User-adjustable parameters for collecting exon sequences include a minimum and maximum acceptable exon length, maximum number of exonic base pairs (bp) to sample per gene, and maximum total bp for the entire collection. It allows for partial sampling of very large exons. It can preferentially sample upstream (5 prime) exons, downstream (3 prime) exons, both external exons, or all internal exons. It is written in the Python programming language using its free libraries. We describe the use of EXONSAMPLER to collect exon sequences from the domestic cow (Bos taurus) genome for the design of an exon-capture microarray to sequence exons from related species, including the zebu cow and wild bison. We collected ~10% of the exome (~3 million bp), including 155 candidate genes, and ~16,000 exons evenly spaced genomewide. We prioritized the collection of 5 prime exons to facilitate discovery and genotyping of SNPs near upstream gene regulatory DNA sequences, which control gene expression and are often under natural selection. © 2014 John Wiley & Sons Ltd.

  20. Tools to Minimize Inter-Laboratory Variability in Vitellogenin Gene Expression Monitoring Programs

    Data.gov (United States)

    U.S. Environmental Protection Agency — All data files are in excel format. Files with names CSU are different mesocosms qPCR data results for vitellogen gene and 18s a house keeping gene. Data files...

  1. A Seasonal Time-Series Model Based on Gene Expression Programming for Predicting Financial Distress

    Directory of Open Access Journals (Sweden)

    Ching-Hsue Cheng

    2018-01-01

    Full Text Available The issue of financial distress prediction plays an important and challenging research topic in the financial field. Currently, there have been many methods for predicting firm bankruptcy and financial crisis, including the artificial intelligence and the traditional statistical methods, and the past studies have shown that the prediction result of the artificial intelligence method is better than the traditional statistical method. Financial statements are quarterly reports; hence, the financial crisis of companies is seasonal time-series data, and the attribute data affecting the financial distress of companies is nonlinear and nonstationary time-series data with fluctuations. Therefore, this study employed the nonlinear attribute selection method to build a nonlinear financial distress prediction model: that is, this paper proposed a novel seasonal time-series gene expression programming model for predicting the financial distress of companies. The proposed model has several advantages including the following: (i the proposed model is different from the previous models lacking the concept of time series; (ii the proposed integrated attribute selection method can find the core attributes and reduce high dimensional data; and (iii the proposed model can generate the rules and mathematical formulas of financial distress for providing references to the investors and decision makers. The result shows that the proposed method is better than the listing classifiers under three criteria; hence, the proposed model has competitive advantages in predicting the financial distress of companies.

  2. A Seasonal Time-Series Model Based on Gene Expression Programming for Predicting Financial Distress

    Science.gov (United States)

    2018-01-01

    The issue of financial distress prediction plays an important and challenging research topic in the financial field. Currently, there have been many methods for predicting firm bankruptcy and financial crisis, including the artificial intelligence and the traditional statistical methods, and the past studies have shown that the prediction result of the artificial intelligence method is better than the traditional statistical method. Financial statements are quarterly reports; hence, the financial crisis of companies is seasonal time-series data, and the attribute data affecting the financial distress of companies is nonlinear and nonstationary time-series data with fluctuations. Therefore, this study employed the nonlinear attribute selection method to build a nonlinear financial distress prediction model: that is, this paper proposed a novel seasonal time-series gene expression programming model for predicting the financial distress of companies. The proposed model has several advantages including the following: (i) the proposed model is different from the previous models lacking the concept of time series; (ii) the proposed integrated attribute selection method can find the core attributes and reduce high dimensional data; and (iii) the proposed model can generate the rules and mathematical formulas of financial distress for providing references to the investors and decision makers. The result shows that the proposed method is better than the listing classifiers under three criteria; hence, the proposed model has competitive advantages in predicting the financial distress of companies. PMID:29765399

  3. A Seasonal Time-Series Model Based on Gene Expression Programming for Predicting Financial Distress.

    Science.gov (United States)

    Cheng, Ching-Hsue; Chan, Chia-Pang; Yang, Jun-He

    2018-01-01

    The issue of financial distress prediction plays an important and challenging research topic in the financial field. Currently, there have been many methods for predicting firm bankruptcy and financial crisis, including the artificial intelligence and the traditional statistical methods, and the past studies have shown that the prediction result of the artificial intelligence method is better than the traditional statistical method. Financial statements are quarterly reports; hence, the financial crisis of companies is seasonal time-series data, and the attribute data affecting the financial distress of companies is nonlinear and nonstationary time-series data with fluctuations. Therefore, this study employed the nonlinear attribute selection method to build a nonlinear financial distress prediction model: that is, this paper proposed a novel seasonal time-series gene expression programming model for predicting the financial distress of companies. The proposed model has several advantages including the following: (i) the proposed model is different from the previous models lacking the concept of time series; (ii) the proposed integrated attribute selection method can find the core attributes and reduce high dimensional data; and (iii) the proposed model can generate the rules and mathematical formulas of financial distress for providing references to the investors and decision makers. The result shows that the proposed method is better than the listing classifiers under three criteria; hence, the proposed model has competitive advantages in predicting the financial distress of companies.

  4. An efficient model for auxiliary diagnosis of hepatocellular carcinoma based on gene expression programming.

    Science.gov (United States)

    Zhang, Li; Chen, Jiasheng; Gao, Chunming; Liu, Chuanmiao; Xu, Kuihua

    2018-03-16

    Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide. The early diagnosis of HCC is greatly helpful to achieve long-term disease-free survival. However, HCC is usually difficult to be diagnosed at an early stage. The aim of this study was to create the prediction model to diagnose HCC based on gene expression programming (GEP). GEP is an evolutionary algorithm and a domain-independent problem-solving technique. Clinical data show that six serum biomarkers, including gamma-glutamyl transferase, C-reaction protein, carcinoembryonic antigen, alpha-fetoprotein, carbohydrate antigen 153, and carbohydrate antigen 199, are related to HCC characteristics. In this study, the prediction of HCC was made based on these six biomarkers (195 HCC patients and 215 non-HCC controls) by setting up optimal joint models with GEP. The GEP model discriminated 353 out of 410 subjects, representing a determination coefficient of 86.28% (283/328) and 85.37% (70/82) for training and test sets, respectively. Compared to the results from the support vector machine, the artificial neural network, and the multilayer perceptron, GEP showed a better outcome. The results suggested that GEP modeling was a promising and excellent tool in diagnosis of hepatocellular carcinoma, and it could be widely used in HCC auxiliary diagnosis. Graphical abstract The process to establish an efficient model for auxiliary diagnosis of hepatocellular carcinoma.

  5. Alternative-splicing in the exon-10 region of GABA(A receptor beta(2 subunit gene: relationships between novel isoforms and psychotic disorders.

    Directory of Open Access Journals (Sweden)

    Cunyou Zhao

    Full Text Available BACKGROUND: Non-coding single nucleotide polymorphisms (SNPs in GABRB2, the gene for beta(2-subunit of gamma-aminobutyric acid type A (GABA(A receptor, have been associated with schizophrenia (SCZ and quantitatively correlated to mRNA expression and alternative splicing. METHODS AND FINDINGS: Expression of the Exon 10 region of GABRB2 from minigene constructs revealed this region to be an "alternative splicing hotspot" that readily gave rise to differently spliced isoforms depending on intron sequences. This led to a search in human brain cDNA libraries, and the discovery of two novel isoforms, beta(2S1 and beta(2S2, bearing variations in the neighborhood of Exon-10. Quantitative real-time PCR analysis of postmortem brain samples showed increased beta(2S1 expression and decreased beta(2S2 expression in both SCZ and bipolar disorder (BPD compared to controls. Disease-control differences were significantly correlated with SNP rs187269 in BPD males for both beta(2S1 and beta(2S2 expressions, and significantly correlated with SNPs rs2546620 and rs187269 in SCZ males for beta(2S2 expression. Moreover, site-directed mutagenesis indicated that Thr(365, a potential phosphorylation site in Exon-10, played a key role in determining the time profile of the ATP-dependent electrophysiological current run-down. CONCLUSION: This study therefore provided experimental evidence for the importance of non-coding sequences in the Exon-10 region in GABRB2 with respect to beta(2-subunit splicing diversity and the etiologies of SCZ and BPD.

  6. Nuclear proliferation and civilian nuclear power: report of the Nonproliferation Alternative Systems Assessment Program. Volume VII. International perspectives

    International Nuclear Information System (INIS)

    1979-12-01

    The purpose of this volume is to assess the proliferation vulnerabilities of the present deployment of civilian nuclear-power systems within the current nonproliferation regime and, in light of their prospective deployment, to consider technical and institutional measures and alternatives which may contribute to an improved regime in which nuclear power could play a significant part. An assessment of these measures must include consideration of their nonproliferation effectiveness as well as their bearing upon energy security, and their operational, economic, and political implications. The nature of these considerations can provide some measure of their likely acceptability to various nations. While any final assessment of such measures and alternatives would have to examine the circumstances particular to each nation, it is hoped that the more generic assessments conducted here will be useful in suggesting guidelines for developing an improved nonproliferation regime which also helps to meet nuclear-energy needs. One chapter outlines the existing nonproliferation regime, including the Treaty for the Non-Proliferation of Nuclear Weapons (NPT), International Atomic Energy Agency (IAEA) safeguards, bilateral and multilateral requirements for agreements of cooperation and transfers of technology, and existing provisons for sanctions for violation of nonproliferation commitments. The chapter then proceeds to an assessment of various alternatives for providing assurance of fuel supply in light of this current regime. Another chapter examines a set of technical and institutional measures and alternatives for various components of once-through and closed fuel cycles. The components of the once-through fuel cycle assessed are enrichment services and spent-fuel management; the components of closed fuel cycles assessed are reprocessing and plutonium management and fast-breeder reactor (FBR) deployment

  7. TCR Signal Strength Regulates Akt Substrate Specificity To Induce Alternate Murine Th and T Regulatory Cell Differentiation Programs.

    Science.gov (United States)

    Hawse, William F; Boggess, William C; Morel, Penelope A

    2017-07-15

    The Akt/mTOR pathway is a key driver of murine CD4 + T cell differentiation, and induction of regulatory T (Treg) cells results from low TCR signal strength and low Akt/mTOR signaling. However, strong TCR signals induce high Akt activity that promotes Th cell induction. Yet, it is unclear how Akt controls alternate T cell fate decisions. We find that the strength of the TCR signal results in differential Akt enzymatic activity. Surprisingly, the Akt substrate networks associated with T cell fate decisions are qualitatively different. Proteomic profiling of Akt signaling networks during Treg versus Th induction demonstrates that Akt differentially regulates RNA processing and splicing factors to drive T cell differentiation. Interestingly, heterogeneous nuclear ribonucleoprotein (hnRNP) L or hnRNP A1 are Akt substrates during Treg induction and have known roles in regulating the stability and splicing of key mRNAs that code for proteins in the canonical TCR signaling pathway, including CD3ζ and CD45. Functionally, inhibition of Akt enzymatic activity results in the dysregulation of splicing during T cell differentiation, and knockdown of hnRNP L or hnRNP A1 results in the lower induction of Treg cells. Together, this work suggests that a switch in substrate specificity coupled to the phosphorylation status of Akt may lead to alternative cell fates and demonstrates that proteins involved with alternative splicing are important factors in T cell fate decisions. Copyright © 2017 by The American Association of Immunologists, Inc.

  8. The immediate early gene product EGR1 and polycomb group proteins interact in epigenetic programming during chondrogenesis.

    Directory of Open Access Journals (Sweden)

    Frank Spaapen

    Full Text Available Initiation of and progression through chondrogenesis is driven by changes in the cellular microenvironment. At the onset of chondrogenesis, resting mesenchymal stem cells are mobilized in vivo and a complex, step-wise chondrogenic differentiation program is initiated. Differentiation requires coordinated transcriptomic reprogramming and increased progenitor proliferation; both processes require chromatin remodeling. The nature of early molecular responses that relay differentiation signals to chromatin is poorly understood. We here show that immediate early genes are rapidly and transiently induced in response to differentiation stimuli in vitro. Functional ablation of the immediate early factor EGR1 severely deregulates expression of key chondrogenic control genes at the onset of differentiation. In addition, differentiating cells accumulate DNA damage, activate a DNA damage response and undergo a cell cycle arrest and prevent differentiation associated hyper-proliferation. Failed differentiation in the absence of EGR1 affects global acetylation and terminates in overall histone hypermethylation. We report novel molecular connections between EGR1 and Polycomb Group function: Polycomb associated histone H3 lysine27 trimethylation (H3K27me3 blocks chromatin access of EGR1. In addition, EGR1 ablation results in abnormal Ezh2 and Bmi1 expression. Consistent with this functional interaction, we identify a number of co-regulated targets genes in a chondrogenic gene network. We here describe an important role for EGR1 in early chondrogenic epigenetic programming to accommodate early gene-environment interactions in chondrogenesis.

  9. Alternative security

    International Nuclear Information System (INIS)

    Weston, B.H.

    1990-01-01

    This book contains the following chapters: The Military and Alternative Security: New Missions for Stable Conventional Security; Technology and Alternative Security: A Cherished Myth Expires; Law and Alternative Security: Toward a Just World Peace; Politics and Alternative Security: Toward a More Democratic, Therefore More Peaceful, World; Economics and Alternative Security: Toward a Peacekeeping International Economy; Psychology and Alternative Security: Needs, Perceptions, and Misperceptions; Religion and Alternative Security: A Prophetic Vision; and Toward Post-Nuclear Global Security: An Overview

  10. Effects of Metabolic Programming on Juvenile Play Behavior and Gene Expression in the Prefrontal Cortex of Rats.

    Science.gov (United States)

    Hehar, Harleen; Ma, Irene; Mychasiuk, Richelle

    2016-01-01

    Early developmental processes, such as metabolic programming, can provide cues to an organism, which allow it to make modifications that are predicted to be beneficial for survival. Similarly, social play has a multifaceted role in promoting survival and fitness of animals. Play is a complex behavior that is greatly influenced by motivational and reward circuits, as well as the energy reserves and metabolism of an organism. This study examined the association between metabolic programming and juvenile play behavior in an effort to further elucidate insight into the consequences that early adaptions have on developmental trajectories. The study also examined changes in expression of four genes (Drd2, IGF1, Opa1, and OxyR) in the prefrontal cortex known to play significant roles in reward, bioenergetics, and social-emotional functioning. Using four distinct variations in developmental programming (high-fat diet, caloric restriction, exercise, or high-fat diet combined with exercise), we found that dietary programming (high-fat diet vs. caloric restriction) had the greatest impact on play behavior and gene expression. However, exercise also induced changes in both measures. This study demonstrates that metabolic programming can alter neural circuits and bioenergetics involved in play behavior, thus providing new insights into mechanisms that allow programming to influence the evolutionary success of an organism. © 2016 S. Karger AG, Basel.

  11. Vehicle Design Evaluation Program (VDEP). A computer program for weight sizing, economic, performance and mission analysis of fuel-conservative aircraft, multibodied aircraft and large cargo aircraft using both JP and alternative fuels

    Science.gov (United States)

    Oman, B. H.

    1977-01-01

    The NASA Langley Research Center vehicle design evaluation program (VDEP-2) was expanded by (1) incorporating into the program a capability to conduct preliminary design studies on subsonic commercial transport type aircraft using both JP and such alternate fuels as hydrogen and methane;(2) incorporating an aircraft detailed mission and performance analysis capability; and (3) developing and incorporating an external loads analysis capability. The resulting computer program (VDEP-3) provides a preliminary design tool that enables the user to perform integrated sizing, structural analysis, and cost studies on subsonic commercial transport aircraft. Both versions of the VDEP-3 Program which are designated preliminary Analysis VDEP-3 and detailed Analysis VDEP utilize the same vehicle sizing subprogram which includes a detailed mission analysis capability, as well as a geometry and weight analysis for multibodied configurations.

  12. Beliefs About a Complementary and Alternative Therapy-Based Chronic Pain Management Program for a Medicaid Population.

    Science.gov (United States)

    Donovan, Elizabeth; Ranney, Megan L; Patry, Emily J; McKenzie, Michelle; Baird, Janette; Green, Traci C

    2017-09-01

    Rhode Island Medicaid offers high emergency department utilizers the opportunity to take part in the Chronic Pain Program, an integrated treatment approach that includes free complementary therapies (massage, chiropractic, and acupuncture). The aim of the current analysis was to understand beliefs about the Rhode Island Chronic Pain Program from the perspective of the patient receiving services, the provider delivering services, and the administrator implementing the program. A qualitative interview-based study. Patients (N = 24), providers (N = 13), and administrators (N = 11) who were already involved, or were eligible to be involved, in the Chronic Pain Program. Semistructured interviews were conducted to elicit information about experiences with the program. Transcriptions of audio recordings were analyzed according to principles of deductive thematic analysis. Patient interviews revealed five themes: 1) relationship between stress and pain, 2) trusting patient-provider relationships, 3) increased quality of life, 4) temporary pain relief, and 5) anxiety and discomfort associated with acupuncture. Provider interviews revealed three themes: 1) a way to reach the disenfranchised, 2) not enough visits with patients, and 3) opportunity to build relationships with patients. Administrator interviews revealed two themes: 1) a means to offer a range of support services to complicated patients and 2) unanswered questions over whether the program adequately serves patients with the greatest needs. Key stakeholders in this new initiative agree that the Rhode Island Chronic Pain Program shows promise and that the holistic approach may be a good match for this hard-to-reach population. © 2017 American Academy of Pain Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

  13. Typical Toddlers' Participation in "Just-in-Time" Programming of Vocabulary for Visual Scene Display Augmentative and Alternative Communication Apps on Mobile Technology: A Descriptive Study.

    Science.gov (United States)

    Holyfield, Christine; Drager, Kathryn; Light, Janice; Caron, Jessica Gosnell

    2017-08-15

    Augmentative and alternative communication (AAC) promotes communicative participation and language development for young children with complex communication needs. However, the motor, linguistic, and cognitive demands of many AAC technologies restrict young children's operational use of and influence over these technologies. The purpose of the current study is to better understand young children's participation in programming vocabulary "just in time" on an AAC application with minimized demands. A descriptive study was implemented to highlight the participation of 10 typically developing toddlers (M age: 16 months, range: 10-22 months) in just-in-time vocabulary programming in an AAC app with visual scene displays. All 10 toddlers participated in some capacity in adding new visual scene displays and vocabulary to the app just in time. Differences in participation across steps were observed, suggesting variation in the developmental demands of controls involved in vocabulary programming. Results from the current study provide clinical insights toward involving young children in AAC programming just in time and steps that may allow for more independent participation or require more scaffolding. Technology designed to minimize motor, cognitive, and linguistic demands may allow children to participate in programming devices at a younger age.

