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Sample records for arabidopsis orphan protein-coding

  1. Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes.

    Directory of Open Access Journals (Sweden)

    Casey R Richardson

    Full Text Available BACKGROUND: MicroRNAs (miRNAs and trans-acting small-interfering RNAs (tasi-RNAs are small (20-22 nt long RNAs (smRNAs generated from hairpin secondary structures or antisense transcripts, respectively, that regulate gene expression by Watson-Crick pairing to a target mRNA and altering expression by mechanisms related to RNA interference. The high sequence homology of plant miRNAs to their targets has been the mainstay of miRNA prediction algorithms, which are limited in their predictive power for other kingdoms because miRNA complementarity is less conserved yet transitive processes (production of antisense smRNAs are active in eukaryotes. We hypothesize that antisense transcription and associated smRNAs are biomarkers which can be computationally modeled for gene discovery. PRINCIPAL FINDINGS: We explored rice (Oryza sativa sense and antisense gene expression in publicly available whole genome tiling array transcriptome data and sequenced smRNA libraries (as well as C. elegans and found evidence of transitivity of MIRNA genes similar to that found in Arabidopsis. Statistical analysis of antisense transcript abundances, presence of antisense ESTs, and association with smRNAs suggests several hundred Arabidopsis 'orphan' hypothetical genes are non-coding RNAs. Consistent with this hypothesis, we found novel Arabidopsis homologues of some MIRNA genes on the antisense strand of previously annotated protein-coding genes. A Support Vector Machine (SVM was applied using thermodynamic energy of binding plus novel expression features of sense/antisense transcription topology and siRNA abundances to build a prediction model of miRNA targets. The SVM when trained on targets could predict the "ancient" (deeply conserved class of validated Arabidopsis MIRNA genes with an accuracy of 84%, and 76% for "new" rapidly-evolving MIRNA genes. CONCLUSIONS: Antisense and smRNA expression features and computational methods may identify novel MIRNA genes and other non

  2. Arabidopsis TH2 Encodes the Orphan Enzyme Thiamin Monophosphate Phosphatase[OPEN

    Science.gov (United States)

    Niehaus, Thomas D.; Hasnain, Ghulam; Gidda, Satinder K.; Nguyen, Thuy N.D.; Anderson, Erin M.; Brown, Greg; Yakunin, Alexander F.; de Crécy-Lagard, Valérie; Gregory, Jesse F.

    2016-01-01

    To synthesize the cofactor thiamin diphosphate (ThDP), plants must first hydrolyze thiamin monophosphate (ThMP) to thiamin, but dedicated enzymes for this hydrolysis step were unknown and widely doubted to exist. The classical thiamin-requiring th2-1 mutation in Arabidopsis thaliana was shown to reduce ThDP levels by half and to increase ThMP levels 5-fold, implying that the THIAMIN REQUIRING2 (TH2) gene product could be a dedicated ThMP phosphatase. Genomic and transcriptomic data indicated that TH2 corresponds to At5g32470, encoding a HAD (haloacid dehalogenase) family phosphatase fused to a TenA (thiamin salvage) family protein. Like the th2-1 mutant, an insertional mutant of At5g32470 accumulated ThMP, and the thiamin requirement of the th2-1 mutant was complemented by wild-type At5g32470. Complementation tests in Escherichia coli and enzyme assays with recombinant proteins confirmed that At5g32470 and its maize (Zea mays) orthologs GRMZM2G148896 and GRMZM2G078283 are ThMP-selective phosphatases whose activity resides in the HAD domain and that the At5g32470 TenA domain has the expected thiamin salvage activity. In vitro and in vivo experiments showed that alternative translation start sites direct the At5g32470 protein to the cytosol and potentially also to mitochondria. Our findings establish that plants have a dedicated ThMP phosphatase and indicate that modest (50%) ThDP depletion can produce severe deficiency symptoms. PMID:27677881

  3. Non-Protein Coding RNAs

    CERN Document Server

    Walter, Nils G; Batey, Robert T

    2009-01-01

    This book assembles chapters from experts in the Biophysics of RNA to provide a broadly accessible snapshot of the current status of this rapidly expanding field. The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, highlighting just one example of a large number of non-protein coding RNAs. Because non-protein coding RNAs outnumber protein coding genes in mammals and other higher eukaryotes, it is now thought that the complexity of organisms is correlated with the fraction of their genome that encodes non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic transposons, higher-level organization of eukaryotic chromosomes, and gene expression itself are found to largely be directed by non-protein coding RNAs. The biophysical study of these RNAs employs X-ray crystallography, NMR, ensemble and single molecule fluorescence spectroscopy, optical tweezers, cryo-electron microscopy, and ot...

  4. Orphan drugs

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    Goločorbin-Kon Svetlana

    2013-01-01

    Full Text Available Introduction. Drugs used for treatment of rare diseases are known worldwide under the term of orphan drugs because pharmaceutical companies have not been interested in ”adopting” them, that is in investing in research, developing and producing these drugs. This kind of policy has been justified by the fact that these drugs are targeted for small markets, that only a small number of patients is available for clinical trials, and that large investments are required for the development of drugs meant to treat diseases whose pathogenesis has not yet been clarified in majority of cases. The aim of this paper is to present previous and present status of orphan drugs in Serbia and other countries. The beginning of orphan drugs development. This problem was first recognized by Congress of the United States of America in January 1983, and when the ”Orphan Drug Act” was passed, it was a turning point in the development of orphan drugs. This law provides pharmaceutical companies with a series of reliefs, both financial ones that allow them to regain funds invested into the research and development and regulatory ones. Seven years of marketing exclusivity, as a type of patent monopoly, is the most important relief that enables companies to make large profits. Conclusion. There are no sufficient funds and institutions to give financial support to the patients. It is therefore necessary to make health professionals much more aware of rare diseases in order to avoid time loss in making the right diagnosis and thus to gain more time to treat rare diseases. The importance of discovery, development and production of orphan drugs lies in the number of patients whose life quality can be improved significantly by administration of these drugs as well as in the number of potential survivals resulting from the treatment with these drugs. [Projekat Ministarstva nauke Republike Srbije, br. III 41012

  5. Fomepizole (orphan medical).

    Science.gov (United States)

    Hantson, P

    2001-06-01

    Orphan Medical has developed fomepizole as a potential treatment for both ethylene glycol and methanol poisoning. The drug was launched as Antizol in January 1998 for the treatment of ethylene glycol poisoning [273949] after US marketing approval was grantedin December 1997 [271563]. It has also received US approval for methanol poisoning [393217] and UK approval for ethylene glycol poisoning [329495]. In 1999, Orphan Medical's partner, Cambridge Laboratories, intended to pursue European approval under the mutual recognition procedure [329495]. However, by September 2000, Cambridge Laboratories had discontinued their involvement with fomepizole and IDIS World Medicines had licensed the rights to distribute the drug in the UK [412142]. In February 2000, the Canadian Therapeutic Products Programme (TPP) granted fomepizole Priority Review, provided that an NDA was submitted by March 14, 2000 [354665]. In August 2000, the TPP accepted this NDA and set a target date for approval in the fourth quarter of 2000 [379474]. The TPP granted fomepizole a Notice of Compliance permitting the sale of fomepizole in Canada in December 2000. The company's marketing partner in Canada, Paladin Labs had launched fomepizole by January 2001 [396953]. In June 2000, Tucker Anthony Cleary Gull stated that the Orphan Drug status which Orphan Medical had obtained for fomepizole would provide marketing exclusivity through December 2004. The analysts also stated that fomepizole had accounted for 40% of Orphan Medical's revenue in financial year 1999, although +/- 30% of sales were estimated to be due to stockpiling [409606].

  6. Modifier effects between regulatory and protein-coding variation.

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    Antigone S Dimas

    2008-10-01

    Full Text Available Genome-wide associations have shown a lot of promise in dissecting the genetics of complex traits in humans with single variants, yet a large fraction of the genetic effects is still unaccounted for. Analyzing genetic interactions between variants (epistasis is one of the potential ways forward. We investigated the abundance and functional impact of a specific type of epistasis, namely the interaction between regulatory and protein-coding variants. Using genotype and gene expression data from the 210 unrelated individuals of the original four HapMap populations, we have explored the combined effects of regulatory and protein-coding single nucleotide polymorphisms (SNPs. We predict that about 18% (1,502 out of 8,233 nsSNPs of protein-coding variants are differentially expressed among individuals and demonstrate that regulatory variants can modify the functional effect of a coding variant in cis. Furthermore, we show that such interactions in cis can affect the expression of downstream targets of the gene containing the protein-coding SNP. In this way, a cis interaction between regulatory and protein-coding variants has a trans impact on gene expression. Given the abundance of both types of variants in human populations, we propose that joint consideration of regulatory and protein-coding variants may reveal additional genetic effects underlying complex traits and disease and may shed light on causes of differential penetrance of known disease variants.

  7. Modifier effects between regulatory and protein-coding variation.

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    Dimas, Antigone S; Stranger, Barbara E; Beazley, Claude; Finn, Robert D; Ingle, Catherine E; Forrest, Matthew S; Ritchie, Matthew E; Deloukas, Panos; Tavaré, Simon; Dermitzakis, Emmanouil T

    2008-10-01

    Genome-wide associations have shown a lot of promise in dissecting the genetics of complex traits in humans with single variants, yet a large fraction of the genetic effects is still unaccounted for. Analyzing genetic interactions between variants (epistasis) is one of the potential ways forward. We investigated the abundance and functional impact of a specific type of epistasis, namely the interaction between regulatory and protein-coding variants. Using genotype and gene expression data from the 210 unrelated individuals of the original four HapMap populations, we have explored the combined effects of regulatory and protein-coding single nucleotide polymorphisms (SNPs). We predict that about 18% (1,502 out of 8,233 nsSNPs) of protein-coding variants are differentially expressed among individuals and demonstrate that regulatory variants can modify the functional effect of a coding variant in cis. Furthermore, we show that such interactions in cis can affect the expression of downstream targets of the gene containing the protein-coding SNP. In this way, a cis interaction between regulatory and protein-coding variants has a trans impact on gene expression. Given the abundance of both types of variants in human populations, we propose that joint consideration of regulatory and protein-coding variants may reveal additional genetic effects underlying complex traits and disease and may shed light on causes of differential penetrance of known disease variants.

  8. The Detectability of Orphan Afterglows

    CERN Document Server

    Piran, E N T

    2002-01-01

    The realization that GRBs release a rather constant amount of energy implies that the post jet-break afterglow evolution would be rather universal and for a given redshift they should be detected up to a fixed observer angle. We estimate the observed magnitude and the implied detectability of orphan afterglows. We show that orphan afterglows would be detectable only up to rather small ($\\sim 10^o$) angles away from the GRB jet axis. Thus a detection orphan afterglow would generally correspond to a "near-miss" of the GRB whose jet was pointing just slightly away from us. Both theoretical and phenomenological estimates of the rate of orphan afterglows suffer from a rather large uncertainty. With our "canonical" parameters we expect a dozen transients that would arise from orphan GRBs in the SDSS and a comparable number of transients in a dedicated 2M class telescope operating full time in an orphan afterglow search.

  9. Orphan regulations for orphan drug development in India

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    D Saikiran Reddy

    2014-01-01

    Full Text Available Through this review article an attempt has been made to put forward the challenges faced by rare disease drug development and the current scenario of orphan drug legislations in India. An orphan drug is a pharmaceutical agent that is used to treat a rare medical condition (viz., glioblastoma multiforme, nocardiosis, Tourette syndrome, etc. Developed countries such as United States (US, Europe, Japan, and Australia have laid down legal framework for combating rare diseases. A path breaking legislation was formulated by the US government way back in 1983, known as "Orphan Drugs Act (ODA." The key purpose of ODA was to incentivize R and D initiatives for such drugs to treat millions of population suffering from "orphan diseases." Though the percentage of patients suffering from "rare diseases" in India is reportedly higher than the world average, unfortunately even today such cases get little help from our government. Indian government should also encourage its domestic pharmaceutical industry to get engaged in research for orphan drugs by putting an "ODA" in place and extending financial support, and regulatory concessions like smaller and shorter clinical trials, without further delay. Thus, India could well-demonstrate that the concept of orphan drugs for orphan diseases is really not orphan in India.

  10. Orphan drugs: the regulatory environment.

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    Franco, Pedro

    2013-02-01

    The definition of a rare disease is not universal and depends on the legislation and policies adopted by each region or country. The main objective of this article is to describe and discuss the legal framework and the regulatory environment of orphan drugs worldwide. Some reflections and discussions on the need for specific orphan drug legislation or policies are described at length. Furthermore, some aspects of the history of each region in respect of the orphan drug legislation evolution are outlined. This article describes and compares the orphan drug legislation or policies of the following countries or regions: United Sates of America (US), European Union (EU), Japan, Australia, Singapore, Taiwan and Canada. The incentives described in the orphan drug legislations or policies, the criteria for designation of orphan status and the authorisation process of an orphan drug are also described and compared. The legislations and policies are to some extent similar but not the same. It is important to understand the main differences among all available legislative systems to improve the international collaboration in the field of orphan drugs and rare diseases.

  11. Drug repositioning for orphan diseases.

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    Sardana, Divya; Zhu, Cheng; Zhang, Minlu; Gudivada, Ranga C; Yang, Lun; Jegga, Anil G

    2011-07-01

    The need and opportunity to discover therapeutics for rare or orphan diseases are enormous. Due to limited prevalence and/or commercial potential, of the approximately 6000 orphan diseases (defined by the FDA Orphan Drug Act as industry. The fact that drug development is complicated, time-consuming and expensive with extremely low success rates only adds to the low rate of therapeutics available for orphan diseases. An alternative and efficient strategy to boost the discovery of orphan disease therapeutics is to find connections between an existing drug product and orphan disease. Drug Repositioning or Drug Repurposing--finding a new indication for a drug--is one way to maximize the potential of a drug. The advantages of this approach are manifold, but rational drug repositioning for orphan diseases is not trivial and poses several formidable challenges--pharmacologically and computationally. Most of the repositioned drugs currently in the market are the result of serendipity. One reason the connection between drug candidates and their potential new applications are not identified in an earlier or more systematic fashion is that the underlying mechanism 'connecting' them is either very intricate and unknown or indirect or dispersed and buried in an ever-increasing sea of information, much of which is emerging only recently and therefore is not well organized. In this study, we will review some of these issues and the current methodologies adopted or proposed to overcome them and translate chemical and biological discoveries into safe and effective orphan disease therapeutics.

  12. Selection on protein-coding genes of natural cyanobacterial populations

    NARCIS (Netherlands)

    Mes, T.H.M.; Doeleman, M.W.; Lodders, N.; Nübel, U.; Stal, L.J.

    2006-01-01

    We examined the distribution of synonymous and non-synonymous changes in 12 protein-coding genes of natural populations of cyanobacteria to infer changes in gene functionality. By comparing mutation distributions within and across species using the McDonald–Kreitman test, we found data sets to conta

  13. AIDS ORPHANS GET SPECIAL VISITOR

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Chinese Premier Wen Jiabao visits AIDS orphans in Shangcai County,central China’s Henan Province,on November 30,a day before the 20th World AIDS Day. The region of Shangcai has the highest concentration of people living with HIV/AIDS in China. The Chinese Government has released a package of policies that offer people living with HIV/AIDS free medicine,health checks and consultations,as well as free schooling to AIDS orphans.

  14. The Detectability of Orphan Afterglows

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    Nakar, Ehud; Piran, Tsvi; Granot, Jonathan

    2002-11-01

    The realization that gamma-ray bursts (GRBs) release a constant amount of energy implies that post-jet-break afterglow evolution is largely universal. For a given redshift, all afterglows should be detected up to a fixed observer angle. We estimate the observed magnitude and the implied detectability of orphan afterglows. We show that for reasonable limiting magnitudes (mlim=25), orphan afterglows will typically be detected from small (~10°) angles away from the GRB jet axis. A detected orphan afterglow generally corresponds to a ``near miss'' of a GRB whose jet is pointing just slightly away from us. With our most optimistic parameters, we expect that 15 orphan afterglows will be recorded in the Sloan Digital Sky Survey, and 35 transients will be recorded in a dedicated 2 m class telescope operating full time for a year in an orphan afterglow search. The rate is smaller by a factor of 15 for our ``canonical'' parameters. We show that for a given facility, an optimal survey should be shallower, covering a larger area, rather than deeper. The limiting magnitude should not be, however, lower than ~23, as in this case, more transients from on-axis GRBs will be discovered than orphan afterglows. About 15% of the transients could be discovered with a second exposure of the same area provided that it follows after 3, 4, and 8 days for mlim=23, 25, and 27, respectively.

  15. Annotation of the protein coding regions of the equine genome

    DEFF Research Database (Denmark)

    Hestand, Matthew S.; Kalbfleisch, Theodore S.; Coleman, Stephen J.

    2015-01-01

    Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced m...... and appear to be small errors in the equine reference genome, since they are also identified as homozygous variants by genomic DNA resequencing of the reference horse. Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross...

  16. Regulatory Proteolysis in Arabidopsis-Pathogen Interactions

    OpenAIRE

    Miklós Pogány; Tamás Dankó; Evelin Kámán-Tóth; Ildikó Schwarczinger; Zoltán Bozsó

    2015-01-01

    Approximately two and a half percent of protein coding genes in Arabidopsis encode enzymes with known or putative proteolytic activity. Proteases possess not only common housekeeping functions by recycling nonfunctional proteins. By irreversibly cleaving other proteins, they regulate crucial developmental processes and control responses to environmental changes. Regulatory proteolysis is also indispensable in interactions between plants and their microbial pathogens. Proteolytic cleavage is s...

  17. RNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes.

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    Zheng, Qi; Rowley, M Jordan; Böhmdorfer, Gudrun; Sandhu, Davinder; Gregory, Brian D; Wierzbicki, Andrzej T

    2013-01-01

    Transcriptional gene silencing controls transposons and other repetitive elements through RNA-directed DNA methylation (RdDM) and heterochromatin formation. A key component of the Arabidopsis RdDM pathway is ARGONAUTE4 (AGO4), which associates with siRNAs to mediate DNA methylation. Here, we show that AGO4 preferentially targets transposable elements embedded within promoters of protein-coding genes. This pattern of AGO4 binding cannot be simply explained by the sequences of AGO4-bound siRNAs; instead, AGO4 binding to specific gene promoters is also mediated by long non-coding RNAs (lncRNAs) produced by RNA polymerase V. lncRNA-mediated AGO4 binding to gene promoters directs asymmetric DNA methylation to these genomic regions and is involved in regulating the expression of targeted genes. Finally, AGO4 binding overlaps sites of DNA methylation affected by the biotic stress response. Based on these findings, we propose that the targets of AGO4-directed RdDM are regulatory units responsible for controlling gene expression under specific environmental conditions.

  18. Are payers treating orphan drugs differently?

    OpenAIRE

    Joshua P. Cohen; Felix, Abigail

    2014-01-01

    Background: Some orphan drugs can cost hundreds of thousands of dollars annually per patient. As a result, payer sensitivity to the cost of orphan drugs is rising, particularly in light of increased numbers of new launches in recent years. In this article, we examine payer coverage in the United States, England and Wales, and the Netherlands of outpatient orphan drugs approved between 1983 and 2012, as well as the 11 most expensive orphan drugs.Methods: We collected data from drug regulatory ...

  19. Orphan drugs: expensive yet necessary.

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    Hyry, H I; Roos, J C P; Cox, T M

    2015-04-01

    Whether the prices of certain orphan treatments are justified is highly controversial. One argument is that such therapies should not be funded through the public purse or private health plans because a patient with a rare disease requires more than their 'fair share' of a limited health care budget. Orphan medications can also be denied because they fare poorly in the cost-effectiveness assessments of drugs. This paper takes the unusual line that life-saving treatments should be provided regardless of their cost. This contention is based on the Harvard philosopher John Rawls' theory of justice. We offer three rules to limit the use of cost-effectiveness approaches: efficiency assessments should not be deployed (i) when the choice is between an only treatment and no treatment, or to (ii) prioritise between different patients and patient groups. However a well considered cost efficiency calculation may have its place (iii) where a patient has a choice between two or more equally safe and effective treatments. We rebut potential objections to this analysis, and conclude that there has been a tendency to classify appeals for orphan treatments as a minority interest and in conflict with the aims of public health and society at large. Rawls' concept of societal justice shows that a distinction between the individual and society in this context is bogus. The funding of orphan therapies is as much a matter for public health as the funding of treatments for other conditions. Treatment must not be withheld on economic grounds.

  20. Evaluating the protein coding potential of exonized transposable element sequences

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    Borodovsky Mark

    2007-11-01

    Full Text Available Abstract Background Transposable element (TE sequences, once thought to be merely selfish or parasitic members of the genomic community, have been shown to contribute a wide variety of functional sequences to their host genomes. Analysis of complete genome sequences have turned up numerous cases where TE sequences have been incorporated as exons into mRNAs, and it is widely assumed that such 'exonized' TEs encode protein sequences. However, the extent to which TE-derived sequences actually encode proteins is unknown and a matter of some controversy. We have tried to address this outstanding issue from two perspectives: i-by evaluating ascertainment biases related to the search methods used to uncover TE-derived protein coding sequences (CDS and ii-through a probabilistic codon-frequency based analysis of the protein coding potential of TE-derived exons. Results We compared the ability of three classes of sequence similarity search methods to detect TE-derived sequences among data sets of experimentally characterized proteins: 1-a profile-based hidden Markov model (HMM approach, 2-BLAST methods and 3-RepeatMasker. Profile based methods are more sensitive and more selective than the other methods evaluated. However, the application of profile-based search methods to the detection of TE-derived sequences among well-curated experimentally characterized protein data sets did not turn up many more cases than had been previously detected and nowhere near as many cases as recent genome-wide searches have. We observed that the different search methods used were complementary in the sense that they yielded largely non-overlapping sets of hits and differed in their ability to recover known cases of TE-derived CDS. The probabilistic analysis of TE-derived exon sequences indicates that these sequences have low protein coding potential on average. In particular, non-autonomous TEs that do not encode protein sequences, such as Alu elements, are frequently

  1. Orphans as agents for change

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    Gjotterud Sigrid Mari

    2015-12-01

    Full Text Available Transformative experiences can happen at unexpected times, in unexpected ways. This paper tells the story of how a gift of a goat can lead to the transformation of a life. Many organisations globally are engaged in a struggle to overcome poverty and injustice by providing livestock as a means for transformation. The animals in themselves are not enough for the transformed lives; they can be a valuable starting point. In the Uluguru Mountains in Tanzania, a Tanzanian and a Norwegian together took one such initiative in order to support teen-age orphans, one of the most vulnerable groups in the community who were struggling to survive. As practitioners and researchers, the four authors had been taking part in the development of the Mgeta Orphan Education Foundation (MOEF, which had developed through action learning/action research. Selected students received a goat and training, and the opportunity to join and develop a network of orphans throughout the region. In this article, we discuss the benefits and challenges the orphaned youngsters face when joining the foundation. How do they benefit from having the goat and what are the challenges, how do they learn and how do they contribute to fellow farmers in their communities? We claim that many of the students have experienced transformation, and provide examples to give evidence of this claim. However, the students are not the only ones who are transforming; so are we who, as co-researchers, have had the opportunity to play a role in and witness their efforts.

  2. "Foreign Mothers" of Chinese Orphans

    Institute of Scientific and Technical Information of China (English)

    1995-01-01

    Since Shanghai opened to the outside, a large number of foreign wives have lived there. They have organized a charitable association which has attracted people’s attention. They donate money and material goods to the Shanghai Children’s Welfare House, as well as contributing their maternal love to the Chinese orphans. Every week, no matter whether it is raining or windy, they visit, holding the children in their arms and feeding them. Some of them

  3. Orphan drug: Development trends and strategies.

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    Sharma, Aarti; Jacob, Abraham; Tandon, Manas; Kumar, Dushyant

    2010-10-01

    The growth of pharma industries has slowed in recent years because of various reasons such as patent expiries, generic competition, drying pipelines, and increasingly stringent regulatory guidelines. Many blockbuster drugs will loose their exclusivity in next 5 years. Therefore, the current economic situation plus the huge generic competition shifted the focus of pharmaceutical companies from the essential medicines to the new business model - niche busters, also called orphan drugs. Orphan drugs may help pharma companies to reduce the impact of revenue loss caused by patent expiries of blockbuster drugs. The new business model of orphan drugs could offer an integrated healthcare solution that enables pharma companies to develop newer areas of therapeutics, diagnosis, treatment, monitoring, and patient support. Incentives for drug development provided by governments, as well as support from the FDA and EU Commission in special protocols, are a further boost for the companies developing orphan drugs. Although there may still be challenges ahead for the pharmaceutical industry, orphan drugs seem to offer the key to recovery and stability within the market. In our study, we have compared the policies and orphan drug incentives worldwide alongwith the challenges faced by the pharmaceutical companies. Recent developments are seen in orphan drug approval, the various drugs in orphan drug pipeline, and the future prospectives for orphan drugs and diseases.

  4. Observations from One Champion of AIDS Orphans

    Institute of Scientific and Technical Information of China (English)

    HUJIA

    2004-01-01

    ON December 1, 2003,the CCTV program News Research aired a special feature on AIDS orphans at the Love and Care Family AIDS orphanage. The public attention this raised brought large social donations for the orphanage and signaled greater public efforts to help AIDS orphans.

  5. 78 FR 35117 - Orphan Drug Regulations

    Science.gov (United States)

    2013-06-12

    ... from companies and trade associations of companies that are marketing or hope to market orphan drugs... trade associations of companies that are marketing or hope to market orphan drugs. On the whole, the..., sponsors could even potentially ``game'' approvals by seeking successive narrow approvals of a drug...

  6. World health dilemmas: Orphan and rare diseases, orphan drugs and orphan patients

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    Kontoghiorghe, Christina N; Andreou, Nicholas; Constantinou, Katerina; Kontoghiorghes, George J

    2014-01-01

    According to global annual estimates hunger/malnutrition is the major cause of death (36 of 62 million). Cardiovascular diseases and cancer (5.44 of 13.43 million) are the major causes of death in developed countries, while lower respiratory tract infections, human immunodeficiency virus infection/acquired immunodeficiency syndrome, diarrhoeal disease, malaria and tuberculosis (10.88 of 27.12 million) are the major causes of death in developing countries with more than 70% of deaths occurring in children. The majority of approximately 800 million people with other rare diseases, including 100000 children born with thalassaemia annually receive no treatment. There are major ethical dilemmas in dealing with global health issues such as poverty and the treatment of orphan and rare diseases. Of approximately 50000 drugs about 10% are orphan drugs, with annual sales of the latter approaching 100 billion USD. In comparison, the annual revenue in 2009 from the top 12 pharmaceutical companies in Western countries was 445 billion USD and the top drug, atorvastatin, reached 100 billion USD. In the same year, the total government expenditure for health in the developing countries was 410 billion USD with only 6%-7% having been received as aid from developed countries. Drugs cost the National Health Service in the United Kingdom more than 20 billion USD or 10% of the annual health budget. Uncontrollable drug prices and marketing policies affect global health budgets, clinical practice, patient safety and survival. Fines of 5.3 billion USD were imposed on two pharmaceutical companies in the United States, the regulatory authority in France was replaced and clinicians were charged with bribery in order to overcome recent illegal practises affecting patient care. High expenditure for drug development is mainly related to marketing costs. However, only 2 million USD was spent developing the drug deferiprone (L1) for thalassaemia up to the stage of multicentre clinical trials. The

  7. Orphans in the Dead Sea Scrolls

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    Gideon R. Kotzé

    2016-05-01

    Full Text Available This study investigates the literary references to orphans in writings amongst the Qumran texts that were written in Hebrew and can be associated with the sectarian Qumran movement. The study focuses on passages where forms of the word יתום are used. These include the Damascus Document (CD 6:16–17, Hodayot (1QHa 13:22 and Barkhi Nafshia (4Q434 1 i 2. The investigation concludes that the references to orphans in these passages do not have the same rhetorical functions. In CD 6, the wordings of authoritative scriptures are adapted to portray orphans and widows as the victims of wrongdoing. In 1QHa and 4Q434, however, orphans are mentioned in hymns that praise the Lord’s positive treatment of needy people

  8. QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions.

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    Li, Ling; Zheng, Wenguang; Zhu, Yanbing; Ye, Huaxun; Tang, Buyun; Arendsee, Zebulun W; Jones, Dallas; Li, Ruoran; Ortiz, Diego; Zhao, Xuefeng; Du, Chuanlong; Nettleton, Dan; Scott, M Paul; Salas-Fernandez, Maria G; Yin, Yanhai; Wurtele, Eve Syrkin

    2015-11-24

    The allocation of carbon and nitrogen resources to the synthesis of plant proteins, carbohydrates, and lipids is complex and under the control of many genes; much remains to be understood about this process. QQS (Qua-Quine Starch; At3g30720), an orphan gene unique to Arabidopsis thaliana, regulates metabolic processes affecting carbon and nitrogen partitioning among proteins and carbohydrates, modulating leaf and seed composition in Arabidopsis and soybean. Here the universality of QQS function in modulating carbon and nitrogen allocation is exemplified by a series of transgenic experiments. We show that ectopic expression of QQS increases soybean protein independent of the genetic background and original protein content of the cultivar. Furthermore, transgenic QQS expression increases the protein content of maize, a C4 species (a species that uses 4-carbon photosynthesis), and rice, a protein-poor agronomic crop, both highly divergent from Arabidopsis. We determine that QQS protein binds to the transcriptional regulator AtNF-YC4 (Arabidopsis nuclear factor Y, subunit C4). Overexpression of AtNF-YC4 in Arabidopsis mimics the QQS-overexpression phenotype, increasing protein and decreasing starch levels. NF-YC, a component of the NF-Y complex, is conserved across eukaryotes. The NF-YC4 homologs of soybean, rice, and maize also bind to QQS, which provides an explanation of how QQS can act in species where it does not occur endogenously. These findings are, to our knowledge, the first insight into the mechanism of action of QQS in modulating carbon and nitrogen allocation across species. They have major implications for the emergence and function of orphan genes, and identify a nontransgenic strategy for modulating protein levels in crop species, a trait of great agronomic significance.

  9. Rare diseases and orphan drugs

    Directory of Open Access Journals (Sweden)

    Domenica Taruscio

    2011-01-01

    Full Text Available According to the Regulation (EC N. 141/2000 of the European Parliament and of the Council, rare diseases are life-threatening or chronically debilitating conditions, affecting no more than 5 in 10 000 persons in the European Community. It is estimated that between 6000 to 8000 distinct rare diseases affect up to 6% of the total EU population. Therefore, these conditions can be considered rare if taken individually but they affect a significant proportion of the European population when considered as a single group. Several initiatives have been undertaken at international, European and national level to tackle public health as well as research issues related to the prevention, diagnosis, treatment and surveillance of these diseases. The development of innovative and effective medical products for their diagnosis and treatment is frequently hampered by several factors, including the limited knowledge of their natural history, the difficulties in setting up clinical studies due to the limited numbers of patients affected by a specific disease, the weak interest of sponsors due to the restricted market opportunities. Therefore, incentives and other facilitations have been adopted in many parts of the world, including in the EU, in order to facilitate the development and commercialization of diagnostic tools and treatments devoted to rare diseases. This paper illustrates mainly the European initiatives and will discuss the problematic and controversial aspects surrounding orphan drugs. Finally, activities and measures adopted in Italy are presented.

  10. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

    DEFF Research Database (Denmark)

    Lin, Michael F; Kheradpour, Pouya; Washietl, Stefan;

    2011-01-01

    conservation compared to typical protein-coding genes—especially at synonymous sites. In this study, we use genome alignments of 29 placental mammals to systematically locate short regions within human ORFs that show conspicuously low estimated rates of synonymous substitution across these species. The 29......-species alignment provides statistical power to locate more than 10,000 such regions with resolution down to nine-codon windows, which are found within more than a quarter of all human protein-coding genes and contain ~2% of their synonymous sites. We collect numerous lines of evidence that the observed...

  11. A-to-I editing of protein coding and noncoding RNAs.

    Science.gov (United States)

    Mallela, Arka; Nishikura, Kazuko

    2012-01-01

    Adenosine deaminase acting on RNA (ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA) substrates. Inosine pairs preferentially with cytidine, as opposed to uridine; therefore, ADAR editing alters the sequence and base pairing properties of both protein-coding and non-coding RNA. Editing can directly alter the sequence of protein-coding transcripts and modify splicing, or affect a variety of non-coding targets, including microRNA, small interfering RNA, viral transcripts, and repeat elements such as Alu and LINE. Such editing has a wide range of physiological effects, including modification of targets in the brain and in disease states.

  12. A survey of orphan enzyme activities

    Directory of Open Access Journals (Sweden)

    Pouliot Yannick

    2007-07-01

    Full Text Available Abstract Background Using computational database searches, we have demonstrated previously that no gene sequences could be found for at least 36% of enzyme activities that have been assigned an Enzyme Commission number. Here we present a follow-up literature-based survey involving a statistically significant sample of such "orphan" activities. The survey was intended to determine whether sequences for these enzyme activities are truly unknown, or whether these sequences are absent from the public sequence databases but can be found in the literature. Results We demonstrate that for ~80% of sampled orphans, the absence of sequence data is bona fide. Our analyses further substantiate the notion that many of these enzyme activities play biologically important roles. Conclusion This survey points toward significant scientific cost of having such a large fraction of characterized enzyme activities disconnected from sequence data. It also suggests that a larger effort, beginning with a comprehensive survey of all putative orphan activities, would resolve nearly 300 artifactual orphans and reconnect a wealth of enzyme research with modern genomics. For these reasons, we propose that a systematic effort to identify the cognate genes of orphan enzymes be undertaken.

  13. ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells

    Science.gov (United States)

    Müller, Raphael; Weirick, Tyler; John, David; Militello, Giuseppe; Chen, Wei; Dimmeler, Stefanie; Uchida, Shizuka

    2016-09-01

    Increasing evidence indicates the presence of long noncoding RNAs (lncRNAs) is specific to various cell types. Although lncRNAs are speculated to be more numerous than protein-coding genes, the annotations of lncRNAs remain primitive due to the lack of well-structured schemes for their identification and description. Here, we introduce a new knowledge database “ANGIOGENES” (http://angiogenes.uni-frankfurt.de) to allow for in silico screening of protein-coding genes and lncRNAs expressed in various types of endothelial cells, which are present in all tissues. Using the latest annotations of protein-coding genes and lncRNAs, publicly-available RNA-seq data was analyzed to identify transcripts that are expressed in endothelial cells of human, mouse and zebrafish. The analyzed data were incorporated into ANGIOGENES to provide a one-stop-shop for transcriptomics data to facilitate further biological validation. ANGIOGENES is an intuitive and easy-to-use database to allow in silico screening of expressed, enriched and/or specific endothelial transcripts under various conditions. We anticipate that ANGIOGENES serves as a starting point for functional studies to elucidate the roles of protein-coding genes and lncRNAs in angiogenesis.

  14. A systematic survey of loss-of-function variants in human protein-coding genes

    NARCIS (Netherlands)

    MacArthur, D.G.; Balasubramanian, S.; Frankish, A.; Huang, N.; Morris, J.; Walter, K.; Jostins, L.; Habegger, L.; Pickrell, J.K.; Montgomery, S.B.; Albers, C.A.; Zhang, Z.D.; Conrad, D.F.; Lunter, G.; Zheng, H.; Ayub, Q.; DePristo, M.A.; Banks, E.; Hu, M.; Handsaker, R.E.; Rosenfeld, J.A.; Fromer, M.; Jin, M.; Mu, X.J.; Khurana, E.; Ye, K.; Kay, M.; Saunders, G.I.; Suner, M.M.; Hunt, T.; Barnes, I.H.; Amid, C.; Carvalho-Silva, D.R.; Bignell, A.H.; Snow, C.; Yngvadottir, B.; Bumpstead, S.; Cooper, D.N.; Xue, Y.; Romero, I.G.; Genomes Project, C.; Wang, J.; Li, Y.; Gibbs, R.A.; McCarroll, S.A.; Dermitzakis, E.T.; Pritchard, J.K.; Barrett, J.C.; Harrow, J.; Hurles, M.E.; Gerstein, M.B.; Tyler-Smith, C.

    2012-01-01

    Genome-sequencing studies indicate that all humans carry many genetic variants predicted to cause loss of function (LoF) of protein-coding genes, suggesting unexpected redundancy in the human genome. Here we apply stringent filters to 2951 putative LoF variants obtained from 185 human genomes to det

  15. ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells.

    Science.gov (United States)

    Müller, Raphael; Weirick, Tyler; John, David; Militello, Giuseppe; Chen, Wei; Dimmeler, Stefanie; Uchida, Shizuka

    2016-09-01

    Increasing evidence indicates the presence of long noncoding RNAs (lncRNAs) is specific to various cell types. Although lncRNAs are speculated to be more numerous than protein-coding genes, the annotations of lncRNAs remain primitive due to the lack of well-structured schemes for their identification and description. Here, we introduce a new knowledge database "ANGIOGENES" (http://angiogenes.uni-frankfurt.de) to allow for in silico screening of protein-coding genes and lncRNAs expressed in various types of endothelial cells, which are present in all tissues. Using the latest annotations of protein-coding genes and lncRNAs, publicly-available RNA-seq data was analyzed to identify transcripts that are expressed in endothelial cells of human, mouse and zebrafish. The analyzed data were incorporated into ANGIOGENES to provide a one-stop-shop for transcriptomics data to facilitate further biological validation. ANGIOGENES is an intuitive and easy-to-use database to allow in silico screening of expressed, enriched and/or specific endothelial transcripts under various conditions. We anticipate that ANGIOGENES serves as a starting point for functional studies to elucidate the roles of protein-coding genes and lncRNAs in angiogenesis.

  16. When everyone is an orphan: against adopting a U.S.-styled orphan drug policy in Canada.

    Science.gov (United States)

    Herder, Matthew

    2013-01-01

    Putting aside whether diseases that affect only small numbers of people ("rare diseases") should be prioritized over diseases that are otherwise orphaned, in this article I argue that a new approach to rare, orphan diseases is needed. The current model, first signaled by the United States' Orphan Drug Act and subsequently emulated by several other jurisdictions, relies on a set of open-ended criteria and market-based incentives in order to define and encourage drug therapies for rare, orphan diseases. Given a) the biopharmaceutical industries' growing interest in orphan diseases, b) progress in the sphere of personalized medicines enabling more and more common diseases to be reclassified as rare, and c) empirical evidence suggesting that the most orphan drugs target only a limited, lucrative subset of rare diseases, I argue that Canada, which recently announced plans to develop its own "orphan drug framework" should not follow the United States' orphan drug model.

  17. Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing.

    Science.gov (United States)

    Kanda, Kojun; Pflug, James M; Sproul, John S; Dasenko, Mark A; Maddison, David R

    2015-01-01

    In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles

  18. Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs.

    Directory of Open Access Journals (Sweden)

    Chen Xie

    2012-09-01

    Full Text Available Tinkering with pre-existing genes has long been known as a major way to create new genes. Recently, however, motherless protein-coding genes have been found to have emerged de novo from ancestral non-coding DNAs. How these genes originated is not well addressed to date. Here we identified 24 hominoid-specific de novo protein-coding genes with precise origination timing in vertebrate phylogeny. Strand-specific RNA-Seq analyses were performed in five rhesus macaque tissues (liver, prefrontal cortex, skeletal muscle, adipose, and testis, which were then integrated with public transcriptome data from human, chimpanzee, and rhesus macaque. On the basis of comparing the RNA expression profiles in the three species, we found that most of the hominoid-specific de novo protein-coding genes encoded polyadenylated non-coding RNAs in rhesus macaque or chimpanzee with a similar transcript structure and correlated tissue expression profile. According to the rule of parsimony, the majority of these hominoid-specific de novo protein-coding genes appear to have acquired a regulated transcript structure and expression profile before acquiring coding potential. Interestingly, although the expression profile was largely correlated, the coding genes in human often showed higher transcriptional abundance than their non-coding counterparts in rhesus macaque. The major findings we report in this manuscript are robust and insensitive to the parameters used in the identification and analysis of de novo genes. Our results suggest that at least a portion of long non-coding RNAs, especially those with active and regulated transcription, may serve as a birth pool for protein-coding genes, which are then further optimized at the transcriptional level.

  19. On the genealogy of the Orphan Stream

    NARCIS (Netherlands)

    Sales, Laura V.; Helmi, Amina; Starkenburg, Else; Morrison, Heather L.; Engle, Ethan; Harding, Paul; Mateo, Mario; Olszewski, Edward W.; Sivarani, Thirupathi

    2008-01-01

    We use N-body simulations to explore the origin and a plausible orbit for the Orphan Stream, one of the faintest substructures discovered so far in the outer halo of our Galaxy. We are able to reproduce its position, velocity and distance measurements by appealing to a single wrap of a double-compon

  20. Next-Generation Sequencing of Protein-Coding and Long Non-protein-Coding RNAs in Two Types of Exosomes Derived from Human Whole Saliva.

    Science.gov (United States)

    Ogawa, Yuko; Tsujimoto, Masafumi; Yanoshita, Ryohei

    2016-01-01

    Exosomes are small extracellular vesicles containing microRNAs and mRNAs that are produced by various types of cells. We previously used ultrafiltration and size-exclusion chromatography to isolate two types of human salivary exosomes (exosomes I, II) that are different in size and proteomes. We showed that salivary exosomes contain large repertoires of small RNAs. However, precise information regarding long RNAs in salivary exosomes has not been fully determined. In this study, we investigated the compositions of protein-coding RNAs (pcRNAs) and long non-protein-coding RNAs (lncRNAs) of exosome I, exosome II and whole saliva (WS) by next-generation sequencing technology. Although 11% of all RNAs were commonly detected among the three samples, the compositions of reads mapping to known RNAs were similar. The most abundant pcRNA is ribosomal RNA protein, and pcRNAs of some salivary proteins such as S100 calcium-binding protein A8 (protein S100-A8) were present in salivary exosomes. Interestingly, lncRNAs of pseudogenes (presumably, processed pseudogenes) were abundant in exosome I, exosome II and WS. Translationally controlled tumor protein gene, which plays an important role in cell proliferation, cell death and immune responses, was highly expressed as pcRNA and pseudogenes in salivary exosomes. Our results show that salivary exosomes contain various types of RNAs such as pseudogenes and small RNAs, and may mediate intercellular communication by transferring these RNAs to target cells as gene expression regulators.

  1. Conserved syntenic clusters of protein coding genes are missing in birds

    OpenAIRE

    Lovell, Peter V.; Wirthlin, Morgan; Wilhelm, Larry; Minx, Patrick; Lazar, Nathan H.; Carbone, Lucia; Warren, Wesley C.; Mello, Claudio V.

    2014-01-01

    Background Birds are one of the most highly successful and diverse groups of vertebrates, having evolved a number of distinct characteristics, including feathers and wings, a sturdy lightweight skeleton and unique respiratory and urinary/excretion systems. However, the genetic basis of these traits is poorly understood. Results Using comparative genomics based on extensive searches of 60 avian genomes, we have found that birds lack approximately 274 protein coding genes that are present in th...

  2. On the genealogy of the Orphan Stream

    CERN Document Server

    Sales, L V; Starkenburg, E; Morrison, H L; Engle, E; Harding, P; Mateo, M; Olszewski, E W; Sivarani, T

    2008-01-01

    We use N-body simulations to explore the origin and a plausible orbit for the Orphan Stream, one of the faintest substructures discovered so far in the outer halo of our Galaxy. We are able to reproduce its position, velocity and distance measurements by appealing to a single wrap of a double-component satellite galaxy. We find that the progenitor of the Orphan Stream could have been an object similar to today's Milky Way dwarfs, such as Carina, Draco, Leo II or Sculptor; and unlikely to be connected to Complex A or Ursa Major II. Our models suggest that such progenitors, if accreted on orbits with apocenters smaller than ~35 kpc, are likely to give rise to very low surface brightness streams, which may be hiding in the outer halo and remain largely undetected with current techniques. The systematic discovery of these ghostly substructures may well require wide field spectroscopic surveys of the Milky Way's outer stellar halo.

  3. Legal and regulatory aspects of orphan drugs.

    Science.gov (United States)

    Shani, Segev; Yahalom, Zohar

    2013-11-01

    Rare (orphan) diseases are defined as diseases whose prevalence is significantly low. Many of these diseases are diagnosed at childhood by pediatricians. Rare diseases pose many obstacles for health care systems in general and patients specifically. As they are rare, they are less investigated, there is less knowledge about the disease and less professionals specializing in it. Furthermore, as for most diseases there is no specific treatment, diagnosis is not relevant. From industry perspective, as the market potential is small, there is no financial incentive to invest in developing treatments for rare diseases. All the above led patients, researchers and policymakers around the world to legislate specific laws designated to encourage and provide incentives for researchers and for the pharmaceutical industry to develop scientific and clinical knowledge as well as potential treatments for these diseases. The objective of this article is to describe the initiation and current status of public health policy concerning orphan disease and drugs.

  4. Orphan enzymes in ether lipid metabolism.

    Science.gov (United States)

    Watschinger, Katrin; Werner, Ernst R

    2013-01-01

    Ether lipids are an emerging class of lipids which have so far not been investigated and understood in every detail. They have important roles as membrane components of e.g. lens, brain and testis, and as mediators such as platelet-activating factor. The metabolic enzymes for biosynthesis and degradation have been investigated to some extent. As most involved enzymes are integral membrane proteins they are tricky to handle in biochemical protocols. The sequence of some ether lipid metabolising enzymes has only recently been reported and other sequences still remain obscure. Defined enzymes without assigned sequence are known as orphan enzymes. One of these enzymes with uncharacterised sequence is plasmanylethanolamine desaturase, a key enzyme for the biosynthesis of one of the most abundant phospholipids in our body, the plasmalogens. This review aims to briefly summarise known functions of ether lipids, give an overview on their metabolism including the most prominent members, platelet-activating factor and the plasmalogens. A special focus is set on the description of orphan enzymes in ether lipid metabolism and on the successful strategies how four previous orphans have recently been assigned a sequence. Only one of these four was characterised by classical protein purification and sequencing, whereas the other three required alternative strategies such as bioinformatic candidate gene selection and recombinant expression or development of an inhibitor and multidimensional metabolic profiling.

  5. The mitochondrial genome of Iberobaenia (Coleoptera: Iberobaeniidae): first rearrangement of protein-coding genes in the beetles.

    Science.gov (United States)

    Andujar, Carmelo; Arribas, Paula; Linard, Benjamin; Kundrata, Robin; Bocak, Ladislav; Vogler, Alfried P

    2017-03-01

    The complete mitochondrial genome of the recently discovered beetle family Iberobaeniidae is described and compared with known coleopteran mitogenomes. The mitochondrial sequence was obtained by shotgun metagenomic sequencing using the Illumina Miseq technology and resulted in an average coverage of 130 × and a minimum coverage of 35×. The mitochondrial genome of Iberobaeniidae includes 13 protein-coding genes, 2 rRNAs, 22 tRNAs genes, and 1 putative control region, and showed a unique rearrangement of protein-coding genes. This is the first rearrangement affecting the relative position of protein-coding and ribosomal genes reported for the order Coleoptera.

  6. The Orbit of the Orphan Stream

    Energy Technology Data Exchange (ETDEWEB)

    Newberg, Heidi Jo; Willett, Benjamin A.; Yanny, Brian; Xu, Yan

    2010-01-01

    We use recent SEGUE spectroscopy and SDSS and SEGUE imaging data to measure the sky position, distance, and radial velocities of stars in the tidal debris stream that is commonly referred to as the 'Orphan Stream.' We fit orbital parameters to the data, and find a prograde orbit with an apogalacticon, perigalacticon, and eccentricity of 90 kpc, 16.4 kpc and e = 0.7, respectively. Neither the dwarf galaxy UMa II nor the Complex A gas cloud have velocities consistent with a kinematic association with the Orphan Stream. It is possible that Segue-1 is associated with the Orphan Stream, but no other known Galactic clusters or dwarf galaxies in the Milky Way lie along its orbit. The detected portion of the stream ranges from 19 to 47 kpc from the Sun and is an indicator of the mass interior to these distances. There is a marked increase in the density of Orphan Stream stars near (l, b) = (253{sup o}; 49{sup o}), which could indicate the presence of the progenitor at the edge of the SDSS data. If this is the progenitor, then the detected portion of the Orphan Stream is a leading tidal tail. We find blue horizontal branch (BHB) stars and F turnoff stars associated with the Orphan Stream. The turnoff color is (g-r){sub 0} = 0.22. The BHB stars have a low metallicity of [Fe/H]{sub WBG} = -2.1. The orbit is best fit to a halo potential with a halo plus disk mass of about 2.6 x 10{sup 11} M{sub {circle_dot}}, integrated to 60 kpc from the Galactic center. Our fits are done to orbits rather than full N-body simulations; we show that if N-body simulations are used, the inferred mass of the galaxy would be slightly smaller. Our best fit is found with a logarithmic halo speed of v{sub halo} = 73 {+-} 24 km s{sup -1}, a disk+bulge mass of M(R < 60 kpc) = 1.3 x 10{sup 11} M{sub {circle_dot}}, and a halo mass of M(R < 60 kpc) = 1.4 x 10{sup 11} M{sub {circle_dot}}. However, we can find similar fits to the data that use an NFW halo profile, or that have smaller disk masses

  7. Transcriptional enhancers in protein-coding exons of vertebrate developmental genes.

    Directory of Open Access Journals (Sweden)

    Deborah I Ritter

    Full Text Available Many conserved noncoding sequences function as transcriptional enhancers that regulate gene expression. Here, we report that protein-coding DNA also frequently contains enhancers functioning at the transcriptional level. We tested the enhancer activity of 31 protein-coding exons, which we chose based on strong sequence conservation between zebrafish and human, and occurrence in developmental genes, using a Tol2 transposable GFP reporter assay in zebrafish. For each exon we measured GFP expression in hundreds of embryos in 10 anatomies via a novel system that implements the voice-recognition capabilities of a cellular phone. We find that 24/31 (77% exons drive GFP expression compared to a minimal promoter control, and 14/24 are anatomy-specific (expression in four anatomies or less. GFP expression driven by these coding enhancers frequently overlaps the anatomies where the host gene is expressed (60%, suggesting self-regulation. Highly conserved coding sequences and highly conserved noncoding sequences do not significantly differ in enhancer activity (coding: 24/31 vs. noncoding: 105/147 or tissue-specificity (coding: 14/24 vs. noncoding: 50/105. Furthermore, coding and noncoding enhancers display similar levels of the enhancer-related histone modification H3K4me1 (coding: 9/24 vs noncoding: 34/81. Meanwhile, coding enhancers are over three times as likely to contain an H3K4me1 mark as other exons of the host gene. Our work suggests that developmental transcriptional enhancers do not discriminate between coding and noncoding DNA and reveals widespread dual functions in protein-coding DNA.

  8. miR-148 targets human DNMT3b protein coding region

    OpenAIRE

    Duursma, Anja M.; Kedde, Martijn; Schrier, Mariette; le Sage, Carlos; Agami, Reuven

    2008-01-01

    MicroRNAs (miRNAs) are small noncoding RNA molecules of 20–24 nucleotides that regulate gene expression. In animals, miRNAs form imperfect interactions with sequences in the 3′ Untranslated region (3′UTR) of mRNAs, causing translational inhibition and mRNA decay. In contrast, plant miRNAs mostly associate with protein coding regions. Here we show that human miR-148 represses DNA methyltransferase 3b (Dnmt3b) gene expression through a region in its coding sequence. This region is evolutionary ...

  9. RNA Editing Sites Exist in Protein-coding Genes in the Chloroplast Genome of Cycas taitungensis

    Institute of Scientific and Technical Information of China (English)

    Haiyan Chen; Likun Deng; Yuan Jiang; Ping Lu; Jianing Yu

    2011-01-01

    RNA editing is a post-transcriptional process that results in modifications of ribonucleotides at specific locations.In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C-to-U changes,especially in seed plants.Using prediction and experimental determination,we investigated RNA editing in 40 protein-coding genes from the chloroplast genome of Cycas taitungensis.A total of 85 editing sites were identified in 25 transcripts.Comparison analysis of the published editotypes of these 25 transcripts in eight species showed that RNA editing events gradually disappear during plant evolution.The editing in the first and third codon position disappeared quicker than that in the second codon position,ndh genes have the highest editing frequency while serine and proline codons were more frequently edited than the codons of other amino acids.These results imply that retained RNA editing sites have imbalanced distribution in genes and most of them may function by changing protein structure or interaction.Mitochondrion protein-coding genes have three times the editing sites compared with chloroplast genes of Cycas,most likely due to slower evolution speed.

  10. Optimization of Mutation Pressure in Relation to Properties of Protein-Coding Sequences in Bacterial Genomes.

    Directory of Open Access Journals (Sweden)

    Paweł Błażej

    Full Text Available Most mutations are deleterious and require energetically costly repairs. Therefore, it seems that any minimization of mutation rate is beneficial. On the other hand, mutations generate genetic diversity indispensable for evolution and adaptation of organisms to changing environmental conditions. Thus, it is expected that a spontaneous mutational pressure should be an optimal compromise between these two extremes. In order to study the optimization of the pressure, we compared mutational transition probability matrices from bacterial genomes with artificial matrices fulfilling the same general features as the real ones, e.g., the stationary distribution and the speed of convergence to the stationarity. The artificial matrices were optimized on real protein-coding sequences based on Evolutionary Strategies approach to minimize or maximize the probability of non-synonymous substitutions and costs of amino acid replacements depending on their physicochemical properties. The results show that the empirical matrices have a tendency to minimize the effects of mutations rather than maximize their costs on the amino acid level. They were also similar to the optimized artificial matrices in the nucleotide substitution pattern, especially the high transitions/transversions ratio. We observed no substantial differences between the effects of mutational matrices on protein-coding sequences in genomes under study in respect of differently replicated DNA strands, mutational cost types and properties of the referenced artificial matrices. The findings indicate that the empirical mutational matrices are rather adapted to minimize mutational costs in the studied organisms in comparison to other matrices with similar mathematical constraints.