  14. Typical Toddlers' Participation in “Just-in-Time” Programming of Vocabulary for Visual Scene Display Augmentative and Alternative Communication Apps on Mobile Technology: A Descriptive Study

    Science.gov (United States)

    Drager, Kathryn; Light, Janice; Caron, Jessica Gosnell

    2017-01-01

    Purpose Augmentative and alternative communication (AAC) promotes communicative participation and language development for young children with complex communication needs. However, the motor, linguistic, and cognitive demands of many AAC technologies restrict young children's operational use of and influence over these technologies. The purpose of the current study is to better understand young children's participation in programming vocabulary “just in time” on an AAC application with minimized demands. Method A descriptive study was implemented to highlight the participation of 10 typically developing toddlers (M age: 16 months, range: 10–22 months) in just-in-time vocabulary programming in an AAC app with visual scene displays. Results All 10 toddlers participated in some capacity in adding new visual scene displays and vocabulary to the app just in time. Differences in participation across steps were observed, suggesting variation in the developmental demands of controls involved in vocabulary programming. Conclusions Results from the current study provide clinical insights toward involving young children in AAC programming just in time and steps that may allow for more independent participation or require more scaffolding. Technology designed to minimize motor, cognitive, and linguistic demands may allow children to participate in programming devices at a younger age. PMID:28586825

  15. Nuclear proliferation and civilian nuclear power. Report of the Nonproliferation Alternative Systems Assessment Program. Volume VII. International perspectives

    Energy Technology Data Exchange (ETDEWEB)

    1980-06-01

    The purpose of this volume is to assess the proliferation vulnerabilities of the present deployment of civilian nuclear-power systems within the current nonproliferation regime and, in light of their prospective deployment, to consider technical and institutional measures and alternatives which may contribute to an improved regime in which nuclear power could play a significant part. An assessment of these measures must include consideration of their nonproliferation effectiveness as well as their bearing upon energy security, and their operational, economic, and political implications. The nature of these considerations can provide some measure of their likely acceptability to various nations.

  16. Nuclear proliferation and civilian nuclear power. Report of the Nonproliferation Alternative Systems Assessment Program. Volume VII. International perspectives

    International Nuclear Information System (INIS)

    1980-06-01

    The purpose of this volume is to assess the proliferation vulnerabilities of the present deployment of civilian nuclear-power systems within the current nonproliferation regime and, in light of their prospective deployment, to consider technical and institutional measures and alternatives which may contribute to an improved regime in which nuclear power could play a significant part. An assessment of these measures must include consideration of their nonproliferation effectiveness as well as their bearing upon energy security, and their operational, economic, and political implications. The nature of these considerations can provide some measure of their likely acceptability to various nations

  17. Reverse engineering model structures for soil and ecosystem respiration: the potential of gene expression programming

    Directory of Open Access Journals (Sweden)

    I. Ilie

    2017-09-01

    Full Text Available Accurate model representation of land–atmosphere carbon fluxes is essential for climate projections. However, the exact responses of carbon cycle processes to climatic drivers often remain uncertain. Presently, knowledge derived from experiments, complemented by a steadily evolving body of mechanistic theory, provides the main basis for developing such models. The strongly increasing availability of measurements may facilitate new ways of identifying suitable model structures using machine learning. Here, we explore the potential of gene expression programming (GEP to derive relevant model formulations based solely on the signals present in data by automatically applying various mathematical transformations to potential predictors and repeatedly evolving the resulting model structures. In contrast to most other machine learning regression techniques, the GEP approach generates readable models that allow for prediction and possibly for interpretation. Our study is based on two cases: artificially generated data and real observations. Simulations based on artificial data show that GEP is successful in identifying prescribed functions, with the prediction capacity of the models comparable to four state-of-the-art machine learning methods (random forests, support vector machines, artificial neural networks, and kernel ridge regressions. Based on real observations we explore the responses of the different components of terrestrial respiration at an oak forest in south-eastern England. We find that the GEP-retrieved models are often better in prediction than some established respiration models. Based on their structures, we find previously unconsidered exponential dependencies of respiration on seasonal ecosystem carbon assimilation and water dynamics. We noticed that the GEP models are only partly portable across respiration components, the identification of a general terrestrial respiration model possibly prevented by equifinality issues. Overall

  18. Neonatal hyper- and hypothyroidism alter the myoglobin gene expression program in adulthood.

    Science.gov (United States)

    Souza, K de Picoli; Nunes, M T

    2014-08-01

    Myoglobin acts as an oxygen store and a reactive oxygen species acceptor in muscles. We examined myoglobin mRNA in rat cardiac ventricle and skeletal muscles during the first 42 days of life and the impact of transient neonatal hypo- and hyperthyroidism on the myoglobin gene expression pattern. Cardiac ventricle and skeletal muscles of Wistar rats at 7-42 days of life were quickly removed, and myoglobin mRNA was determined by Northern blot analysis. Rats were treated with propylthiouracil (5-10 mg/100 g) and triiodothyronine (0.5-50 µg/100 g) for 5, 15, or 30 days after birth to induce hypo- and hyperthyroidism and euthanized either just after treatment or at 90 days. During postnatal (P) days 7-28, the ventricle myoglobin mRNA remained unchanged, but it gradually increased in skeletal muscle (12-fold). Triiodothyronine treatment, from days P0-P5, increased the skeletal muscle myoglobin mRNA 1.5- to 4.5-fold; a 2.5-fold increase was observed in ventricle muscle, but only when triiodothyronine treatment was extended to day P15. Conversely, hypothyroidism at P5 markedly decreased (60%) ventricular myoglobin mRNA. Moreover, transient hyperthyroidism in the neonatal period increased ventricle myoglobin mRNA (2-fold), and decreased heart rate (5%), fast muscle myoglobin mRNA (30%) and body weight (20%) in adulthood. Transient hypothyroidism in the neonatal period also permanently decreased fast muscle myoglobin mRNA (30%) and body weight (14%). These results indicated that changes in triiodothyronine supply in the neonatal period alter the myoglobin expression program in ventricle and skeletal muscle, leading to specific physiological repercussions and alterations in other parameters in adulthood.

  19. Reverse engineering model structures for soil and ecosystem respiration: the potential of gene expression programming

    Science.gov (United States)

    Ilie, Iulia; Dittrich, Peter; Carvalhais, Nuno; Jung, Martin; Heinemeyer, Andreas; Migliavacca, Mirco; Morison, James I. L.; Sippel, Sebastian; Subke, Jens-Arne; Wilkinson, Matthew; Mahecha, Miguel D.

    2017-09-01

    Accurate model representation of land-atmosphere carbon fluxes is essential for climate projections. However, the exact responses of carbon cycle processes to climatic drivers often remain uncertain. Presently, knowledge derived from experiments, complemented by a steadily evolving body of mechanistic theory, provides the main basis for developing such models. The strongly increasing availability of measurements may facilitate new ways of identifying suitable model structures using machine learning. Here, we explore the potential of gene expression programming (GEP) to derive relevant model formulations based solely on the signals present in data by automatically applying various mathematical transformations to potential predictors and repeatedly evolving the resulting model structures. In contrast to most other machine learning regression techniques, the GEP approach generates readable models that allow for prediction and possibly for interpretation. Our study is based on two cases: artificially generated data and real observations. Simulations based on artificial data show that GEP is successful in identifying prescribed functions, with the prediction capacity of the models comparable to four state-of-the-art machine learning methods (random forests, support vector machines, artificial neural networks, and kernel ridge regressions). Based on real observations we explore the responses of the different components of terrestrial respiration at an oak forest in south-eastern England. We find that the GEP-retrieved models are often better in prediction than some established respiration models. Based on their structures, we find previously unconsidered exponential dependencies of respiration on seasonal ecosystem carbon assimilation and water dynamics. We noticed that the GEP models are only partly portable across respiration components, the identification of a general terrestrial respiration model possibly prevented by equifinality issues. Overall, GEP is a promising

  20. Neonatal hyper- and hypothyroidism alter the myoglobin gene expression program in adulthood

    International Nuclear Information System (INIS)

    Picoli Souza, K. de; Nunes, M.T.

    2014-01-01

    Myoglobin acts as an oxygen store and a reactive oxygen species acceptor in muscles. We examined myoglobin mRNA in rat cardiac ventricle and skeletal muscles during the first 42 days of life and the impact of transient neonatal hypo- and hyperthyroidism on the myoglobin gene expression pattern. Cardiac ventricle and skeletal muscles of Wistar rats at 7-42 days of life were quickly removed, and myoglobin mRNA was determined by Northern blot analysis. Rats were treated with propylthiouracil (5-10 mg/100 g) and triiodothyronine (0.5-50 µg/100 g) for 5, 15, or 30 days after birth to induce hypo- and hyperthyroidism and euthanized either just after treatment or at 90 days. During postnatal (P) days 7-28, the ventricle myoglobin mRNA remained unchanged, but it gradually increased in skeletal muscle (12-fold). Triiodothyronine treatment, from days P0-P5, increased the skeletal muscle myoglobin mRNA 1.5- to 4.5-fold; a 2.5-fold increase was observed in ventricle muscle, but only when triiodothyronine treatment was extended to day P15. Conversely, hypothyroidism at P5 markedly decreased (60%) ventricular myoglobin mRNA. Moreover, transient hyperthyroidism in the neonatal period increased ventricle myoglobin mRNA (2-fold), and decreased heart rate (5%), fast muscle myoglobin mRNA (30%) and body weight (20%) in adulthood. Transient hypothyroidism in the neonatal period also permanently decreased fast muscle myoglobin mRNA (30%) and body weight (14%). These results indicated that changes in triiodothyronine supply in the neonatal period alter the myoglobin expression program in ventricle and skeletal muscle, leading to specific physiological repercussions and alterations in other parameters in adulthood

  1. Neonatal hyper- and hypothyroidism alter the myoglobin gene expression program in adulthood

    Energy Technology Data Exchange (ETDEWEB)

    Picoli Souza, K. de [Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados, Dourados, MS (Brazil); Nunes, M.T. [Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade de São Paulo, São Paulo, SP (Brazil)

    2014-06-24

    Myoglobin acts as an oxygen store and a reactive oxygen species acceptor in muscles. We examined myoglobin mRNA in rat cardiac ventricle and skeletal muscles during the first 42 days of life and the impact of transient neonatal hypo- and hyperthyroidism on the myoglobin gene expression pattern. Cardiac ventricle and skeletal muscles of Wistar rats at 7-42 days of life were quickly removed, and myoglobin mRNA was determined by Northern blot analysis. Rats were treated with propylthiouracil (5-10 mg/100 g) and triiodothyronine (0.5-50 µg/100 g) for 5, 15, or 30 days after birth to induce hypo- and hyperthyroidism and euthanized either just after treatment or at 90 days. During postnatal (P) days 7-28, the ventricle myoglobin mRNA remained unchanged, but it gradually increased in skeletal muscle (12-fold). Triiodothyronine treatment, from days P0-P5, increased the skeletal muscle myoglobin mRNA 1.5- to 4.5-fold; a 2.5-fold increase was observed in ventricle muscle, but only when triiodothyronine treatment was extended to day P15. Conversely, hypothyroidism at P5 markedly decreased (60%) ventricular myoglobin mRNA. Moreover, transient hyperthyroidism in the neonatal period increased ventricle myoglobin mRNA (2-fold), and decreased heart rate (5%), fast muscle myoglobin mRNA (30%) and body weight (20%) in adulthood. Transient hypothyroidism in the neonatal period also permanently decreased fast muscle myoglobin mRNA (30%) and body weight (14%). These results indicated that changes in triiodothyronine supply in the neonatal period alter the myoglobin expression program in ventricle and skeletal muscle, leading to specific physiological repercussions and alterations in other parameters in adulthood.

  2. Neonatal hyper- and hypothyroidism alter the myoglobin gene expression program in adulthood

    Directory of Open Access Journals (Sweden)

    K. de Picoli Souza

    2014-08-01

    Full Text Available Myoglobin acts as an oxygen store and a reactive oxygen species acceptor in muscles. We examined myoglobin mRNA in rat cardiac ventricle and skeletal muscles during the first 42 days of life and the impact of transient neonatal hypo- and hyperthyroidism on the myoglobin gene expression pattern. Cardiac ventricle and skeletal muscles of Wistar rats at 7-42 days of life were quickly removed, and myoglobin mRNA was determined by Northern blot analysis. Rats were treated with propylthiouracil (5-10 mg/100 g and triiodothyronine (0.5-50 µg/100 g for 5, 15, or 30 days after birth to induce hypo- and hyperthyroidism and euthanized either just after treatment or at 90 days. During postnatal (P days 7-28, the ventricle myoglobin mRNA remained unchanged, but it gradually increased in skeletal muscle (12-fold. Triiodothyronine treatment, from days P0-P5, increased the skeletal muscle myoglobin mRNA 1.5- to 4.5-fold; a 2.5-fold increase was observed in ventricle muscle, but only when triiodothyronine treatment was extended to day P15. Conversely, hypothyroidism at P5 markedly decreased (60% ventricular myoglobin mRNA. Moreover, transient hyperthyroidism in the neonatal period increased ventricle myoglobin mRNA (2-fold, and decreased heart rate (5%, fast muscle myoglobin mRNA (30% and body weight (20% in adulthood. Transient hypothyroidism in the neonatal period also permanently decreased fast muscle myoglobin mRNA (30% and body weight (14%. These results indicated that changes in triiodothyronine supply in the neonatal period alter the myoglobin expression program in ventricle and skeletal muscle, leading to specific physiological repercussions and alterations in other parameters in adulthood.

  3. Production of alcohols and other oxygenates from fossil fuels and renewables : final report for IEA Alternative Motor Fuels Agreement Program of research and development on alternative motor fuels, Annex 4/Phase 2

    Energy Technology Data Exchange (ETDEWEB)

    Vancea, L. (comp.) [Natural Resources Canada, Ottawa, ON (Canada)

    1995-07-01

    The objective of the International Energy Agency's (IEA's) Alternative Motor Fuels Agreement Program was to exchange information on the production of alcohols and other oxygenates between 6 participating countries including Canada, Italy, Japan, New Zealand, Sweden and the United States. Various production methods were reviewed in an effort to identify potential areas of cooperative research programs. The original scope was to examine the production of alcohols and other oxygenates from fossil fuels only, but some participants examined their production from renewables. This report provided a brief description of the Annex and the list of participants. It presented the Operating Agent's Report and contained a summary of the contributions submitted by participating countries by topic. In Canada, Iogen of Ottawa, Ontario has conducted a study on the energy, carbon and economic budgets estimated for wheat grain, corn grain, wheat straw, and switchgrass. Iogen has developed a process for fermenting wheat straw and switchgrass into ethanol. Most research has focused on enzymatic hydrolysis processes because of the low yields inherent in dilute acid hydrolysis processes. Enzymes hydrolyze the cellulose to glucose without producing any degradation products, thereby yielding high quantity products with no toxicity. Future bioethanol production will probably be cellulosic-based rather than grain-based. refs., tabs., figs.

  4. Production of alcohols and other oxygenates from fossil fuels and renewables : final report for IEA Alternative Motor Fuels Agreement Program of research and development on alternative motor fuels, Annex 4/Phase 2

    Energy Technology Data Exchange (ETDEWEB)

    Vancea, L [Natural Resources Canada, Ottawa, ON (Canada)

    1995-07-01

    The objective of the International Energy Agency's (IEA's) Alternative Motor Fuels Agreement Program was to exchange information on the production of alcohols and other oxygenates between 6 participating countries including Canada, Italy, Japan, New Zealand, Sweden and the United States. Various production methods were reviewed in an effort to identify potential areas of cooperative research programs. The original scope was to examine the production of alcohols and other oxygenates from fossil fuels only, but some participants examined their production from renewables. This report provided a brief description of the Annex and the list of participants. It presented the Operating Agent's Report and contained a summary of the contributions submitted by participating countries by topic. In Canada, Iogen of Ottawa, Ontario has conducted a study on the energy, carbon and economic budgets estimated for wheat grain, corn grain, wheat straw, and switchgrass. Iogen has developed a process for fermenting wheat straw and switchgrass into ethanol. Most research has focused on enzymatic hydrolysis processes because of the low yields inherent in dilute acid hydrolysis processes. Enzymes hydrolyze the cellulose to glucose without producing any degradation products, thereby yielding high quantity products with no toxicity. Future bioethanol production will probably be cellulosic-based rather than grain-based. refs., tabs., figs.

  5. Mentor Advice Giving in an Alternative Certification Program for Secondary Science Teaching: Opportunities and Roadblocks in Developing a Knowledge Base for Teaching

    Science.gov (United States)

    Upson Bradbury, Leslie; Koballa, Thomas R., Jr.

    2007-12-01

    Mentoring is often an important component of alternative certification programs, yet little is known about what novices learn about science teaching through mentoring relationships. This study investigated the advice given by two mentor science teachers to their protégés. Findings indicate that mentors gave more advice related to general pedagogical knowledge than science-specific pedagogical content knowledge. Specifically, there was little to no advice related to the topics of inquiry, the nature of science, or the development of scientific literacy. Implications call for an increase in communication between university teacher education programs and school-based mentors, the development of benchmarks to help guide mentor-protégé interactions, and the importance of a multiyear induction process.

  6. Real-time PCR based on SYBR-Green I fluorescence: An alternative to the TaqMan assay for a relative quantification of gene rearrangements, gene amplifications and micro gene deletions

    Directory of Open Access Journals (Sweden)

    Puisieux Alain

    2003-10-01

    Full Text Available Abstract Background Real-time PCR is increasingly being adopted for RNA quantification and genetic analysis. At present the most popular real-time PCR assay is based on the hybridisation of a dual-labelled probe to the PCR product, and the development of a signal by loss of fluorescence quenching as PCR degrades the probe. Though this so-called 'TaqMan' approach has proved easy to optimise in practice, the dual-labelled probes are relatively expensive. Results We have designed a new assay based on SYBR-Green I binding that is quick, reliable, easily optimised and compares well with the published assay. Here we demonstrate its general applicability by measuring copy number in three different genetic contexts; the quantification of a gene rearrangement (T-cell receptor excision circles (TREC in peripheral blood mononuclear cells; the detection and quantification of GLI, MYC-C and MYC-N gene amplification in cell lines and cancer biopsies; and detection of deletions in the OPA1 gene in dominant optic atrophy. Conclusion Our assay has important clinical applications, providing accurate diagnostic results in less time, from less biopsy material and at less cost than assays currently employed such as FISH or Southern blotting.

  7. Transcriptional regulatory program in wild-type and retinoblastoma gene-deficient mouse embryonic fibroblasts during adipocyte differentiation

    DEFF Research Database (Denmark)

    Hakim-Weber, Robab; Krogsdam, Anne-M; Jørgensen, Claus

    2011-01-01

    Although many molecular regulators of adipogenesis have been identified a comprehensive catalogue of components is still missing. Recent studies showed that the retinoblastoma protein (pRb) was expressed in the cell cycle and late cellular differentiation phase during adipogenesis. To investigate...... this dual role of pRb in the early and late stages of adipogenesis we used microarrays to perform a comprehensive systems-level analysis of the common transcriptional program of the classic 3T3-L1 preadipocyte cell line, wild-type mouse embryonic fibroblasts (MEFs), and retinoblastoma gene-deficient MEFs...... of experimental data and computational analyses pinpointed a feedback-loop between Pparg and Foxo1.To analyze the effects of the retinoblastoma protein at the transcriptional level we chose a perturbated system (Rb-/- MEFs) for comparison to the transcriptional program of wild-type MEFs. Gene ontology analysis...

  8. Efficiency of Do-It-Yourself Slide-Tape Programs as an Alternative to the Lecture in Medical Biochemistry

    Science.gov (United States)

    Baggott, James; And Others

    1977-01-01

    Evidence suggests that a well-developed lecture script on a topic in medical biochemistry can quickly and easily be converted into an effective slide-tape program that is as educationally effective and well-received as one that is painstakingly tailored to the nature of the medium. (LBH)

  9. Distinct gene regulatory programs define the inhibitory effects of liver X receptors and PPARG on cancer cell proliferation.

    Science.gov (United States)

    Savic, Daniel; Ramaker, Ryne C; Roberts, Brian S; Dean, Emma C; Burwell, Todd C; Meadows, Sarah K; Cooper, Sara J; Garabedian, Michael J; Gertz, Jason; Myers, Richard M

    2016-07-11

    The liver X receptors (LXRs, NR1H2 and NR1H3) and peroxisome proliferator-activated receptor gamma (PPARG, NR1C3) nuclear receptor transcription factors (TFs) are master regulators of energy homeostasis. Intriguingly, recent studies suggest that these metabolic regulators also impact tumor cell proliferation. However, a comprehensive temporal molecular characterization of the LXR and PPARG gene regulatory responses in tumor cells is still lacking. To better define the underlying molecular processes governing the genetic control of cellular growth in response to extracellular metabolic signals, we performed a comprehensive, genome-wide characterization of the temporal regulatory cascades mediated by LXR and PPARG signaling in HT29 colorectal cancer cells. For this analysis, we applied a multi-tiered approach that incorporated cellular phenotypic assays, gene expression profiles, chromatin state dynamics, and nuclear receptor binding patterns. Our results illustrate that the activation of both nuclear receptors inhibited cell proliferation and further decreased glutathione levels, consistent with increased cellular oxidative stress. Despite a common metabolic reprogramming, the gene regulatory network programs initiated by these nuclear receptors were widely distinct. PPARG generated a rapid and short-term response while maintaining a gene activator role. By contrast, LXR signaling was prolonged, with initial, predominantly activating functions that transitioned to repressive gene regulatory activities at late time points. Through the use of a multi-tiered strategy that integrated various genomic datasets, our data illustrate that distinct gene regulatory programs elicit common phenotypic effects, highlighting the complexity of the genome. These results further provide a detailed molecular map of metabolic reprogramming in cancer cells through LXR and PPARG activation. As ligand-inducible TFs, these nuclear receptors can potentially serve as attractive therapeutic

  10. Energy alternatives

    International Nuclear Information System (INIS)

    1981-01-01

    English. A special committe of the Canadian House of Commons was established on 23 May 1980 to investigate the use of alternative energy sources such as 'gasohol', liquified coal, solar energy, methanol, wind and tidal power, biomass, and propane. In its final report, the committee envisions an energy system for Canada based on hydrogen and electricity, using solar and geothermal energy for low-grade heat. The committe was not able to say which method of generating electricty would dominate in the next century, although it recommends that fossil fuels should not be used. The fission process is not specifically discussed, but the outlook for fusion was investigated, and continued governmental support of fusion research is recommended. The report proposes some improvements in governmental energy organizations and programs

  11. Accident analysis for transuranic waste management alternatives in the U.S. Department of Energy waste management program

    International Nuclear Information System (INIS)

    Nabelssi, B.; Mueller, C.; Roglans-Ribas, J.; Folga, S.; Tompkins, M.; Jackson, R.

    1995-01-01

    Preliminary accident analyses and radiological source term evaluations have been conducted for transuranic waste (TRUW) as part of the US Department of Energy (DOE) effort to manage storage, treatment, and disposal of radioactive wastes at its various sites. The approach to assessing radiological releases from facility accidents was developed in support of the Office of Environmental Management Programmatic Environmental Impact Statement (EM PEIS). The methodology developed in this work is in accordance with the latest DOE guidelines, which consider the spectrum of possible accident scenarios in the implementation of various actions evaluated in an EIS. The radiological releases from potential risk-dominant accidents in storage and treatment facilities considered in the EM PEIS TRUW alternatives are described in this paper. The results show that significant releases can be predicted for only the most severe and extremely improbable accidents sequences

  12. Evaluating bacterial gene-finding HMM structures as probabilistic logic programs

    DEFF Research Database (Denmark)

    Mørk, Søren; Holmes, Ian

    2012-01-01

    , a probabilistic dialect of Prolog. Results: We evaluate Hidden Markov Model structures for bacterial protein-coding gene potential, including a simple null model structure, three structures based on existing bacterial gene finders and two novel model structures. We test standard versions as well as ADPH length...

  13. Alternative additives; Alternative additiver

    Energy Technology Data Exchange (ETDEWEB)

    2007-08-15

    In this project a number of industrial and agricultural waste products have been characterised and evaluated in terms of alkali-getter performance. The intended use is for biomass-fired power stations aiming at reducing corrosion or slagging related problems. The following products have been obtained, characterised and evaluated: 1) Brewery draff 2) Danish de-gassed manure 3) Paper sludge 4) Moulding sand 5) Spent bleaching earth 6) Anorthosite 7) Sand 8) Clay-sludge. Most of the above alternative additive candidates are deemed unsuitable due to insufficient chemical effect and/or expensive requirements for pre-treatment (such as drying and transportation). 3 products were selected for full-scale testing: de-gassed manure, spent bleaching earth and clay slugde. The full scale tests were undertaken at the biomass-fired power stations in Koege, Slagelse and Ensted. Spent bleaching earth (SBE) and clay sludge were the only tested additive candidates that had a proven ability to react with KCl, to thereby reduce Cl-concentrations in deposits, and reduce the deposit flux to superheater tubes. Their performance was shown to nearly as good as commercial additives. De-gassed manure, however, did not evaluate positively due to inhibiting effects of Ca in the manure. Furthermore, de-gassed manure has a high concentration of heavy metals, which imposes a financial burden with regard to proper disposal of the ash by-products. Clay-sludge is a wet clay slurring, and drying and transportation of this product entails substantial costs. Spent bleaching does not require much pre-treatment and is therefore the most promising alternative additive. On the other hand, bleaching earth contains residual plant oil which means that a range of legislation relating to waste combustion comes into play. Not least a waste combustion fee of 330 DKK/tonne. For all alternative (and commercial) additives disposal costs of the increase ash by-products represents a significant cost. This is

  14. Nuclear proliferation and civilian nuclear power. Report of the Nonproliferation Alternative Systems Assessment Program. Volume II. Proliferation resistance

    International Nuclear Information System (INIS)

    1980-06-01

    The purpose of this volume is limited to an assessment of the relative effects that particular choices of nuclear-power systems, for whatever reasons, may have on the possible spread of nuclear-weapons capabilities. This volume addresses the concern that non-nuclear-weapons states may be able to initiate efforts to acquire or to improve nuclear-weapons capabilities through civilian nuclear-power programs; it also addresses the concern that subnational groups may obtain and abuse the nuclear materials or facilities of such programs, whether in nuclear-weapons states (NWS's) or nonnuclear-weapons states (NNW's). Accordingly, this volume emphasizes one important factor in such decisions, the resistance of nuclear-power systems to the proliferation of nuclear-weapons capabilities

  15. The U.S. Marine Corps Combined Action Program (CAP): A Proposed Alternative Strategy for the Vietnam War

    Science.gov (United States)

    2002-05-01

    Vietnamese men abstained from premarital sex, they openly practiced mutual masturbation . 62 In western culture, a man’s business was a man’s business, but... practice of integrating Marine with native forces marked the beginning of a nearly six year endeavor entitled the Combined Action Program or CAP. Embraced...chain of command. While the CAP platoons drew from infantry battalions primarily, their ties to them remained administrative and informal in practice

  16. Nuclear proliferation and civilian nuclear power: report of the Nonproliferation Alternative Systems Assessment Program. Volume IV. Commercial potential

    International Nuclear Information System (INIS)

    1979-12-01

    Volume IV 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

  17. Expression profiling of FLOWERING LOCUS T-like gene in alternate bearing 'Hass' avocado trees suggests a role for PaFT in avocado flower induction.

    Directory of Open Access Journals (Sweden)

    Dafna Ziv

    Full Text Available In many perennials, heavy fruit load on a shoot decreases the ability of the plant to undergo floral induction in the following spring, resulting in a pattern of crop production known as alternate bearing. Here, we studied the effects of fruit load on floral determination in 'Hass' avocado (Persea americana. De-fruiting experiments initially confirmed the negative effects of fruit load on return to flowering. Next, we isolated a FLOWERING LOCUS T-like gene, PaFT, hypothesized to act as a phloem-mobile florigen signal and examined its expression profile in shoot tissues of on (fully loaded and off (fruit-lacking trees. Expression analyses revealed a strong peak in PaFT transcript levels in leaves of off trees from the end of October through November, followed by a return to starting levels. Moreover and concomitant with inflorescence development, only off buds displayed up-regulation of the floral identity transcripts PaAP1 and PaLFY, with significant variation being detected from October and November, respectively. Furthermore, a parallel microscopic study of off apical buds revealed the presence of secondary inflorescence axis structures that only appeared towards the end of November. Finally, ectopic expression of PaFT in Arabidopsis resulted in early flowering transition. Together, our data suggests a link between increased PaFT expression observed during late autumn and avocado flower induction. Furthermore, our results also imply that, as in the case of other crop trees, fruit-load might affect flowering by repressing the expression of PaFT in the leaves. Possible mechanism(s by which fruit crop might repress PaFT expression, are discussed.

  18. Expression Profiling of FLOWERING LOCUS T-Like Gene in Alternate Bearing ‘Hass' Avocado Trees Suggests a Role for PaFT in Avocado Flower Induction

    Science.gov (United States)

    Ziv, Dafna; Zviran, Tali; Zezak, Oshrat; Samach, Alon; Irihimovitch, Vered

    2014-01-01

    In many perennials, heavy fruit load on a shoot decreases the ability of the plant to undergo floral induction in the following spring, resulting in a pattern of crop production known as alternate bearing. Here, we studied the effects of fruit load on floral determination in ‘Hass' avocado (Persea americana). De-fruiting experiments initially confirmed the negative effects of fruit load on return to flowering. Next, we isolated a FLOWERING LOCUS T-like gene, PaFT, hypothesized to act as a phloem-mobile florigen signal and examined its expression profile in shoot tissues of on (fully loaded) and off (fruit-lacking) trees. Expression analyses revealed a strong peak in PaFT transcript levels in leaves of off trees from the end of October through November, followed by a return to starting levels. Moreover and concomitant with inflorescence development, only off buds displayed up-regulation of the floral identity transcripts PaAP1 and PaLFY, with significant variation being detected from October and November, respectively. Furthermore, a parallel microscopic study of off apical buds revealed the presence of secondary inflorescence axis structures that only appeared towards the end of November. Finally, ectopic expression of PaFT in Arabidopsis resulted in early flowering transition. Together, our data suggests a link between increased PaFT expression observed during late autumn and avocado flower induction. Furthermore, our results also imply that, as in the case of other crop trees, fruit-load might affect flowering by repressing the expression of PaFT in the leaves. Possible mechanism(s) by which fruit crop might repress PaFT expression, are discussed. PMID:25330324

  19. Expression profiling of FLOWERING LOCUS T-like gene in alternate bearing 'Hass' avocado trees suggests a role for PaFT in avocado flower induction.

    Science.gov (United States)

    Ziv, Dafna; Zviran, Tali; Zezak, Oshrat; Samach, Alon; Irihimovitch, Vered

    2014-01-01

    In many perennials, heavy fruit load on a shoot decreases the ability of the plant to undergo floral induction in the following spring, resulting in a pattern of crop production known as alternate bearing. Here, we studied the effects of fruit load on floral determination in 'Hass' avocado (Persea americana). De-fruiting experiments initially confirmed the negative effects of fruit load on return to flowering. Next, we isolated a FLOWERING LOCUS T-like gene, PaFT, hypothesized to act as a phloem-mobile florigen signal and examined its expression profile in shoot tissues of on (fully loaded) and off (fruit-lacking) trees. Expression analyses revealed a strong peak in PaFT transcript levels in leaves of off trees from the end of October through November, followed by a return to starting levels. Moreover and concomitant with inflorescence development, only off buds displayed up-regulation of the floral identity transcripts PaAP1 and PaLFY, with significant variation being detected from October and November, respectively. Furthermore, a parallel microscopic study of off apical buds revealed the presence of secondary inflorescence axis structures that only appeared towards the end of November. Finally, ectopic expression of PaFT in Arabidopsis resulted in early flowering transition. Together, our data suggests a link between increased PaFT expression observed during late autumn and avocado flower induction. Furthermore, our results also imply that, as in the case of other crop trees, fruit-load might affect flowering by repressing the expression of PaFT in the leaves. Possible mechanism(s) by which fruit crop might repress PaFT expression, are discussed.

  20. Set points, settling points and some alternative models: theoretical options to understand how genes and environments combine to regulate body adiposity

    Directory of Open Access Journals (Sweden)

    John R. Speakman

    2011-11-01

    Full Text Available The close correspondence between energy intake and expenditure over prolonged time periods, coupled with an apparent protection of the level of body adiposity in the face of perturbations of energy balance, has led to the idea that body fatness is regulated via mechanisms that control intake and energy expenditure. Two models have dominated the discussion of how this regulation might take place. The set point model is rooted in physiology, genetics and molecular biology, and suggests that there is an active feedback mechanism linking adipose tissue (stored energy to intake and expenditure via a set point, presumably encoded in the brain. This model is consistent with many of the biological aspects of energy balance, but struggles to explain the many significant environmental and social influences on obesity, food intake and physical activity. More importantly, the set point model does not effectively explain the ‘obesity epidemic’ – the large increase in body weight and adiposity of a large proportion of individuals in many countries since the 1980s. An alternative model, called the settling point model, is based on the idea that there is passive feedback between the size of the body stores and aspects of expenditure. This model accommodates many of the social and environmental characteristics of energy balance, but struggles to explain some of the biological and genetic aspects. The shortcomings of these two models reflect their failure to address the gene-by-environment interactions that dominate the regulation of body weight. We discuss two additional models – the general intake model and the dual intervention point model – that address this issue and might offer better ways to understand how body fatness is controlled.

  1. NFIA co-localizes with PPARγ and transcriptionally controls the brown fat gene program

    DEFF Research Database (Denmark)

    Hiraike, Yuta; Waki, Hironori; Yu, Jing

    2017-01-01

    . NFIA and the master transcriptional regulator of adipogenesis, PPARγ, co-localize at the brown-fat-specific enhancers. Moreover, the binding of NFIA precedes and facilitates the binding of PPARγ, leading to increased chromatin accessibility and active transcription. Introduction of NFIA into myoblasts...... results in brown adipocyte differentiation. Conversely, the brown fat of NFIA-knockout mice displays impaired expression of the brown-fat-specific genes and reciprocal elevation of muscle genes. Finally, expression of NFIA and the brown-fat-specific genes is positively correlated in human brown fat...

  2. Gene expression profiling analysis of CRTC1-MAML2 fusion oncogene-induced transcriptional program in human mucoepidermoid carcinoma cells

    International Nuclear Information System (INIS)

    Chen, Jie; Li, Jian-Liang; Chen, Zirong; Griffin, James D.; Wu, Lizi

    2015-01-01

    Mucoepidermoid carcinoma (MEC) arises from multiple organs and accounts for the most common types of salivary gland malignancies. Currently, patients with unresectable and metastatic MEC have poor long-term clinical outcomes and no targeted therapies are available. The majority of MEC tumors contain a t(11;19) chromosomal translocation that fuses two genes, CRTC1 and MAML2, to generate the chimeric protein CRTC1-MAML2. CRTC1-MAML2 displays transforming activity in vitro and is required for human MEC cell growth and survival, partially due to its ability to constitutively activate CREB-mediated transcription. Consequently, CRTC1-MAML2 is implicated as a major etiologic molecular event and a therapeutic target for MEC. However, the molecular mechanisms underlying CRTC1-MAML2 oncogenic action in MEC have not yet been systematically analyzed. Elucidation of the CRTC1-MAML2-regulated transcriptional program and its underlying mechanisms will provide important insights into MEC pathogenesis that are essential for the development of targeted therapeutics. Transcriptional profiling was performed on human MEC cells with the depletion of endogenous CRTC1-MAML2 fusion or its interacting partner CREB via shRNA-mediated gene knockdown. A subset of target genes was validated via real-time RT-PCR assays. CRTC1-MAML2-perturbed molecular pathways in MEC were identified through pathway analyses. Finally, comparative analysis of CRTC1-MAML2-regulated and CREB-regulated transcriptional profiles was carried out to assess the contribution of CREB in mediating CRTC1-MAML2-induced transcription. A total of 808 differentially expressed genes were identified in human MEC cells after CRTC1-MAML2 knockdown and a subset of known and novel fusion target genes was confirmed by real-time RT-PCR. Pathway Analysis revealed that CRTC1-MAML2-regulated genes were associated with network functions that are important for cell growth, proliferation, survival, migration, and metabolism. Comparison of CRTC

  3. The Chromatin Remodeler BPTF Activates a Stemness Gene-Expression Program Essential for the Maintenance of Adult Hematopoietic Stem Cells

    Directory of Open Access Journals (Sweden)

    Bowen Xu

    2018-03-01

    Full Text Available Summary: Self-renewal and differentiation of adult stem cells are tightly regulated partly through configuration of chromatin structure by chromatin remodelers. Using knockout mice, we here demonstrate that bromodomain PHD finger transcription factor (BPTF, a component of the nucleosome remodeling factor (NURF chromatin-remodeling complex, is essential for maintaining the population size of hematopoietic stem/progenitor cells (HSPCs, including long-term hematopoietic stem cells (HSCs. Bptf-deficient HSCs are defective in reconstituted hematopoiesis, and hematopoietic-specific knockout of Bptf caused profound defects including bone marrow failure and anemia. Genome-wide transcriptome profiling revealed that BPTF loss caused downregulation of HSC-specific gene-expression programs, which contain several master transcription factors (Meis1, Pbx1, Mn1, and Lmo2 required for HSC maintenance and self-renewal. Furthermore, we show that BPTF potentiates the chromatin accessibility of key HSC “stemness” genes. These results demonstrate an essential requirement of the chromatin remodeler BPTF and NURF for activation of “stemness” gene-expression programs and proper function of adult HSCs. : Wang and colleagues show that a chromatin remodeler, BPTF, sustains appropriate functions of hematopoietic stem/progenitor cells (HSPCs. BPTF loss causes bone marrow failure and anemia. The authors further define a BPTF-dependent gene-expression program in HSPCs, which contains key HSC stemness factors. These results demonstrate an essential requirement of the BPTF-associated chromatin remodelers for HSC functionality and adult hematopoiesis. Keywords: Bptf, hematopoietic stem cells, chromatin remodeler, Meis1, Pbx1, Mn1, DNA accessibility, NURF, AP1 complex

  4. Deep Sequence Analysis of Non-Small Cell Lung Cancer: Integrated Analysis of Gene Expression, Alternative Splicing, and Single Nucleotide Variations in Lung Adenocarcinomas with and without Oncogenic KRAS Mutations

    International Nuclear Information System (INIS)

    Kalari, Krishna R.; Rossell, David; Necela, Brian M.; Asmann, Yan W.; Nair, Asha

    2012-01-01

    KRAS mutations are highly prevalent in non-small cell lung cancer (NSCLC), and tumors harboring these mutations tend to be aggressive and resistant to chemotherapy. We used next-generation sequencing technology to identify pathways that are specifically altered in lung tumors harboring a KRAS mutation. Paired-end RNA-sequencing of 15 primary lung adenocarcinoma tumors (8 harboring mutant KRAS and 7 with wild-type KRAS) were performed. Sequences were mapped to the human genome, and genomic features, including differentially expressed genes, alternate splicing isoforms and single nucleotide variants, were determined for tumors with and without KRAS mutation using a variety of computational methods. Network analysis was carried out on genes showing differential expression (374 genes), alternate splicing (259 genes), and SNV-related changes (65 genes) in NSCLC tumors harboring a KRAS mutation. Genes exhibiting two or more connections from the lung adenocarcinoma network were used to carry out integrated pathway analysis. The most significant signaling pathways identified through this analysis were the NFκB, ERK1/2, and AKT pathways. A 27 gene mutant KRAS-specific sub network was extracted based on gene–gene connections from the integrated network, and interrogated for druggable targets. Our results confirm previous evidence that mutant KRAS tumors exhibit activated NFκB, ERK1/2, and AKT pathways and may be preferentially sensitive to target therapeutics toward these pathways. In addition, our analysis indicates novel, previously unappreciated links between mutant KRAS and the TNFR and PPARγ signaling pathways, suggesting that targeted PPARγ antagonists and TNFR inhibitors may be useful therapeutic strategies for treatment of mutant KRAS lung tumors. Our study is the first to integrate genomic features from RNA-Seq data from NSCLC and to define a first draft genomic landscape model that is unique to tumors with oncogenic KRAS mutations.