  11. Analysis of protein-coding genetic variation in 60,706 humans.

    Science.gov (United States)

    Lek, Monkol; Karczewski, Konrad J; Minikel, Eric V; Samocha, Kaitlin E; Banks, Eric; Fennell, Timothy; O'Donnell-Luria, Anne H; Ware, James S; Hill, Andrew J; Cummings, Beryl B; Tukiainen, Taru; Birnbaum, Daniel P; Kosmicki, Jack A; Duncan, Laramie E; Estrada, Karol; Zhao, Fengmei; Zou, James; Pierce-Hoffman, Emma; Berghout, Joanne; Cooper, David N; Deflaux, Nicole; DePristo, Mark; Do, Ron; Flannick, Jason; Fromer, Menachem; Gauthier, Laura; Goldstein, Jackie; Gupta, Namrata; Howrigan, Daniel; Kiezun, Adam; Kurki, Mitja I; Moonshine, Ami Levy; Natarajan, Pradeep; Orozco, Lorena; Peloso, Gina M; Poplin, Ryan; Rivas, Manuel A; Ruano-Rubio, Valentin; Rose, Samuel A; Ruderfer, Douglas M; Shakir, Khalid; Stenson, Peter D; Stevens, Christine; Thomas, Brett P; Tiao, Grace; Tusie-Luna, Maria T; Weisburd, Ben; Won, Hong-Hee; Yu, Dongmei; Altshuler, David M; Ardissino, Diego; Boehnke, Michael; Danesh, John; Donnelly, Stacey; Elosua, Roberto; Florez, Jose C; Gabriel, Stacey B; Getz, Gad; Glatt, Stephen J; Hultman, Christina M; Kathiresan, Sekar; Laakso, Markku; McCarroll, Steven; McCarthy, Mark I; McGovern, Dermot; McPherson, Ruth; Neale, Benjamin M; Palotie, Aarno; Purcell, Shaun M; Saleheen, Danish; Scharf, Jeremiah M; Sklar, Pamela; Sullivan, Patrick F; Tuomilehto, Jaakko; Tsuang, Ming T; Watkins, Hugh C; Wilson, James G; Daly, Mark J; MacArthur, Daniel G

    2016-08-18

    Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes.

  12. Optimization of Mutation Pressure in Relation to Properties of Protein-Coding Sequences in Bacterial Genomes.

    Science.gov (United States)

    Błażej, Paweł; Miasojedow, Błażej; Grabińska, Małgorzata; Mackiewicz, Paweł

    2015-01-01

    Most mutations are deleterious and require energetically costly repairs. Therefore, it seems that any minimization of mutation rate is beneficial. On the other hand, mutations generate genetic diversity indispensable for evolution and adaptation of organisms to changing environmental conditions. Thus, it is expected that a spontaneous mutational pressure should be an optimal compromise between these two extremes. In order to study the optimization of the pressure, we compared mutational transition probability matrices from bacterial genomes with artificial matrices fulfilling the same general features as the real ones, e.g., the stationary distribution and the speed of convergence to the stationarity. The artificial matrices were optimized on real protein-coding sequences based on Evolutionary Strategies approach to minimize or maximize the probability of non-synonymous substitutions and costs of amino acid replacements depending on their physicochemical properties. The results show that the empirical matrices have a tendency to minimize the effects of mutations rather than maximize their costs on the amino acid level. They were also similar to the optimized artificial matrices in the nucleotide substitution pattern, especially the high transitions/transversions ratio. We observed no substantial differences between the effects of mutational matrices on protein-coding sequences in genomes under study in respect of differently replicated DNA strands, mutational cost types and properties of the referenced artificial matrices. The findings indicate that the empirical mutational matrices are rather adapted to minimize mutational costs in the studied organisms in comparison to other matrices with similar mathematical constraints.

  13. Modeling compositional dynamics based on GC and purine contents of protein-coding sequences

    KAUST Repository

    Zhang, Zhang

    2010-11-08

    Background: Understanding the compositional dynamics of genomes and their coding sequences is of great significance in gaining clues into molecular evolution and a large number of publically-available genome sequences have allowed us to quantitatively predict deviations of empirical data from their theoretical counterparts. However, the quantification of theoretical compositional variations for a wide diversity of genomes remains a major challenge.Results: To model the compositional dynamics of protein-coding sequences, we propose two simple models that take into account both mutation and selection effects, which act differently at the three codon positions, and use both GC and purine contents as compositional parameters. The two models concern the theoretical composition of nucleotides, codons, and amino acids, with no prerequisite of homologous sequences or their alignments. We evaluated the two models by quantifying theoretical compositions of a large collection of protein-coding sequences (including 46 of Archaea, 686 of Bacteria, and 826 of Eukarya), yielding consistent theoretical compositions across all the collected sequences.Conclusions: We show that the compositions of nucleotides, codons, and amino acids are largely determined by both GC and purine contents and suggest that deviations of the observed from the expected compositions may reflect compositional signatures that arise from a complex interplay between mutation and selection via DNA replication and repair mechanisms.Reviewers: This article was reviewed by Zhaolei Zhang (nominated by Mark Gerstein), Guruprasad Ananda (nominated by Kateryna Makova), and Daniel Haft. 2010 Zhang and Yu; licensee BioMed Central Ltd.

  14. Revisiting the missing protein-coding gene catalog of the domestic dog

    Directory of Open Access Journals (Sweden)

    Galibert Francis

    2009-02-01

    Full Text Available Abstract Background Among mammals for which there is a high sequence coverage, the whole genome assembly of the dog is unique in that it predicts a low number of protein-coding genes, ~19,000, compared to the over 20,000 reported for other mammalian species. Of particular interest are the more than 400 of genes annotated in primates and rodent genomes, but missing in dog. Results Using over 14,000 orthologous genes between human, chimpanzee, mouse rat and dog, we built multiple pairwise synteny maps to infer short orthologous intervals that were targeted for characterizing the canine missing genes. Based on gene prediction and a functionality test using the ratio of replacement to silent nucleotide substitution rates (dN/dS, we provide compelling structural and functional evidence for the identification of 232 new protein-coding genes in the canine genome and 69 gene losses, characterized as undetected gene or pseudogenes. Gene loss phyletic pattern analysis using ten species from chicken to human allowed us to characterize 28 canine-specific gene losses that have functional orthologs continuously from chicken or marsupials through human, and 10 genes that arose specifically in the evolutionary lineage leading to rodent and primates. Conclusion This study demonstrates the central role of comparative genomics for refining gene catalogs and exploring the evolutionary history of gene repertoires, particularly as applied for the characterization of species-specific gene gains and losses.

  15. Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing

    Directory of Open Access Journals (Sweden)

    Peng Huiru

    2011-04-01

    Full Text Available Abstract Background Biotic and abiotic stresses, such as powdery mildew infection and high temperature, are important limiting factors for yield and grain quality in wheat production. Emerging evidences suggest that long non-protein coding RNAs (npcRNAs are developmentally regulated and play roles in development and stress responses of plants. However, identification of long npcRNAs is limited to a few plant species, such as Arabidopsis, rice and maize, no systematic identification of long npcRNAs and their responses to abiotic and biotic stresses is reported in wheat. Results In this study, by using computational analysis and experimental approach we identified 125 putative wheat stress responsive long npcRNAs, which are not conserved among plant species. Among them, some were precursors of small RNAs such as microRNAs and siRNAs, two long npcRNAs were identified as signal recognition particle (SRP 7S RNA variants, and three were characterized as U3 snoRNAs. We found that wheat long npcRNAs showed tissue dependent expression patterns and were responsive to powdery mildew infection and heat stress. Conclusion Our results indicated that diverse sets of wheat long npcRNAs were responsive to powdery mildew infection and heat stress, and could function in wheat responses to both biotic and abiotic stresses, which provided a starting point to understand their functions and regulatory mechanisms in the future.

  16. Fact or fiction: updates on how protein-coding genes might emerge de novo from previously non-coding DNA

    Science.gov (United States)

    Schmitz, Jonathan F; Bornberg-Bauer, Erich

    2017-01-01

    Over the last few years, there has been an increasing amount of evidence for the de novo emergence of protein-coding genes, i.e. out of non-coding DNA. Here, we review the current literature and summarize the state of the field. We focus specifically on open questions and challenges in the study of de novo protein-coding genes such as the identification and verification of de novo-emerged genes. The greatest obstacle to date is the lack of high-quality genomic data with very short divergence times which could help precisely pin down the location of origin of a de novo gene. We conclude that, while there is plenty of evidence from a genetics perspective, there is a lack of functional studies of bona fide de novo genes and almost no knowledge about protein structures and how they come about during the emergence of de novo protein-coding genes. We suggest that future studies should concentrate on the functional and structural characterization of de novo protein-coding genes as well as the detailed study of the emergence of functional de novo protein-coding genes.

  17. Interpreting the role of de novo protein-coding mutations in neuropsychiatric disease.

    Science.gov (United States)

    Gratten, Jacob; Visscher, Peter M; Mowry, Bryan J; Wray, Naomi R

    2013-03-01

    Pedigree, linkage and association studies are consistent with heritable variation for complex disease due to the segregation of genetic factors in families and in the population. In contrast, de novo mutations make only minor contributions to heritability estimates for complex traits. Nonetheless, some de novo variants are known to be important in disease etiology. The identification of risk-conferring de novo variants will contribute to the discovery of etiologically relevant genes and pathways and may help in genetic counseling. There is considerable interest in the role of such mutations in complex neuropsychiatric disease, largely driven by new genotyping and sequencing technologies. An important role for large de novo copy number variations has been established. Recently, whole-exome sequencing has been used to extend the investigation of de novo variation to point mutations in protein-coding regions. Here, we consider several challenges for the interpretation of such mutations in the context of their role in neuropsychiatric disease.

  18. A human-specific de novo protein-coding gene associated with human brain functions.

    Directory of Open Access Journals (Sweden)

    Chuan-Yun Li

    2010-03-01

    Full Text Available To understand whether any human-specific new genes may be associated with human brain functions, we computationally screened the genetic vulnerable factors identified through Genome-Wide Association Studies and linkage analyses of nicotine addiction and found one human-specific de novo protein-coding gene, FLJ33706 (alternative gene symbol C20orf203. Cross-species analysis revealed interesting evolutionary paths of how this gene had originated from noncoding DNA sequences: insertion of repeat elements especially Alu contributed to the formation of the first coding exon and six standard splice junctions on the branch leading to humans and chimpanzees, and two subsequent substitutions in the human lineage escaped two stop codons and created an open reading frame of 194 amino acids. We experimentally verified FLJ33706's mRNA and protein expression in the brain. Real-Time PCR in multiple tissues demonstrated that FLJ33706 was most abundantly expressed in brain. Human polymorphism data suggested that FLJ33706 encodes a protein under purifying selection. A specifically designed antibody detected its protein expression across human cortex, cerebellum and midbrain. Immunohistochemistry study in normal human brain cortex revealed the localization of FLJ33706 protein in neurons. Elevated expressions of FLJ33706 were detected in Alzheimer's brain samples, suggesting the role of this novel gene in human-specific pathogenesis of Alzheimer's disease. FLJ33706 provided the strongest evidence so far that human-specific de novo genes can have protein-coding potential and differential protein expression, and be involved in human brain functions.

  19. OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences

    Directory of Open Access Journals (Sweden)

    Grossman Lawrence I

    2007-09-01

    Full Text Available Abstract Background Rapidly accumulating genome sequence data from multiple species offer powerful opportunities for the detection of DNA sequence evolution. Phylogenetic tree construction and codon-based tests for natural selection are the prevailing tools used to detect functionally important evolutionary change in protein coding sequences. These analyses often require multiple DNA sequence alignments that maintain the correct reading frame for each collection of putative orthologous sequences. Since this feature is not available in most alignment tools, codon reading frames often must be checked manually before evolutionary analyses can commence. Results Here we report an online codon-preserved alignment tool (OCPAT that generates multiple sequence alignments automatically from the coding sequences of any list of human gene IDs and their putative orthologs from genomes of other vertebrate tetrapods. OCPAT is programmed to extract putative orthologous genes from genomes and to align the orthologs with the reading frame maintained in all species. OCPAT also optimizes the alignment by trimming the most variable alignment regions at the 5' and 3' ends of each gene. The resulting output of alignments is returned in several formats, which facilitates further molecular evolutionary analyses by appropriate available software. Alignments are generally robust and reliable, retaining the correct reading frame. The tool can serve as the first step for comparative genomic analyses of protein-coding gene sequences including phylogenetic tree reconstruction and detection of natural selection. We aligned 20,658 human RefSeq mRNAs using OCPAT. Most alignments are missing sequence(s from at least one species; however, functional annotation clustering of the ~1700 transcripts that were alignable to all species shows that genes involved in multi-subunit protein complexes are highly conserved. Conclusion The OCPAT program facilitates large-scale evolutionary and

  20. DNA methylation patterns of protein coding genes and long noncoding RNAs in female schizophrenic patients.

    Science.gov (United States)

    Liao, Qi; Wang, Yunliang; Cheng, Jia; Dai, Dongjun; Zhou, Xingyu; Zhang, Yuzheng; Gao, Shugui; Duan, Shiwei

    2015-02-01

    Schizophrenia (SCZ) is a complex mental disorder contributed by both genetic and epigenetic factors. Long noncoding RNAs (lncRNAs) was recently found playing an important regulatory role in mental disorders. However, little was known about the DNA methylation of lncRNAs, although numerous SCZ studies have been performed on genetic polymorphisms or epigenetic marks in protein coding genes. We presented a comprehensive genome wide DNA methylation study of both protein coding genes and lncRNAs in female patients with paranoid and undifferentiated SCZ. Using the methyl-CpG binding domain (MBD) protein-enriched genome sequencing (MBD-seq), 8,163 and 764 peaks were identified in paranoid and undifferentiated SCZ, respectively (p Gene ontology analysis showed that the hypermethylated regions were enriched in the genes related to neuron system and brain for both paranoid and undifferentiated SCZ (p gene promoter regions that might affect gene expression and influence the SCZ related pathways. Interestingly, DNA methylation of 136 and 23 known lncRNAs in Refseq database were identified in paranoid and undifferentiated SCZ, respectively. In addition, ∼20% of intergenic peaks annotated based on Refseq genes were overlapped with lncRNAs in UCSC and gencode databases. In order to show the results well for most biological researchers, we created an online database to display and visualize the information of DNA methyation peaks in both types of SCZ (http://www.bioinfo.org/scz/scz.htm). Our results showed that the aberrant DNA methylation of lncRNAs might be another important epigenetic factor for SCZ.

  1. Imperfect DNA mirror repeats in E. coli TnsA and other protein-coding DNA.

    Science.gov (United States)

    Lang, Dorothy M

    2005-09-01

    DNA imperfect mirror repeats (DNA-IMRs) are ubiquitous in protein-coding DNA. However, they overlap and often have different centers of symmetry, making it difficult to evaluate their relationship to each other and to specific DNA and protein motifs and structures. This paper describes a systematic method of determining a hierarchy for DNA-IMRs and evaluates their relationship to protein structural elements (PSEs)--helices, turns and beta-sheets. DNA-IMRs are identifed by two different methods--DNA-IMRs terminated by reverse dinucleotides (rd-IMRs) and DNA-IMRs terminated by a single (mono) matching nucleotide (m-IMRs). Both rd-IMRs and m-IMRs are evaluated in 17 proteins, and illustrated in detail for TnsA. For each of the proteins, Fisher's exact test (FET) is used to measure the coincidence between the terminal dinucleotides of rd-IMRs and the terminal amino acids of individual PSEs. A significant correlation over a span of about 3 nt was found for each protein. The correlation is robust and for most genes, all rd-IMRs16 nt contain approximately 88% of the potential functional motifs. The protein translation of the longest rd- and m-IMRs span sequences important to the protein's structure and function. In all 17 proteins studied, the population of rd-IMRs is substantially less than the expected number and the population of m-IMRs greater than the expected number, indicating strong selective pressures. The association of rd-IMRs with PSEs restricts their spatial distribution, and therefore, their number. The greater than predicted number of m-IMRs indicates that DNA symmetry exists throughout the entire protein-coding region and may stabilize the sequence.

  2. Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposable element of C. elegans

    Directory of Open Access Journals (Sweden)

    Pupko Tal

    2008-10-01

    Full Text Available Abstract Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals. Here, we report that the Turmoil-1 transposable element in C. elegans has incorporated two protein-coding sequences into its inverted terminal repeat (ITR sequences. The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM that originated from the rsp-2 gene and a fragment from the protein-coding region of the cpg-3 gene. We further report that an open reading frame specific to C. elegans may have been created as a result of a Turmoil-1 insertion. Mutations at the 5' splice site of this open reading frame may have reactivated the transduplicated RRM motif. Reviewers This article was reviewed by Dan Graur and William Martin. For the full reviews, please go to the Reviewers' Reports section.

  3. Some Numbers behind Canada's Decision to Adopt an Orphan Drug Policy: US Orphan Drug Approvals in Canada, 1997-2012.

    Science.gov (United States)

    Herder, Matthew; Krahn, Timothy Mark

    2016-05-01

    We examined whether access to US-approved orphan drugs in Canada has changed between 1997 (when Canada chose not to adopt an orphan drug policy) and 2012 (when Canada reversed its policy decision). Specifically, we looked at two dimensions of access to US-approved orphan drugs in Canada: (1) regulatory access; and (2) temporal access. Whereas only 63% of US-approved orphan drugs were granted regulatory approval in 1997, we found that regulatory access to US-approved orphan drugs in Canada increased to 74% between 1997 and 2012. However, temporal access to orphan drugs is slower in Canada: in a head-on comparison of 40 matched drugs, only two were submitted and four were approved first in Canada; moreover, the mean review time in Canada (423 days) was longer than that in the US (mean = 341 days), a statistically significant difference (t[39] = 2.04, p = 0.048). These results raise questions about what motivated Canada's apparent shift in orphan drug policy.

  4. From novice to expert: agroecological competences of children orphaned by AIDS compared to non-orphans in Benin

    Directory of Open Access Journals (Sweden)

    Price Lisa L

    2011-01-01

    Full Text Available Abstract Background AIDS has created new vulnerabilities for rural African households due to prime-age adult mortality and is assumed to lead to impairment of the intergenerational transfer of farming knowledge. There has been scant research to date, however, on the impacts of parental death on farming knowledge of children made orphans by AIDS. The question we investigate is if there is a difference in agricultural expertise between AIDS affected and non-affected adults and children. Methods The research was carried out in rural Benin with 77 informants randomly selected according to their AIDS status: 13 affected and 13 non-affected adults; 13 paternal, 13 maternal and 13 double orphans; and 12 non-orphan children. Informants descriptions from pile sorting exercises of maize and cowpea pests were categorized and then aggregated into descriptions based form (morphology and function (utility and used to determine whether the moving from novice to expert is impaired by children orphaned by AIDS. Differences and similarities in responses were determined using the Fischer exact test and the Cochran-Mantzel-Haenszel test. Results No significant differences were found between AIDS affected and non-affected adults. Results of the study do reveal differences in the use of form and function descriptors among the children. There is a statistically significant difference in the use of form descriptors between one-parent orphans and non-orphans and in descriptors of specific damages to maize. One-parent paternal orphans were exactly like non-affected adults in their 50/50 balanced expertise in the use of both form and function descriptors. One-parent orphans also had the highest number of descriptors used by children overall and these descriptors are spread across the various aspects of the knowledge domain relative to non-orphans. Conclusions Rather than a knowledge loss for one-parent orphans, particularly paternal orphans, we believe we are witnessing

  5. The many "small COPDs": COPD should be an orphan disease

    DEFF Research Database (Denmark)

    Rennard, Stephen I; Vestbo, Jørgen

    2008-01-01

    status, therefore, could facilitate the development of treatments for both phenotypic subsets of COPD patients as well as aid the development of agents to alter the natural history of the disease. Post-drug approval regulations could require that agents approved under the orphan provisions......COPD is one of the most common causes of morbidity and mortality. Perhaps paradoxically, COPD also should be an orphan disease. Importantly, this could advance the development of treatments for COPD. There are two criteria for orphan status in the United States. Most widely known is the criterion...... groups based on mechanism sets the stage for the rational development of therapeutics. In addition, many candidate treatments may alter the natural history of COPD. Testing them, however, will require large studies for a duration that will compromise the commercial life of any resulting product. Orphan...

  6. Accelerated evolution in the protein-coding regions is universal in crotalinae snake venom gland phospholipase A2 isozyme genes.

    Science.gov (United States)

    Nakashima, K; Nobuhisa, I; Deshimaru, M; Nakai, M; Ogawa, T; Shimohigashi, Y; Fukumaki, Y; Hattori, M; Sakaki, Y; Hattori, S

    1995-06-06

    The nucleotide sequences of four genes encoding Trimeresurus gramineus (green habu snake, crotalinae) venom gland phospholipase A2 (PLA2; phosphatidylcholine 2-acylhydrolase, EC 3.1.1.4) isozymes were compared internally and externally with those of six genes encoding Trimeresurus flavoviridis (habu snake, crotalinae) venom gland PLA2 isozymes. The numbers of nucleotide substitutions per site (KN) for the noncoding regions including introns were one-third to one-eighth of the numbers of nucleotide substitutions per synonymous site (KS) for the protein-coding regions of exons, indicating that the noncoding regions are much more conserved than the protein-coding regions. The KN values for the introns were found to be nearly equivalent to those of introns of T. gramineus and T. flavoviridis TATA box-binding protein genes, which are assumed to be a general (nonvenomous) gene. Thus, it is evident that the introns of venom gland PLA2 isozyme genes have evolved at a similar rate to those of nonvenomous genes. The numbers of nucleotide substitutions per nonsynonymous site (KA) were close to or larger than the KS values for the protein-coding regions in venom gland PLA2 isozyme genes. All of the data combined reveal that Darwinian-type accelerated evolution has universally occurred only in the protein-coding regions of crotalinae snake venom PLA2 isozyme genes.

  7. Biological basis of miRNA action when their targets are located in human protein coding region.

    Directory of Open Access Journals (Sweden)

    Wanjun Gu

    Full Text Available Recent analyses have revealed many functional microRNA (miRNA targets in mammalian protein coding regions. But, the mechanisms that ensure miRNA function when their target sites are located in protein coding regions of mammalian mRNA transcripts are largely unknown. In this paper, we investigate some potential biological factors, such as target site accessibility and local translation efficiency. We computationally analyze these two factors using experimentally identified miRNA targets in human protein coding region. We find site accessibility is significantly increased in miRNA target region to facilitate miRNA binding. At the mean time, local translation efficiency is also selectively decreased near miRNA target region. GC-poor codons are preferred in the flank region of miRNA target sites to ease the access of miRNA targets. Within-genome analysis shows substantial variations of site accessibility and local translation efficiency among different miRNA targets in the genome. Further analyses suggest target gene's GC content and conservation level could explain some of the differences in site accessibility. On the other hand, target gene's functional importance and conservation level can affect local translation efficiency near miRNA target region. We hence propose both site accessibility and local translation efficiency are important in miRNA action when miRNA target sites are located in mammalian protein coding regions.

  8. WISCOD: A Statistical Web-Enabled Tool for the Identification of Significant Protein Coding Regions

    Directory of Open Access Journals (Sweden)

    Mireia Vilardell

    2014-01-01

    Full Text Available Classically, gene prediction programs are based on detecting signals such as boundary sites (splice sites, starts, and stops and coding regions in the DNA sequence in order to build potential exons and join them into a gene structure. Although nowadays it is possible to improve their performance with additional information from related species or/and cDNA databases, further improvement at any step could help to obtain better predictions. Here, we present WISCOD, a web-enabled tool for the identification of significant protein coding regions, a novel software tool that tackles the exon prediction problem in eukaryotic genomes. WISCOD has the capacity to detect real exons from large lists of potential exons, and it provides an easy way to use global P value called expected probability of being a false exon (EPFE that is useful for ranking potential exons in a probabilistic framework, without additional computational costs. The advantage of our approach is that it significantly increases the specificity and sensitivity (both between 80% and 90% in comparison to other ab initio methods (where they are in the range of 70–75%. WISCOD is written in JAVA and R and is available to download and to run in a local mode on Linux and Windows platforms.

  9. Non-random retention of protein-coding overlapping genes in Metazoa

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    Bork Peer

    2008-04-01

    Full Text Available Abstract Background Although the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a comparative analysis of overlaps between genes coding for well-annotated proteins in five metazoan genomes (human, mouse, zebrafish, fruit fly and worm. Results For all analyzed species the observed number of overlapping genes is always lower than expected assuming functional neutrality, suggesting that gene overlap is negatively selected. The comparison to the random distribution also shows that retained overlaps do not exhibit random features: antiparallel overlaps are significantly enriched, while overlaps lying on the same strand and those involving coding sequences are highly underrepresented. We confirm that overlap is mostly species-specific and provide evidence that it frequently originates through the acquisition of terminal, non-coding exons. Finally, we show that overlapping genes tend to be significantly co-expressed in a breast cancer cDNA library obtained by 454 deep sequencing, and that different overlap types display different patterns of reciprocal expression. Conclusion Our data suggest that overlap between protein-coding genes is selected against in Metazoa. However, when retained it may be used as a species-specific mechanism for the reciprocal regulation of neighboring genes. The tendency of overlaps to involve non-coding regions of the genes leads to the speculation that the advantages achieved by an overlapping arrangement may be optimized by evolving regulatory non-coding transcripts.

  10. miR-148 targets human DNMT3b protein coding region.

    Science.gov (United States)

    Duursma, Anja M; Kedde, Martijn; Schrier, Mariette; le Sage, Carlos; Agami, Reuven

    2008-05-01

    MicroRNAs (miRNAs) are small noncoding RNA molecules of 20-24 nucleotides that regulate gene expression. In animals, miRNAs form imperfect interactions with sequences in the 3' Untranslated region (3'UTR) of mRNAs, causing translational inhibition and mRNA decay. In contrast, plant miRNAs mostly associate with protein coding regions. Here we show that human miR-148 represses DNA methyltransferase 3b (Dnmt3b) gene expression through a region in its coding sequence. This region is evolutionary conserved and present in the Dnmt3b splice variants Dnmt3b1, Dnmt3b2, and Dnmt3b4, but not in the abundantly expressed Dnmt3b3. Whereas overexpression of miR-148 results in decreased DNMT3b1 expression, short-hairpin RNA-mediated miR-148 repression leads to an increase in DNMT3b1 expression. Interestingly, mutating the putative miR-148 target site in Dnmt3b1 abolishes regulation by miR-148. Moreover, endogenous Dnmt3b3 mRNA, which lacks the putative miR-148 target site, is resistant to miR-148-mediated regulation. Thus, our results demonstrate that the coding sequence of Dnmt3b mediates regulation by the miR-148 family. More generally, we provide evidence that coding regions of human genes can be targeted by miRNAs, and that such a mechanism might play a role in determining the relative abundance of different splice variants.