  5. The Chromatin Remodeler BPTF Activates a Stemness Gene-Expression Program Essential for the Maintenance of Adult Hematopoietic Stem Cells.

    Science.gov (United States)

    Xu, Bowen; Cai, Ling; Butler, Jason M; Chen, Dongliang; Lu, Xiongdong; Allison, David F; Lu, Rui; Rafii, Shahin; Parker, Joel S; Zheng, Deyou; Wang, Gang Greg

    2018-03-13

    Self-renewal and differentiation of adult stem cells are tightly regulated partly through configuration of chromatin structure by chromatin remodelers. Using knockout mice, we here demonstrate that bromodomain PHD finger transcription factor (BPTF), a component of the nucleosome remodeling factor (NURF) chromatin-remodeling complex, is essential for maintaining the population size of hematopoietic stem/progenitor cells (HSPCs), including long-term hematopoietic stem cells (HSCs). Bptf-deficient HSCs are defective in reconstituted hematopoiesis, and hematopoietic-specific knockout of Bptf caused profound defects including bone marrow failure and anemia. Genome-wide transcriptome profiling revealed that BPTF loss caused downregulation of HSC-specific gene-expression programs, which contain several master transcription factors (Meis1, Pbx1, Mn1, and Lmo2) required for HSC maintenance and self-renewal. Furthermore, we show that BPTF potentiates the chromatin accessibility of key HSC "stemness" genes. These results demonstrate an essential requirement of the chromatin remodeler BPTF and NURF for activation of "stemness" gene-expression programs and proper function of adult HSCs. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  6. The expression of petunia strigolactone pathway genes is altered as part of the endogenous developmental program

    Directory of Open Access Journals (Sweden)

    Revel S M Drummond

    2012-01-01

    Full Text Available Analysis of mutants with increased branching has revealed the strigolactone synthesis/perception pathway which regulates branching in plants. However, whether variation in this well conserved developmental signalling system contributes to the unique plant architectures of different species is yet to be determined. We examined petunia orthologues of the Arabidopsis MAX1 and MAX2 genes to characterise their role in petunia architecture. A single orthologue of MAX1, PhMAX1 which encodes a cytochrome P450, was identified and was able to complement the max1 mutant of Arabidopsis. Petunia has two copies of the MAX2 gene, PhMAX2A and PhMAX2B which encode F-Box proteins. Differences in the transcript levels of these two MAX2-like genes suggest diverging functions. Unlike PhMAX2B, PhMAX2A mRNA levels increase as leaves age. Nonetheless, this gene functionally complements the Arabidopsis max2 mutant indicating that the biochemical activity of the PhMAX2A protein is not significantly different from MAX2. The expression of the petunia strigolactone pathway genes (PhCCD7, PhCCD8, PhMAX1, PhMAX2A, and PhMAX2B was then further investigated throughout the development of wild-type petunia plants. Three of these genes showed changes in mRNA levels over the development series. Alterations to the expression of these genes over time, or in different regions of the plant, may influence the branching growth habit of the plant. Alterations to strigolactone production and/or sensitivity could allow both subtle and dramatic changes to branching within and between species.

  7. RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing.

    Science.gov (United States)

    Gupta, Vikas; Estrada, April D; Blakley, Ivory; Reid, Rob; Patel, Ketan; Meyer, Mason D; Andersen, Stig Uggerhøj; Brown, Allan F; Lila, Mary Ann; Loraine, Ann E

    2015-01-01

    Blueberries are a rich source of antioxidants and other beneficial compounds that can protect against disease. Identifying genes involved in synthesis of bioactive compounds could enable the breeding of berry varieties with enhanced health benefits. Toward this end, we annotated a previously sequenced draft blueberry genome assembly using RNA-Seq data from five stages of berry fruit development and ripening. Genome-guided assembly of RNA-Seq read alignments combined with output from ab initio gene finders produced around 60,000 gene models, of which more than half were similar to proteins from other species, typically the grape Vitis vinifera. Comparison of gene models to the PlantCyc database of metabolic pathway enzymes identified candidate genes involved in synthesis of bioactive compounds, including bixin, an apocarotenoid with potential disease-fighting properties, and defense-related cyanogenic glycosides, which are toxic. Cyanogenic glycoside (CG) biosynthetic enzymes were highly expressed in green fruit, and a candidate CG detoxification enzyme was up-regulated during fruit ripening. Candidate genes for ethylene, anthocyanin, and 400 other biosynthetic pathways were also identified. Homology-based annotation using Blast2GO and InterPro assigned Gene Ontology terms to around 15,000 genes. RNA-Seq expression profiling showed that blueberry growth, maturation, and ripening involve dynamic gene expression changes, including coordinated up- and down-regulation of metabolic pathway enzymes and transcriptional regulators. Analysis of RNA-seq alignments identified developmentally regulated alternative splicing, promoter use, and 3' end formation. We report genome sequence, gene models, functional annotations, and RNA-Seq expression data that provide an important new resource enabling high throughput studies in blueberry.

  8. The histone demethylase Kdm6b regulates a mature gene expression program in differentiating cerebellar granule neurons.

    Science.gov (United States)

    Wijayatunge, Ranjula; Liu, Fang; Shpargel, Karl B; Wayne, Nicole J; Chan, Urann; Boua, Jane-Valeriane; Magnuson, Terry; West, Anne E

    2018-03-01

    The histone H3 lysine 27 (H3K27) demethylase Kdm6b (Jmjd3) can promote cellular differentiation, however its physiological functions in neurons remain to be fully determined. We studied the expression and function of Kdm6b in differentiating granule neurons of the developing postnatal mouse cerebellum. At postnatal day 7, Kdm6b is expressed throughout the layers of the developing cerebellar cortex, but its expression is upregulated in newborn cerebellar granule neurons (CGNs). Atoh1-Cre mediated conditional knockout of Kdm6b in CGN precursors either alone or in combination with Kdm6a did not disturb the gross morphological development of the cerebellum. Furthermore, RNAi-mediated knockdown of Kdm6b in cultured CGN precursors did not alter the induced expression of early neuronal marker genes upon cell cycle exit. By contrast, knockdown of Kdm6b significantly impaired the induction of a mature neuronal gene expression program, which includes gene products required for functional synapse maturation. Loss of Kdm6b also impaired the ability of Brain-Derived Neurotrophic Factor (BDNF) to induce expression of Grin2c and Tiam1 in maturing CGNs. Taken together, these data reveal a previously unknown role for Kdm6b in the postmitotic stages of CGN maturation and suggest that Kdm6b may work, at least in part, by a transcriptional mechanism that promotes gene sensitivity to regulation by BDNF. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Npas4 regulates excitatory-inhibitory balance within neural circuits through cell-type-specific gene programs.

    Science.gov (United States)

    Spiegel, Ivo; Mardinly, Alan R; Gabel, Harrison W; Bazinet, Jeremy E; Couch, Cameron H; Tzeng, Christopher P; Harmin, David A; Greenberg, Michael E

    2014-05-22

    The nervous system adapts to experience by inducing a transcriptional program that controls important aspects of synaptic plasticity. Although the molecular mechanisms of experience-dependent plasticity are well characterized in excitatory neurons, the mechanisms that regulate this process in inhibitory neurons are only poorly understood. Here, we describe a transcriptional program that is induced by neuronal activity in inhibitory neurons. We find that, while neuronal activity induces expression of early-response transcription factors such as Npas4 in both excitatory and inhibitory neurons, Npas4 activates distinct programs of late-response genes in inhibitory and excitatory neurons. These late-response genes differentially regulate synaptic input to these two types of neurons, promoting inhibition onto excitatory neurons while inducing excitation onto inhibitory neurons. These findings suggest that the functional outcomes of activity-induced transcriptional responses are adapted in a cell-type-specific manner to achieve a circuit-wide homeostatic response. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. Clean/alternative fueled fleet programs - 1990 Amendments to the Clean Air Act, the Colorado Air Pollution Prevention and Control Act, and Denver City and County regulations

    International Nuclear Information System (INIS)

    Bowles, S.L.; Manderino, L.A.

    1993-01-01

    Despite substantial regulations for nearly two decades, attainment of this ambient standards for ozone and carbon monoxide (CO) remain difficult goals to achieve, Even with of ozone precursors and CO. The 1990 Amendments to the Clean Air Act (CAA90) prescribe further reductions of mobile source emissions. One such reduction strategy is using clean fuels, such as methanol, ethanol, or other alcohols (in blends of 85 percent or more alcohol with gasoline or other fuel), reformulated gasoline or diesel, natural gas, liquified petroleum gas, hydrogen, or electricity. There are regulatory measures involving special fuels which will be required in areas heavily polluted with ozone and CO. The state of Colorado recently passed the 1992 Air Pollution Prevention and Control Act which included provisions for the use of alternative fuels which will be implemented in 1994. In addition to adhering to the Colorado state regulations, the city and county of Denver also have regulations pertaining to the use of alternative fuels in fleets of 10 or more vehicles. Denver's program began in 1992. This paper will address the issue of fleet conversion and its impact on industry in Colorado, and Denver in particular

  11. Evaluation of retinoids for induction of the redundant gene ABCD2 as an alternative treatment option in X-linked adrenoleukodystrophy.

    Directory of Open Access Journals (Sweden)

    Franziska D Weber

    Full Text Available X-linked adrenoleukodystrophy (X-ALD, the most common peroxisomal disorder, is a clinically heterogeneous disease that can manifest as devastating inflammatory cerebral demyelination (CALD leading to death of affected males. Currently, the only curative treatment is allogeneic hematopoietic stem cell transplantation (HSCT. However, HSCT is only effective when performed at an early stage because the inflammation may progress for eighteen months after HSCT. Thus, alternative treatment options able to immediately halt the progression are urgently needed. X-ALD is caused by mutations in the ABCD1 gene, encoding the peroxisomal membrane protein ABCD1, resulting in impaired very long-chain fatty acid metabolism. The related ABCD2 protein is able to functionally compensate for ABCD1-deficiency both in vitro and in vivo. Recently, we demonstrated that of the cell types derived from CD34+ stem cells, predominantly monocytes but not lymphocytes are metabolically impaired in X-ALD. As ABCD2 is virtually not expressed in these cells, we hypothesize that a pharmacological up-regulation of ABCD2 should compensate metabolically and halt the inflammation in CALD. Retinoids are anti-inflammatory compounds known to act on ABCD2. Here, we investigated the capacity of selected retinoids for ABCD2 induction in human monocytes/macrophages. In THP-1 cells, 13-cis-retinoic acid reached the highest, fivefold, increase in ABCD2 expression. To test the efficacy of retinoids in vivo, we analyzed ABCD2 mRNA levels in blood cells isolated from acne patients receiving 13-cis-retinoic acid therapy. In treated acne patients, ABCD2 mRNA levels were comparable to pre-treatment levels in monocytes and lymphocytes. Nevertheless, when primary monocytes were in vitro differentiated into macrophages and treated with 13-cis-retinoic acid, we observed a fourfold induction of ABCD2. However, the level of ABCD2 induction obtained by retinoids alone is probably not of therapeutic relevance

  12. Optimal planning of co-firing alternative fuels with coal in a power plant by grey nonlinear mixed integer programming model

    Energy Technology Data Exchange (ETDEWEB)

    Koa, A.S.; Chang, N.B. [University of Central Florida, Orlando, FL (United States). Dept. for Civil & Environmental Engineering

    2008-07-15

    Energy supply and use is of fundamental importance to society. Although the interactions between energy and environment were originally local in character, they have now widened to cover regional and global issues, such as acid rain and the greenhouse effect. It is for this reason that there is a need for covering the direct and indirect economic and environmental impacts of energy acquisition, transport, production and use. In this paper, particular attention is directed to ways of resolving conflict between economic and environmental goals by encouraging a power plant to consider co-firing biomass and refuse-derived fuel (RDF) with coal simultaneously. It aims at reducing the emission level of sulfur dioxide (SO{sub 2}) in an uncertain environment, using the power plant in Michigan City, Indiana as an example. To assess the uncertainty by a comparative way both deterministic and grey nonlinear mixed integer programming (MIP) models were developed to minimize the net operating cost with respect to possible fuel combinations. It aims at generating the optimal portfolio of alternative fuels while maintaining the same electricity generation simultaneously. To case the solution procedure stepwise relaxation algorithm was developed for solving the grey nonlinear MIP model. Breakeven alternative fuel value can be identified in the post-optimization stage for decision-making. Research findings show that the inclusion of RDF does not exhibit comparative advantage in terms of the net cost, albeit relatively lower air pollution impact. Yet it can be sustained by a charge system, subsidy program, or emission credit as the price of coal increases over time.

  13. Optimal planning of co-firing alternative fuels with coal in a power plant by grey nonlinear mixed integer programming model.

    Science.gov (United States)

    Ko, Andi Setiady; Chang, Ni-Bin

    2008-07-01

    Energy supply and use is of fundamental importance to society. Although the interactions between energy and environment were originally local in character, they have now widened to cover regional and global issues, such as acid rain and the greenhouse effect. It is for this reason that there is a need for covering the direct and indirect economic and environmental impacts of energy acquisition, transport, production and use. In this paper, particular attention is directed to ways of resolving conflict between economic and environmental goals by encouraging a power plant to consider co-firing biomass and refuse-derived fuel (RDF) with coal simultaneously. It aims at reducing the emission level of sulfur dioxide (SO(2)) in an uncertain environment, using the power plant in Michigan City, Indiana as an example. To assess the uncertainty by a comparative way both deterministic and grey nonlinear mixed integer programming (MIP) models were developed to minimize the net operating cost with respect to possible fuel combinations. It aims at generating the optimal portfolio of alternative fuels while maintaining the same electricity generation simultaneously. To ease the solution procedure stepwise relaxation algorithm was developed for solving the grey nonlinear MIP model. Breakeven alternative fuel value can be identified in the post-optimization stage for decision-making. Research findings show that the inclusion of RDF does not exhibit comparative advantage in terms of the net cost, albeit relatively lower air pollution impact. Yet it can be sustained by a charge system, subsidy program, or emission credit as the price of coal increases over time.

  14. Teacher Identity and Self-efficacy Development in an Alternative Licensure Program for Middle and High School Math and Science Teachers

    Science.gov (United States)

    West, Robert J.

    This mixed-method case study focused on the phenomenon of the transition from student to teacher. The educational system in the United States is constantly shifting to provide the correct number of teachers for our nations' schools. There is no simple formula for this process and occasionally an area of need arises that is not being met. Recently, the demand for science and math teachers in the K-12 system has outpaced the supply of new teachers (Business-Higher Education Forum, 2011). To complicate the problem further, teachers are leaving the field in record numbers both through retirement and attrition (National Commission on Teaching and America's Future, 2007). Particularly hard hit are poor rural schools with low-performing students, such as the schools of Appalachia (Barley, 2009; Goodpaster, Adedokun, & Weaver, 2012). Out of this need, alternative licensure programs for teachers have developed. The alternative teacher-training program studied in this research is the Woodrow Wilson Teaching Fellowship (WWTF) website, "The Woodrow Wilson Ohio Teaching Fellowship seeks to attract talented, committed individuals with backgrounds in the STEM fields---science, technology, engineering, and mathematics---into teaching in high-need Ohio secondary schools" (para. 2) . The researcher was interested in the formation of teacher identity and self-efficacy as these constructs have been shown to manifest in highly effective teachers that are likely to remain in the field of teaching (Beaucamp & Thomas 2009; Klassen, Tze, Betts, & Gordon, 2010). The research method included in-depth interviews, mixed with pretest/posttest administrations of the Teacher Sense of Efficacy Scale (TSES) (Tschannen-Moran & Woolfolk Hoy 2001) given during the teacher-training period and again following the first year of professional teaching. Results from both the TSES and the interviews indicate that the participants had a successful transition into teaching. They both felt and demonstrated that

  15. Alternative indicators for monitoring the quality of a continuous intervention program on antibiotic prescribing during changing healthcare conditions.

    Science.gov (United States)

    Bantar, C; Franco, D; Heft, C; Vesco, E; Arango, C; Izaguirre, M; Alcázar, G; Boleas, M; Oliva, M E

    2005-06-01

    We recently published on the impact of a four-phase hospital-wide intervention program designed to optimize the quality of antibiotic use, where a multidisciplinary team (MDT) could modify prescription at the last phase. Because health care quality was changing during the last 5 years (late 1999 to early 2004), we developed certain indicators to monitor the quality of our intervention over time. Different periods were defined as baseline (pre-intervention), initial intervention-active control, pre-crisis control, crisis control, post-crisis control and end of crisis control. Major indicators were rates of prescription modification by the MDT; prescription for an uncertain infection and a novel index formula (RIcarb) to estimate the rationale for carbapenem use. We assessed 2115 antimicrobial prescriptions. Modification of prescription rate was 30% at the beginning and decreased thereafter up to stable levels. Rate of prescriptions ordered for cases of both uncertain infection and unknown source of infection decreased significantly after intervention (i.e. from baseline to active control). In contrast, a doubling of culture-directed prescriptions was observed between these periods. RIcarb values lower and higher than 60% (modal, cut-off) were assumed as carbapenem overuse and underuse, respectively. Overuse was observed at the pre-intervention, while pronounced underuse was shown during the crisis (RIcarb, 45% and 87%, respectively). The present study demonstrates that certain indicators, other than the widely adopted impact outcomes, are a suitable tool for monitoring the quality of a continuous, long-term, active intervention on antimicrobial prescribing practice, especially when applied in a changing healthcare setting.

  16. Alternative Remedies

    Science.gov (United States)

    ... Home › Aging & Health A to Z › Alternative Remedies Font ... medical treatment prescribed by their healthcare provider. Using this type of alternative therapy along with traditional treatments is ...

  17. Alternative Fuels

    Science.gov (United States)

    Alternative fuels include gaseous fuels such as hydrogen, natural gas, and propane; alcohols such as ethanol, methanol, and butanol; vegetable and waste-derived oils; and electricity. Overview of alternative fuels is here.

  18. Alternating Hemiplegia

    Science.gov (United States)

    ... to the symptoms of the disorder. View Full Definition Treatment Drug therapy including verapamil may help to reduce the ... the more serious form of alternating hemiplegia × ... Definition Alternating hemiplegia is a rare neurological disorder that ...

  19. Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain.

    Directory of Open Access Journals (Sweden)

    Nicole C Riddle

    2012-09-01

    Full Text Available Chromatin environments differ greatly within a eukaryotic genome, depending on expression state, chromosomal location, and nuclear position. In genomic regions characterized by high repeat content and high gene density, chromatin structure must silence transposable elements but permit expression of embedded genes. We have investigated one such region, chromosome 4 of Drosophila melanogaster. Using chromatin-immunoprecipitation followed by microarray (ChIP-chip analysis, we examined enrichment patterns of 20 histone modifications and 25 chromosomal proteins in S2 and BG3 cells, as well as the changes in several marks resulting from mutations in key proteins. Active genes on chromosome 4 are distinct from those in euchromatin or pericentric heterochromatin: while there is a depletion of silencing marks at the transcription start sites (TSSs, HP1a and H3K9me3, but not H3K9me2, are enriched strongly over gene bodies. Intriguingly, genes on chromosome 4 are less frequently associated with paused polymerase. However, when the chromatin is altered by depleting HP1a or POF, the RNA pol II enrichment patterns of many chromosome 4 genes shift, showing a significant decrease over gene bodies but not at TSSs, accompanied by lower expression of those genes. Chromosome 4 genes have a low incidence of TRL/GAGA factor binding sites and a low T(m downstream of the TSS, characteristics that could contribute to a low incidence of RNA polymerase pausing. Our data also indicate that EGG and POF jointly regulate H3K9 methylation and promote HP1a binding over gene bodies, while HP1a targeting and H3K9 methylation are maintained at the repeats by an independent mechanism. The HP1a-enriched, POF-associated chromatin structure over the gene bodies may represent one type of adaptation for genes embedded in repetitive DNA.

  20. Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen

    Science.gov (United States)

    Airoldi, Edoardo M.; Miller, Darach; Athanasiadou, Rodoniki; Brandt, Nathan; Abdul-Rahman, Farah; Neymotin, Benjamin; Hashimoto, Tatsu; Bahmani, Tayebeh; Gresham, David

    2016-01-01

    Cell growth rate is regulated in response to the abundance and molecular form of essential nutrients. In Saccharomyces cerevisiae (budding yeast), the molecular form of environmental nitrogen is a major determinant of cell growth rate, supporting growth rates that vary at least threefold. Transcriptional control of nitrogen use is mediated in large part by nitrogen catabolite repression (NCR), which results in the repression of specific transcripts in the presence of a preferred nitrogen source that supports a fast growth rate, such as glutamine, that are otherwise expressed in the presence of a nonpreferred nitrogen source, such as proline, which supports a slower growth rate. Differential expression of the NCR regulon and additional nitrogen-responsive genes results in >500 transcripts that are differentially expressed in cells growing in the presence of different nitrogen sources in batch cultures. Here we find that in growth rate–controlled cultures using nitrogen-limited chemostats, gene expression programs are strikingly similar regardless of nitrogen source. NCR expression is derepressed in all nitrogen-limiting chemostat conditions regardless of nitrogen source, and in these conditions, only 34 transcripts exhibit nitrogen source–specific differential gene expression. Addition of either the preferred nitrogen source, glutamine, or the nonpreferred nitrogen source, proline, to cells growing in nitrogen-limited chemostats results in rapid, dose-dependent repression of the NCR regulon. Using a novel means of computational normalization to compare global gene expression programs in steady-state and dynamic conditions, we find evidence that the addition of nitrogen to nitrogen-limited cells results in the transient overproduction of transcripts required for protein translation. Simultaneously, we find that that accelerated mRNA degradation underlies the rapid clearing of a subset of transcripts, which is most pronounced for the highly expressed NCR

  1. Structural organization of the human and mouse laminin beta2 chain genes, and alternative splicing at the 5' end of the human transcript

    DEFF Research Database (Denmark)

    Durkin, M E; Gautam, M; Loechel, F

    1996-01-01

    We have determined the structural organization of the human and mouse genes that encode the laminin beta2 chain (s-laminin), an essential component of the basement membranes of the neuromuscular synapse and the kidney glomerulus. The human and mouse genes have a nearly identical exon-intron organ......We have determined the structural organization of the human and mouse genes that encode the laminin beta2 chain (s-laminin), an essential component of the basement membranes of the neuromuscular synapse and the kidney glomerulus. The human and mouse genes have a nearly identical exon...

  2. Developmental status of bioassays in genetic toxicology: a report of Phase II of the US Environmental Protection Agency Gene-Tox program

    Energy Technology Data Exchange (ETDEWEB)

    Brusick, D; Auletta, A

    1985-01-01

    The Gene-Tox Program was structured around two phases of genetic test data evaluation. The first phase consisted of 36 Work Group reports, each evaluating the results and performance of a specific bioassay. The second phase consisted of a plan to summarize the information provided by the Work Groups. The Gene-Tox Coordinating Committee was to be responsible for Phase II, and several subgroups were assigned specific goals in implementing this analysis. This report deals with Goal I which is to identify the developmental status of the individual bioassays reviewed by the Gene-Tox Work Groups in the first phase of the Program. 5 references, 6 tables.

  3. Nuclear proliferation and civilian nuclear power: report of the Nonproliferation Alternative Systems Assessment Program. Volume IX. Reactor and fuel cycle descriptions

    Energy Technology Data Exchange (ETDEWEB)

    1979-12-01

    The Nonproliferation Alternative Systems Assessment Program (NASAP) has characterized and assessed various reactor/fuel-cycle systems. Volume IX provides, in summary form, the technical descriptions of the reactor/fuel-cycle systems studied. This includes the status of the system technology, as well as a discussion of the safety, environmental, and licensing needs from a technical perspective. This information was then used in developing the research, development, and demonstration (RD and D) program, including its cost and time frame, to advance the existing technology to the level needed for commercial use. Wherever possible, the cost data are given as ranges to reflect the uncertainties in the estimates. Volume IX is divided into three sections: Chapter 1, Reactor Systems; Chapter 2, Fuel-Cycle Systems; and the Appendixes. Chapter 1 contains the characterizations of the following 12 reactor types: light-water reactor; heavy-water reactor; water-cooled breeder reactor; high-temperature gas-cooled reactor; gas-cooled fast reactor; liquid-metal fast breeder reactor; spectral-shift-controlled reactor; accelerator-driven reactor; molten-salt reactor; gaseous-core reactor; tokamak fusion-fisson hybrid reactor; and fast mixed-spectrum reactor. Chapter 2 contains similar information developed for fuel-cycle facilities in the following categories: mining and milling; conversion and enrichment; fuel fabrication; spent fuel reprocessing; waste handling and disposal; and transportation of nuclear materials.

  4. Nuclear proliferation and civilian nuclear power: report of the Nonproliferation Alternative Systems Assessment Program. Volume IX. Reactor and fuel cycle descriptions

    International Nuclear Information System (INIS)

    1979-12-01

    The Nonproliferation Alternative Systems Assessment Program (NASAP) has characterized and assessed various reactor/fuel-cycle systems. Volume IX provides, in summary form, the technical descriptions of the reactor/fuel-cycle systems studied. This includes the status of the system technology, as well as a discussion of the safety, environmental, and licensing needs from a technical perspective. This information was then used in developing the research, development, and demonstration (RD and D) program, including its cost and time frame, to advance the existing technology to the level needed for commercial use. Wherever possible, the cost data are given as ranges to reflect the uncertainties in the estimates. Volume IX is divided into three sections: Chapter 1, Reactor Systems; Chapter 2, Fuel-Cycle Systems; and the Appendixes. Chapter 1 contains the characterizations of the following 12 reactor types: light-water reactor; heavy-water reactor; water-cooled breeder reactor; high-temperature gas-cooled reactor; gas-cooled fast reactor; liquid-metal fast breeder reactor; spectral-shift-controlled reactor; accelerator-driven reactor; molten-salt reactor; gaseous-core reactor; tokamak fusion-fisson hybrid reactor; and fast mixed-spectrum reactor. Chapter 2 contains similar information developed for fuel-cycle facilities in the following categories: mining and milling; conversion and enrichment; fuel fabrication; spent fuel reprocessing; waste handling and disposal; and transportation of nuclear materials

  5. Evidence of cardiac involvement in the fetal inflammatory response syndrome: disruption of gene networks programming cardiac development in nonhuman primates.

    Science.gov (United States)

    Mitchell, Timothy; MacDonald, James W; Srinouanpranchanh, Sengkeo; Bammler, Theodor K; Merillat, Sean; Boldenow, Erica; Coleman, Michelle; Agnew, Kathy; Baldessari, Audrey; Stencel-Baerenwald, Jennifer E; Tisoncik-Go, Jennifer; Green, Richard R; Gale, Michael J; Rajagopal, Lakshmi; Adams Waldorf, Kristina M

    2018-04-01

    Most early preterm births are associated with intraamniotic infection and inflammation, which can lead to systemic inflammation in the fetus. The fetal inflammatory response syndrome describes elevations in the fetal interleukin-6 level, which is a marker for inflammation and fetal organ injury. An understanding of the effects of inflammation on fetal cardiac development may lead to insight into the fetal origins of adult cardiovascular disease. The purpose of this study was to determine whether the fetal inflammatory response syndrome is associated with disruptions in gene networks that program fetal cardiac development. We obtained fetal cardiac tissue after necropsy from a well-described pregnant nonhuman primate model (pigtail macaque, Macaca nemestrina) of intrauterine infection (n=5) and controls (n=5). Cases with the fetal inflammatory response syndrome (fetal plasma interleukin-6 >11 pg/mL) were induced by either choriodecidual inoculation of a hypervirulent group B streptococcus strain (n=4) or intraamniotic inoculation of Escherichia coli (n=1). RNA and protein were extracted from fetal hearts and profiled by microarray and Luminex (Millipore, Billerica, MA) for cytokine analysis, respectively. Results were validated by quantitative reverse transcriptase polymerase chain reaction. Statistical and bioinformatics analyses included single gene analysis, gene set analysis, Ingenuity Pathway Analysis (Qiagen, Valencia, CA), and Wilcoxon rank sum. Severe fetal inflammation developed in the context of intraamniotic infection and a disseminated bacterial infection in the fetus. Interleukin-6 and -8 in fetal cardiac tissues were elevated significantly in fetal inflammatory response syndrome cases vs controls (P1.5-fold change, P<.05) in the fetal heart (analysis of variance). Altered expression of select genes was validated by quantitative reverse transcriptase polymerase chain reaction that included several with known functions in cardiac injury, morphogenesis

  6. Alternative RNA splicing and cancer

    Science.gov (United States)

    Liu, Sali; Cheng, Chonghui

    2015-01-01

    Alternative splicing of pre-messenger RNA (mRNA) is a fundamental mechanism by which a gene can give rise to multiple distinct mRNA transcripts, yielding protein isoforms with different, even opposing, functions. With the recognition that alternative splicing occurs in nearly all human genes, its relationship with cancer-associated pathways has emerged as a rapidly growing field. In this review, we summarize recent findings that have implicated the critical role of alternative splicing in cancer and discuss current understandings of the mechanisms underlying dysregulated alternative splicing in cancer cells. PMID:23765697

  7. Gene Expression Programs in Response to Hypoxia: Cell Type Specificity and Prognostic Significance in Human Cancers.

    Directory of Open Access Journals (Sweden)

    2006-01-01

    Full Text Available BACKGROUND: Inadequate oxygen (hypoxia triggers a multifaceted cellular response that has important roles in normal physiology and in many human diseases. A transcription factor, hypoxia-inducible factor (HIF, plays a central role in the hypoxia response; its activity is regulated by the oxygen-dependent degradation of the HIF-1alpha protein. Despite the ubiquity and importance of hypoxia responses, little is known about the variation in the global transcriptional response to hypoxia among different cell types or how this variation might relate to tissue- and cell-specific diseases. METHODS AND FINDINGS: We analyzed the temporal changes in global transcript levels in response to hypoxia in primary renal proximal tubule epithelial cells, breast epithelial cells, smooth muscle cells, and endothelial cells with DNA microarrays. The extent of the transcriptional response to hypoxia was greatest in the renal tubule cells. This heightened response was associated with a uniquely high level of HIF-1alpha RNA in renal cells, and it could be diminished by reducing HIF-1alpha expression via RNA interference. A gene-expression signature of the hypoxia response, derived from our studies of cultured mammary and renal tubular epithelial cells, showed coordinated variation in several human cancers, and was a strong predictor of clinical outcomes in breast and ovarian cancers. In an analysis of a large, published gene-expression dataset from breast cancers, we found that the prognostic information in the hypoxia signature was virtually independent of that provided by the previously reported wound signature and more predictive of outcomes than any of the clinical parameters in current use. CONCLUSIONS: The transcriptional response to hypoxia varies among human cells. Some of this variation is traceable to variation in expression of the HIF1A gene. A gene-expression signature of the cellular response to hypoxia is associated with a significantly poorer prognosis

  8. Cell-Type-Specific Gene Programs of the Normal Human Nephron Define Kidney Cancer Subtypes.

    Science.gov (United States)

    Lindgren, David; Eriksson, Pontus; Krawczyk, Krzysztof; Nilsson, Helén; Hansson, Jennifer; Veerla, Srinivas; Sjölund, Jonas; Höglund, Mattias; Johansson, Martin E; Axelson, Håkan

    2017-08-08

    Comprehensive transcriptome studies of cancers often rely on corresponding normal tissue samples to serve as a transcriptional reference. In this study, we performed in-depth analyses of normal kidney tissue transcriptomes from the TCGA and demonstrate that the histological variability in cellularity, inherent in the kidney architecture, lead to considerable transcriptional differences between samples. This should be considered when comparing expression profiles of normal and cancerous kidney tissues. We exploited these differences to define renal-cell-specific gene signatures and used these as a framework to analyze renal cell carcinoma (RCC) ontogeny. Chromophobe RCCs express FOXI1-driven genes that define collecting duct intercalated cells, whereas HNF-regulated genes, specific for proximal tubule cells, are an integral part of clear cell and papillary RCC transcriptomes. These networks may be used as a framework for understanding the interplay between genomic changes in RCC subtypes and the lineage-defining regulatory machinery of their non-neoplastic counterparts. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  9. Intersection of FOXO- and RUNX1-mediated gene expression programs in single breast epithelial cells during morphogenesis and tumor progression.

    Science.gov (United States)

    Wang, Lixin; Brugge, Joan S; Janes, Kevin A

    2011-10-04

    Gene expression networks are complicated by the assortment of regulatory factors that bind DNA and modulate transcription combinatorially. Single-cell measurements can reveal biological mechanisms hidden by population averages, but their value has not been fully explored in the context of mRNA regulation. Here, we adapted a single-cell expression profiling technique to examine the gene expression program downstream of Forkhead box O (FOXO) transcription factors during 3D breast epithelial acinar morphogenesis. By analyzing patterns of mRNA fluctuations among individual matrix-attached epithelial cells, we found that a subset of FOXO target genes was jointly regulated by the transcription factor Runt-related transcription factor 1 (RUNX1). Knockdown of RUNX1 causes hyperproliferation and abnormal morphogenesis, both of which require normal FOXO function. Down-regulating RUNX1 and FOXOs simultaneously causes widespread oxidative stress, which arrests proliferation and restores normal acinar morphology. In hormone-negative breast cancers lacking human epidermal growth factor receptor 2 (HER2) amplification, we find that RUNX1 down-regulation is strongly associated with up-regulation of FOXO1, which may be required to support growth of RUNX1-negative tumors. The coordinate function of these two tumor suppressors may provide a failsafe mechanism that inhibits cancer progression.

  10. Identification of reference genes for RT-qPCR in ovine mammary tissue during late pregnancy and lactation and in response to maternal nutritional programming.

    Science.gov (United States)

    Paten, A M; Pain, S J; Peterson, S W; Blair, H T; Kenyon, P R; Dearden, P K; Duncan, E J

    2014-08-01

    The mammary gland is a complex tissue consisting of multiple cell types which, over the lifetime of an animal, go through repeated cycles of development associated with pregnancy, lactation and involution. The mammary gland is also known to be sensitive to maternal programming by environmental stimuli such as nutrition. The molecular basis of these adaptations is of significant interest, but requires robust methods to measure gene expression. Reverse-transcription quantitative PCR (RT-qPCR) is commonly used to measure gene expression, and is currently the method of choice for validating genome-wide expression studies. RT-qPCR requires the selection of reference genes that are stably expressed over physiological states and treatments. In this study we identify suitable reference genes to normalize RT-qPCR data for the ovine mammary gland in two physiological states; late pregnancy and lactation. Biopsies were collected from offspring of ewes that had been subjected to different nutritional paradigms during pregnancy to examine effects of maternal programming on the mammary gland of the offspring. We evaluated eight candidate reference genes and found that two reference genes (PRPF3 and CUL1) are required for normalising RT-qPCR data from pooled RNA samples, but five reference genes are required for analyzing gene expression in individual animals (SENP2, EIF6, MRPL39, ATP1A1, CUL1). Using these stable reference genes, we showed that TET1, a key regulator of DNA methylation, is responsive to maternal programming and physiological state. The identification of these novel reference genes will be of utility to future studies of gene expression in the ovine mammary gland. Copyright © 2014 the American Physiological Society.

  11. A tomato metacaspase gene is upregulated during programmed cell death in Botrytis cinerea-infected leaves

    NARCIS (Netherlands)

    Hoeberichts, F.A.; Have, ten A.; Woltering, E.J.

    2003-01-01

    Programmed cell death (PCD) in plant cells is often accompanied by biochemical and morphological hallmarks similar to those of animal apoptosis. However, orthologs of animal caspases, cysteinyl aspartate-specific proteases that constitute the core component of animal apoptosis, have not yet been

  12. cudaMap: a GPU accelerated program for gene expression connectivity mapping.

    Science.gov (United States)

    McArt, Darragh G; Bankhead, Peter; Dunne, Philip D; Salto-Tellez, Manuel; Hamilton, Peter; Zhang, Shu-Dong

    2013-10-11

    Modern cancer research often involves large datasets and the use of sophisticated statistical techniques. Together these add a heavy computational load to the analysis, which is often coupled with issues surrounding data accessibility. Connectivity mapping is an advanced bioinformatic and computational technique dedicated to therapeutics discovery and drug re-purposing around differential gene expression analysis. On a normal desktop PC, it is common for the connectivity mapping task with a single gene signature to take > 2h to complete using sscMap, a popular Java application that runs on standard CPUs (Central Processing Units). Here, we describe new software, cudaMap, which has been implemented using CUDA C/C++ to harness the computational power of NVIDIA GPUs (Graphics Processing Units) to greatly reduce processing times for connectivity mapping. cudaMap can identify candidate therapeutics from the same signature in just over thirty seconds when using an NVIDIA Tesla C2050 GPU. Results from the analysis of multiple gene signatures, which would previously have taken several days, can now be obtained in as little as 10 minutes, greatly facilitating candidate therapeutics discovery with high throughput. We are able to demonstrate dramatic speed differentials between GPU assisted performance and CPU executions as the computational load increases for high accuracy evaluation of statistical significance. Emerging 'omics' technologies are constantly increasing the volume of data and information to be processed in all areas of biomedical research. Embracing the multicore functionality of GPUs represents a major avenue of local accelerated computing. cudaMap will make a strong contribution in the discovery of candidate therapeutics by enabling speedy execution of heavy duty connectivity mapping tasks, which are increasingly required in modern cancer research. cudaMap is open source and can be freely downloaded from http://purl.oclc.org/NET/cudaMap.