  11. Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.

    Directory of Open Access Journals (Sweden)

    Sanzo Miyazawa

    Full Text Available BACKGROUND: A mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the average fixation probability depending on the type of amino acid replacement, has advantages over nucleotide, amino acid, and empirical codon substitution models in evolutionary analysis of protein-coding sequences. It can approximate a wide range of codon substitution processes. If no selection pressure on amino acids is taken into account, it will become equivalent to a nucleotide substitution model. If mutation rates are assumed not to depend on the codon type, then it will become essentially equivalent to an amino acid substitution model. Mutation at the nucleotide level and selection at the amino acid level can be separately evaluated. RESULTS: The present scheme for single nucleotide mutations is equivalent to the general time-reversible model, but multiple nucleotide changes in infinitesimal time are allowed. Selective constraints on the respective types of amino acid replacements are tailored to each gene in a linear function of a given estimate of selective constraints. Their good estimates are those calculated by maximizing the respective likelihoods of empirical amino acid or codon substitution frequency matrices. Akaike and Bayesian information criteria indicate that the present model performs far better than the other substitution models for all five phylogenetic trees of highly-divergent to highly-homologous sequences of chloroplast, mitochondrial, and nuclear genes. It is also shown that multiple nucleotide changes in infinitesimal time are significant in long branches, although they may be caused by compensatory substitutions or other mechanisms. The variation of selective constraint over sites fits the datasets significantly better than variable mutation rates, except for 10 slow-evolving nuclear genes of 10 mammals. An critical finding for phylogenetic analysis is that

  12. Distinguishing protein-coding from non-coding RNAs through support vector machines.

    Directory of Open Access Journals (Sweden)

    Jinfeng Liu

    2006-04-01

    Full Text Available RIKEN's FANTOM project has revealed many previously unknown coding sequences, as well as an unexpected degree of variation in transcripts resulting from alternative promoter usage and splicing. Ever more transcripts that do not code for proteins have been identified by transcriptome studies, in general. Increasing evidence points to the important cellular roles of such non-coding RNAs (ncRNAs. The distinction of protein-coding RNA transcripts from ncRNA transcripts is therefore an important problem in understanding the transcriptome and carrying out its annotation. Very few in silico methods have specifically addressed this problem. Here, we introduce CONC (for "coding or non-coding", a novel method based on support vector machines that classifies transcripts according to features they would have if they were coding for proteins. These features include peptide length, amino acid composition, predicted secondary structure content, predicted percentage of exposed residues, compositional entropy, number of homologs from database searches, and alignment entropy. Nucleotide frequencies are also incorporated into the method. Confirmed coding cDNAs for eukaryotic proteins from the Swiss-Prot database constituted the set of true positives, ncRNAs from RNAdb and NONCODE the true negatives. Ten-fold cross-validation suggested that CONC distinguished coding RNAs from ncRNAs at about 97% specificity and 98% sensitivity. Applied to 102,801 mouse cDNAs from the FANTOM3 dataset, our method reliably identified over 14,000 ncRNAs and estimated the total number of ncRNAs to be about 28,000.

  13. Poly(T) variation within mitochondrial protein-coding genes in Globodera (Nematoda: Heteroderidae).

    Science.gov (United States)

    Riepsamen, Angelique H; Blok, Vivian C; Phillips, Mark; Gibson, Tracey; Dowton, Mark

    2008-03-01

    We sequenced a mitochondrial subgenome from the nematode Globodera rostochiensis, in two overlapping pieces. The subgenome was 9210 bp and contained four protein-coding genes (ND4, COIII, ND3, Cytb) and two tRNA genes (tRNA(Thr), tRNA(Gln)). Genome organization was similar to that of Globodera pallida, which is multipartite. Together with the small number of genes on this subgenome, this suggests that the mitochondrial genome of G. rostochiensis is also multipartite. In the initial clones sequenced, COIII and ND3 were full-length, while ND4 and Cytb were interrupted by premature stop codons and contained point indels that disrupted the reading frame. However, sequencing of multiple clones, from DNA extracted both from multiple individuals and from single cysts, revealed a predominant source of variation-in the length of polythymidine tracts. Comparison of our genomic sequences with ESTs similarly revealed variation in the length of polythymidine tracts. We subsequently sequenced both genomic DNA and mRNA from populations of G. pallida. In each case, variation in the length of polythymidine tracts was observed. The levels of expression of mitochondrial genes in G. pallida were representative of the subgenomes present: little evidence of differential expression was observed. These observations are consistent with the operation of posttranscriptional editing in Globodera mitochondria, although this is difficult to show conclusively in the presence of intraindividual gene sequence variation. Further, alternative explanations cannot be discounted; these include the operation of slippage during translation or that genomic copies of most genes are pseudogenes with a small proportion of full-length sequences able to maintain mitochondrial function.

  14. Legal assessment of current situation on orphan patients in Lithuania.

    Science.gov (United States)

    Spokiene, Indre

    2008-01-01

    After Lithuania joined the European Union, the Regulation (EC) No. 141/2000 on orphan medicinal products and Commission Regulation (EC) No. 847/2000 came into force as part of national legislation. Member States must adopt specific measures to increase knowledge on rare diseases and to improve their detection, diagnosis, and treatment. The aim of this article was to present and to assess the current legal situation on orphan patients and their treatment in Lithuania, to identify legislation gaps, and to propose some ideas how to facilitate the solution of the existing problems in this field. For this purpose, European Union and Lithuanian legal documents on rare medicinal products are examined using a comparative method. With reference to inventory of Member States' incentives for rare diseases in national level, the most important issues, which orphan patients face to in Lithuania, are singled out. In Lithuania, the situation of orphan patients in terms of protection of patient rights is insufficiently determined. The access to effective health care services or approved therapies in some cases is restricted. Working relationships between genetic services and various clinical specialists as well as with those in primary care are not legally determined; the number of clinical trials aimed at orphan medicinal products is low. These results suggest a need for awareness raising among Lithuanian Government, health care specialists, patient organizations about the importance to improve practical implementation of European Union legislation and progressive experience of some European countries in this field.

  15. Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes

    KAUST Repository

    Alam, Tanvir

    2014-10-02

    Transcriptional regulation of protein-coding genes is increasingly well-understood on a global scale, yet no comparable information exists for long non-coding RNA (lncRNA) genes, which were recently recognized to be as numerous as protein-coding genes in mammalian genomes. We performed a genome-wide comparative analysis of the promoters of human lncRNA and protein-coding genes, finding global differences in specific genetic and epigenetic features relevant to transcriptional regulation. These two groups of genes are hence subject to separate transcriptional regulatory programs, including distinct transcription factor (TF) proteins that significantly favor lncRNA, rather than coding-gene, promoters. We report a specific signature of promoter-proximal transcriptional regulation of lncRNA genes, including several distinct transcription factor binding sites (TFBS). Experimental DNase I hypersensitive site profiles are consistent with active configurations of these lncRNA TFBS sets in diverse human cell types. TFBS ChIP-seq datasets confirm the binding events that we predicted using computational approaches for a subset of factors. For several TFs known to be directly regulated by lncRNAs, we find that their putative TFBSs are enriched at lncRNA promoters, suggesting that the TFs and the lncRNAs may participate in a bidirectional feedback loop regulatory network. Accordingly, cells may be able to modulate lncRNA expression levels independently of mRNA levels via distinct regulatory pathways. Our results also raise the possibility that, given the historical reliance on protein-coding gene catalogs to define the chromatin states of active promoters, a revision of these chromatin signature profiles to incorporate expressed lncRNA genes is warranted in the future.

  16. What Can Big Data Offer the Pharmacovigilance of Orphan Drugs?

    Science.gov (United States)

    Price, John

    2016-12-01

    The pharmacovigilance of drugs for orphan diseases presents problems related to the small patient population. Obtaining high-quality information on individual reports of suspected adverse reactions is of particular importance for the pharmacovigilance of orphan drugs. The possibility of mining "big data" to detect suspected adverse reactions is being explored in pharmacovigilance generally but may have limited application to orphan drugs. Sources of big data such as social media may be infrequently used as communication channels by patients with rare disease or their caregivers or by health care providers; any adverse reactions identified are likely to reflect what is already known about the safety of the drug from the network of support that grows up around these patients. Opportunities related to potential future big data sources are discussed.

  17. Estimation of the detectability of optical orphan afterglows

    CERN Document Server

    Zou, Y C; Dai, Z G

    2006-01-01

    Considering two main assumptions: no sideways expansion and the distribution of half-opening angle of jetted ejecta of gamma-ray bursts, we estimate the detectability of optical orphan afterglows. We show that the former assumption leads to more orphans to be detected while the latter greatly depresses the detectability compared with one single opening angle $\\theta_j=0.1$ model. We also consider the influence of other parameters, and find that the effects of ejecta energy $E_j$, post-jet-break temporal index $-\\alpha_2$ and the distribution of half-opening angle of the jet are important while the index of electron energy distribution $p$, electron energy equipartition factor $\\epsilon_e$ and environment density $n$ are insignificant. If the $E_j$ and $\\alpha_2$ are determined by other methods, one can constrain the distribution of half-opening angle of jets by observation of orphan afterglows.

  18. EU marketing authorization review of orphan and non-orphan drugs does not differ.

    Science.gov (United States)

    Putzeist, M; Mantel-Teeuwisse, A K; Llinares, J; Gispen-De Wied, C C; Hoes, A W; Leufkens, H G M

    2013-10-01

    Marketing authorization application dossiers of 17 orphan drugs (ODs) and 51 non-ODs evaluated by the European Medicines Agency (EMA) in the period 2009-2010 were compared. We aimed to identify whether any differences existed between ODs and non-ODs in number and type of deficits brought forward during the EMA review, regarding the clinical development plan, clinical outcome and medical need and studied whether these deficits were similarly associated with marketing approval in the EU. In 71% of the ODs dossiers and 65% of the non-ODs dossiers marketing approval was granted. Differences in deficits were found, but similarities in the way ODs and non-ODs were reviewed and marketing approval decisions were taken, underline that regulatory standards are equally high.

  19. Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina

    Directory of Open Access Journals (Sweden)

    Ussery David

    2007-09-01

    Full Text Available Abstract Background Several dozen fungi encompassing traditional model organisms, industrial production organisms and human and plant pathogens have been sequenced recently and their particular genomic features analysed in detail. In addition comparative genomics has been used to analyse specific sub groups of fungi. Notably, analysis of the phylum Saccharomycotina has revealed major events of evolution such as the recent genome duplication and subsequent gene loss. However, little has been done to gain a comprehensive comparative view to the fungal kingdom. We have carried out a computational genome wide comparison of protein coding gene content of Saccharomycotina and Pezizomycotina, which include industrially important yeasts and filamentous fungi, respectively. Results Our analysis shows that based on genome redundancy, the traditional model organisms Saccharomyces cerevisiae and Neurospora crassa are exceptional among fungi. This can be explained by the recent genome duplication in S. cerevisiae and the repeat induced point mutation mechanism in N. crassa. Interestingly in Pezizomycotina a subset of protein families related to plant biomass degradation and secondary metabolism are the only ones showing signs of recent expansion. In addition, Pezizomycotina have a wealth of phylum specific poorly characterised genes with a wide variety of predicted functions. These genes are well conserved in Pezizomycotina, but show no signs of recent expansion. The genes found in all fungi except Saccharomycotina are slightly better characterised and predicted to encode mainly enzymes. The genes specific to Saccharomycotina are enriched in transcription and mitochondrion related functions. Especially mitochondrial ribosomal proteins seem to have diverged from those of Pezizomycotina. In addition, we highlight several individual gene families with interesting phylogenetic distributions. Conclusion Our analysis predicts that all Pezizomycotina unlike

  20. The correlation between HTA recommendations and reimbursement status of orphan drugs in Europe

    OpenAIRE

    Kawalec, Paweł; Sagan, Anna; Pilc, Andrzej

    2016-01-01

    Background The aim of this study was to review and compare types of reimbursement recommendations for orphan drugs issued by eight European health technology assessment (HTA) agencies and the reimbursement status of these drugs in the corresponding countries. Separate calculations were also performed for three sub-groups: ultra-orphan drugs, oncology orphan drugs and other (non-ultra, non-oncology) orphan drugs. Results We reviewed drugs authorized by the European Medicine Agency (EMA) betwee...

  1. Accessing Social Grants to Meet Orphan Children School Needs: Namibia and South Africa Perspective

    Science.gov (United States)

    Taukeni, Simon; Matshidiso, Taole

    2013-01-01

    In this comparative paper we interrogate the access of social grants to meet orphan children school needs in Namibia and South Africa. We noted that the two governments are committed to provide orphan children with social grants to enable them to meet the school needs. However, accessing social grant to benefit most vulnerable orphan children…

  2. Orphan drugs expenditure in the Netherlands in the period 2006-2012

    NARCIS (Netherlands)

    T.A. Kanters (Tim A.); A. Steenhoek (Adri); L. van Hakkaart-van Roijen (Leona)

    2014-01-01

    textabstractBackground: The relatively low budget impact of orphan drugs is often used as an argument in reimbursement decisions. However, overall, the budget impact of orphan drugs can still be substantial. In this study, we assess the uptake and budget impact of orphan drugs in the Netherlands.Met

  3. The importance of HIV prevention messaging for orphaned youth in Zimbabwe.

    Science.gov (United States)

    Haney, Erica; Singh, Kavita

    2012-01-01

    The AIDS epidemic has contributed to a drastic increase in the number of orphans in Zimbabwe. Female adolescent orphans are particularly in jeopardy of contracting HIV due to disadvantages including extreme poverty, low education, and the absent of parental oversight which can lead to higher risk-taking sexual behaviors. By understanding where girls receive education about HIV and who they rely on for information, organizations can effectively modify existing programs to better target this at-risk population. For this study a household survey was conducted which included 216 orphans and 324 non-orphans (n=540), aged 12-17 years, in the resource-poor setting of Hwange District, Zimbabwe. The aims of this article were to examine the differences between orphans and non-orphans in HIV prevention message exposure, level of motivation for learning about HIV, and communication with caregivers about safe sex. The household survey revealed that younger orphans, aged 12-15 years, were more motivated to learn about HIV and had greater HIV messaging exposure in school than non-orphans. These exposure and differences in the levels of motivation between groups dissipated at older ages. Our research also discovered less caregiver communication among orphans than non-orphans. Our findings suggest that HIV programs targeting orphans need to do a better job at keeping older orphans interested in HIV prevention at a time when it matters most. Furthermore, intervention strategies that provide caregiver support are instrumental in effectively delivering prevention messages to girls at home.

  4. Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence.

    Science.gov (United States)

    Regier, Jerome C; Shultz, Jeffrey W; Ganley, Austen R D; Hussey, April; Shi, Diane; Ball, Bernard; Zwick, Andreas; Stajich, Jason E; Cummings, Michael P; Martin, Joel W; Cunningham, Clifford W

    2008-12-01

    This study attempts to resolve relationships among and within the four basal arthropod lineages (Pancrustacea, Myriapoda, Euchelicerata, Pycnogonida) and to assess the widespread expectation that remaining phylogenetic problems will yield to increasing amounts of sequence data. Sixty-eight regions of 62 protein-coding nuclear genes (approximately 41 kilobases (kb)/taxon) were sequenced for 12 taxonomically diverse arthropod taxa and a tardigrade outgroup. Parsimony, likelihood, and Bayesian analyses of total nucleotide data generally strongly supported the monophyly of each of the basal lineages represented by more than one species. Other relationships within the Arthropoda were also supported, with support levels depending on method of analysis and inclusion/exclusion of synonymous changes. Removing third codon positions, where the assumption of base compositional homogeneity was rejected, altered the results. Removing the final class of synonymous mutations--first codon positions encoding leucine and arginine, which were also compositionally heterogeneous--yielded a data set that was consistent with a hypothesis of base compositional homogeneity. Furthermore, under such a data-exclusion regime, all 68 gene regions individually were consistent with base compositional homogeneity. Restricting likelihood analyses to nonsynonymous change recovered trees with strong support for the basal lineages but not for other groups that were variably supported with more inclusive data sets. In a further effort to increase phylogenetic signal, three types of data exploration were undertaken. (1) Individual genes were ranked by their average rate of nonsynonymous change, and three rate categories were assigned--fast, intermediate, and slow. Then, bootstrap analysis of each gene was performed separately to see which taxonomic groups received strong support. Five taxonomic groups were strongly supported independently by two or more genes, and these genes mostly belonged to the slow

  5. Orphan receptor ligand discovery by pickpocketing pharmacological neighbors.

    Science.gov (United States)

    Ngo, Tony; Ilatovskiy, Andrey V; Stewart, Alastair G; Coleman, James L J; McRobb, Fiona M; Riek, R Peter; Graham, Robert M; Abagyan, Ruben; Kufareva, Irina; Smith, Nicola J

    2017-02-01

    Understanding the pharmacological similarity of G protein-coupled receptors (GPCRs) is paramount for predicting ligand off-target effects, drug repurposing, and ligand discovery for orphan receptors. Phylogenetic relationships do not always correctly capture pharmacological similarity. Previous family-wide attempts to define pharmacological relationships were based on three-dimensional structures and/or known receptor-ligand pairings, both unavailable for orphan GPCRs. Here, we present GPCR-CoINPocket, a novel contact-informed neighboring pocket metric of GPCR binding-site similarity that is informed by patterns of ligand-residue interactions observed in crystallographically characterized GPCRs. GPCR-CoINPocket is applicable to receptors with unknown structure or ligands and accurately captures known pharmacological relationships between GPCRs, even those undetected by phylogeny. When applied to orphan receptor GPR37L1, GPCR-CoINPocket identified its pharmacological neighbors, and transfer of their pharmacology aided in discovery of the first surrogate ligands for this orphan with a 30% success rate. Although primarily designed for GPCRs, the method is easily transferable to other protein families.

  6. Chinese Company Doubles as “Mother” of Orphans

    Institute of Scientific and Technical Information of China (English)

    JU JIUJIANG; WANG GUILAN

    2011-01-01

    The story goes back to the end of 2007,when Yang Min,Party secretary and deputy chief manager of the Nantong Times Clothing Co.,Ltd.in Rugao,Jiangsu Province,heard what had happened to an orphan in the city.

  7. 77 FR 64555 - Orphan Works and Mass Digitization

    Science.gov (United States)

    2012-10-22

    ... short, the Office concluded that the problem of orphan works is pervasive; it affects a broad cross... potentially at issue, from music to books to film clips. That said, the Report also reflects that a... particularly challenging because they affect a vast variety of images, from historically important...

  8. Pricing and reimbursement of orphan drugs: the need for more transparency

    Directory of Open Access Journals (Sweden)

    Simoens Steven

    2011-06-01

    Full Text Available Abstract Pricing and reimbursement of orphan drugs are an issue of high priority for policy makers, legislators, health care professionals, industry leaders, academics and patients. This study aims to conduct a literature review to provide insight into the drivers of orphan drug pricing and reimbursement. Although orphan drug pricing follows the same economic logic as drug pricing in general, the monopolistic power of orphan drugs results in high prices: a orphan drugs benefit from a period of marketing exclusivity; b few alternative health technologies are available; c third-party payers and patients have limited negotiating power; d manufacturers attempt to maximise orphan drug prices within the constraints of domestic pricing and reimbursement policies; and e substantial R&D costs need to be recouped from a small number of patients. Although these conditions apply to some orphan drugs, they do not apply to all orphan drugs. Indeed, the small number of patients treated with an orphan drug and the limited economic viability of orphan drugs can be questioned in a number of cases. Additionally, manufacturers have an incentive to game the system by artificially creating monopolistic market conditions. Given their high price for an often modest effectiveness, orphan drugs are unlikely to provide value for money. However, additional criteria are used to inform reimbursement decisions in some countries. These criteria may include: the seriousness of the disease; the availability of other therapies to treat the disease; and the cost to the patient if the medicine is not reimbursed. Therefore, the maximum cost per unit of outcome that a health care payer is willing to pay for a drug could be set higher for orphan drugs to which society attaches a high social value. There is a need for a transparent and evidence-based approach towards orphan drug pricing and reimbursement. Such an approach should be targeted at demonstrating the relative effectiveness

  9. Pricing and reimbursement of orphan drugs: the need for more transparency.

    Science.gov (United States)

    Simoens, Steven

    2011-06-17

    Pricing and reimbursement of orphan drugs are an issue of high priority for policy makers, legislators, health care professionals, industry leaders, academics and patients. This study aims to conduct a literature review to provide insight into the drivers of orphan drug pricing and reimbursement. Although orphan drug pricing follows the same economic logic as drug pricing in general, the monopolistic power of orphan drugs results in high prices: a) orphan drugs benefit from a period of marketing exclusivity; b) few alternative health technologies are available; c) third-party payers and patients have limited negotiating power; d) manufacturers attempt to maximise orphan drug prices within the constraints of domestic pricing and reimbursement policies; and e) substantial R&D costs need to be recouped from a small number of patients. Although these conditions apply to some orphan drugs, they do not apply to all orphan drugs. Indeed, the small number of patients treated with an orphan drug and the limited economic viability of orphan drugs can be questioned in a number of cases. Additionally, manufacturers have an incentive to game the system by artificially creating monopolistic market conditions. Given their high price for an often modest effectiveness, orphan drugs are unlikely to provide value for money. However, additional criteria are used to inform reimbursement decisions in some countries. These criteria may include: the seriousness of the disease; the availability of other therapies to treat the disease; and the cost to the patient if the medicine is not reimbursed. Therefore, the maximum cost per unit of outcome that a health care payer is willing to pay for a drug could be set higher for orphan drugs to which society attaches a high social value. There is a need for a transparent and evidence-based approach towards orphan drug pricing and reimbursement. Such an approach should be targeted at demonstrating the relative effectiveness, cost-effectiveness and

  10. Proteomic detection of non-annotated protein-coding genes in Pseudomonas fluorescens Pf0-1.

    Science.gov (United States)

    Kim, Wook; Silby, Mark W; Purvine, Sam O; Nicoll, Julie S; Hixson, Kim K; Monroe, Matt; Nicora, Carrie D; Lipton, Mary S; Levy, Stuart B

    2009-12-24

    Genome sequences are annotated by computational prediction of coding sequences, followed by similarity searches such as BLAST, which provide a layer of possible functional information. While the existence of processes such as alternative splicing complicates matters for eukaryote genomes, the view of bacterial genomes as a linear series of closely spaced genes leads to the assumption that computational annotations that predict such arrangements completely describe the coding capacity of bacterial genomes. We undertook a proteomic study to identify proteins expressed by Pseudomonas fluorescens Pf0-1 from genes that were not predicted during the genome annotation. Mapping peptides to the Pf0-1 genome sequence identified sixteen non-annotated protein-coding regions, of which nine were antisense to predicted genes, six were intergenic, and one read in the same direction as an annotated gene but in a different frame. The expression of all but one of the newly discovered genes was verified by RT-PCR. Few clues as to the function of the new genes were gleaned from informatic analyses, but potential orthologs in other Pseudomonas genomes were identified for eight of the new genes. The 16 newly identified genes improve the quality of the Pf0-1 genome annotation, and the detection of antisense protein-coding genes indicates the under-appreciated complexity of bacterial genome organization.

  11. Proteomic detection of non-annotated protein-coding genes in Pseudomonas fluorescens Pf0-1.

    Directory of Open Access Journals (Sweden)

    Wook Kim

    Full Text Available Genome sequences are annotated by computational prediction of coding sequences, followed by similarity searches such as BLAST, which provide a layer of possible functional information. While the existence of processes such as alternative splicing complicates matters for eukaryote genomes, the view of bacterial genomes as a linear series of closely spaced genes leads to the assumption that computational annotations that predict such arrangements completely describe the coding capacity of bacterial genomes. We undertook a proteomic study to identify proteins expressed by Pseudomonas fluorescens Pf0-1 from genes that were not predicted during the genome annotation. Mapping peptides to the Pf0-1 genome sequence identified sixteen non-annotated protein-coding regions, of which nine were antisense to predicted genes, six were intergenic, and one read in the same direction as an annotated gene but in a different frame. The expression of all but one of the newly discovered genes was verified by RT-PCR. Few clues as to the function of the new genes were gleaned from informatic analyses, but potential orthologs in other Pseudomonas genomes were identified for eight of the new genes. The 16 newly identified genes improve the quality of the Pf0-1 genome annotation, and the detection of antisense protein-coding genes indicates the under-appreciated complexity of bacterial genome organization.

  12. Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Wook; Silby, Mark W.; Purvine, Samuel O.; Nicoll, Julie S.; Hixson, Kim K.; Monroe, Matthew E.; Nicora, Carrie D.; Lipton, Mary S.; Levy, Stuart B.

    2009-12-24

    Genome sequences are annotated by computational prediction of coding sequences, followed by similarity searches such as BLAST, which provide a layer of (possible) functional information. While the existence of processes such as alternative splicing complicates matters for eukaryote genomes, the view of bacterial genomes as a linear series of closely spaced genes leads to the assumption that computational annotations which predict such arrangements completely describe the coding capacity of bacterial genomes. We undertook a proteomic study to identify proteins expressed by Pseudomonas fluorescens Pf0-1 from genes which were not predicted during the genome annotation. Mapping peptides to the Pf0-1 genome sequence identified sixteen non-annotated protein-coding regions, of which nine were antisense to predicted genes, six were intergenic, and one read in the same direction as an annotated gene but in a different frame. The expression of all but one of the newly discovered genes was verified by RT-PCR. Few clues as to the function of the new genes were gleaned from informatic analyses, but potential orthologues in other Pseudomonas genomes were identified for eight of the new genes. The 16 newly identified genes improve the quality of the Pf0-1 genome annotation, and the detection of antisense protein-coding genes indicates the under-appreciated complexity of bacterial genome organization.

  13. Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq.

    Science.gov (United States)

    Zhu, Jinhang; Chen, Geng; Zhu, Sibo; Li, Suqing; Wen, Zhuo; Bin Li; Zheng, Yuanting; Shi, Leming

    2016-06-22

    Many diseases and adverse drug reactions exhibit tissue specificity. To better understand the tissue-specific expression characteristics of transcripts in different human tissues, we deeply sequenced RNA samples from 14 different human tissues. After filtering many lowly expressed transcripts, 24,729 protein-coding transcripts and 1,653 noncoding transcripts were identified. By analyzing highly expressed tissue-specific protein-coding transcripts (TSCTs) and noncoding transcripts (TSNTs), we found that testis expressed the highest numbers of TSCTs and TSNTs. Brain, monocytes, ovary, and heart expressed more TSCTs than the rest tissues, whereas brain, placenta, heart, and monocytes expressed more TSNTs than other tissues. Co-expression network constructed based on the TSCTs and TSNTs showed that each hub TSNT was co-expressed with several TSCTs, allowing functional annotation of TSNTs. Important biological processes and KEGG pathways highly related to the specific functions or diseases of each tissue were enriched with the corresponding TSCTs. These TSCTs and TSNTs may participate in the tissue-specific physiological or pathological processes. Our study provided a unique data set and systematic analysis of expression characteristics and functions of both TSCTs and TSNTs based on 14 distinct human tissues, and could facilitate future investigation of the mechanisms behind tissue-specific diseases and adverse drug reactions.

  14. Orphan neuropeptides. Novel neuropeptides modulating sleep or feeding.

    Science.gov (United States)

    Chung, Shinjae; Civelli, Olivier

    2006-08-01

    Neuropeptides form the largest family of modulators of synaptic transmission. Until 1995 some 60 different neuropeptides had been found. With the recognition that all neuropeptides act by binding to G protein coupled receptors (GPCRs), a new approach relying on the use of orphan GPCRs as targets was designed to identify novel neuropeptides. Thirteen new neuropeptide families have since been discovered. In this review we will describe the orphan GPCR-based approach that led to these discoveries and present its impact on two specific physiological responses, feeding and sleep. In particular, we will discuss the modulatory roles of the hypocretins/orexins and of neuropeptide S in sleep and awakening and those of ghrelin and melanin concentrating hormone in food intake.

  15. Duals of Orphan-Free Anisotropic Voronoi Diagrams are Triangulations

    CERN Document Server

    Canas, Guillermo D

    2011-01-01

    We show that, under mild conditions on the underlying metric, duals of appropriately defined anisotropic Voronoi diagrams are embedded triangulations. Furthermore, they always triangulate the convex hull of the vertices, and have other properties that parallel those of ordinary Delaunay triangulations. These results apply to the duals of anisotropic Voronoi diagrams of any set of vertices, so long as the diagram is orphan-free.

  16. Challenges in orphan drug development and regulatory policy in China

    OpenAIRE

    Cheng, Alice; Xie, Zhi

    2017-01-01

    While regulatory policy is well defined for orphan drug development in the United States and Europe, rare disease policy in China is still evolving. Many Chinese patients currently pay out of pocket for international treatments that are not yet approved in China. The lack of a clear definition and therefore regulatory approval process for rare diseases has, until now, de-incentivized pharmaceutical companies to pursue rare disease drug development in China. In turn, many grassroots movements ...

  17. Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation.

    Science.gov (United States)

    Xing, Chuanhua; Bitzer, Donald L; Alexander, Winser E; Vouk, Mladen A; Stomp, Anne-Marie

    2009-02-01

    We introduce a new approach in this article to distinguish protein-coding sequences from non-coding sequences utilizing a period-3, free energy signal that arises from the interactions of the 3'-terminal nucleotides of the 18S rRNA with mRNA. We extracted the special features of the amplitude and the phase of the period-3 signal in protein-coding regions, which is not found in non-coding regions, and used them to distinguish protein-coding sequences from non-coding sequences. We tested on all the experimental genes from Saccharomyces cerevisiae and Schizosaccharomyces pombe. The identification was consistent with the corresponding information from GenBank, and produced better performance compared to existing methods that use a period-3 signal. The primary tests on some fly, mouse and human genes suggests that our method is applicable to higher eukaryotic genes. The tests on pseudogenes indicated that most pseudogenes have no period-3 signal. Some exploration of the 3'-tail of 18S rRNA and pattern analysis of protein-coding sequences supported further our assumption that the 3'-tail of 18S rRNA has a role of synchronization throughout translation elongation process. This, in turn, can be utilized for the identification of protein-coding sequences.

  18. Influence of the Leader protein coding region of foot-and-mouth disease virus on virus replication

    DEFF Research Database (Denmark)

    Belsham, Graham

    2013-01-01

    The foot-and-mouth disease virus (FMDV) Leader (L) protein is produced in two forms, Lab and Lb, differing only at their amino-termini, due to the use of separate initiation codons, usually 84 nt apart. It has been shown previously, and confirmed here, that precise deletion of the Lab coding......, in the context of the virus lacking the Lb coding region, was also tolerated by the virus within BHK cells. However, precise loss of the Lb coding sequence alone blocked FMDV replication in primary bovine thyroid cells. Thus, the requirement for the Leader protein coding sequences is highly dependent...... on the nature and extent of the residual Leader protein sequences and on the host cell system used. FMDVs precisely lacking Lb and with the Lab initiation codon modified may represent safer seed viruses for vaccine production....

  19. Analysis of protein-coding mutations in hiPSCs and their possible role during somatic cell reprogramming.

    Science.gov (United States)

    Ruiz, Sergio; Gore, Athurva; Li, Zhe; Panopoulos, Athanasia D; Montserrat, Nuria; Fung, Ho-Lim; Giorgetti, Alessandra; Bilic, Josipa; Batchelder, Erika M; Zaehres, Holm; Schöler, Hans R; Zhang, Kun; Izpisua Belmonte, Juan Carlos

    2013-01-01

    Recent studies indicate that human-induced pluripotent stem cells contain genomic structural variations and point mutations in coding regions. However, these studies have focused on fibroblast-derived human induced pluripotent stem cells, and it is currently unknown whether the use of alternative somatic cell sources with varying reprogramming efficiencies would result in different levels of genetic alterations. Here we characterize the genomic integrity of eight human induced pluripotent stem cell lines derived from five different non-fibroblast somatic cell types. We show that protein-coding mutations are a general feature of the human induced pluripotent stem cell state and are independent of somatic cell source. Furthermore, we analyse a total of 17 point mutations found in human induced pluripotent stem cells and demonstrate that they do not generally facilitate the acquisition of pluripotency and thus are not likely to provide a selective advantage for reprogramming.

  20. Complex interplay among DNA modification, noncoding RNA expression and protein-coding RNA expression in Salvia miltiorrhiza chloroplast genome.

    Directory of Open Access Journals (Sweden)

    Haimei Chen

    Full Text Available Salvia miltiorrhiza is one of the most widely used medicinal plants. As a first step to develop a chloroplast-based genetic engineering method for the over-production of active components from S. miltiorrhiza, we have analyzed the genome, transcriptome, and base modifications of the S. miltiorrhiza chloroplast. Total genomic DNA and RNA were extracted from fresh leaves and then subjected to strand-specific RNA-Seq and Single-Molecule Real-Time (SMRT sequencing analyses. Mapping the RNA-Seq reads to the genome assembly allowed us to determine the relative expression levels of 80 protein-coding genes. In addition, we identified 19 polycistronic transcription units and 136 putative antisense and intergenic noncoding RNA (ncRNA genes. Comparison of the abundance of protein-coding transcripts (cRNA with and without overlapping antisense ncRNAs (asRNA suggest that the presence of asRNA is associated with increased cRNA abundance (p<0.05. Using the SMRT Portal software (v1.3.2, 2687 potential DNA modification sites and two potential DNA modification motifs were predicted. The two motifs include a TATA box-like motif (CPGDMM1, "TATANNNATNA", and an unknown motif (CPGDMM2 "WNYANTGAW". Specifically, 35 of the 97 CPGDMM1 motifs (36.1% and 91 of the 369 CPGDMM2 motifs (24.7% were found to be significantly modified (p<0.01. Analysis of genes downstream of the CPGDMM1 motif revealed the significantly increased abundance of ncRNA genes that are less than 400 bp away from the significantly modified CPGDMM1motif (p<0.01. Taking together, the present study revealed a complex interplay among DNA modifications, ncRNA and cRNA expression in chloroplast genome.

  1. Development-related expression patterns of protein-coding and miRNA genes involved in porcine muscle growth.

    Science.gov (United States)

    Wang, F J; Jin, L; Guo, Y Q; Liu, R; He, M N; Li, M Z; Li, X W

    2014-01-01

    Muscle growth and development is associated with remarkable changes in protein-coding and microRNA (miRNA) gene expression. To determine the expression patterns of genes and miRNAs related to muscle growth and development, we measured the expression levels of 25 protein-coding and 16 miRNA genes in skeletal and cardiac muscles throughout 5 developmental stages by quantitative reverse transcription-polymerase chain reaction. The Short Time-Series Expression Miner (STEM) software clustering results showed that growth-related genes were downregulated at all developmental stages in both the psoas major and longissimus dorsi muscles, indicating their involvement in early developmental stages. Furthermore, genes related to muscle atrophy, such as forkhead box 1 and muscle ring finger, showed unregulated expression with increasing age, suggesting a decrease in protein synthesis during the later stages of skeletal muscle development. We found that development of the cardiac muscle was a complex process in which growth-related genes were highly expressed during embryonic development, but they did not show uniform postnatal expression patterns. Moreover, the expression level of miR-499, which enhances the expression of the β-myosin heavy chain, was significantly different in the psoas major and longissimus dorsi muscles, suggesting the involvement of miR-499 in the determination of skeletal muscle fiber types. We also performed correlation analyses of messenger RNA and miRNA expression. We found negative relationships between miR-486 and forkhead box 1, and miR-133a and serum response factor at all developmental stages, suggesting that forkhead box 1 and serum response factor are potential targets of miR-486 and miR-133a, respectively.

  2. Arabidopsis hybrid speciation processes.

    Science.gov (United States)

    Schmickl, Roswitha; Koch, Marcus A

    2011-08-23

    The genus Arabidopsis provides a unique opportunity to study fundamental biological questions in plant sciences using the diploid model species Arabidopsis thaliana and Arabidopsis lyrata. However, only a few studies have focused on introgression and hybrid speciation in Arabidopsis, although polyploidy is a common phenomenon within this genus. More recently, there is growing evidence of significant gene flow between the various Arabidopsis species. So far, we know Arabidopsis suecica and Arabidopsis kamchatica as fully stabilized allopolyploid species. Both species evolved during Pleistocene glaciation and deglaciation cycles in Fennoscandinavia and the amphi-Beringian region, respectively. These hybrid studies were conducted either on a phylogeographic scale or reconstructed experimentally in the laboratory. In our study we focus at a regional and population level. Our research area is located in the foothills of the eastern Austrian Alps, where two Arabidopsis species, Arabidopsis arenosa and A. lyrata ssp. petraea, are sympatrically distributed. Our hypothesis of genetic introgression, migration, and adaptation to the changing environment during the Pleistocene has been confirmed: We observed significant, mainly unidirectional gene flow between the two species, which has given rise to the tetraploid A. lyrata. This cytotype was able to escape from the narrow ecological niche occupied by diploid A. lyrata ssp. petraea on limestone outcrops by migrating northward into siliceous areas, leaving behind a trail of genetic differentiation.

  3. Orphan drugs for rare diseases: is it time to revisit their special market access status?

    Science.gov (United States)

    Simoens, Steven; Cassiman, David; Dooms, Marc; Picavet, Eline

    2012-07-30

    Orphan drugs are intended for diseases with a very low prevalence, and many countries have implemented legislation to support market access of orphan drugs. We argue that it is time to revisit the special market access status of orphan drugs. Indeed, evidence suggests that there is no societal preference for treating rare diseases. Although society appears to assign a greater value to severity of disease, this criterion is equally relevant to many common diseases. Furthermore, the criterion of equity in access to treatment, which underpins orphan drug legislation, puts more value on health improvement in rare diseases than in common diseases and implies that population health is not maximized. Finally, incentives for the development, pricing and reimbursement of orphan drugs have created market failures, including monopolistic prices and the artificial creation of rare diseases. We argue that, instead of awarding special market access status to orphan drugs, there is scope to optimize research and development (R&D) of orphan drugs and to control prices of orphan drugs by means of, for example, patent auctions, advance purchase commitments, pay-as-you-go schemes and dose-modification studies. Governments should consider carefully the right incentive strategy for R&D of orphan drugs in rare diseases.

  4. Significant Comparative Characteristics between Orphan and Nonorphan Genes in the Rice (Oryza sativa L. Genome

    Directory of Open Access Journals (Sweden)

    Wen-Jiu Guo

    2007-01-01

    Full Text Available Microsatellites are short tandem repeats of one to six bases in genomic DNA. As microsatellites are highly polymorphic and play a vital role in gene function and recombination, they are an attractive subject for research in evolution and in the genetics and breeding of animals and plants. Orphan genes have no known homologs in existing databases. Using bioinformatic computation and statistical analysis, we identified 19,26 orphan genes in the rice (Oryza sativa ssp. Japanica cv. Nipponbare proteome. We found that a larger proportion of orphan genes are expressed after sexual maturation and under environmental pressure than nonorphan genes. Orphan genes generally have shorter protein lengths and intron size, and are faster evolving. Additionally, orphan genes have fewer PROSITE patterns with larger pattern sizes than those in nonorphan genes. The average microsatellite content and the percentage of trinucleotide repeats in orphan genes are also significantly higher than in nonorphan genes. Microsatellites are found less often in PROSITE patterns in orphan genes. Taken together, these orphan gene characteristics suggest that microsatellites play an important role in orphan gene evolution and expression.

  5. Conceptions of mental health among Ugandan youth orphaned by AIDS.

    Science.gov (United States)

    Harms, Sheila; Kizza, Ruth; Sebunnya, Joshua; Jack, Susan

    2009-03-01

    The AIDS epidemic has disproportionately affected developing or low-income sub-Saharan African countries. Within the context of the epidemic, children and youth are at risk of losing their parents at an early age. The experience of orphanhood due to AIDS has the potential to negatively impact on a child's mental health. A qualitative study was conducted to comprehensively describe the experience of orphanhood and its impact on mental health from the culturally specific perspective of Ugandan youths. We conducted interviews with a purposeful sample of 13 youths (ages 12 to 18) who had lost one or both parents to AIDS illness and who were also affiliated with a non-governmental organisation providing support to orphans. The orphaned youths experienced significant ongoing emotional difficulties following the death of their parent(s). The youths in this study were unfamiliar with the term 'mental health,' however they easily identified factors associated with good or poor mental health. In general, good mental health was associated with social conduct that is culturally appropriate. Poor mental health was perceived as a form of madness or insanity and it was associated with a loss of basic life necessities, such as access to food, education or shelter. The youths also identified factors that promote more successful orphans. The findings of this study suggest that Western terminologies and symptom constellations in the Diagnostic and Statistical Manual IV may not be applicable in an African cultural context. There are several clinical implications, including the development of a mental health intervention paradigm that emphasises resilience.

  6. Orphan protein function and its relation to glycosylation

    DEFF Research Database (Denmark)

    Gupta, Ramneek; Jensen, Lars Juhl; Brunak, Søren

    2002-01-01

    , and inference of protein function by exploiting direct sequence similarity indeed goes a long way in describing a proteome’s functional capacity. However, at least 40% of the gene products in newly sequenced genomes typically remain uncharacterised. Proteins without an annotated function are also known...... as orphan proteins since they do not belong to a functionally characterised protein family. Many sequences must, therefore, be compared using their features rather than by direct comparison in the conventional sequence space. Here we focus on one such feature — glycosylation — that is common in eukaryotic...

  7. Children, foundlings and orphans in 19th Century Montevideo

    Directory of Open Access Journals (Sweden)

    María Laura Osta Vázquez

    2016-12-01

    Full Text Available Our aim is to shed light on orphan children in 19th century Montevideo from the vantage points of the history of childhood, the history of concepts, and other methodological perspectives. The first orphanage, called ‘La Inclusa’, was founded in 1818. Its activities revolved around a turnstile system wherein babies were left mostly anonymously, by their parents, relatives, neighbors or midwives. Our goal is to deconstruct concepts commonly used today and to historically contextualize them in relation to such practices. We seek to quantitatively visualize these children, parents and wet nurses through charts based on adoption and vital records. 

  8. Random forest classification of etiologies for an orphan disease.

    Science.gov (United States)

    Speiser, Jaime Lynn; Durkalski, Valerie L; Lee, William M

    2015-02-28

    Classification of objects into pre-defined groups based on known information is a fundamental problem in the field of statistics. Although approaches for solving this problem exist, finding an accurate classification method can be challenging in an orphan disease setting, where data are minimal and often not normally distributed. The purpose of this paper is to illustrate the application of the random forest (RF) classification procedure in a real clinical setting and discuss typical questions that arise in the general classification framework as well as offer interpretations of RF results. This paper includes methods for assessing predictive performance, importance of predictor variables, and observation-specific information.

  9. 78 FR 44016 - Exclusion of Orphan Drugs for Certain Covered Entities Under 340B Program

    Science.gov (United States)

    2013-07-23

    ... HUMAN SERVICES 42 CFR Part 10 RIN 0906-AA94 Exclusion of Orphan Drugs for Certain Covered Entities Under... exclusion requirements. This rule will provide clarity in the marketplace, maintain the 340B savings for... 340B(e) of the PHSA (42 U.S.C. 256b(e)) states the following: EXCLUSION OF ORPHAN DRUGS FOR...

  10. 21 CFR 316.30 - Annual reports of holder of orphan-drug designation.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Annual reports of holder of orphan-drug designation. 316.30 Section 316.30 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... of holder of orphan-drug designation. Within 14 months after the date on which a drug was...

  11. Diversity and mobility in households with children orphaned by AIDS in Couffo, Benin

    NARCIS (Netherlands)

    Fagbemissi, R.C.; Lie, R.; Leeuwis, C.

    2009-01-01

    This paper characterises children orphaned by AIDS in the Couffo region of Benin. A 2006 census conducted for the research revealed a total of 315 such orphans, aged 0 to 14 years, within 88 households. Seventy-one percent of these children were under the care of their mothers or grandmothers, 68% w

  12. Neglect and perceived stigmatization impact psychological distress of orphans in Tanzania

    Directory of Open Access Journals (Sweden)

    Katharin Hermenau

    2015-11-01

    Full Text Available Background: Research has shown that orphans in sub-Saharan Africa are at increased risk for mental health problems. Exposure to maltreatment and HIV/AIDS-related stigmatization are related to orphans’ psychological distress. Yet, researchers stress the need for more research in low-income countries to identify which factors of being an orphan may lead to psychological distress. Objectives: The present study aims to systematically investigate orphans’ experiences of maltreatment and stigmatization to identify factors that relate to their psychological distress. Methods: In total, 89 Tanzanian children who had lost at least one parent were compared to 89 matched non-orphans (mean age: 11 years; 51% boys. We measured exposure to maltreatment and perceived stigmatization as an orphan. Mental health was assessed using the Strengths and Difficulties Questionnaire, the Children's Depression Inventory, the UCLA PTSD Index for Children, and the Reactive–Proactive Questionnaire. Results: Orphans reported significantly more experiences of neglect, but not of abuse. A group comparison revealed more depressive symptoms, posttraumatic stress symptoms, and aggressive behavior among orphans. Neglect, abuse, and stigmatization correlated with orphans’ internalizing and externalizing problems, yet only neglect and stigmatization were related to orphans’ depression severity. Perceived stigmatization moderated the relationship between neglect and depression. Conclusions: Our findings suggest that orphans in Tanzania are at increased risk of experiencing neglect. Maltreatment and perceived stigmatization may play a role in orphans’ psychological distress. Culturally appropriate and evidence-based interventions may help to prevent maltreatment and stigmatization of orphans.

  13. Elucidation of primary metabolic pathways in Aspergillus species: Orphaned research in characterizing orphan genes

    DEFF Research Database (Denmark)

    Andersen, Mikael Rørdam

    2014-01-01

    of cellular function. However, several methods can be employed to use the metabolic networks in tandem with comparative genomics to accelerate functional assignment of genes in primary metabolism. In particular, gaps in metabolic pathways can be used to assign functions to orphan genes. In this review......Primary metabolism affects all phenotypical traits of filamentous fungi. Particular examples include reacting to extracellular stimuli, producing precursor molecules required for cell division and morphological changes as well as providing monomer building blocks for production of secondary...

  14. Rare, Low-Frequency, and Common Variants in the Protein-Coding Sequence of Biological Candidate Genes from GWASs Contribute to Risk of Rheumatoid Arthritis

    NARCIS (Netherlands)

    Diogo, Dorothee; Kurreeman, Fina; Stahl, Eli A.; Liao, Katherine P.; Gupta, Namrata; Greenberg, Jeffrey D.; Rivas, Manuel A.; Hickey, Brendan; Flannick, Jason; Thomson, Brian; Guiducci, Candace; Ripke, Stephan; Adzhubey, Ivan; Barton, Anne; Kremer, Joel M.; Alfredsson, Lars; Sunyaev, Shamil; Martin, Javier; Zhernakova, Alexandra; Bowes, John; Eyre, Steve; Siminovitch, Katherine A.; Gregersen, Peter K.; Worthington, Jane; Klareskog, Lars; Padyukov, Leonid; Raychaudhuri, Soumya; Plenge, Robert M.

    2013-01-01

    The extent to which variants in the protein-coding sequence of genes contribute to risk of rheumatoid arthritis (RA) is unknown. In this study, we addressed this issue by deep exon sequencing and large-scale genotyping of 25 biological candidate genes located within RA risk loci discovered by genome

  15. A study of descriptive data for orphans and non-orphans on key criteria of economic vulnerability in two municipalities in South Africa

    Directory of Open Access Journals (Sweden)

    Donald Skinner

    2013-01-01

    Full Text Available Background: It is generally assumed that orphan status increases the risk to children of a range of negative outcomes. In South Africa, death of parents due to HIV-related illness is contributing to a rapid increase in the prevalence of orphans. This paper presents descriptive data from two South African communities, namely Kopanong, in the Free State and Kanana in the North West province, characterising the differences between orphans (double, maternal and paternal and non-orphans on key criteria of social vulnerability.Objectives: The objective was to obtain a better understanding of how different types of orphans and non-orphans may differ in these key areas as a crucial starting point for addressing the devastating consequences the AIDS epidemic has on these children’s lives. While the study focuses on two specific areas these will provide insight into the general situation of orphans in South Africa.Methods: A cross-sectional census survey was conducted in the two communities of Kopanong, comprising n = 5254 households and Kanana, comprising n = 12 984 households.Results: In Kopanong, 8.2% of children had lost both parents, 19.1% had lost their father and 6.5% their mother only, whilst in Kanana the results were 6.5%, 28.1% and 3.7% respectively. Loss of both parents appeared to have a consistent impact on material need, including access to food, clothing and essential services, whilst loss of a single parent seems to have a more variable impact. At present, there are very few child headed households, but this constitutes a risk in the longer term.Conclusions: Orphans appear to be more vulnerable in terms of material need. Children assessed in this study as being most in need were not accessing adequately many services directed at them. There is a need to extend understanding and measurement of emotional need and abuse. 

  16. A study of descriptive data for orphans and non-orphans on key criteria of economic vulnerability in two municipalities in South Africa

    Directory of Open Access Journals (Sweden)

    Donald Skinner

    2013-05-01

    Full Text Available Background: It is generally assumed that orphan status increases the risk to children of a range of negative outcomes. In South Africa, death of parents due to HIV-related illness is contributing to a rapid increase in the prevalence of orphans. This paper presents descriptive data from two South African communities, namely Kopanong, in the Free State and Kanana in the North West province, characterising the differences between orphans (double, maternal and paternal and non-orphans on key criteria of social vulnerability.Objectives: The objective was to obtain a better understanding of how different types of orphans and non-orphans may differ in these key areas as a crucial starting point for addressing the devastating consequences the AIDS epidemic has on these children’s lives. While the study focuses on two specific areas these will provide insight into the general situation of orphans in South Africa.Methods: A cross-sectional census survey was conducted in the two communities of Kopanong, comprising n = 5254 households and Kanana, comprising n = 12 984 households.Results: In Kopanong, 8.2% of children had lost both parents, 19.1% had lost their father and 6.5% their mother only, whilst in Kanana the results were 6.5%, 28.1% and 3.7% respectively. Loss of both parents appeared to have a consistent impact on material need, including access to food, clothing and essential services, whilst loss of a single parent seems to have a more variable impact. At present, there are very few child headed households, but this constitutes a risk in the longer term. Conclusions: Orphans appear to be more vulnerable in terms of material need. Children assessed in this study as being most in need were not accessing adequately many services directed at them. There is a need to extend understanding and measurement of emotional need and abuse.

  17. The role of globalization in drug development and access to orphan drugs: orphan drug legislation in the US/EU and in Latin America

    OpenAIRE

    Arnold, Renée J.G.; Lida Bighash; Alejandro Bryón Nieto; Gabriela Tannus Branco de Araújo; Juan Gabriel Gay-Molina; Federico Augustovski

    2015-01-01

    Compared to a decade ago, nearly three times as many drugs for rare diseases are slated for development. This article addresses the market access issues associated with orphan drug status in Europe and the United States in contrast to the legislation in five Latin American (LA) countries that have made strides in this regard--Mexico, Brazil, Colombia, Chile and Argentina. Based on the success of orphan drug legislation in the EU and US, LA countries should strive to adopt similar strategies w...

  18. Formation of a solar Ha filament from orphan penumbrae

    CERN Document Server

    Buehler, D; van Noort, M; Solanki, S K

    2016-01-01

    The formation of an Ha filament in active region (AR) 10953 is described. Observations from the Solar Optical Telescope (SOT) aboard the Hinode satellite starting on 27th April 2007 until 1st May 2007 were analysed. 20 scans of the 6302A Fe I line pair recorded by SOT/SP were inverted using the SPINOR code. The inversions were analysed together with SOT/BFI G-band and Ca II H and SOT/NFI Ha observations. Following the disappearance of an initial Ha filament aligned along the polarity inversion line (PIL) of the AR, a new Ha filament formed in its place some 20 hours later, which remained stable for at least 1.5 days. The creation of the new Ha filament was driven by the ascent of horizontal magnetic fields from the photosphere into the chromosphere at three separate locations along the PIL. The magnetic fields at two of these locations were situated directly underneath the initial Ha filament and formed orphan penumbrae already aligned along the Ha filament channel. The 700 G orphan penumbrae were stable and ...

  19. Orphan Sources. Extending Radiological Protection outside the Regulatory Framework

    Energy Technology Data Exchange (ETDEWEB)

    Eugenio Gil [Deputy Director for Emergency, Spanish Nuclear Safety Council (Spain)

    2006-07-01

    Radioactive sources that are not under appropriate regulatory control-Orphan sources- can result in a number of undesirable consequences including human health impacts, socio-psychological impacts, political and economic impacts, as well as environmental impacts. Many countries are now in the process of introducing the necessary measures to regain an appropriate level of control over them. For a variety of historical and economic reasons, there could already be sources in any specific country that are not within the usual regulatory system. Some of these may be known about, others may not. Therefore a national strategy is needed to ascertain the likelihood and magnitude of the issue of radioactive source control problem within a country and the priorities necessary to address the problems identified. A well-developed plan for improving control over all relevant radioactive sources tailored to the national situation will ensure optimum use of resources such as time, money and personnel. It will allow these limited resources to be allocated appropriately to ensure that control is first regained over those sources presenting the highest risks. This lecture shows a way to develop an appropriate national strategy for regaining control over orphan sources. The methodology described in this lecture is basically based in the IAEA Recommendations. (author)

  20. Unveiling the population of orphan Gamma Ray Bursts

    CERN Document Server

    Ghirlanda, G; Campana, S; Vergani, S D; Japelj, J; Bernardini, M G; Burlon, D; D'Avanzo, P; Melandri, A; Gomboc, A; Nappo, F; Paladini, R; Pescalli, A; Salafia, O S; Tagliaferri, G

    2015-01-01

    Gamma Ray Bursts are detectable in the gamma-ray band if their jets are oriented towards the observer. However, for each GRB with a typical theta_jet, there should be ~2/theta_jet^2 bursts whose emission cone is oriented elsewhere in space. These off-axis bursts can be eventually detected when, due to the deceleration of their relativistic jets, the beaming angle becomes comparable to the viewing angle. Orphan Afterglows (OA) should outnumber the current population of bursts detected in the gamma-ray band even if they have not been conclusively observed so far at any frequency. We compute the expected flux of the population of orphan afterglows in the mm, optical and X-ray bands through a population synthesis code of GRBs and the standard afterglow emission model. We estimate the detection rate of OA by on-going and forthcoming surveys. The average duration of OA as transients above a given limiting flux is derived and described with analytical expressions: in general OA should appear as daily transients in o...