  13. Developmental programming: gestational bisphenol-A treatment alters trajectory of fetal ovarian gene expression.

    Science.gov (United States)

    Veiga-Lopez, Almudena; Luense, Lacey J; Christenson, Lane K; Padmanabhan, Vasantha

    2013-05-01

    Bisphenol-A (BPA), a ubiquitous environmental endocrine disrupting chemical, is a component of polycarbonate plastic and epoxy resins. Because of its estrogenic properties, there is increasing concern relative to risks from exposures during critical periods of early organ differentiation. Prenatal BPA treatment in sheep results in low birth weight, hypergonadotropism, and ovarian cycle disruptions. This study tested the hypothesis that gestational exposure to bisphenol A, at an environmentally relevant dose, induces early perturbations in the ovarian transcriptome (mRNA and microRNA). Pregnant Suffolk ewes were treated with bisphenol A (0.5 mg/kg, sc, daily, produced ∼2.6 ng/mL of unconjugated BPA in umbilical arterial samples of BPA treated fetuses approaching median levels of BPA measured in maternal circulation) from days 30 to 90 of gestation. Expression of steroidogenic enzymes, steroid/gonadotropin receptors, key ovarian regulators, and microRNA biogenesis components were measured by RT-PCR using RNA derived from fetal ovaries collected on gestational days 65 and 90. An age-dependent effect was evident in most steroidogenic enzymes, steroid receptors, and key ovarian regulators. Prenatal BPA increased Cyp19 and 5α-reductase expression in day 65, but not day 90, ovaries. Fetal ovarian microRNA expression was altered by prenatal BPA with 45 down-regulated (>1.5-fold) at day 65 and 11 down-regulated at day 90 of gestation. These included microRNAs targeting Sry-related high-mobility-group box (SOX) family genes, kit ligand, and insulin-related genes. The results of this study demonstrate that exposure to BPA at an environmentally relevant dose alters fetal ovarian steroidogenic gene and microRNA expression of relevance to gonadal differentiation, folliculogenesis, and insulin homeostasis.

  14. Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization

    Directory of Open Access Journals (Sweden)

    McDonald Karen

    2011-08-01

    Full Text Available Abstract Background Direct gene synthesis is becoming more popular owing to decreases in gene synthesis pricing. Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific applications. In order to facilitate gene optimization, we have developed a stand-alone software called Visual Gene Developer. Results The software not only provides general functions for gene analysis and optimization along with an interactive user-friendly interface, but also includes unique features such as programming capability, dedicated mRNA secondary structure prediction, artificial neural network modeling, network & multi-threaded computing, and user-accessible programming modules. The software allows a user to analyze and optimize a sequence using main menu functions or specialized module windows. Alternatively, gene optimization can be initiated by designing a gene construct and configuring an optimization strategy. A user can choose several predefined or user-defined algorithms to design a complicated strategy. The software provides expandable functionality as platform software supporting module development using popular script languages such as VBScript and JScript in the software programming environment. Conclusion Visual Gene Developer is useful for both researchers who want to quickly analyze and optimize genes, and those who are interested in developing and testing new algorithms in bioinformatics. The software is available for free download at http://www.visualgenedeveloper.net.

  15. A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Apel, Amanda Reider; d'Espaux, Leo; Wehrs, Maren

    2017-01-01

    of these parts via a web-based tool, that automates the generation of DNA fragments for integration. Our system builds upon existing gene editing methods in the thoroughness with which the parts are standardized and characterized, the types and number of parts available and the ease with which our methodology...... can be used to perform genetic edits in yeast. We demonstrated the applicability of this toolkit by optimizing the expression of a challenging but industrially important enzyme, taxadiene synthase (TXS). This approach enabled us to diagnose an issue with TXS solubility, the resolution of which yielded...

  16. Technology choice and development in Brazil: An assessment of Brazil's alternative fuel program and the agriculture, manufacturing, energy, and service sectors

    Science.gov (United States)

    Nolan, Lucy A.

    Technology choice profoundly affects a country's development process because capital-intensive and labor-intensive technologies have different socioeconomic linkages within the economy. This research examines the impacts of technology choice through the use of a social accounting matrix (SAM) framework. SAM-based modeling determines the direct and indirect effects of technology choice on development, particularly poverty alleviation in Brazil. Brazil's alternative fuel program was analyzed as a special example of technology choice. Two ethanol production technologies and the gasoline sector were compared; to make the study more robust, labor and capital intensive technologies were evaluated in the production of agriculture, manufacturing, energy, and services. Growth in these economic sectors was examined to assess the effects on employment, factor and household income, energy intensity, and carbon dioxide costs. Poverty alleviation was a focus, so income to unskilled agriculture labor, unskilled non-agriculture labor, and income to rural and urban households in poverty was also analyzed. The major research finding is that overall, labor-intensive technologies generate more employment, factor and household income, environmental and energy benefits to Brazil's economy than capital-intensive technologies. In addition, labor-intensive technologies make a particular contribution to poverty alleviation. The results suggest that policies to encourage the adoption of these technologies, especially in the agriculture and renewable energy sectors, are important because of their intersectoral linkages within the economy. Many studies have shown that Brazil's fuel ethanol program has helped to realize multiple macroeconomic objectives. However, this is the first empirical study to quantify its household income effects. The ethanol industry generated the most household income of the energy sectors. The research confirms a key finding of the appropriate technology literature

  17. Alternative fuel cycles

    International Nuclear Information System (INIS)

    Penn, W.J.

    1979-05-01

    Uranium resource utilization and economic considerations provide incentives to study alternative fuel cycles as future options to the PHWR natural uranium cycle. Preliminary studies to define the most favourable alternatives and their possible introduction dates are discussed. The important and uncertain components which influence option selection are reviewed, including nuclear capacity growth, uranium availability and demand, economic potential, and required technological developments. Finally, a summary of Ontario Hydro's program to further assess cycle selection and define development needs is given. (auth)

  18. TALE factors use two distinct functional modes to control an essential zebrafish gene expression program.

    Science.gov (United States)

    Ladam, Franck; Stanney, William; Donaldson, Ian J; Yildiz, Ozge; Bobola, Nicoletta; Sagerström, Charles G

    2018-06-18

    TALE factors are broadly expressed embryonically and known to function in complexes with transcription factors (TFs) like Hox proteins at gastrula/segmentation stages, but it is unclear if such generally expressed factors act by the same mechanism throughout embryogenesis. We identify a TALE-dependent gene regulatory network (GRN) required for anterior development and detect TALE occupancy associated with this GRN throughout embryogenesis. At blastula stages, we uncover a novel functional mode for TALE factors, where they occupy genomic DECA motifs with nearby NF-Y sites. We demonstrate that TALE and NF-Y form complexes and regulate chromatin state at genes of this GRN. At segmentation stages, GRN-associated TALE occupancy expands to include HEXA motifs near PBX:HOX sites. Hence, TALE factors control a key GRN, but utilize distinct DNA motifs and protein partners at different stages - a strategy that may also explain their oncogenic potential and may be employed by other broadly expressed TFs. © 2018, Ladam et al.

  19. Child hunger and the protective effects of Supplemental Nutrition Assistance Program (SNAP) and alternative food sources among Mexican-origin families in Texas border colonias.

    Science.gov (United States)

    Sharkey, Joseph R; Dean, Wesley R; Nalty, Courtney C

    2013-09-13

    Nutritional health is essential for children's growth and development. Many Mexican-origin children who reside in limited-resource colonias along the Texas-Mexico border are at increased risk for poor nutrition as a result of household food insecurity. However, little is known about the prevalence of child hunger or its associated factors among children of Mexican immigrants. This study determines the prevalence of child hunger and identifies protective and risk factors associated with it in two Texas border areas. This study uses 2009 Colonia Household and Community Food Resource Assessment (C-HCFRA) data from 470 mothers who were randomly recruited by promotora-researchers. Participants from colonias near two small towns in two South Texas counties participated in an in-home community and household assessment. Interviewer-administered surveys collected data in Spanish on sociodemographics, federal food assistance program participation, and food security status. Frequencies and bivariate correlations were examined while a random-effects logistic regression model with backward elimination was used to determine correlates of childhood hunger. Hunger among children was reported in 51% (n = 239) of households in this C-HCFRA sample. Bivariate analyses revealed that hunger status was associated with select maternal characteristics, such as lower educational attainment and Mexican nativity, and household characteristics, including household composition, reliance on friend or neighbor for transportation, food purchase at dollar stores and from neighbors, and participation in school-based nutrition programs. A smaller percentage of households with child hunger participated in school-based nutrition programs (51%) or used alternative food sources, while 131 households were unable to give their child or children a balanced meal during the school year and 145 households during summer months. In the random effects model (RE = small town), increased household

  20. Alternative wastewatersystems

    DEFF Research Database (Denmark)

    Dyck-Madsen, Søren; Hoffmann, Birgitte; Gabriel, Søren

    1999-01-01

    The report:-  Communicates experiences from Swedish buildings from the establishment and running of alternative wastewater systems. Communicates pictures of alternative buildings and wastewater systems in Sweden. Gives a short evaluation of the performance and the sustainability of the systems....

  1. LPS injection reprograms the expression and the 3' UTR of a CAP gene by alternative polyadenylation and the formation of a GAIT element in Ciona intestinalis.

    Science.gov (United States)

    Vizzini, Aiti; Bonura, Angela; Longo, Valeria; Sanfratello, Maria Antonietta; Parrinello, Daniela; Cammarata, Matteo; Colombo, Paolo

    2016-09-01

    The diversification of cellular functions is one of the major characteristics of multicellular organisms which allow cells to modulate their gene expression, leading to the formation of transcripts and proteins with different functions and concentrations in response to different stimuli. CAP genes represent a widespread family of proteins belonging to the cysteine-rich secretory protein, antigen 5 and pathogenesis-related 1 superfamily which, it has been proposed, play key roles in the infection process and the modulation of immune responses in host animals. The ascidian Ciona intestinalis represents a group of proto-chordates with an exclusively innate immune system that has been widely studied in the field of comparative and developmental immunology. Using this biological system, we describe the identification of a novel APA mechanism by which an intronic polyadenylation signal is activated by LPS injection, leading to the formation of a shorter CAP mRNA capable of expressing the first CAP exon plus 19 amino acid residues whose sequence is contained within the first intron of the annotated gene. Furthermore, such an APA event causes the expression of a translational controlling cis-acting GAIT element which is not present in the previously isolated CAP isoform and identified in the 3'-UTR of other immune-related genes, suggesting an intriguing scenario in which both transcriptional and post-transcriptional control mechanisms are involved in the activation of the CAP gene during inflammatory response in C. intestinalis. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Cloning and functional expression of the mitochondrial alternative oxidase gene (aox1) of Aspergillus niger in Lactococcus lactis and its induction by oxidizing conditions.

    Science.gov (United States)

    Papagianni, Maria; Avramidis, Nicholaos

    2012-01-05

    Lactococcus lactis is a widely used food bacterium mainly known for its fermentation metabolism. An important, and for long time overlooked, trait of this species is its ability to perform respiratory metabolism in the presence of heme and under aerobic conditions. There is no evidence however for the presence of an alternative respiration pathway and AOX activity. In this study, a cDNA fragment encoding the mitochondrial alternative oxidase, the enzyme responsible for alternative respiration, from a citric acid producing Aspergillus niger strain was cloned and expressed in L. lactis as a host strain. Expression of aox1 conferred on this organism cyanide-resistant and salicylhydroxamate-sensitive growth. Bioreactor cultures under fully aerobic conditions of the transformed L. lactis showed that the alternative respiratory pathway operates and improves significantly the microorganism's response to oxidizing stress conditions as it enhances biomass production, suppresses lactate formation, and leads to accumulation of large amounts of nisin. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. Detection and quantification of alternative splice sites in Arabidopsis genes AtDCL2 and AtPTB2 with highly sensitive surface enhanced Raman spectroscopy (SERS) and gold nanoprobes.

    Science.gov (United States)

    Kadam, Ulhas S; Schulz, Burkhard; Irudayaraj, Joseph

    2014-05-02

    Alternative splicing (AS) increases the size of the transcriptome and proteome to enhance the physiological capacity of cells. We demonstrate surface enhanced Raman spectroscopy (SERS) in combination with a DNA hybridization analytical platform to identify and quantify AS genes in plants. AS in AtDCL2 and AtPTB2 were investigated using non-fluorescent Raman probes using a 'sandwich assay'. Utilizing Raman probes conjugated to gold nanoparticles we demonstrate the recognition of RNA sequences specific to AtDCL2 and AtPTB2 splice junction variants with detection sensitivity of up to 0.1 fM. Published by Elsevier B.V.

  4. Gene expression programming approach for the estimation of moisture ratio in herbal plants drying with vacuum heat pump dryer

    Science.gov (United States)

    Dikmen, Erkan; Ayaz, Mahir; Gül, Doğan; Şahin, Arzu Şencan

    2017-07-01

    The determination of drying behavior of herbal plants is a complex process. In this study, gene expression programming (GEP) model was used to determine drying behavior of herbal plants as fresh sweet basil, parsley and dill leaves. Time and drying temperatures are input parameters for the estimation of moisture ratio of herbal plants. The results of the GEP model are compared with experimental drying data. The statistical values as mean absolute percentage error, root-mean-squared error and R-square are used to calculate the difference between values predicted by the GEP model and the values actually observed from the experimental study. It was found that the results of the GEP model and experimental study are in moderately well agreement. The results have shown that the GEP model can be considered as an efficient modelling technique for the prediction of moisture ratio of herbal plants.

  5. Forecasting Water Level Fluctuations of Urmieh Lake Using Gene Expression Programming and Adaptive Neuro-Fuzzy Inference System

    Directory of Open Access Journals (Sweden)

    Sepideh Karimi

    2012-06-01

    Full Text Available Forecasting lake level at various prediction intervals is an essential issue in such industrial applications as navigation, water resource planning and catchment management. In the present study, two data driven techniques, namely Gene Expression Programming and Adaptive Neuro-Fuzzy Inference System, were applied for predicting daily lake levels for three prediction intervals. Daily water-level data from Urmieh Lake in Northwestern Iran were used to train, test and validate the used techniques. Three statistical indexes, coefficient of determination, root mean square error and variance accounted for were used to assess the performance of the used techniques. Technique inter-comparisons demonstrated that the GEP surpassed the ANFIS model at each of the prediction intervals. A traditional auto regressive moving average model was also applied to the same data sets; the obtained results were compared with those of the data driven approaches demonstrating superiority of the data driven models to ARMA.

  6. Treatment of Diabetic Mice with a Combination of Ketogenic Diet and Aerobic Exercise via Modulations of PPARs Gene Programs

    Science.gov (United States)

    Xu, Lingyan; Xia, Jie; Wang, Dongmei; Qian, Min

    2018-01-01

    Type 2 diabetes is a prevalent chronic disease arising as a serious public health problem worldwide. Diet intervention is considered to be a critical strategy in glycemic control of diabetic patients. Recently, the low-carbohydrate ketogenic diet is shown to be effective in glycemic control and weight loss. However, hepatic lipid accumulation could be observed in mice treated with ketogenic diet. On the other hand, exercise is a well-known approach for treating nonalcoholic fatty liver disease. We thus hypothesize that the combination of ketogenic diet and exercise could improve insulin sensitivity, while minimizing adverse effect of hepatic steatosis. In order to test this hypothesis, we established diabetic mice model with streptozotocin (STZ) and divided them into control group, ketogenic diet group, and ketogenic diet with aerobic exercise group. We found that after six weeks of intervention, mice treated with ketogenic diet and ketogenic diet combined with exercise both have lower body weights, HbAlc level, HOMA index, and improvements in insulin sensitivity, compared with diabetes group. In addition, mice in ketogenic diet intervention exhibited hepatic steatosis shown by serum and hepatic parameters, as well as histochemistry staining in the liver, which could be largely relieved by exercise. Furthermore, gene analysis revealed that ketogenic diet in combination with exercise reduced PPARγ and lipid synthetic genes, as well as enhancing PPARα and lipid β-oxidation gene program in the liver compared to those in ketogenic diet without exercise. Overall, the present study demonstrated that the combination of ketogenic diet and a moderate-intensity aerobic exercise intervention improved insulin sensitivity in diabetic mice, while avoiding hepatic steatosis, which provided a novel strategy in the combat of diabetes. PMID:29743883

  7. Treatment of Diabetic Mice with a Combination of Ketogenic Diet and Aerobic Exercise via Modulations of PPARs Gene Programs.

    Science.gov (United States)

    Zhang, Qiang; Xu, Lingyan; Xia, Jie; Wang, Dongmei; Qian, Min; Ding, Shuzhe

    2018-01-01

    Type 2 diabetes is a prevalent chronic disease arising as a serious public health problem worldwide. Diet intervention is considered to be a critical strategy in glycemic control of diabetic patients. Recently, the low-carbohydrate ketogenic diet is shown to be effective in glycemic control and weight loss. However, hepatic lipid accumulation could be observed in mice treated with ketogenic diet. On the other hand, exercise is a well-known approach for treating nonalcoholic fatty liver disease. We thus hypothesize that the combination of ketogenic diet and exercise could improve insulin sensitivity, while minimizing adverse effect of hepatic steatosis. In order to test this hypothesis, we established diabetic mice model with streptozotocin (STZ) and divided them into control group, ketogenic diet group, and ketogenic diet with aerobic exercise group. We found that after six weeks of intervention, mice treated with ketogenic diet and ketogenic diet combined with exercise both have lower body weights, HbAlc level, HOMA index, and improvements in insulin sensitivity, compared with diabetes group. In addition, mice in ketogenic diet intervention exhibited hepatic steatosis shown by serum and hepatic parameters, as well as histochemistry staining in the liver, which could be largely relieved by exercise. Furthermore, gene analysis revealed that ketogenic diet in combination with exercise reduced PPAR γ and lipid synthetic genes, as well as enhancing PPAR α and lipid β -oxidation gene program in the liver compared to those in ketogenic diet without exercise. Overall, the present study demonstrated that the combination of ketogenic diet and a moderate-intensity aerobic exercise intervention improved insulin sensitivity in diabetic mice, while avoiding hepatic steatosis, which provided a novel strategy in the combat of diabetes.

  8. How alternative are alternative fuels?

    OpenAIRE

    Soffritti, Tiziana; Danielis, Romeo

    1998-01-01

    Could alternative fuel vehicles contribute to a substantial reduction of air pollution? Is there a market for alternative fuel vehicles? Could a market be created via a pollution tax? The article answers these questions on the basis of the available estimates.