  1. Gender Differences in Maladaptive Cognitive Schema in Orphans in Dakahlia, Egypt

    Directory of Open Access Journals (Sweden)

    Abdel-Hady El-Gilany

    2013-01-01

    Full Text Available The objective of this study was to assess the gender differences of maladaptive cognitive schema among orphans in Dakahlia governorate orphanages. A cross-sectional comparative study included 152 orphan boys and 48 orphan girls in all orphanages homes in Dakahlia governorate, Egypt. Data collection tools included a structured interview questionnaire for personal data; early maladaptive schema questionnaire-short form (EMSQ-SF. The mean score of the total YSQ and all the subscales, except self-sacrifice and unrelenting standards, are significantly higher among females than males. Attention should be given to the psychological care of the orphans especially security, trust, confidence, and autonomy with more attention to orphan girls.

  2. Orphan drug development: an economically viable strategy for biopharma R&D.

    Science.gov (United States)

    Meekings, Kiran N; Williams, Cory S M; Arrowsmith, John E

    2012-07-01

    Orphan drug incentives have stimulated research into diseases with significant unmet medical need. Although the targeting of orphan diseases is seen by industry as an attractive strategy, there are limited economic data available to support its use. In this paper we show that the revenue-generating potential of orphan drugs is as great as for non-orphan drugs, even though patient populations for rare diseases are significantly smaller. Moreover, we suggest that orphan drugs have greater profitability when considered in the full context of developmental drivers including government financial incentives, smaller clinical trial sizes, shorter clinical trial times and higher rates of regulatory success. The data support the targeting of rare diseases as an important component of a successful biopharma R&D strategy.

  3. The experiences of AIDS orphans living in a township

    Directory of Open Access Journals (Sweden)

    Esmeralda Ricks

    2012-02-01

    Full Text Available An overwhelming challenge to health-care professionals today, is the rendering of care services to AIDS orphans. This article is based on a study that explored and described the lived experiences of AIDS orphans in a township in order to understand their ‘life world’ as AIDS orphans. A further purpose was to provide information to primary health-care nurses (PHCNs, related professionals and partners involved in the care of these children, so that they could plan a care response to meet the orphans’ unique needs. A qualitative research design that used an explorative, descriptive, contextual and phenomenological strategy of inquiry was employed. Data were collected by means of in-depth interviews from a purposively selected sample, and were analysed according to the steps of qualitative data analysis proposed by Tesch (Creswell 1994. Guba’s model was used to ensure the trustworthiness of the qualitative data. Two main themes and their sub-themes were identified. The first theme was that children experience devastating changes in their life circumstances when they become AIDS orphans. The second theme highlighted how the participants rediscovered hope to persevere. Recommendations directed at nursing practice, education and research, were made based upon the findings.

    Opsomming

    ‘n Uitdaging wat professionele gesondheidswerkers huidiglik oorweldig, is dienslewering aan VIGS weeskinders. Die doel van die studie was om die geleefde ervaring van kinders wat in dorpsgebiede woon en VIGS weeskinders geword het, te verken en te beskryf ten einde hul leefwêreld te verstaan. Hierdie inligting kan deur Primêre Gesondheidsorg Verpleegkundiges (PVGs, verwante beroepslui en vennote betrokke by die versorging van hierdie kinders, gebruik word as basis om versorging te beplan wat in die kinders se unieke behoeftes sal voorsien. ‘n Kwalitatiewe navorsingsontwerp met verkennende, beskrywende, kontekstuele en fenomologiese

  4. Phylogenetic relationships within Echinococcus and Taenia tapeworms (Cestoda: Taeniidae): an inference from nuclear protein-coding genes.

    Science.gov (United States)

    Knapp, Jenny; Nakao, Minoru; Yanagida, Tetsuya; Okamoto, Munehiro; Saarma, Urmas; Lavikainen, Antti; Ito, Akira

    2011-12-01

    The family Taeniidae of tapeworms is composed of two genera, Echinococcus and Taenia, which obligately parasitize mammals including humans. Inferring phylogeny via molecular markers is the only way to trace back their evolutionary histories. However, molecular dating approaches are lacking so far. Here we established new markers from nuclear protein-coding genes for RNA polymerase II second largest subunit (rpb2), phosphoenolpyruvate carboxykinase (pepck) and DNA polymerase delta (pold). Bayesian inference and maximum likelihood analyses of the concatenated gene sequences allowed us to reconstruct phylogenetic trees for taeniid parasites. The tree topologies clearly demonstrated that Taenia is paraphyletic and that the clade of Echinococcus oligarthrus and Echinococcusvogeli is sister to all other members of Echinococcus. Both species are endemic in Central and South America, and their definitive hosts originated from carnivores that immigrated from North America after the formation of the Panamanian land bridge about 3 million years ago (Ma). A time-calibrated phylogeny was estimated by a Bayesian relaxed-clock method based on the assumption that the most recent common ancestor of E. oligarthrus and E. vogeli existed during the late Pliocene (3.0 Ma). The results suggest that a clade of Taenia including human-pathogenic species diversified primarily in the late Miocene (11.2 Ma), whereas Echinococcus started to diversify later, in the end of the Miocene (5.8 Ma). Close genetic relationships among the members of Echinococcus imply that the genus is a young group in which speciation and global radiation occurred rapidly.

  5. A New Aspergillus fumigatus Typing Method Based on Hypervariable Tandem Repeats Located within Exons of Surface Protein Coding Genes (TRESP)

    Science.gov (United States)

    Garcia-Rubio, Rocio; Gil, Horacio; Monteiro, Maria Candida; Pelaez, Teresa; Mellado, Emilia

    2016-01-01

    Aspergillus fumigatus is a saprotrophic mold fungus ubiquitously found in the environment and is the most common species causing invasive aspergillosis in immunocompromised individuals. For A. fumigatus genotyping, the short tandem repeat method (STRAf) is widely accepted as the first choice. However, difficulties associated with PCR product size and required technology have encouraged the development of novel typing techniques. In this study, a new genotyping method based on hypervariable tandem repeats within exons of surface protein coding genes (TRESP) was designed. A. fumigatus isolates were characterized by PCR amplification and sequencing with a panel of three TRESP encoding genes: cell surface protein A; MP-2 antigenic galactomannan protein; and hypothetical protein with a CFEM domain. The allele sequence repeats of each of the three targets were combined to assign a specific genotype. For the evaluation of this method, 126 unrelated A. fumigatus strains were analyzed and 96 different genotypes were identified, showing a high level of discrimination [Simpson’s index of diversity (D) 0.994]. In addition, 49 azole resistant strains were analyzed identifying 26 genotypes and showing a lower D value (0.890) among them. This value could indicate that these resistant strains are closely related and share a common origin, although more studies are needed to confirm this hypothesis. In summary, a novel genotyping method for A. fumigatus has been developed which is reproducible, easy to perform, highly discriminatory and could be especially useful for studying outbreaks. PMID:27701437

  6. Influence of the Leader protein coding region of foot-and-mouth disease virus on virus replication.

    Science.gov (United States)

    Belsham, Graham J

    2013-07-01

    The foot-and-mouth disease virus (FMDV) Leader (L) protein is produced in two forms, Lab and Lb, differing only at their amino-termini, due to the use of separate initiation codons, usually 84 nt apart. It has been shown previously, and confirmed here, that precise deletion of the Lab coding sequence is lethal for the virus, whereas loss of the Lb coding sequence results in a virus that is viable in BHK cells. In addition, it is now shown that deletion of the 'spacer' region between these two initiation codons can be tolerated. Growth of the virus precisely lacking just the Lb coding sequence resulted in a previously undetected accumulation of frameshift mutations within the 'spacer' region. These mutations block the inappropriate fusion of amino acid sequences to the amino-terminus of the capsid protein precursor. Modification, by site-directed mutagenesis, of the Lab initiation codon, in the context of the virus lacking the Lb coding region, was also tolerated by the virus within BHK cells. However, precise loss of the Lb coding sequence alone blocked FMDV replication in primary bovine thyroid cells. Thus, the requirement for the Leader protein coding sequences is highly dependent on the nature and extent of the residual Leader protein sequences and on the host cell system used. FMDVs precisely lacking Lb and with the Lab initiation codon modified may represent safer seed viruses for vaccine production.

  7. The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes

    Science.gov (United States)

    Pantano, Lorena; Jodar, Meritxell; Bak, Mads; Ballescà, Josep Lluís; Tommerup, Niels; Oliva, Rafael; Vavouri, Tanya

    2015-01-01

    At the end of mammalian sperm development, sperm cells expel most of their cytoplasm and dispose of the majority of their RNA. Yet, hundreds of RNA molecules remain in mature sperm. The biological significance of the vast majority of these molecules is unclear. To better understand the processes that generate sperm small RNAs and what roles they may have, we sequenced and characterized the small RNA content of sperm samples from two human fertile individuals. We detected 182 microRNAs, some of which are highly abundant. The most abundant microRNA in sperm is miR-1246 with predicted targets among sperm-specific genes. The most abundant class of small noncoding RNAs in sperm are PIWI-interacting RNAs (piRNAs). Surprisingly, we found that human sperm cells contain piRNAs processed from pseudogenes. Clusters of piRNAs from human testes contain pseudogenes transcribed in the antisense strand and processed into small RNAs. Several human protein-coding genes contain antisense predicted targets of pseudogene-derived piRNAs in the male germline and these piRNAs are still found in mature sperm. Our study provides the most extensive data set and annotation of human sperm small RNAs to date and is a resource for further functional studies on the roles of sperm small RNAs. In addition, we propose that some of the pseudogene-derived human piRNAs may regulate expression of their parent gene in the male germline. PMID:25904136

  8. Molecular Detection of Methicillin-Resistant Staphylococcus aureus by Non-Protein Coding RNA-Mediated Monoplex Polymerase Chain Reaction

    Science.gov (United States)

    Soo Yean, Cheryl Yeap; Selva Raju, Kishanraj; Xavier, Rathinam; Subramaniam, Sreeramanan; Gopinath, Subash C. B.; Chinni, Suresh V.

    2016-01-01

    Non-protein coding RNA (npcRNA) is a functional RNA molecule that is not translated into a protein. Bacterial npcRNAs are structurally diversified molecules, typically 50–200 nucleotides in length. They play a crucial physiological role in cellular networking, including stress responses, replication and bacterial virulence. In this study, by using an identified npcRNA gene (Sau-02) in Methicillin-resistant Staphylococcus aureus (MRSA), we identified the Gram-positive bacteria S. aureus. A Sau-02-mediated monoplex Polymerase Chain Reaction (PCR) assay was designed that displayed high sensitivity and specificity. Fourteen different bacteria and 18 S. aureus strains were tested, and the results showed that the Sau-02 gene is specific to S. aureus. The detection limit was tested against genomic DNA from MRSA and was found to be ~10 genome copies. Further, the detection was extended to whole-cell MRSA detection, and we reached the detection limit with two bacteria. The monoplex PCR assay demonstrated in this study is a novel detection method that can replicate other npcRNA-mediated detection assays. PMID:27367909

  9. DNA methylation patterns of protein-coding genes and long non-coding RNAs in males with schizophrenia.

    Science.gov (United States)

    Liao, Qi; Wang, Yunliang; Cheng, Jia; Dai, Dongjun; Zhou, Xingyu; Zhang, Yuzheng; Li, Jinfeng; Yin, Honglei; Gao, Shugui; Duan, Shiwei

    2015-11-01

    Schizophrenia (SCZ) is one of the most complex mental illnesses affecting ~1% of the population worldwide. SCZ pathogenesis is considered to be a result of genetic as well as epigenetic alterations. Previous studies have aimed to identify the causative genes of SCZ. However, DNA methylation of long non-coding RNAs (lncRNAs) involved in SCZ has not been fully elucidated. In the present study, a comprehensive genome-wide analysis of DNA methylation was conducted using samples from two male patients with paranoid and undifferentiated SCZ, respectively. Methyl-CpG binding domain protein-enriched genome sequencing was used. In the two patients with paranoid and undifferentiated SCZ, 1,397 and 1,437 peaks were identified, respectively. Bioinformatic analysis demonstrated that peaks were enriched in protein-coding genes, which exhibited nervous system and brain functions. A number of these peaks in gene promoter regions may affect gene expression and, therefore, influence SCZ-associated pathways. Furthermore, 7 and 20 lncRNAs, respectively, in the Refseq database were hypermethylated. According to the lncRNA dataset in the NONCODE database, ~30% of intergenic peaks overlapped with novel lncRNA loci. The results of the present study demonstrated that aberrant hypermethylation of lncRNA genes may be an important epigenetic factor associated with SCZ. However, further studies using larger sample sizes are required.

  10. The prevalence and cost of unapproved uses of top-selling orphan drugs.

    Directory of Open Access Journals (Sweden)

    Aaron S Kesselheim

    Full Text Available INTRODUCTION: The Orphan Drug Act encourages drug development for rare conditions. However, some orphan drugs become top sellers for unclear reasons. We sought to evaluate the extent and cost of approved and unapproved uses of orphan drugs with the highest unit sales. METHODS: We assessed prescription patterns for four top-selling orphan drugs: lidocaine patch (Lidoderm approved for post-herpetic neuralgia, modafinil (Provigil approved for narcolepsy, cinacalcet (Sensipar approved for hypercalcemia of parathyroid carcinoma, and imatinib (Gleevec approved for chronic myelogenous leukemia and gastrointestinal stromal tumor. We pooled patient-specific diagnosis and prescription data from two large US state pharmaceutical benefit programs for the elderly. We analyzed the number of new and total patients using each drug and patterns of reimbursement for approved and unapproved uses. For lidocaine patch, we subcategorized approved prescriptions into two subtypes of unapproved uses: neuropathic pain, for which some evidence of efficacy exists, and non-neuropathic pain. RESULTS: We found that prescriptions for lidocaine patch, modafinil, and cinacalcet associated with non-orphan diagnoses rose at substantially higher rates (average monthly increases in number of patients of 14.6, 1.45, and 1.58 than prescriptions associated with their orphan diagnoses (3.12, 0.24, and 0.03, respectively (p75%. Increases in lidocaine patch use for non-neuropathic pain far exceeded neuropathic pain (10.2 vs. 3.6 patients, p<0.001. DISCUSSION: In our sample, three of four top-selling orphan drugs were used more commonly for non-orphan indications. These orphan drugs treated common clinical symptoms (pain and fatigue or laboratory abnormalities. We should continue to monitor orphan drug use after approval to identify products that come to be widely used for non-FDA approved indications, particularly those without adequate evidence of efficacy.

  11. Children, AIDS and the politics of orphan care in Ethiopia: the extended family revisited.

    Science.gov (United States)

    Abebe, Tatek; Aase, Asbjorn

    2007-05-01

    The astounding rise in the number of orphans due to the HIV/AIDS epidemic has left many Ethiopian families and communities with enormous childcare problems. Available studies on the capacity and sustainability of the extended family system, which culturally performs the role of care for children in need, suggest two competing theories. The first is grounded in the social rupture thesis and assumes that the traditional system of orphan care is stretched by the impact of the epidemic, and is actually collapsing. By contrast, the second theory counter-suggests that the flexibility and strength of the informal childcare practise, if supported by appropriate interventions, can still support a large number of orphans. Based on a seven-month period of child-focused, qualitative research fieldwork in Ethiopia involving observations; in-depth interviews with orphans (42), social workers (12) and heads of households (18); focus group discussions with orphans (8), elderly people and community leaders (6); and story-writing by children in school contexts, this article explores the trade-offs and social dynamics of orphan care within extended family structures in Ethiopia. It argues that there is a rural-urban divide in the capacity to cater for orphans that emanates from structural differences as well as the socio-cultural and economic values associated with children. The care of orphans within extended family households is also characterised by multiple and reciprocal relationships in care-giving and care-receiving practices. By calling for a contextual understanding of the 'orphan burden', the paper concludes that interventions for orphans may consider care as a continuum in the light of four profiles of extended families, namely rupturing, transient, adaptive, and capable families.

  12. Inverse association of natural mentoring relationship with distress mental health in children orphaned by AIDS

    Directory of Open Access Journals (Sweden)

    Munakata Tsunetsugu

    2010-01-01

    Full Text Available Abstract Background The magnitude of the AIDS-orphaned children crisis in sub-Saharan Africa has so overstretched the resource of most families that the collapse of fostering in the sub-region seems imminent (UNICEF, 2003, fueling the need for a complementary/alternative care. This paper examines the probability of the natural mentoring care to ameliorate distress mental health in children orphaned by AIDS. Methods 952 children, mean age about 14 years, from local community schools and child-care centers in Kampala (Uganda and Mafikeng/Klerksdorp (South Africa towns participated in the study. The design has AIDS-orphaned group (n = 373 and two control groups: Other-causes orphaned (n = 287 and non-orphaned (n = 290 children. We use measures of child abuse, depression, social discrimination, anxiety, parental/foster care, self-esteem, and social support to estimate mental health. Natural mentoring care is measured with the Ragins and McFarlin (1990 Mentor Role Instrument as adapted. Results AIDS-orphaned children having a natural mentor showed significant decreased distress mental health factors. Similar evidence was not observed in the control groups. Also being in a natural mentoring relationship inversely related to distress mental health factors in the AIDS-orphaned group, in particular. AIDS-orphaned children who scored high mentoring relationship showed significant lowest distress mental health factors that did those who scored moderate and low mentoring relationship. Conclusions Natural mentoring care seems more beneficial to ameliorate distress mental health in AIDS-orphaned children (many of whom are double-orphans, having no biological parents than in children in the control groups.

  13. Oxytocin receptor gene sequences in owl monkeys and other primates show remarkable interspecific regulatory and protein coding variation.

    Science.gov (United States)

    Babb, Paul L; Fernandez-Duque, Eduardo; Schurr, Theodore G

    2015-10-01

    The oxytocin (OT) hormone pathway is involved in numerous physiological processes, and one of its receptor genes (OXTR) has been implicated in pair bonding behavior in mammalian lineages. This observation is important for understanding social monogamy in primates, which occurs in only a small subset of taxa, including Azara's owl monkey (Aotus azarae). To examine the potential relationship between social monogamy and OXTR variation, we sequenced its 5' regulatory (4936bp) and coding (1167bp) regions in 25 owl monkeys from the Argentinean Gran Chaco, and examined OXTR sequences from 1092 humans from the 1000 Genomes Project. We also assessed interspecific variation of OXTR in 25 primate and rodent species that represent a set of phylogenetically and behaviorally disparate taxa. Our analysis revealed substantial variation in the putative 5' regulatory region of OXTR, with marked structural differences across primate taxa, particularly for humans and chimpanzees, which exhibited unique patterns of large motifs of dinucleotide A+T repeats upstream of the OXTR 5' UTR. In addition, we observed a large number of amino acid substitutions in the OXTR CDS region among New World primate taxa that distinguish them from Old World primates. Furthermore, primate taxa traditionally defined as socially monogamous (e.g., gibbons, owl monkeys, titi monkeys, and saki monkeys) all exhibited different amino acid motifs for their respective OXTR protein coding sequences. These findings support the notion that monogamy has evolved independently in Old World and New World primates, and that it has done so through different molecular mechanisms, not exclusively through the oxytocin pathway.

  14. Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms.

    Directory of Open Access Journals (Sweden)

    Roshan Mascarenhas

    Full Text Available mRNA translation into proteins is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs, and genetic variants remains poorly understood. mRNA levels on polysomes have been shown to correlate well with expressed protein levels, pointing to polysomal loading as a critical factor. To study regulation and genetic factors of protein translation we measured levels and allelic ratios of mRNAs and ncRNAs (including microRNAs in lymphoblast cell lines (LCL and in polysomal fractions. We first used targeted assays to measure polysomal loading of mRNA alleles, confirming reported genetic effects on translation of OPRM1 and NAT1, and detecting no effect of rs1045642 (3435C>T in ABCB1 (MDR1 on polysomal loading while supporting previous results showing increased mRNA turnover of the 3435T allele. Use of high-throughput sequencing of complete transcript profiles (RNA-Seq in three LCLs revealed significant differences in polysomal loading of individual RNA classes and isoforms. Correlated polysomal distribution between protein-coding and non-coding RNAs suggests interactions between them. Allele-selective polysome recruitment revealed strong genetic influence for multiple RNAs, attributable either to differential expression of RNA isoforms or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Genes identified by different allelic RNA ratios between cytosol and polysomes were enriched with published expression quantitative trait loci (eQTLs affecting RNA functions, and associations with clinical phenotypes. Polysomal RNA-Seq combined with allelic ratio analysis provides a powerful approach to study polysomal RNA recruitment and regulatory variants affecting protein translation.

  15. Sources of signal in 62 protein-coding nuclear genes for higher-level phylogenetics of arthropods.

    Directory of Open Access Journals (Sweden)

    Jerome C Regier

    Full Text Available BACKGROUND: This study aims to investigate the strength of various sources of phylogenetic information that led to recent seemingly robust conclusions about higher-level arthropod phylogeny and to assess the role of excluding or downweighting synonymous change for arriving at those conclusions. METHODOLOGY/PRINCIPAL FINDINGS: The current study analyzes DNA sequences from 68 gene segments of 62 distinct protein-coding nuclear genes for 80 species. Gene segments analyzed individually support numerous nodes recovered in combined-gene analyses, but few of the higher-level nodes of greatest current interest. However, neither is there support for conflicting alternatives to these higher-level nodes. Gene segments with higher rates of nonsynonymous change tend to be more informative overall, but those with lower rates tend to provide stronger support for deeper nodes. Higher-level nodes with bootstrap values in the 80% - 99% range for the complete data matrix are markedly more sensitive to substantial drops in their bootstrap percentages after character subsampling than those with 100% bootstrap, suggesting that these nodes are likely not to have been strongly supported with many fewer data than in the full matrix. Data set partitioning of total data by (mostly synonymous and (mostly nonsynonymous change improves overall node support, but the result remains much inferior to analysis of (unpartitioned nonsynonymous change alone. Clusters of genes with similar nonsynonymous rate properties (e.g., faster vs. slower show some distinct patterns of node support but few conflicts. Synonymous change is shown to contribute little, if any, phylogenetic signal to the support of higher-level nodes, but it does contribute nonphylogenetic signal, probably through its underlying heterogeneous nucleotide composition. Analysis of seemingly conservative indels does not prove useful. CONCLUSIONS: Generating a robust molecular higher-level phylogeny of Arthropoda is

  16. Some Information about the Opening of Erzincan Orphan School

    Directory of Open Access Journals (Sweden)

    Galip EKEN

    2013-06-01

    Full Text Available The necessity of answering the orphan children’s material andspiritual needs which had increased at important measureduring the World War I become an important social problem inthat era. Not ignoring that important problem did the Ottomanstate opened many orphanages in many province and cities inAnatolia especially in Istanbul. One of them was established inErzincan in 1918. Establishing an orphanage in which the girlsand boys could have live together safely and which had 500beds had started with a decision taken by the central government.In this article some of the ranks about supplying of thefinancial source of the orphanage and the efforts spent for theproviding of the available built shed lights on.

  17. Cholesterol and male fertility: what about orphans and adopted?

    Science.gov (United States)

    Maqdasy, Salwan; Baptissart, Marine; Vega, Aurélie; Baron, Silvère; Lobaccaro, Jean-Marc A; Volle, David H

    2013-04-10

    The link between cholesterol homeostasis and male fertility has been clearly suggested in patients who suffer from hyperlipidemia and metabolic syndrome. This has been confirmed by the generation of several transgenic mouse models or in animals fed with high cholesterol diet. Next to the alteration of the endocrine signaling pathways through steroid receptors (androgen and estrogen receptors); "orphan" and "adopted" nuclear receptors, such as the Liver X Receptors (LXRs), the Proliferating Peroxisomal Activated Receptors (PPARs) or the Liver Receptor Homolog-1 (LRH-1), have been involved in this cross-talk. These transcription factors show distinct expression patterns in the male genital tract, explaining the large panel of phenotypes observed in transgenic male mice and highlighting the importance of lipid homesostasis and the complexity of the molecular pathways involved. Increasing our knowledge of the roles of these nuclear receptors in male germ cell differentiation could help in proposing new approaches to either treat infertile men or define new strategies for contraception.

  18. The impact of the declining extended family support system on the education of orphans in Lesotho.

    Science.gov (United States)

    Tanga, Pius T

    2013-09-01

    This paper examines the impact of the weakening of the extended family on the education of double orphans in Lesotho through in-depth interviews with participants from 3 of the 10 districts in Lesotho. The findings reveal that in Lesotho the extended family has not yet disintegrated as the literature suggests. However, it shows signs of rupturing, as many orphans reported that they are being taken into extended family households, the incentive for these households being, presumably, the financial and other material assistance that they receive from the government and non-governmental organisations (NGOs) which supplements household income and material wellbeing. The findings show that financial and other assistance given by the government and NGOs have resulted in conflict between the orphans and caregivers. This has also prompted many extended families to shift responsibilities to the government and NGOs. Most of the extended households provided the orphans with poor living conditions, such as unhygienic houses, poor nutrition, and little or no provision of school materials, which has had a negative impact on the education of the orphans. The combined effects of economic crisis and HIV and AIDS have resulted in extended families not being able to care for the needs of the orphans adequately, whilst continuing to accept them into their households. It is recommended that although extended families are still accepting orphans, the government should strengthen and recognise the important role played by families and the communities in caring for these vulnerable children. The government should also introduce social grants for orphans and other vulnerable children and review the current meagre public assistance (R100) it provides for orphans and vulnerable children in Lesotho. Other stakeholders should concentrate on strengthening the capacity of families and communities through programmes and projects which could be more sustainable than the current handouts given by

  19. AIDS orphans and vulnerable children in India: problems, prospects, and concerns.

    Science.gov (United States)

    Kumar, Anant

    2012-01-01

    This article reviews and discusses the problems, responses, and concerns of orphans and vulnerable children in India. The article shows that HIV/AIDS programs and interventions are vital for survival and welfare of orphan and vulnerable children, but they have reached only to a small fraction of the most vulnerable children. The article suggests a number of measures that government and civil society could take to address the problems and emphasizes the need to learn from other countries' experience and initiatives in developing appropriate policy and programmes for orphan and vulnerable children.

  20. Community-based capital cash transfer to support orphans in Western Kenya

    DEFF Research Database (Denmark)

    Skovdal, Morten; Mwasiaji, W.; Morrison, J.;

    2008-01-01

    Various types of 'cash transfer' are currently receiving much attention as a way of helping orphans and vulnerable children in Africa. Drawing on a qualitative study conducted in Western Kenya, this paper points to the strategy of community-based capital cash transfers (CCCT) as a particularly...... promising method of supporting orphans and carers. Qualitative data were obtained from 15 orphans and 26 caregivers in Bondo District, Kenya, beneficiaries of a CCCT programme run by a partnership between the community, the government social services department and a foreign donor. Our findings suggest...

  1. Morphometric Analysis of Recognized Genes for Autism Spectrum Disorders and Obesity in Relationship to the Distribution of Protein-Coding Genes on Human Chromosomes

    Directory of Open Access Journals (Sweden)

    Austen B. McGuire

    2016-05-01

    Full Text Available Mammalian chromosomes are comprised of complex chromatin architecture with the specific assembly and configuration of each chromosome influencing gene expression and function in yet undefined ways by varying degrees of heterochromatinization that result in Giemsa (G negative euchromatic (light bands and G-positive heterochromatic (dark bands. We carried out morphometric measurements of high-resolution chromosome ideograms for the first time to characterize the total euchromatic and heterochromatic chromosome band length, distribution and localization of 20,145 known protein-coding genes, 790 recognized autism spectrum disorder (ASD genes and 365 obesity genes. The individual lengths of G-negative euchromatin and G-positive heterochromatin chromosome bands were measured in millimeters and recorded from scaled and stacked digital images of 850-band high-resolution ideograms supplied by the International Society of Chromosome Nomenclature (ISCN 2013. Our overall measurements followed established banding patterns based on chromosome size. G-negative euchromatic band regions contained 60% of protein-coding genes while the remaining 40% were distributed across the four heterochromatic dark band sub-types. ASD genes were disproportionately overrepresented in the darker heterochromatic sub-bands, while the obesity gene distribution pattern did not significantly differ from protein-coding genes. Our study supports recent trends implicating genes located in heterochromatin regions playing a role in biological processes including neurodevelopment and function, specifically genes associated with ASD.

  2. Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome.

    Science.gov (United States)

    Chen, Meili; Hu, Yibo; Liu, Jingxing; Wu, Qi; Zhang, Chenglin; Yu, Jun; Xiao, Jingfa; Wei, Fuwen; Wu, Jiayan

    2015-12-11

    High-quality and complete gene models are the basis of whole genome analyses. The giant panda (Ailuropoda melanoleuca) genome was the first genome sequenced on the basis of solely short reads, but the genome annotation had lacked the support of transcriptomic evidence. In this study, we applied RNA-seq to globally improve the genome assembly completeness and to detect novel expressed transcripts in 12 tissues from giant pandas, by using a transcriptome reconstruction strategy that combined reference-based and de novo methods. Several aspects of genome assembly completeness in the transcribed regions were effectively improved by the de novo assembled transcripts, including genome scaffolding, the detection of small-size assembly errors, the extension of scaffold/contig boundaries, and gap closure. Through expression and homology validation, we detected three groups of novel full-length protein-coding genes. A total of 12.62% of the novel protein-coding genes were validated by proteomic data. GO annotation analysis showed that some of the novel protein-coding genes were involved in pigmentation, anatomical structure formation and reproduction, which might be related to the development and evolution of the black-white pelage, pseudo-thumb and delayed embryonic implantation of giant pandas. The updated genome annotation will help further giant panda studies from both structural and functional perspectives.

  3. Morphometric Analysis of Recognized Genes for Autism Spectrum Disorders and Obesity in Relationship to the Distribution of Protein-Coding Genes on Human Chromosomes.

    Science.gov (United States)

    McGuire, Austen B; Rafi, Syed K; Manzardo, Ann M; Butler, Merlin G

    2016-05-05

    Mammalian chromosomes are comprised of complex chromatin architecture with the specific assembly and configuration of each chromosome influencing gene expression and function in yet undefined ways by varying degrees of heterochromatinization that result in Giemsa (G) negative euchromatic (light) bands and G-positive heterochromatic (dark) bands. We carried out morphometric measurements of high-resolution chromosome ideograms for the first time to characterize the total euchromatic and heterochromatic chromosome band length, distribution and localization of 20,145 known protein-coding genes, 790 recognized autism spectrum disorder (ASD) genes and 365 obesity genes. The individual lengths of G-negative euchromatin and G-positive heterochromatin chromosome bands were measured in millimeters and recorded from scaled and stacked digital images of 850-band high-resolution ideograms supplied by the International Society of Chromosome Nomenclature (ISCN) 2013. Our overall measurements followed established banding patterns based on chromosome size. G-negative euchromatic band regions contained 60% of protein-coding genes while the remaining 40% were distributed across the four heterochromatic dark band sub-types. ASD genes were disproportionately overrepresented in the darker heterochromatic sub-bands, while the obesity gene distribution pattern did not significantly differ from protein-coding genes. Our study supports recent trends implicating genes located in heterochromatin regions playing a role in biological processes including neurodevelopment and function, specifically genes associated with ASD.

  4. Phylogenetic performance of mitochondrial protein-coding genes of Oncomelania hupensis in resolving relationships between landscape populations

    Institute of Scientific and Technical Information of China (English)

    Shi-Zhu LI; Li ZHANG; Lin MA; Wei HU; Shan LV; Qin LIU; Ying-Jun QIAN

    2013-01-01

    Oncomelania hupensis is the unique intermediate host of Schistosomajaponicum,which plays a key role in the transmission of human blood fluke Schistosoma.The complete mitochondrial (mt) genome of O.hupensis has been characterized; however,the phylogenetic performance of mt protein-coding genes (PCGs) of the snail remain unclear.In this study,11 whole mt genomes of snails collected from four different ecological settings in China and the Philippines were sequenced.The mt genome sizes ranged from 15 183 to 15 216 bp,with the G + C contents from 32.4% to 33.4%.A total of 15 251 characters were generated from the multiple sequence alignment.Of 2711 (17.8%)polymorphic sites,56.22% (1524) were parsimony sites.The mt genomes' phylogenetic trees were reconstructed using minimum evolution,neighbor joining,maximum likelihood,maximum parsimony,and Bayesian tree estimate methods,and two main distinct clades were identified:(i) the isolate from mountainous regions; (ii) the remaining isolate which included three inner branches.All phylogenetic trees of the 13 PCGs were generated by running 1000 bootstrap replicates and compared with the complete mtDNA tree,the classification accuracy ranging from 21.23% to 87.87%,the topological distance of phylogenetic trees between PCGs ranging from 5 to 14.Therefore,the performance of PCGs can be divided into good condition (COⅠ,ND2,ND5,and ND3),medium (COⅡ,ATP6,ND1,ND6,Cytb,ND4,and COⅢ),poor (ATP8 and ND4L).This study represents the first analysis ofmt genome diversity of the O.hupensis snail and phylogenetic performance of mt PCGs.It presents clear evidence that the snail populations can be separated into four landscape genetic populations in mainland China based on whole mt genomes.The identification of the phylogenetic performance of PCGs provides new insight into the intensive genetic diversity study using mtDNA markers for the snail.

  5. Systematic review of available evidence on 11 high-priced inpatient orphan drugs

    NARCIS (Netherlands)

    T.A. Kanters (Tim A.); C. de Sonneville (Caroline); W.K. Redekop (Ken); L. van Hakkaart-van Roijen (Leona)

    2013-01-01

    markdownabstract__Abstract__ __Background__: Attention for Evidence Based Medicine (EBM) is growing, but evidence for orphan drugs is argued to be limited and inferior. This study systematically reviews the available evidence on clinical effectiveness, costeffectiveness and budget impact for orph

  6. 78 FR 35277 - Agency Information Collection Activities; Proposed Collection; Comment Request; Orphan Drugs...

    Science.gov (United States)

    2013-06-12

    ... HUMAN SERVICES Food and Drug Administration Agency Information Collection Activities; Proposed... document. FOR FURTHER INFORMATION CONTACT: Jonna Capezzuto, Office of Information Management, Food and Drug... appropriate, and other forms of information technology. Orphan Drugs; Common EMA/FDA Application Form...

  7. 76 FR 3910 - Agency Information Collection Activities; Proposed Collection; Comment Request; Orphan Drugs...

    Science.gov (United States)

    2011-01-21

    ... HUMAN SERVICES Food and Drug Administration Agency Information Collection Activities; Proposed... document. FOR FURTHER INFORMATION CONTACT: Jonna Capezzuto, Office of Information Management, Food and Drug... appropriate, and other forms of information technology. ] Orphan Drugs; Common EMA/FDA Application Form...

  8. Community-based capital cash transfer to support orphans in Western Kenya

    DEFF Research Database (Denmark)

    Skovdal, Morten; Mwasiaji, W.; Morrison, J.

    2008-01-01

    Various types of 'cash transfer' are currently receiving much attention as a way of helping orphans and vulnerable children in Africa. Drawing on a qualitative study conducted in Western Kenya, this paper points to the strategy of community-based capital cash transfers (CCCT) as a particularly...... that the programme not only increased food availability, but also enhanced social capital. Further research is needed to explore the potential of CCCT in supporting orphans and vulnerable children in countries with high orphanhood rates....

  9. Grow Together under the Sunshine——The 4th Summer Camp for AIDS Orphaned Children

    Institute of Scientific and Technical Information of China (English)

    NING LILI

    2007-01-01

    @@ The 4th summer camp for AIDS-orphaned children was held in Beijing from August 2-8,2007.Co-sponsored by the China Youth Concern Commission and China Foundation for the Prevention and Control of STDs (sexually transmitted disease) and AIDS,the event was attended by 80 AIDS-orphaned children aged 8-16 from 18 counties and cities of 8 provinces of Shanxi,Yunnan,Henan,Jilin,Liaoning,Guizhou,Sichuan and Anhui.

  10. Oral lesions and dental status among institutionalized orphans in Yemen: A matched case-control study

    Directory of Open Access Journals (Sweden)

    Sadeq Ali Al-Maweri

    2014-01-01

    Full Text Available Objectives: The aim of this study was to assess the prevalence of oral mucosal lesions (OMLs and dental caries and to evaluate oral health practices among institutionalized orphan-children in Sana′a city, Yemen. Subjects and Methods: A sample of 202 institutionalized male-orphan-children in the main orphanage in Sana′a city, were matched to 202 non-orphan schoolchildren. Clinical examination included assessment of OMLs based on standard international diagnostic criteria and evaluation of dental status using the Decayed/decayed, Missed/missed and Filled/filled (DMFT/dmft index according to World Health Organization recommendations. Demographic data and oral hygiene practices were obtained by interviewing each subject using special questionnaire form. Results: Majority of children were in the 12-15 year age group. Nine types of lesions were reported among orphans; the most common lesions were fissured tongue (24.3%, herpes labialis (7.9% and traumatic ulcers (2.5%. The occurrence of herpes labialis was found to be significantly higher in orphans than in controls (P < 0.01. The prevalence of dental caries was insignificantly lower among the orphans (84.7% compared with the non-orphans (89.61%; P = 0.136. The mean dmft score was significantly lower in orphans than in controls (2.28 vs. 3.82; P = 0.001. Conclusions: The institutionalized children in this orphanage had a high prevalence of OMLs but low prevalence of dental caries, though they revealed poor oral hygiene practices. Effective oral health promotion strategies need to be implemented to improve the oral health and oral health practices of children living in orphanages.

  11. The evolving drug development landscape: from blockbusters to niche busters in the orphan drug space.

    Science.gov (United States)

    Kumar Kakkar, Ashish; Dahiya, Neha

    2014-06-01

    Strategy, Management and Health Policy Large pharmaceutical companies have traditionally focused on the development of blockbuster drugs that target disease states with large patient populations. However, with large-scale patent expirations and competition from generics and biosimilars, anemic pipelines, escalating clinical trial costs, and global health-care reform, the blockbuster model has become less viable. Orphan drug initiatives and the incentives accompanied by these have fostered renewed research efforts in the area of rare diseases and have led to the approval of more than 400 orphan products. Despite targeting much smaller patient populations, the revenue-generating potential of orphan drugs has been shown to be huge, with a greater return on investment than non-orphan drugs. The success of these "niche buster" therapeutics has led to a renewed interest from "Big Pharma" in the rare disease landscape. This article reviews the key drivers for orphan drug research and development, their profitability, and issues surrounding the emergence of large pharmaceutical firms into the orphan drug space.

  12. The Burden of Orphans and Vulnerable Children Due to HIV/AIDS in Cameroon.

    Science.gov (United States)

    Nsagha, Dickson S; Bissek, Anne-Cécile Zk; Nsagha, Sarah M; Assob, Jules-Clement N; Kamga, Henri-Lucien F; Njamnshi, Dora M; Njunda, Anna L; Obama, Marie-Thérèse O; Njamnshi, Alfred K

    2012-01-01

    HIV/AIDS is a major public health problem in Cameroon and Africa, and the challenges of orphans and vulnerable children are a threat to child survival, growth and development. The HIV prevalence in Cameroon was estimated at 5.1% in 2010. The objective of this study was to assess the burden of orphans and vulnerable children due to HIV/AIDS in Cameroon. A structured search to identify publications on orphans and other children made vulnerable by AIDS was carried out. A traditional literature search on google, PubMed and Medline using the keywords: orphans, vulnerable children, HIV/AIDS and Cameroon was conducted to identify potential AIDS orphans publications, we included papers on HIV prevalence in Cameroon, institutional versus integrated care of orphans, burden of children orphaned by AIDS and projections, impact of AIDS orphans on Cameroon, AIDS orphans assisted through the integrated care approach, and comparism of the policies of orphans care in the central African sub-region. We also used our participatory approach working experience with traditional rulers, administrative authorities and health stakeholders in Yaounde I and Yaounde VI Councils, Nanga Eboko Health District, Isangelle and Ekondo Titi Health Areas, Bafaka-Balue, PLAN Cameroon, the Pan African Institute for Development-West Africa, Save the orphans Foundation, Ministry of Social Affairs, and the Ministry of Public Health. Results show that only 9% of all OVC in Cameroon are given any form of support. AIDS death continue to rise in Cameroon. In 1995, 7,900 people died from AIDS in the country; and the annual number rose to 25,000 in 2000. Out of 1,200,000 orphans and vulnerable children in Cameroon in 2010, 300,000(25%) were AIDS orphans. Orphans and the number of children orphaned by AIDS has increased dramatically from 13,000 in 1995 to 304,000 in 2010. By 2020, this number is projected to rise to 350,000. These deaths profoundly affect families, which often are split up and left without any

  13. Exiling children, creating orphans: when immigration policies hurt citizens.

    Science.gov (United States)

    Zayas, Luis H; Bradlee, Mollie H

    2014-04-01

    Citizen-children born in the United States to undocumented immigrants have become collateral damage of immigration enforcement. These children suffer the effects of immigration laws designed to deport large numbers of people. In removal proceedings, parents often must decide to either leave their citizen-children behind in the care of others or take them to a country the child may have never known. Accordingly, immigration policy frequently creates two de facto classes of children: exiles and orphans. In discussing these classes, the authors offer a summary of how U.S. citizen-children come into contact with the immigration enforcement system. The article explores the impact of detention and deportation on the health, mental health, and developmental trajectories of citizen-children and argues for reforms in policy and practice that will adhere to the highest standards of child welfare practice. By integrating these children into the immigration discourse, practitioners and policymakers will be better able to understand the effects of immigration enforcement, reduce harm to children, and provide for the protection of their rights.

  14. Cutting-edge technology may yield elephants in Orphan basin

    Energy Technology Data Exchange (ETDEWEB)

    Reid, W.

    2006-10-15

    Controlled source electromagnetic survey (CSEM) technology may soon supply vital information to oil companies about Newfoundland's offshore basins. The technology shoots low-frequency electromagnetic signals at the sea-floor to measure resistivity. Natural gas, crude oil and water each have a particular strength to resist the power of an electromagnetic signal, and leave a unique signature. To collect data, the electromagnetic pulse emitter is towed back and forth over an area of seabed potentially holding hydrocarbons. Connected to the ship by a long tether, the emitter hangs approximately 30 to 50 m above the ocean floor, and reaches depths of 2.4 km. The sea floor has 36 receivers anchored to it in a grid of concrete blocks that dissolve within 3 months of installation. The test blocks are first dropped overboard to verify current speed and strength in order to calculate exactly where on the water's surface the concrete blocks will be lowered. The Canada Newfoundland and Labrador Offshore Petroleum Board (CNLOPB) has deemed the technology environmentally safe. Eight land parcels have now been leased for exploration in the Orphan Basin and are expected to receive approval for seismic and electromagnetic surveys. Industry players have shown unusual optimism about the basin's potential, which is estimated to contain 4 oilfields containing a billion barrels of oil each. 2 figs.

  15. Preeclampsia – Will Orphan Drug Status Facilitate Innovative Biological Therapies?

    Science.gov (United States)

    Hahn, Sinuhe

    2015-01-01

    It is generally accepted that the development of novel therapies to treat pregnancy-related disorders, such as preeclampsia, is hampered by the paucity of research funding. Hence, it is with great interest to become aware of at least three novel therapeutic approaches for the treatment of this disorder: exploiting either the anticoagulant activity of antithrombin, the free radical scavenging activity of alpha-1-microglobulin, or the regenerative capacity of placenta-derived mesenchymal stem cells. As these projects are being carried out by small biotech enterprises, the question arises of how they are able to fund such undertakings. A novel strategy adopted by two of these companies is that they successfully petitioned US and EU agencies in order that preeclampsia is accepted in the register of rare or orphan diseases. This provides a number of benefits including market exclusivity, assistance with clinical trials, and dedicated funding schemes. Other strategies to supplement meager research funds, especially to test novel approaches, could be crowdfunding, a venture that relies on intimate interaction with advocacy groups. In other words, preeclampsia meets Facebook. Perhaps similar strategies can be adopted to examine novel therapies targeting either the imbalance in pro- or anti-angiogenic growth factors, complement activation, reduced levels of placenta protein 13, or excessive neutrophil activation evident in preeclampsia. PMID:25767802

  16. Preeclampsia - will orphan drug status facilitate innovative biological therapies?

    Science.gov (United States)

    Hahn, Sinuhe

    2015-01-01

    It is generally accepted that the development of novel therapies to treat pregnancy-related disorders, such as preeclampsia, is hampered by the paucity of research funding. Hence, it is with great interest to become aware of at least three novel therapeutic approaches for the treatment of this disorder: exploiting either the anticoagulant activity of antithrombin, the free radical scavenging activity of alpha-1-microglobulin, or the regenerative capacity of placenta-derived mesenchymal stem cells. As these projects are being carried out by small biotech enterprises, the question arises of how they are able to fund such undertakings. A novel strategy adopted by two of these companies is that they successfully petitioned US and EU agencies in order that preeclampsia is accepted in the register of rare or orphan diseases. This provides a number of benefits including market exclusivity, assistance with clinical trials, and dedicated funding schemes. Other strategies to supplement meager research funds, especially to test novel approaches, could be crowdfunding, a venture that relies on intimate interaction with advocacy groups. In other words, preeclampsia meets Facebook. Perhaps similar strategies can be adopted to examine novel therapies targeting either the imbalance in pro- or anti-angiogenic growth factors, complement activation, reduced levels of placenta protein 13, or excessive neutrophil activation evident in preeclampsia.

  17. Preeclampsia – will Orphan Drug Status facilitate innovative biological therapies?

    Directory of Open Access Journals (Sweden)

    Sinuhe eHahn

    2015-02-01

    Full Text Available It is generally accepted that development of novel therapies to treat pregnancy-relates disorders, such as preeclampsia, is hampered to the paucity of research funding. Hence, it is with great interest to become aware of at least three novel therapeutic approaches for the treatment of this disorder, exploiting either the anticoagulant activity of antithrombin, the free radical scavenging activity of alpha-1-microglobulin, or the regenerative capacity of placenta-derived mesenchymal stem cells. As these projects are being carried out by small biotech enterprises, the question arises of how they are able to fund such undertakings. A novel strategy adopted by two of these companies is that they successfully petitioned US and EU agencies in order that preeclampsia be accepted in the register of rare or orphan diseases. This provides a number of benefits including market exclusivity, assistance with clinical trials and dedicated funding schemes. Other strategies to supplement meager research funds, especially to test novel approaches, could be crowdfunding, a venture which relies on intimate interaction with advocacy groups. In other words, preeclampsia meets Facebook. Perhaps similar strategies can be adopted to examine novel therapies targeting either the imbalance in angiogenic growth factors, complement activation, reduced levels of placenta protein 13 or excessive neutrophil activation evident in preeclampsia.

  18. Post-marketing access to orphan drugs: a critical analysis of health technology assessment and reimbursement decision-making considerations

    Directory of Open Access Journals (Sweden)

    Iskrov G

    2014-01-01

    Full Text Available Georgi Iskrov, Rumen Stefanov Department of Social Medicine and Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria Abstract: This study aims to explore the current rationale of post-marketing access to orphan drugs. As access to orphan medicinal products depends on assessment and appraisal by health authorities, this article is focused on health technology assessment (HTA and reimbursement decision-making considerations for orphan drugs. A critical analysis may identify important factors that could predetermine the combined outcomes of these two processes. Following this objective, an analytical framework was developed, comprising three overlaying issues: to outline what is currently done and what needs to be done in the field of HTA of orphan drugs, to synthesize important variables relevant to the reimbursement decision-making about orphan drugs, and to unveil relationships between theory and practice. Methods for economic evaluation, cost-effectiveness threshold, budget impact, uncertainty of evidence, criteria in reimbursement decision-making, and HTA research agenda are all explored and discussed from an orphan drug perspective. Reimbursement decision-making for orphan drugs is a debate of policy priorities, health system specifics, and societal attitudes. Health authorities need to pursue a multidisciplinary analysis on a range of criteria, ensuring an explicit understanding of the trade-offs for decisions related to eligibility for reimbursement. The only reasonable way to accept a higher valuation of orphan drug benefits is if these are demonstrated empirically. Rarity means that the quality of orphan drug evidence is not the same as for conventional therapies. Closing this gap is another crucial point for the timely access to these products. The generation of evidence goes far beyond pre-market authorization trials and requires transnational cooperation and coordination. Early constructive dialogue among orphan drug

  19. Reference: 517 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available d isolated aleurone layers of Arabidopsis (Arabidopsis thaliana) were used in experiments designed to iden...tify components of the Arabidopsis seed that contribute to seed dormancy and to lea

  20. What makes orphans in Kigali, Rwanda, non-adherent to antiretroviral therapy? Perspectives of their caregivers

    Directory of Open Access Journals (Sweden)

    Kimiyo Kikuchi

    2014-12-01

    Full Text Available Introduction: Every year, approximately 260,000 children are infected with HIV in low- and middle-income countries. The timely initiation and high level of maintenance of antiretroviral therapy (ART are crucial to reducing the suffering of HIV-positive children. We need to develop a better understanding of the background of children's ART non-adherence because it is not well understood. The purpose of this study is to explore the background related to ART non-adherence, specifically in relation to the orphan status of children in Kigali, Rwanda. Methods: We conducted 19 focus group discussions with a total of 121 caregivers of HIV-positive children in Kigali. The primary data for analysis were verbatim transcripts and socio-demographic data. A content analysis was performed for qualitative data analysis and interpretation. Results: The study found several contextual factors that influenced non-adherence: among double orphans, there was psychological distance between the caregivers and children, whereas economic burden was the primary issue among paternal orphans. The factors promoting adherence also were unique to each orphan status, such as the positive attitude about disclosing serostatus to the child by double orphans’ caregivers, and feelings of guilt about the child's condition among non-orphaned caregivers. Conclusions: Knowledge of orphan status is essential to elucidate the factors influencing ART adherence among HIV-positive children. In this qualitative study, we identified the orphan-related contextual factors that influenced ART adherence. Understanding the social context is important in dealing with the challenges to ART adherence among HIV-positive children.

  1. Cbln1 and the δ2 glutamate receptor--an orphan ligand and an orphan receptor find their partners.

    Science.gov (United States)

    Matsuda, Keiko; Yuzaki, Michisuke

    2012-03-01

    Cerebellin was originally discovered as a Purkinje cell-specific peptide more than two decades ago. Later, its precursor protein precerebellin (Cbln1) was found to be produced in cerebellar granule cells. It has become increasingly clear that although the cerebellin peptide may have certain functions, Cbln1 is an actual signaling molecule that belongs to the C1q family. However, the precise function of Cbln1 has been unresolved. Cbln1 is released from granule cells, and disruption of the cbln1 gene in mice causes a severe reduction in the number of synapses between Purkinje cells and parallel fibers (PFs; axons of granule cells) and results in cerebellar ataxia. The glutamate receptor δ2 (GluD2) is highly expressed on Purkinje cells' dendritic spines which make synapses with PFs. Although GluD2 was identified as a member of the ionotropic glutamate receptors more than 15 years ago, it has been referred to as an orphan receptor because its endogenous ligands are unclear. Interestingly, GluD2-null mice phenocopy cbln1-null mice precisely. Cbln1 and GluD2 have therefore been thought to participate in a common signaling pathway that is required for the formation of PF synapses. We recently established a direct ligand-receptor relationship between Cbln1 and GluD2. The Cbln1-GluD2 complex is located at the cleft of PF-Purkinje cell synapses and bidirectionally regulates both presynaptic and postsynaptic differentiation.

  2. A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.

    Directory of Open Access Journals (Sweden)

    Ai-bing Zhang

    Full Text Available Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish and two representing non-coding ITS barcodes (rust fungi and brown algae. Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ and Maximum likelihood (ML methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI of 99.75-100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62-98.40% for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60-99.37% for 1094 brown algae queries, both using ITS barcodes.

  3. Emerging putative associations between non-coding RNAs and protein-coding genes in Neuropathic Pain. Added value from re-using microarray data.