  9. Alternative detox.

    Science.gov (United States)

    Ernst, E

    2012-01-01

    The concept that alternative therapies can eliminate toxins and toxicants from the body, i.e. 'alternative detox' (AD) is popular. Selected textbooks and articles on the subject of AD. The principles of AD make no sense from a scientific perspective and there is no clinical evidence to support them. The promotion of AD treatments provides income for some entrepreneurs but has the potential to cause harm to patients and consumers. In alternative medicine, simplistic but incorrect concepts such as AD abound. AREAS TIMELY FOR RESEARCH: All therapeutic claims should be scientifically tested before being advertised-and AD cannot be an exception.

  10. Prognostic significance of equivocal human epidermal growth factor receptor 2 results and clinical utility of alternative chromosome 17 genes in patients with invasive breast cancer: A cohort study.

    Science.gov (United States)

    Sneige, Nour; Hess, Kenneth R; Multani, Asha S; Gong, Yun; Ibrahim, Nuhad K

    2017-04-01

    The 2013 testing guidelines for determining the human epidermal growth factor receptor 2 (HER2) status include new cutoff points for the HER2/chromosome enumeration probe 17 (CEP17) ratio and the average HER2 copy number per cell, and they recommend using a reflex test with alternative chromosome 17 probes (Ch17Ps) to resolve equivocal HER2 results. This study sought to determine the clinical utility of alternative Ch17Ps in equivocal cases and the effects of equivocal results and/or a change in the HER2 status on patients' outcomes. The University of Texas MD Anderson Cancer Center database of HER2 dual-probe fluorescence in situ hybridization results from 2000 to 2010 was searched for cases of invasive breast cancer with HER2/CEP17 ratios Cancer 2017;123:1115-1123. © 2016 American Cancer Society. © 2016 American Cancer Society.

  11. The function and developmental expression of alternatively spliced isoforms of amphioxus and Xenopus laevis Pax2/5/8 genes: revealing divergence at the invertebrate to vertebrate transition

    Czech Academy of Sciences Publication Activity Database

    Short, S.; Kozmik, Zbyněk; Holland, L. Z.

    2012-01-01

    Roč. 318, č. 7 (2012), s. 555-571 ISSN 1552-5007 R&D Projects: GA ČR GAP305/10/2141; GA MŠk LH12047 Grant - others:NSF(US) MCB 06-20019 Institutional research plan: CEZ:AV0Z50520514 Keywords : Pax2/5/8 * alternative splicing * eye development * amphioxus * Xenopus laevis Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.123, year: 2012

  12. Differential tissue distribution, developmental programming, estrogen regulation and promoter characteristics of cyp19 genes in teleost fish.

    Science.gov (United States)

    Callard, G V; Tchoudakova, A V; Kishida, M; Wood, E

    2001-12-01

    Teleost fish are characterized by exceptionally high levels of brain estrogen biosynthesis when compared to the brains of other vertebrates or to the ovaries of the same fish. Goldfish (Carassius auratus) and zebrafish (Danio rerio) have utility as complementary models for understanding the molecular basis and functional significance of exaggerated neural estrogen biosynthesis. Multiple cytochrome P450 aromatase (P450arom) cDNAs that derive from separate gene loci (cyp19a and cyp19b) are differentially expressed in brain (P450aromB>A) and ovary (P450aromA>B) and have a different developmental program (B>A) and response to estrogen upregulation (B only). As measured by increased P450aromB mRNA, a functional estrogen response system is first detected 24-48 h post-fertilization (hpf), consistent with the onset of estrogen receptor (ER) expression (alpha, beta, and gamma). The 5'-flanking region of the cyp19b gene has a TATA box, two estrogen response elements (EREs), an ERE half-site (ERE1/2), a nerve growth factor inducible-B protein (NGFI-B)/Nur77 responsive element (NBRE) binding site, and a sequence identical to the zebrafish GATA-2 gene neural specific enhancer. The cyp19a promoter region has TATA and CAAT boxes, a steroidogenic factor-1 (SF-1) binding site, and two aryl hydrocarbon receptor (AhR)/AhR nuclear translocator factor (ARNT) binding motifs. Both genes have multiple potential SRY/SOX binding sites (16 and 8 in cyp19b and cyp19a, respectively). Luciferase reporters have basal promoter activity in GH3 cells, but differences (a>b) are opposite to fish pituitary (b>a). When microinjected into fertilized zebrafish eggs, a cyp19b promoter-driven green fluorescent protein (GFP) reporter (but not cyp19a) is expressed in neurons of 30-48 hpf embryos, most prominently in retinal ganglion cells (RGCs) and their projections to optic tectum. Further studies are required to identify functionally relevant cis-elements and cellular factors, and to determine the

  13. Visual expression analysis of the responses of the alternative oxidase gene (aox1) to heat shock, oxidative, and osmotic stresses in conidia of citric acid-producing Aspergillus niger.

    Science.gov (United States)

    Honda, Yuki; Hattori, Takasumi; Kirimura, Kohtaro

    2012-03-01

    The citric acid-producing filamentous fungus Aspergillus niger WU-2223L shows cyanide-insensitive respiration catalyzed by alternative oxidase in addition to the cytochrome pathway. Sequence analysis of the 5' flanking region of the alternative oxidase gene (aox1) revealed a potential heat shock element (HSE) and a stress response element (STRE). We have previously confirmed aox1 expression in conidia. In this study, to confirm whether the upstream region of aox1 responds to various stresses, we used a visual expression analysis system for single-cell conidia of the A. niger strain AOXEGFP-1. This strain harbored a fusion gene comprising aox1 and egfp, which encodes the enhanced green fluorescent protein (EGFP). The fluorescence intensity of EGFP increased in conidia of A. niger AOXEGFP-1 that were subjected to heat shock at 35-45 °C, oxidative stress by exposure to 5mM paraquat or 1 mM t-butylhydroperoxide, or osmotic stresses by exposure to 0.5 M KCl or 1.0 M mannitol. These results indicate that the putative HSE and STRE in the upstream region of aox1 directly or indirectly respond to heat shock, oxidative, and osmotic stresses. Copyright © 2011 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  14. Employee use and perceived benefit of a complementary and alternative medicine wellness clinic at a major military hospital: evaluation of a pilot program.

    Science.gov (United States)

    Duncan, Alaine D; Liechty, Janet M; Miller, Cathy; Chinoy, Gail; Ricciardi, Richard

    2011-09-01

    The objectives of this study were to examine the feasibility of a weekly on-site complementary and alternative medicine (CAM) wellness clinic for staff at a military hospital, and to describe employees' perceptions of program effectiveness. The study setting was the Restore & Renew(®) Wellness Clinic at a United States Department of Defense hospital. The subjects were hospital nurses, physicians, clinicians, support staff, and administrators. The walk-in wellness clinic was open 8:00 am-2:00 pm 1 day a week. Participants selected one or more modalities each visit: ear acupuncture, clinical acupressure, and Zero Balancing.(®) A self-report survey was done after each clinic visit to evaluate clinic features and perceived impact on stress-related symptoms, compassion for patients, sleep, and workplace or personal relationships. Surveys completed after first-time and repeat visits (n=2,756 surveys) indicated that most participants agreed or strongly agreed they felt more relaxed after sessions (97.9%), less stress (94.5%), more energy (84.3%), and less pain (78.8%). Ninety-seven percent (97%) would recommend it to a co-worker. Among surveys completed after five or more visits, more than half (59%-85%) strongly agreed experiencing increased compassion with patients, better sleep, improved mood, and more ease in relations with co-workers. Perceived benefits were sustained and enhanced by number of visits. The most frequently reported health habit changes were related to exercise, stress reduction, diet/nutrition, and weight loss. This evaluation suggests that a hospital-based wellness clinic based on CAM principles and modalities is feasible, well-utilized, and perceived by most participants to have positive health benefits related to stress reduction at work, improved mood and sleep, and lifestyle.

  15. Asymmetric division and differential gene expression during a bacterial developmental program requires DivIVA.

    Directory of Open Access Journals (Sweden)

    Prahathees Eswaramoorthy

    2014-08-01

    Full Text Available Sporulation in the bacterium Bacillus subtilis is a developmental program in which a progenitor cell differentiates into two different cell types, the smaller of which eventually becomes a dormant cell called a spore. The process begins with an asymmetric cell division event, followed by the activation of a transcription factor, σF, specifically in the smaller cell. Here, we show that the structural protein DivIVA localizes to the polar septum during sporulation and is required for asymmetric division and the compartment-specific activation of σF. Both events are known to require a protein called SpoIIE, which also localizes to the polar septum. We show that DivIVA copurifies with SpoIIE and that DivIVA may anchor SpoIIE briefly to the assembling polar septum before SpoIIE is subsequently released into the forespore membrane and recaptured at the polar septum. Finally, using super-resolution microscopy, we demonstrate that DivIVA and SpoIIE ultimately display a biased localization on the side of the polar septum that faces the smaller compartment in which σF is activated.

  16. Caenorhabditis elegans expressing the Saccharomyces cerevisiae NADH alternative dehydrogenase Ndi1p, as a tool to identify new genes involved in complex I related diseases

    Directory of Open Access Journals (Sweden)

    Raynald eCossard

    2015-06-01

    Full Text Available Isolated complex I deficiencies are one of the most commonly observed biochemical features in patients suffering from mitochondrial disorders. In the majority of these clinical cases the molecular bases of the diseases remain unknown suggesting the involvement of unidentified factors that are critical for complex I function.The Saccharomyces cerevisiae NDI1 gene, encoding the mitochondrial internal NADH dehydrogenase was previously shown to complement a complex I deficient strain in Caenorhabitis elegans with notable improvements in reproduction, whole organism respiration. These features indicate that Ndi1p can functionally integrate the respiratory chain, allowing complex I deficiency complementation. Taking into account the Ndi1p ability to bypass complex I, we evaluate the possibility to extend the range of defects/mutations causing complex I deficiencies that can be alleviated by NDI1 expression.We report here that NDI1 expressing animals unexpectedly exhibit a slightly shortened lifespan, a reduction in the progeny and a depletion of the mitochondrial genome. However, Ndi1p is expressed and targeted to the mitochondria as a functional protein that confers rotenone resistance to those animals and without affecting their respiration rate and ATP content.We show that the severe embryonic lethality level caused by the RNAi knockdowns of complex I structural subunit encoding genes (e.g. NDUFV1, NDUFS1, NDUFS6, NDUFS8 or GRIM-19 human orthologs in wild type animals is significantly reduced in the Ndi1p expressing worm.All together these results open up the perspective to identify new genes involved in complex I function, assembly or regulation by screening an RNAi library of genes leading to embryonic lethality that should be rescued by NDI1 expression.

  17. Retrotransposons of the Tnt1B family are mobile in Nicotiana plumbaginifolia and can induce alternative splicing of the host gene upon insertion.

    Science.gov (United States)

    Leprinc, A S; Grandbastien, M A; Christian, M

    2001-11-01

    Active retrotransposons have been identified in Nicotiana plumbaginifolia by their ability to disrupt the nitrate reductase gene in chlorate-resistant mutants selected from protoplast-derived cultures. In mutants E23 and F97, two independent insertions of Tnp2, a new retrotransposon closely related to the tobacco Tnt1 elements, were detected in the nitrate reductase gene. These two Tnp2 elements are members of the Tnt1B subfamily which shows that Tnt1B elements can be active and mutagenic in the N. plumbaginifolia genome. Furthermore, these results suggest that Tnt1B is the most active family of Tntl elements in N. plumbaginifolia, whereas in tobacco only members of the Tnt1A subfamily were found inserted in the nitrate reductase gene. The transcriptional regulations of Tnp2 and Tnt1A elements are most probably different due to non-conserved U3 regions. Our results thus support the hypothesis that different Nicotiana species contain different active Tntl subfamilies and that only one active Tntl subfamily might be maintained in each of these species. The Tnp2 insertion found in the F97 mutant was found to be spliced out of the nitrate reductase mRNA by activation of cryptic donor and acceptor sites in the nitrate reductase and the Tnp2 sequences respectively.

  18. Alternative REST Splicing Underappreciated

    OpenAIRE

    Chen, Guo-Lin; Miller, Gregory

    2017-01-01

    As a major orchestrator of the cellular epigenome, the repressor element-1 silencing transcription factor (REST) can either repress or activate thousands of genes depending on cellular context, suggesting a highly context-dependent REST function tuned by environmental cues. While REST shows cell-type non-selective active transcription, an N-terminal REST4 isoform caused by alternative splicing - inclusion of an extra exon (N3c) which introduces a pre-mature stop codon - has been implicated in...

  19. Monthly streamflow forecasting using continuous wavelet and multi-gene genetic programming combination

    Science.gov (United States)

    Hadi, Sinan Jasim; Tombul, Mustafa

    2018-06-01

    Streamflow is an essential component of the hydrologic cycle in the regional and global scale and the main source of fresh water supply. It is highly associated with natural disasters, such as droughts and floods. Therefore, accurate streamflow forecasting is essential. Forecasting streamflow in general and monthly streamflow in particular is a complex process that cannot be handled by data-driven models (DDMs) only and requires pre-processing. Wavelet transformation is a pre-processing technique; however, application of continuous wavelet transformation (CWT) produces many scales that cause deterioration in the performance of any DDM because of the high number of redundant variables. This study proposes multigene genetic programming (MGGP) as a selection tool. After the CWT analysis, it selects important scales to be imposed into the artificial neural network (ANN). A basin located in the southeast of Turkey is selected as case study to prove the forecasting ability of the proposed model. One month ahead downstream flow is used as output, and downstream flow, upstream, rainfall, temperature, and potential evapotranspiration with associated lags are used as inputs. Before modeling, wavelet coherence transformation (WCT) analysis was conducted to analyze the relationship between variables in the time-frequency domain. Several combinations were developed to investigate the effect of the variables on streamflow forecasting. The results indicated a high localized correlation between the streamflow and other variables, especially the upstream. In the models of the standalone layout where the data were entered to ANN and MGGP without CWT, the performance is found poor. In the best-scale layout, where the best scale of the CWT identified as the highest correlated scale is chosen and enters to ANN and MGGP, the performance increased slightly. Using the proposed model, the performance improved dramatically particularly in forecasting the peak values because of the inclusion

  20. Genetic analysis of complement C1s deficiency associated with systemic lupus erythematosus highlights alternative splicing of normal C1s gene

    DEFF Research Database (Denmark)

    Amano, Mariane T; Ferriani, Virgínia P L; Florido, Marlene P C

    2008-01-01

    Deficiencies of complement proteins of the classical pathway are strongly associated with the development of autoimmune diseases. Deficiency of C1r has been observed to occur concomitantly with deficiency in C1s and 9 out of 15 reported cases presented systemic lupus erythematosus (SLE). Here, we...... describe a family in which all four children are deficient in C1s but only two of them developed SLE. Hemolytic activity mediated by the alternative and the lectin pathways were normal, but classical pathway activation was absent in all children's sera. C1s was undetectable, while in the parents' sera...

  1. Genomewide Analysis of Aryl Hydrocarbon Receptor Binding Targets Reveals an Extensive Array of Gene Clusters that Control Morphogenetic and Developmental Programs

    Science.gov (United States)

    Sartor, Maureen A.; Schnekenburger, Michael; Marlowe, Jennifer L.; Reichard, John F.; Wang, Ying; Fan, Yunxia; Ma, Ci; Karyala, Saikumar; Halbleib, Danielle; Liu, Xiangdong; Medvedovic, Mario; Puga, Alvaro

    2009-01-01

    Background The vertebrate aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that regulates cellular responses to environmental polycyclic and halogenated compounds. The naive receptor is believed to reside in an inactive cytosolic complex that translocates to the nucleus and induces transcription of xenobiotic detoxification genes after activation by ligand. Objectives We conducted an integrative genomewide analysis of AHR gene targets in mouse hepatoma cells and determined whether AHR regulatory functions may take place in the absence of an exogenous ligand. Methods The network of AHR-binding targets in the mouse genome was mapped through a multipronged approach involving chromatin immunoprecipitation/chip and global gene expression signatures. The findings were integrated into a prior functional knowledge base from Gene Ontology, interaction networks, Kyoto Encyclopedia of Genes and Genomes pathways, sequence motif analysis, and literature molecular concepts. Results We found the naive receptor in unstimulated cells bound to an extensive array of gene clusters with functions in regulation of gene expression, differentiation, and pattern specification, connecting multiple morphogenetic and developmental programs. Activation by the ligand displaced the receptor from some of these targets toward sites in the promoters of xenobiotic metabolism genes. Conclusions The vertebrate AHR appears to possess unsuspected regulatory functions that may be potential targets of environmental injury. PMID:19654925

  2. Engineering the central pathways in Lactococcus lactis: functional expression of the phosphofructokinase (pfk) and alternative oxidase (aox1) genes from Aspergillus niger in Lactococcus lactis facilitates improved carbon conversion rates under oxidizing conditions.

    Science.gov (United States)

    Papagianni, Maria; Avramidis, Nicholaos

    2012-08-10

    The present work describes a novel central pathway engineering method that has been designed with the aim to increase the carbon conversion rates under oxidizing conditions in L. lactis fermentations. The nisin producer L. lactis ATCC11454 strain has been genetically engineered by cloning a truncated version of the phosphofructokinase gene (pfk13), along with the pkaC, encoding for the catalytic subunit of cAMP-dependent protein kinase, and the alternative oxidase (aox1) genes of A. niger. Functional expression of the above genes resulted in enhanced PFK activity and the introduction of AOX activity and alternative respiration in the presence of a source of heme in the substrate, under fully aerobic growth conditions. The constructed strain is capable of fermenting high concentrations of glucose as was demonstrated in a series of glucostat fed-batch fermentations with glucose levels maintained at 55, 138 and 277 mM. The high maximum specific uptake rate of glucose of 1.8 mMs(-1)gCDW(-1) at 277 mM glucose is characteristic of the improved ability of the microorganism to handle elevated glucose concentrations under conditions otherwise causing severe reduction of PFK activity. The increased carbon flow through glycolysis led to increased protein synthesis that was reflected in increased biomass and nisin levels. The pfk 13-pkaC-aox1-transformant strain's fermentation at 277 mM glucose gave a final biomass concentration of 7.5 g/l and nisin activity of 14,000 IU/ml which is, compared to the parental strain's production levels at its optimal 55 mM glucose, increased by a factor of 2.34 for biomass and 4.37 for nisin. Copyright © 2012 Elsevier Inc. All rights reserved.

  3. Cosmic alternatives?

    Science.gov (United States)

    Gregory, Ruth

    2009-04-01

    "Cosmologists are often in error but never in doubt." This pithy characterization by the Soviet physicist Lev Landau sums up the raison d'être of Facts and Speculations in Cosmology. Authors Jayant Narlikar and Geoffrey Burbidge are proponents of a "steady state" theory of cosmology, and they argue that the cosmological community has become fixated on a "Big Bang" dogma, suppressing alternative viewpoints. This book very much does what it says on the tin: it sets out what is known in cosmology, and puts forward the authors' point of view on an alternative to the Big Bang.

  4. Cardiac-enriched BAF chromatin-remodeling complex subunit Baf60c regulates gene expression programs essential for heart development and function

    Directory of Open Access Journals (Sweden)

    Xin Sun

    2018-01-01

    Full Text Available How chromatin-remodeling complexes modulate gene networks to control organ-specific properties is not well understood. For example, Baf60c (Smarcd3 encodes a cardiac-enriched subunit of the SWI/SNF-like BAF chromatin complex, but its role in heart development is not fully understood. We found that constitutive loss of Baf60c leads to embryonic cardiac hypoplasia and pronounced cardiac dysfunction. Conditional deletion of Baf60c in cardiomyocytes resulted in postnatal dilated cardiomyopathy with impaired contractile function. Baf60c regulates a gene expression program that includes genes encoding contractile proteins, modulators of sarcomere function, and cardiac metabolic genes. Many of the genes deregulated in Baf60c null embryos are targets of the MEF2/SRF co-factor Myocardin (MYOCD. In a yeast two-hybrid screen, we identified MYOCD as a BAF60c interacting factor; we showed that BAF60c and MYOCD directly and functionally interact. We conclude that Baf60c is essential for coordinating a program of gene expression that regulates the fundamental functional properties of cardiomyocytes.

  5. The mouse Gtl2 gene is differentially expressed during embryonic development, encodes multiple alternatively spliced transcripts, and may act as an RNA.

    Science.gov (United States)

    Schuster-Gossler, K; Bilinski, P; Sado, T; Ferguson-Smith, A; Gossler, A

    1998-06-01

    We have isolated a novel mouse gene (Gtl2) from the site of a gene trap integration (Gtl2lacZ) that gave rise to developmentally regulated lacZ expression, and a dominant parental-origin-dependent phenotype. Heterozygous Gtl2lacZ mice that inherited the transgene from the father showed a proportionate dwarfism phenotype, whereas the penetrance and expressivity of the phenotype was strongly reduced in Gtl2lacZ mice that inherited the transgene from the mother. Gtl2 expression is highly similar to the beta-galactosidase staining pattern, and is down-regulated but not abolished in mice carrying the Gtl2lacZ insertion. In early postimplantation embryos, Gtl2 is expressed in the visceral yolk sac and embryonic ectoderm. During subsequent development and organogenesis, Gtl2 transcripts are abundant in the paraxial mesoderm closely correlated with myogenic differentiation, in parts of the central nervous system, and in the epithelial ducts of developing excretory organs. The Gtl2 gene gives rise to various differentially spliced transcripts, which contain multiple small open reading frames (ORF). However, none of the ATG codons of these ORFs is in the context of a strong Kozak consensus sequence for initiation of translation, suggesting that Gtl2 might function as an RNA. Nuclear Gtl2 RNA was detected in a temporally and spatially regulated manner, and partially processed Gtl2 transcripts were readily detected in Northern blot hybridizations of polyadenylated RNA, suggesting that primary Gtl2 transcripts are differently processed in various cell types during development. Gtl2 transcript levels are present in parthenogenic embryos but may be reduced, consistent with the pattern of inheritance of the Gtl2lacZ phenotype.

  6. Development of an objective gene expression panel as an alternative to self-reported symptom scores in human influenza challenge trials.

    Science.gov (United States)

    Muller, Julius; Parizotto, Eneida; Antrobus, Richard; Francis, James; Bunce, Campbell; Stranks, Amanda; Nichols, Marshall; McClain, Micah; Hill, Adrian V S; Ramasamy, Adaikalavan; Gilbert, Sarah C

    2017-06-08

    Influenza challenge trials are important for vaccine efficacy testing. Currently, disease severity is determined by self-reported scores to a list of symptoms which can be highly subjective. A more objective measure would allow for improved data analysis. Twenty-one volunteers participated in an influenza challenge trial. We calculated the daily sum of scores (DSS) for a list of 16 influenza symptoms. Whole blood collected at baseline and 24, 48, 72 and 96 h post challenge was profiled on Illumina HT12v4 microarrays. Changes in gene expression most strongly correlated with DSS were selected to train a Random Forest model and tested on two independent test sets consisting of 41 individuals profiled on a different microarray platform and 33 volunteers assayed by qRT-PCR. 1456 probes are significantly associated with DSS at 1% false discovery rate. We selected 19 genes with the largest fold change to train a random forest model. We observed good concordance between predicted and actual scores in the first test set (r = 0.57; RMSE = -16.1%) with the greatest agreement achieved on samples collected approximately 72 h post challenge. Therefore, we assayed samples collected at baseline and 72 h post challenge in the second test set by qRT-PCR and observed good concordance (r = 0.81; RMSE = -36.1%). We developed a 19-gene qRT-PCR panel to predict DSS, validated on two independent datasets. A transcriptomics based panel could provide a more objective measure of symptom scoring in future influenza challenge studies. Trial registration Samples were obtained from a clinical trial with the ClinicalTrials.gov Identifier: NCT02014870, first registered on December 5, 2013.

  7. Duplicated Gephyrin Genes Showing Distinct Tissue Distribution and Alternative Splicing Patterns Mediate Molybdenum Cofactor Biosynthesis, Glycine Receptor Clustering, and Escape Behavior in Zebrafish*

    Science.gov (United States)

    Ogino, Kazutoyo; Ramsden, Sarah L.; Keib, Natalie; Schwarz, Günter; Harvey, Robert J.; Hirata, Hiromi

    2011-01-01

    Gephyrin mediates the postsynaptic clustering of glycine receptors (GlyRs) and GABAA receptors at inhibitory synapses and molybdenum-dependent enzyme (molybdoenzyme) activity in non-neuronal tissues. Gephyrin knock-out mice show a phenotype resembling both defective glycinergic transmission and molybdenum cofactor (Moco) deficiency and die within 1 day of birth due to starvation and dyspnea resulting from deficits in motor and respiratory networks, respectively. To address whether gephyrin function is conserved among vertebrates and whether gephyrin deficiency affects molybdoenzyme activity and motor development, we cloned and characterized zebrafish gephyrin genes. We report here that zebrafish have two gephyrin genes, gphna and gphnb. The former is expressed in all tissues and has both C3 and C4 cassette exons, and the latter is expressed predominantly in the brain and spinal cord and harbors only C4 cassette exons. We confirmed that all of the gphna and gphnb splicing isoforms have Moco synthetic activity. Antisense morpholino knockdown of either gphna or gphnb alone did not disturb synaptic clusters of GlyRs in the spinal cord and did not affect touch-evoked escape behaviors. However, on knockdown of both gphna and gphnb, embryos showed impairments in GlyR clustering in the spinal cord and, as a consequence, demonstrated touch-evoked startle response behavior by contracting antagonistic muscles simultaneously, instead of displaying early coiling and late swimming behaviors, which are executed by side-to-side muscle contractions. These data indicate that duplicated gephyrin genes mediate Moco biosynthesis and control postsynaptic clustering of GlyRs, thereby mediating key escape behaviors in zebrafish. PMID:20843816

  8. Flagellar-phase variation: isolation of the rh1 gene

    International Nuclear Information System (INIS)

    Silverman, M.; Zieg, J.; Simon, M.

    1979-01-01

    In Salmonella, expression of flagellar antigen alternates between two serotypes (phases) encoded by two genes, H1 and H2. The mechanism which controls the alternative expression of the H1 and H2 genes was examined by cloning these genes and the genetic elements which control their activity on hybrid vehicles in Escherichia coli. H2 gene activity was shown to be controlled by a recombinational switch located adjacent to the H2 gene. Activity of the H1 gene is thought to be repressed, when the H2 gene is expressed, by the product of another gene, rhl (repressor of H1), which is controlled coordinately with the H2 gene. In this report, we describe the construction of hybrid lambda vehicles which contain, in addition to the H2 gene, a genetic activity corresponding to rhl. Variation of flagellar antigens analogous to that observed in Salmonella was observed when E. coli strains were transduced with the hybrid lambda. By using the lambda H2rhl hybrid to program protein syntheis in uv-irradiated cells, the synthesis of a polypeptide was correlated with rhl gene product activity. We conclude that the H2 region consists of two cotranscribed genes, H2 and rhl. The expression of both gene products is regulated by the same recombinational event

  9. Growing Alternatives

    DEFF Research Database (Denmark)

    Bagger-Petersen, Mai Corlin

    2014-01-01

    From 2014, Anhui Province will pilot a reform of the residential land market in China, thus integrating rural Anhui in the national housing market. In contrast, artist and activist Ou Ning has proposed the Bishan time money currency, intending to establish an alternative economic circuit in Bishan...

  10. Alternative Veier

    DEFF Research Database (Denmark)

    Kruse, Tove Elisabeth; Salamonsen, Anita

    reflektioner omkring patienters brug af og erfaringer med alternativ behandling. Patientorganisationer, organisatoner for alternative behandlere og organisationer for læger og medicinstuderende har læst bogens patienthistorier og deres perspektiver lægges frem. Til slut i bogen diskuteres betydningen af de...

  11. Activity-Dependent NPAS4 Expression and the Regulation of Gene Programs Underlying Plasticity in the Central Nervous System

    Directory of Open Access Journals (Sweden)

    José Fernando Maya-Vetencourt

    2013-01-01

    Full Text Available The capability of the brain to change functionally in response to sensory experience is most active during early stages of development but it decreases later in life when major alterations of neuronal network structures no longer take place in response to experience. This view has been recently challenged by experimental strategies based on the enhancement of environmental stimulation levels, genetic manipulations, and pharmacological treatments, which all have demonstrated that the adult brain retains a degree of plasticity that allows for a rewiring of neuronal circuitries over the entire life course. A hot spot in the field of neuronal plasticity centres on gene programs that underlie plastic phenomena in adulthood. Here, I discuss the role of the recently discovered neuronal-specific and activity-dependent transcription factor NPAS4 as a critical mediator of plasticity in the nervous system. A better understanding of how modifications in the connectivity of neuronal networks occur may shed light on the treatment of pathological conditions such as brain damage or disease in adult life, some of which were once considered untreatable.

  12. Evaluation of liquefaction potential of soil based on standard penetration test using multi-gene genetic programming model

    Science.gov (United States)

    Muduli, Pradyut; Das, Sarat

    2014-06-01

    This paper discusses the evaluation of liquefaction potential of soil based on standard penetration test (SPT) dataset using evolutionary artificial intelligence technique, multi-gene genetic programming (MGGP). The liquefaction classification accuracy (94.19%) of the developed liquefaction index (LI) model is found to be better than that of available artificial neural network (ANN) model (88.37%) and at par with the available support vector machine (SVM) model (94.19%) on the basis of the testing data. Further, an empirical equation is presented using MGGP to approximate the unknown limit state function representing the cyclic resistance ratio (CRR) of soil based on developed LI model. Using an independent database of 227 cases, the overall rates of successful prediction of occurrence of liquefaction and non-liquefaction are found to be 87, 86, and 84% by the developed MGGP based model, available ANN and the statistical models, respectively, on the basis of calculated factor of safety (F s) against the liquefaction occurrence.

  13. Programming of stress-related behavior and epigenetic neural gene regulation in mice offspring through maternal exposure to predator odor

    Science.gov (United States)

    St-Cyr, Sophie; McGowan, Patrick O.

    2015-01-01

    Perinatal stress mediated through the mother can lead to long-term alterations in stress-related phenotypes in offspring. The capacity for adaptation to adversity in early life depends in part on the life history of the animal. This study was designed to examine the behavioral and neural response in adult offspring to prenatal exposure to predator odor: an ethologically-relevant psychological stressor. Pregnant mice were exposed daily to predator odors or distilled water control over the second half of the pregnancy. Predator odor exposure lead to a transient decrease in maternal care in the mothers. As adults, the offspring of predator odor-exposed mothers showed increased anti-predator behavior, a predator-odor induced decrease in activity and, in female offspring, an increased corticosterone (CORT) response to predator odor exposure. We found a highly specific response among stress-related genes within limbic brain regions. Transcript abundance of Corticotropin-releasing hormone receptor 1 (CRHR1) was elevated in the amygdala in adult female offspring of predator odor-exposed mothers. In the hippocampus of adult female offspring, decreased Brain-derived neurotrophic factor (BDNF) transcript abundance was correlated with a site-specific decrease in DNA methylation in Bdnf exon IV, indicating the potential contribution of this epigenetic mechanism to maternal programming by maternal predator odor exposure. These data indicate that maternal predator odor exposure alone is sufficient to induce an altered stress-related phenotype in adulthood, with implications for anti-predator behavior in offspring. PMID:26082698

  14. A potential benefit of albinism in Astyanax cavefish: downregulation of the oca2 gene increases tyrosine and catecholamine levels as an alternative to melanin synthesis.

    Science.gov (United States)

    Bilandžija, Helena; Ma, Li; Parkhurst, Amy; Jeffery, William R

    2013-01-01

    Albinism, the loss of melanin pigmentation, has evolved in a diverse variety of cave animals but the responsible evolutionary mechanisms are unknown. In Astyanax mexicanus, which has a pigmented surface dwelling form (surface fish) and several albino cave-dwelling forms (cavefish), albinism is caused by loss of function mutations in the oca2 gene, which operates during the first step of the melanin synthesis pathway. In addition to albinism, cavefish have evolved differences in behavior, including feeding and sleep, which are under the control of the catecholamine system. The catecholamine and melanin synthesis pathways diverge after beginning with the same substrate, L-tyrosine. Here we describe a novel relationship between the catecholamine and melanin synthesis pathways in Astyanax. Our results show significant increases in L-tyrosine, dopamine, and norepinephrine in pre-feeding larvae and adult brains of Pachón cavefish relative to surface fish. In addition, norepinephrine is elevated in cavefish adult kidneys, which contain the teleost homologs of catecholamine synthesizing adrenal cells. We further show that the oca2 gene is expressed during surface fish development but is downregulated in cavefish embryos. A key finding is that knockdown of oca2 expression in surface fish embryos delays the development of pigmented melanophores and simultaneously increases L-tyrosine and dopamine. We conclude that a potential evolutionary benefit of albinism in Astyanax cavefish may be to provide surplus L-tyrosine as a precursor for the elevated catecholamine synthesis pathway, which could be important for adaptation to the challenging cave environment.

  15. A potential benefit of albinism in Astyanax cavefish: downregulation of the oca2 gene increases tyrosine and catecholamine levels as an alternative to melanin synthesis.

    Directory of Open Access Journals (Sweden)

    Helena Bilandžija

    Full Text Available Albinism, the loss of melanin pigmentation, has evolved in a diverse variety of cave animals but the responsible evolutionary mechanisms are unknown. In Astyanax mexicanus, which has a pigmented surface dwelling form (surface fish and several albino cave-dwelling forms (cavefish, albinism is caused by loss of function mutations in the oca2 gene, which operates during the first step of the melanin synthesis pathway. In addition to albinism, cavefish have evolved differences in behavior, including feeding and sleep, which are under the control of the catecholamine system. The catecholamine and melanin synthesis pathways diverge after beginning with the same substrate, L-tyrosine. Here we describe a novel relationship between the catecholamine and melanin synthesis pathways in Astyanax. Our results show significant increases in L-tyrosine, dopamine, and norepinephrine in pre-feeding larvae and adult brains of Pachón cavefish relative to surface fish. In addition, norepinephrine is elevated in cavefish adult kidneys, which contain the teleost homologs of catecholamine synthesizing adrenal cells. We further show that the oca2 gene is expressed during surface fish development but is downregulated in cavefish embryos. A key finding is that knockdown of oca2 expression in surface fish embryos delays the development of pigmented melanophores and simultaneously increases L-tyrosine and dopamine. We conclude that a potential evolutionary benefit of albinism in Astyanax cavefish may be to provide surplus L-tyrosine as a precursor for the elevated catecholamine synthesis pathway, which could be important for adaptation to the challenging cave environment.

  16. Alternative expression of vacuolar iron transporter and ferritin genes leads to blue/purple coloration of flowers in tulip cv. 'Murasakizuisho'.

    Science.gov (United States)

    Shoji, Kazuaki; Momonoi, Kazumi; Tsuji, Tosiaki

    2010-02-01

    Flowers of tulip cv. 'Murasakizuisho' have a purple perianth except for the bottom region, which is blue in color even though it has the same anthocyanin, delphinidin 3-O-rutinoside, as the entire perianth. The development of the blue coloration in the perianth bottom is due to complexation by anthocyanin, flavonol and iron (Fe), as well as a vacuolar iron transporter, TgVit1. Although transient expression of TgVit1 in the purple cells led to a color change to light blue, the coloration of the transformed cells did not coincide with the dark blue color of the cells of the perianth bottom. We thought that another factor is required for the blue coloration of the cells of perianth bottom. To examine the effect of ferritin (FER), an Fe storage protein, on blue color development, we cloned an FER gene (TgFER1) and performed expression analyses. TgFER1 transcripts were found in the cells located in the upper region of the petals along with purple color development by anthocyanin and were not found in the blue cells of the perianth bottom. This gene expression is in contrast to that of TgVit1, expressed only in the cells of the perianth bottom. Co-expression of TgVIT1 and TgFER-RNAi, constructed for suppressing endogenous TgFER1 by RNA interference (RNAi), changed the purple petal cells to a dark blue color similar to that of the natural perianth bottom. These results strongly suggest that TgVit1 expression and TgFER1 suppression are critical for the development of blue color in the perianth bottom.

  17. Energy alternatives

    International Nuclear Information System (INIS)

    Sweet, C.

    1987-01-01

    The designated successor to fossil fuels is nuclear fission/fusion and that turns out to be problematic. Alternative Energy Systems have great potential but political forces seem to be hampering their development and introduction. The technologies are flexible in their use and scale of operation. The learning curve will not be short but neither will it be as long and as costly as nuclear power. It is time that this is recognised and some serious rethinking takes place in what presently passes for energy policies both in the industrialised countries and in the Third World. Alternative energy systems are defined and some of them which are relevant to the United Kingdom are discussed. (author)

  18. Alternative Fuel News, Vol. 3 No. 2

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-09-23

    This special issue of Alternative Fuel News highlights the Fifth National Clean Cities Conference held in Louisville, Kentucky. The momentum for the program is stronger than ever and the coalitions are working to propel the alternative fuel industry forward.

  19. Alternative splicing of exon 17 and a missense mutation in exon 20 of the insulin receptor gene in two brothers with a novel syndrome of insulin resistance (congenital fiber-type disproportion myopathy)

    DEFF Research Database (Denmark)

    Vorwerk, P; Christoffersen, C T; Müller, J

    1999-01-01

    to be compound heterozygotes for mutations in the IR gene. The maternal allele was alternatively spliced in exon 17 due to a point mutation in the -1 donor splice site of the exon. The abnormal skipping of exon 17 shifts the amino acid reading frame and leads to a truncated IR, missing the entire tyrosine kinase......The insulin receptor (IR) in two brothers with a rare syndrome of congenital muscle fiber type disproportion myopathy (CFTDM) associated with diabetes and severe insulin resistance was studied. By direct sequencing of Epstein-Barr virus-transformed lymphocytes both patients were found...... domain. In the correct spliced variant, the point mutation is silent and results in a normally translated IR. The paternal allele carries a missense mutation in the tyrosine kinase domain. All three cDNA variants were present in the lymphocytes of the patients. Purified IR from 293 cells overexpressing...

  20. Alternative Learning Environments in the Elementary School.

    Science.gov (United States)

    Davis, Eugene D.

    This paper outlines a program utilized in the Countryside School which offers alternative learning environments in the elementary school. The program includes (1) semi-departmentalization; (2) team teaching; and (3) an open-alternatives program. Each of these areas is outlined and fully discussed in terms of student and parent needs. (YRJ)