    Directory of Open Access Journals (Sweden)

    Enrico Capobianco

    2016-10-01

    Full Text Available Regeneration of injured nerves is likely occurring in the peripheral nervous system, but not in the central nervous system. Although protein-coding gene expression has been assessed during nerve regeneration, little is currently known about the role of non-coding RNAs (ncRNAs. This leaves open questions about the potential effects of ncRNAs at transcriptome level. Due to the limited availability of human neuropathic pain data, we have identified the most comprehensive time-course gene expression profile referred to sciatic nerve injury, and studied in a rat model, using two neuronal tissues, namely dorsal root ganglion (DRG and sciatic nerve (SN. We have developed a methodology to identify differentially expressed bioentities starting from microarray probes, and re-purposing them to annotate ncRNAs, while analyzing the expression profiles of protein-coding genes. The approach is designed to reuse microarray data and perform first profiling and then meta-analysis through three main steps. First, we used contextual analysis to identify what we considered putative or potential protein coding targets for selected ncRNAs. Relevance was therefore assigned to differential expression of neighbor protein-coding genes, with neighborhood defined by a fixed genomic distance from long or antisense ncRNA loci, and of parent genes associated with pseudogenes. Second, connectivity among putative targets was used to build networks, in turn useful to conduct inference at interactomic scale. Last, network paths were annotated to assess relevance to neuropathic pain. We found significant differential expression in long-intergenic ncRNAs (32 lincRNAs in SN, and 8 in DRG, antisense RNA (31 asRNA in SN, and 12 in DRG and pseudogenes (456 in SN, 56 in DRG. In particular, contextual analysis centered on pseudogenes revealed some targets with known association to neurodegeneration and/or neurogenesis processes. While modules of the olfactory receptors were clearly

  4. Emerging Putative Associations between Non-Coding RNAs and Protein-Coding Genes in Neuropathic Pain: Added Value from Reusing Microarray Data

    Science.gov (United States)

    Raju, Hemalatha B.; Tsinoremas, Nicholas F.; Capobianco, Enrico

    2016-01-01

    Regeneration of injured nerves is likely occurring in the peripheral nervous system, but not in the central nervous system. Although protein-coding gene expression has been assessed during nerve regeneration, little is currently known about the role of non-coding RNAs (ncRNAs). This leaves open questions about the potential effects of ncRNAs at transcriptome level. Due to the limited availability of human neuropathic pain (NP) data, we have identified the most comprehensive time-course gene expression profile referred to sciatic nerve (SN) injury and studied in a rat model using two neuronal tissues, namely dorsal root ganglion (DRG) and SN. We have developed a methodology to identify differentially expressed bioentities starting from microarray probes and repurposing them to annotate ncRNAs, while analyzing the expression profiles of protein-coding genes. The approach is designed to reuse microarray data and perform first profiling and then meta-analysis through three main steps. First, we used contextual analysis to identify what we considered putative or potential protein-coding targets for selected ncRNAs. Relevance was therefore assigned to differential expression of neighbor protein-coding genes, with neighborhood defined by a fixed genomic distance from long or antisense ncRNA loci, and of parental genes associated with pseudogenes. Second, connectivity among putative targets was used to build networks, in turn useful to conduct inference at interactomic scale. Last, network paths were annotated to assess relevance to NP. We found significant differential expression in long-intergenic ncRNAs (32 lincRNAs in SN and 8 in DRG), antisense RNA (31 asRNA in SN and 12 in DRG), and pseudogenes (456 in SN and 56 in DRG). In particular, contextual analysis centered on pseudogenes revealed some targets with known association to neurodegeneration and/or neurogenesis processes. While modules of the olfactory receptors were clearly identified in protein

  5. Utilizing the Antarctic Master Directory to find orphan datasets

    Science.gov (United States)

    Bonczkowski, J.; Carbotte, S. M.; Arko, R. A.; Grebas, S. K.

    2011-12-01

    While most Antarctic data are housed at an established disciplinary-specific data repository, there are data types for which no suitable repository exists. In some cases, these "orphan" data, without an appropriate national archive, are served from local servers by the principal investigators who produced the data. There are many pitfalls with data served privately, including the frequent lack of adequate documentation to ensure the data can be understood by others for re-use and the impermanence of personal web sites. For example, if an investigator leaves an institution and the data moves, the link published is no longer accessible. To ensure continued availability of data, submission to long-term national data repositories is needed. As stated in the National Science Foundation Office of Polar Programs (NSF/OPP) Guidelines and Award Conditions for Scientific Data, investigators are obligated to submit their data for curation and long-term preservation; this includes the registration of a dataset description into the Antarctic Master Directory (AMD), http://gcmd.nasa.gov/Data/portals/amd/. The AMD is a Web-based, searchable directory of thousands of dataset descriptions, known as DIF records, submitted by scientists from over 20 countries. It serves as a node of the International Directory Network/Global Change Master Directory (IDN/GCMD). The US Antarctic Program Data Coordination Center (USAP-DCC), http://www.usap-data.org/, funded through NSF/OPP, was established in 2007 to help streamline the process of data submission and DIF record creation. When data does not quite fit within any existing disciplinary repository, it can be registered within the USAP-DCC as the fallback data repository. Within the scope of the USAP-DCC we undertook the challenge of discovering and "rescuing" orphan datasets currently registered within the AMD. In order to find which DIF records led to data served privately, all records relating to US data within the AMD were parsed. After

  6. Genomewide analysis of intronic microRNAs in rice and Arabidopsis

    Indian Academy of Sciences (India)

    G. D. Yang; K. Yan; B. J. Wu; Y. H. Wang; Y. X. Gao; C. C. Zheng

    2012-12-01

    MicroRNAs (miRNAs) are potent regulators of gene transcription and posttranscriptional processes. The majority of miRNAs are localized within intronic regions of protein-coding genes (host genes) and have diverse functions in regulating important cellular processes in animals. To date, few plant intronic miRNAs have been studied functionally. Here we report a comprehensive computational analysis to characterize intronic miRNAs in rice and Arabidopsis. RT-PCR analysis confirmed that the identified intronic miRNAs were derived from the real introns of host genes. Interestingly, 13 intronic miRNAs in rice and two in Arabidopsis were located within seven clusters, of which four polycistronic clusters contain miRNAs derived from different families, suggesting that these clustered intronic miRNAs might be involved in extremely complex regulation in rice. Length analysis of miRNA-carrying introns, promoter prediction and qRT-PCR analysis results indicated that intronic miRNAs are coexpressed with their host genes. Expression pattern analysis demonstrated that host genes had a very broad expression spectrum in different stages of development, suggesting the intronic miRNAs might play an important role in plant development. This comparative genomics analysis of intronic miRNAs in rice and Arabidopsis provides new insight into the functions and regulatory mechanisms of intronic miRNAs in monocots and dicots.

  7. Orphan drugs in development for urea cycle disorders: current perspectives

    Directory of Open Access Journals (Sweden)

    Häberle J

    2014-09-01

    therapy, are reviewed. Keywords: urea cycle disorders, inherited hyperammonemias, orphan drugs, phenylbutyrate, N-carbamyl-l-glutamate

  8. Haitian orphan population and protective factors against caries

    Directory of Open Access Journals (Sweden)

    Madelyn Rea

    2016-04-01

    Full Text Available Objective In Haiti, families were torn apart and children were left orphans after the 2010 earthquake. In the aftermath of this natural disaster many children were relocated to orphanages across the country and adopted internationally. Years later these children find themselves catching up in growth physically, mentally and emotionally after an extremely traumatic event during a crucial time in their health development. Another important marker of development is the primary dentition and the presence of caries.  We report estimates of early childhood caries (ECC frequency, risk factors and quality of health among Haitian children. Methods Medical and dental professionals conducted a descriptive cross sectional study through the Pittsburgh Kids Foundation and their partnership with IDADEE children’s home, EBAC orphanage and New Vision Children’s home. Vital signs were taken and recorded to create a health/growth history for each child. Brief dental screenings were conducted and topical fluoride treatments were administered. Risk factors and quality of health information was obtained from discussions with the caregivers present. The children and caregivers were given oral hygiene education and supplies (i.e. toothbrushes, toothpaste, floss.  Results Physical exams and dental screenings were conducted on the 40 children ages 3-10 years of age living in the IDADEE children’s home. Two children had cavitated teeth. Eight children had teeth that were stained. Four children had evidence of dental trauma. 26 out of the 40 children had otherwise healthy dentition. Conclusion The IDADEE children’s home and New Vision Children’s home have hopes to expand their capacity with new construction scheduled to be finished in 2016. As more children enter these homes action is needed to educate caregivers on ways to identify high-risk children to prevent ECC and ways they can be treated before irreversible damage is done to the developing permanent

  9. Hunting the parent of the Orphan stream. II. The first high-resolution spectroscopic study

    Energy Technology Data Exchange (ETDEWEB)

    Casey, Andrew R.; Keller, Stefan C.; Da Costa, Gary; Maunder, Elizabeth [Research School of Astronomy and Astrophysics, Australian National University, Canberra, ACT 2611 (Australia); Frebel, Anna, E-mail: andrew.casey@anu.edu.au [Department of Physics, Massachusetts Institute of Technology and Kavli Institute for Astrophysics and Space Research, Cambridge, MA 02139 (United States)

    2014-03-20

    We present the first high-resolution spectroscopic study on the Orphan stream for five stream candidates, observed with the Magellan Inamori Kyocera Echelle spectrograph on the Magellan Clay telescope. The targets were selected from the low-resolution catalog of Casey et al.: three high-probability members, one medium, and one low-probability stream candidate were observed. Our analysis indicates that the low- and medium-probability targets are metal-rich field stars. The remaining three high-probability targets range over ∼1 dex in metallicity, and are chemically distinct compared to the other two targets and all standard stars: low [α/Fe] abundance ratios are observed, and lower limits are ascertained for [Ba/Y], which sit well above the Milky Way trend. These chemical signatures demonstrate that the undiscovered parent system is unequivocally a dwarf spheroidal galaxy, consistent with dynamical constraints inferred from the stream width and arc. As such, we firmly exclude the proposed association between NGC 2419 and the Orphan stream. A wide range in metallicities adds to the similarities between the Orphan stream and Segue 1, although the low [α/Fe] abundance ratios in the Orphan stream are in tension with the high [α/Fe] values observed in Segue 1. Open questions remain before Segue 1 could possibly be claimed as the 'parent' of the Orphan stream. The parent system could well remain undiscovered in the southern sky.

  10. Rapid identification of sequences for orphan enzymes to power accurate protein annotation.

    Directory of Open Access Journals (Sweden)

    Kevin R Ramkissoon

    Full Text Available The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the "back catalog" of enzymology--"orphan enzymes," those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC database alone. In this study, we demonstrate how this orphan enzyme "back catalog" is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology's "back catalog" another powerful tool to drive accurate genome annotation.

  11. Database identifies FDA-approved drugs with potential to be repurposed for treatment of orphan diseases.

    Science.gov (United States)

    Xu, Kui; Coté, Timothy R

    2011-07-01

    Facing substantial obstacles to developing new therapies for rare diseases, some sponsors are looking to 'repurpose' drugs already approved for other conditions and use those therapies to treat rare diseases. In an effort to facilitate such repurposing and speed the delivery of new therapies to people who need them, we have established a new resource, the Rare Disease Repurposing Database (RDRD). The advantages of repurposed compounds include their demonstrated efficacy (in some clinical contexts), their observed toxicity profiles and their clearly described manufacturing controls. To create the RDRD, we matched the US Food and Drug Administration (FDA) orphan designation database to FDA drug and biological product approval lists. The RDRD lists 236 products that have received orphan status designation--that is, were found to be 'promising' for the treatment of a rare disease--and though not yet approved for marketing for that rare disease, they are already approved for marketing to treat some other disease or condition. The RDRD contains three tables: Orphan-designated products with at least one marketing approval for a common disease indication (N = 109); orphan-designated products with at least one marketing approval for a rare disease indication (N = 76); and orphan-designated products with marketing approvals for both common and rare disease indications (N = 51). While the data included in the database is a re-configuration/cross-indexing of information already released by the FDA, it offers sponsors a new tool for finding special opportunities to develop niche therapies for rare disease patients.

  12. Rapid identification of sequences for orphan enzymes to power accurate protein annotation.

    Science.gov (United States)

    Ramkissoon, Kevin R; Miller, Jennifer K; Ojha, Sunil; Watson, Douglas S; Bomar, Martha G; Galande, Amit K; Shearer, Alexander G

    2013-01-01

    The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the "back catalog" of enzymology--"orphan enzymes," those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC) database alone. In this study, we demonstrate how this orphan enzyme "back catalog" is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis) to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology's "back catalog" another powerful tool to drive accurate genome annotation.

  13. Identifying ligands at orphan GPCRs: current status using structure-based approaches.

    Science.gov (United States)

    Ngo, Tony; Kufareva, Irina; Coleman, James Lj; Graham, Robert M; Abagyan, Ruben; Smith, Nicola J

    2016-10-01

    GPCRs are the most successful pharmaceutical targets in history. Nevertheless, the pharmacology of many GPCRs remains inaccessible as their endogenous or exogenous modulators have not been discovered. Tools that explore the physiological functions and pharmacological potential of these 'orphan' GPCRs, whether they are endogenous and/or surrogate ligands, are therefore of paramount importance. Rates of receptor deorphanization determined by traditional reverse pharmacology methods have slowed, indicating a need for the development of more sophisticated and efficient ligand screening approaches. Here, we discuss the use of structure-based ligand discovery approaches to identify small molecule modulators for exploring the function of orphan GPCRs. These studies have been buoyed by the growing number of GPCR crystal structures solved in the past decade, providing a broad range of template structures for homology modelling of orphans. This review discusses the methods used to establish the appropriate signalling assays to test orphan receptor activity and provides current examples of structure-based methods used to identify ligands of orphan GPCRs. Linked Articles This article is part of a themed section on Molecular Pharmacology of G Protein-Coupled Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v173.20/issuetoc.

  14. Grieving experiences amongst adolescents orphaned by AIDS: Analysis from event history calendars

    Directory of Open Access Journals (Sweden)

    Gloria Thupayagale-Tshweneagae

    2012-05-01

    Full Text Available Mental health is an essential component of adolescent health and wellbeing. Mental health practitioners assess adolescents’ mental health status to identify possible issues that may lead to mental health problems. However, very few of the tools used to assess the mental health status of adolescents include assessment for grieving and coping patterns. The current tools used for assessing an individual’s mental health are lengthy and not comprehensive. The purpose of this study was to assess grieving patterns of adolescents orphaned by AIDS and to appraise the sefulness of an event history calendar as an assessment tool for identifying grieving experiences, in order to guide and support these adolescents through the grieving process. One hundred and two adolescents aged 14–18 years, who had been orphaned by AIDS, completed an event history calendar, reviewed it with the researcher and reported their perceptions of it. Thematic analysis of the event history calendar content revealed that it is an effective, time-efficient, adolescent-friendly tool that facilitated identification and discussion of the orphaned adolescents’ grieving patterns. Crying, isolation, silence and violent outbursts were the main grieving patterns reported by adolescents orphaned by AIDS. The researcher recommends use of the event history calendar for identification of orphaned adolescents’ grieving experiences. Early identification would enable mental health practitioners to support them in order to prevent the occurrence of mental illness due to maladaptive grieving.

  15. Grieving experiences amongst adolescents orphaned by AIDS: Analysis from event history calendars.

    Science.gov (United States)

    Thupayagale-Tshweneagae, Gloria

    2012-09-07

    Mental health is an essential component of adolescent health and wellbeing. Mental health practitioners assess adolescents' mental health status to identify possible issues that may lead to mental health problems. However, very few of the tools used to assess the mental health status of adolescents include assessment for grieving and coping patterns. The current tools used for assessing an individual's mental health are lengthy and not comprehensive. The purpose of this study was to assess grieving patterns of adolescents orphaned by AIDS and to appraise the usefulness of an event history calendar as an assessment tool for identifying grieving experiences, in order to guide and support these adolescents through the grieving process. One hundred and two adolescents aged 14-18 years, who had been orphaned by AIDS, completed an event history calendar, reviewed it with the researcher and reported their perceptions of it. Thematic analysis of the event history calendar content revealed that it is an effective, time-efficient, adolescent-friendly tool that facilitated identification and discussion of the orphaned adolescents' grieving patterns. Crying, isolation, silence and violent outbursts were the main grieving patterns reported by adolescents orphaned by AIDS. The researcher recommends use of the event history calendar for identification of orphaned adolescents' grieving experiences. Early identification would enable mental health practitioners to support them in order to prevent the occurrence of mental illness due to maladaptive grieving.

  16. Psychosocial support and parents' social life determine the self-esteem of orphan children.

    Science.gov (United States)

    Erango, Markos Abiso; Ayka, Zikie Ataro

    2015-01-01

    Parental death affects the life of children in many ways, one of which is self-esteem problems. Providing psychosocial support and equipping orphans play a vital role in their lifes. A cross-sectional study was conducted on 7-18-year-old orphans at 17 local districts of Gamo Gofa Zone, Southern Regional State of Ethiopia. From a total of 48,270 orphans in these areas, 4,368 were selected using stratified simple random sampling technique. Data were collected with a designed questionnaire based on the Rosenberg's rating scale to measure their self-esteem levels. Self-esteem with a score less than or equal to an average score was considered to be low self-esteem in the analysis. Binary logistic regression model was used to analyze the data using the SPSS software. The results of the study revealed that the probability of orphans suffering from low self-esteem was 0.59. Several risk factors were found to be significant at the level of 5%. Psychosocial support (good guidance, counseling and treatment, physical protection and amount of love shared, financial and material support, and fellowship with other children), parents living together before death, strong relationship between parents before death, high average monthly income, voluntary support, and consideration from the society are some of the factors that decrease the risk of being low in self-esteem. There are many orphans with low self-esteem in the study areas. The factors negatively affecting the self-esteem of orphans include the lack of psychosocial support, poor social life of parents, and death of parents due to AIDS. Society and parents should be aware of the consequences of these factors which can influence their children's future self-esteem.

  17. Tectono-stratigraphic evolution and crustal architecture of the Orphan Basin during North Atlantic rifting

    Science.gov (United States)

    Gouiza, Mohamed; Hall, Jeremy; Welford, J. Kim

    2016-06-01

    The Orphan Basin is located in the deep offshore of the Newfoundland margin, and it is bounded by the continental shelf to the west, the Grand Banks to the south, and the continental blocks of Orphan Knoll and Flemish Cap to the east. The Orphan Basin formed in Mesozoic time during the opening of the North Atlantic Ocean between eastern Canada and western Iberia-Europe. This work, based on well data and regional seismic reflection profiles across the basin, indicates that the continental crust was affected by several extensional episodes between the Jurassic and the Early Cretaceous, separated by events of uplift and erosion. The preserved tectono-stratigraphic sequences in the basin reveal that deformation initiated in the eastern part of the Orphan Basin in the Jurassic and spread towards the west in the Early Cretaceous, resulting in numerous rift structures filled with a Jurassic-Lower Cretaceous syn-rift succession and overlain by thick Upper Cretaceous to Cenozoic post-rift sediments. The seismic data show an extremely thinned crust (4-16 km thick) underneath the eastern and western parts of the Orphan Basin, forming two sub-basins separated by a wide structural high with a relatively thick crust (17 km thick). Quantifying the crustal architecture in the basin highlights the large discrepancy between brittle extension localized in the upper crust and the overall crustal thinning. This suggests that continental deformation in the Orphan Basin involved, in addition to the documented Jurassic and Early Cretaceous rifting, an earlier brittle rift phase which is unidentifiable in seismic data and a depth-dependent thinning of the crust driven by localized lower crust ductile flow.

  18. Effectiveness of the Group Play Therapy on the Insecure Attachment and Social Skills of Orphans in Ahvaz City

    Science.gov (United States)

    Mousavi, Bahareh; Safarzadeh, Sahar

    2016-01-01

    This study aimed to determine the effectiveness of the group play therapy on the insecure attachment and social skills of orphans in Ahvaz city. Statistical population included all orphans in Ahvaz city, of whom 30 students were selected whose scores in insecure attachment and in social skills were one standard deviation higher and one standard…

  19. Orphans and Vulnerable Children Affected by Human Immunodeficiency Virus in Sub-Saharan Africa.

    Science.gov (United States)

    Bryant, Malcolm; Beard, Jennifer

    2016-02-01

    In Sub-Saharan Africa, 15.1 million children have been orphaned because of human immunodeficiency virus (HIV). They face significant vulnerabilities, including stigma and discrimination, trauma and stress, illness, food insecurity, poverty, and difficulty accessing education. Millions of additional children who have living parents are vulnerable because their parents or other relatives are infected. This article reviews the current situation of orphans and vulnerable children, explores the underlying determinants of vulnerability and resilience, describes the response by the global community, and highlights the challenges as the HIV pandemic progresses through its fourth decade.

  20. The Roles of Orphan Nuclear Receptors in the Development and Function of the Immune System

    Institute of Scientific and Technical Information of China (English)

    Ivan Dzhagalov; Nu Zhang; You-Wen He

    2004-01-01

    Hormones and their receptors regulate cell growth, differentiation and apoptosis and also play important roles in immune function. Recent studies on the subfamily of the orphan nuclear receptors known as retinoid-acid related orphan receptors (ROR) have shed important insights on the roles of this group of nuclear proteins in the development and function of the immune system. RORα regulates inflammatory cytokine production in both innate and adaptive immune system while RORγ regulates the normal development of T lymphocyte repertoire and secondary lymphoid organs. Cellular & Molecular Immunology. 2004;1(6):401-407.

  1. The Roles of Orphan Nuclear Receptors in the Development and Function of the Immune System

    Institute of Scientific and Technical Information of China (English)

    IvanDzhagalov; NuZhang; You-WenHe

    2004-01-01

    Hormones and their receptors regulate cell growth, differentiation and apoptosis and also play important roles in immune function. Recent studies on the subfamily of the orphan nuclear receptors known as retinoid-acid related orphan receptors (ROR) have shed important insights on the roles of this group of nuclear proteins in the development and function of the immune system. RORα regulates inflammatory cytokine production in both innate and adaptive immune system while RORγ, regulates the normal development of T lymphocyte repertoire and secondary lymphoid organs. Cellular & Molecular Immunology. 2004;1(6):401-407.

  2. The role of globalization in drug development and access to orphan drugs: orphan drug legislation in the US/EU and in Latin America.

    Science.gov (United States)

    Arnold, Renée J G; Bighash, Lida; Bryón Nieto, Alejandro; Tannus Branco de Araújo, Gabriela; Gay-Molina, Juan Gabriel; Augustovski, Federico

    2015-01-01

    Compared to a decade ago, nearly three times as many drugs for rare diseases are slated for development. This article addresses the market access issues associated with orphan drug status in Europe and the United States in contrast to the legislation in five Latin American (LA) countries that have made strides in this regard--Mexico, Brazil, Colombia, Chile and Argentina. Based on the success of orphan drug legislation in the EU and US, LA countries should strive to adopt similar strategies with regard to rare diseases and drug development. With the implementation of new targeted regulations, reimbursement strategies, and drug approvals, accessibility to treatment will be improved for people afflicted with rare diseases in these developing countries.

  3. Psychological well-being and socio-economic hardship among AIDS orphans and other vulnerable children in Guinea.

    Science.gov (United States)

    Delva, Wim; Vercoutere, An; Loua, Catherine; Lamah, Jonas; Vansteelandt, Stijn; De Koker, Petra; Claeys, Patricia; Temmerman, Marleen; Annemans, Lieven

    2009-12-01

    Over the past decade, the effects of AIDS-related parental death on children's socio-economic, educational and psychological well-being have become apparent. Most studies, however, have compared the plight of so-called AIDS orphans with non-orphaned children only. Consequently, such study designs are unable to establish if the AIDS-related cause of death of the parents confers effects additional to those of parent-bereavement. We therefore conducted a cross-sectional survey to assess the psychological well-being and socio-economic hardship among 140 non-orphaned children, 133 children orphaned by causes other than AIDS (O) and 124 children orphaned by AIDS (O-A) in Conakry, N'Zerekore and the villages around N'Zerekore, Guinea. Multi-way analysis of variance and multiple (ordinal) logistic regression models were applied to measure the association between the orphan status and psychological well-being, school attendance, economic activities, frequency of going to bed hungry and sleeping commodity. After adjustment for confounding factors, the psychological well-being score (PWS) was significantly lower among AIDS-orphaned children than among O (Pchildren were more likely to be engaged in economic activities (adjusted odds ratio (AOR) = 3.04; 95% CI: 1.45-6.36) and to go to bed hungry on a daily basis (AOR = 2.73; 95% CI: 1.24-6.02) than other orphans. The differences in school attendance and the proportion of children with a bed or couch to sleep between AIDS-orphaned children and O were not statistically significant. This situation calls for sustainable and holistic approaches to ensure the psychological and socio-economic stability of AIDS orphans and other vulnerable children.

  4. Multiple reference genomes and transcriptomes for Arabidopsis thaliana

    KAUST Repository

    Gan, Xiangchao

    2011-08-28

    Genetic differences between Arabidopsis thaliana accessions underlie the plants extensive phenotypic variation, and until now these have been interpreted largely in the context of the annotated reference accession Col-0. Here we report the sequencing, assembly and annotation of the genomes of 18 natural A. thaliana accessions, and their transcriptomes. When assessed on the basis of the reference annotation, one-third of protein-coding genes are predicted to be disrupted in at least one accession. However, re-annotation of each genome revealed that alternative gene models often restore coding potential. Gene expression in seedlings differed for nearly half of expressed genes and was frequently associated with cis variants within 5 kilobases, as were intron retention alternative splicing events. Sequence and expression variation is most pronounced in genes that respond to the biotic environment. Our data further promote evolutionary and functional studies in A. thaliana, especially the MAGIC genetic reference population descended from these accessions. ©2011 Macmillan Publishers Limited. All rights reserved.

  5. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis

    Directory of Open Access Journals (Sweden)

    Mount Stephen M

    2006-12-01

    Full Text Available Abstract Background Recently, genomic sequencing efforts were finished for Oryza sativa (cultivated rice and Arabidopsis thaliana (Arabidopsis. Additionally, these two plant species have extensive cDNA and expressed sequence tag (EST libraries. We employed the Program to Assemble Spliced Alignments (PASA to identify and analyze alternatively spliced isoforms in both species. Results A comprehensive analysis of alternative splicing was performed in rice that started with >1.1 million publicly available spliced ESTs and over 30,000 full length cDNAs in conjunction with the newly enhanced PASA software. A parallel analysis was performed with Arabidopsis to compare and ascertain potential differences between monocots and dicots. Alternative splicing is a widespread phenomenon (observed in greater than 30% of the loci with transcript support and we have described nine alternative splicing variations. While alternative splicing has the potential to create many RNA isoforms from a single locus, the majority of loci generate only two or three isoforms and transcript support indicates that these isoforms are generally not rare events. For the alternate donor (AD and acceptor (AA classes, the distance between the splice sites for the majority of events was found to be less than 50 basepairs (bp. In both species, the most frequent distance between AA is 3 bp, consistent with reports in mammalian systems. Conversely, the most frequent distance between AD is 4 bp in both plant species, as previously observed in mouse. Most alternative splicing variations are localized to the protein coding sequence and are predicted to significantly alter the coding sequence. Conclusion Alternative splicing is widespread in both rice and Arabidopsis and these species share many common features. Interestingly, alternative splicing may play a role beyond creating novel combinations of transcripts that expand the proteome. Many isoforms will presumably have negative

  6. The orphaning experience: descriptions from Ugandan youth who have lost parents to HIV/AIDS

    Directory of Open Access Journals (Sweden)

    Ssebunnya Joshua

    2010-02-01

    Full Text Available Abstract The HIV/AIDS epidemic has continued to pose significant challenges to countries in Sub-Saharan Africa. Millions of African children and youth have lost parents to HIV/AIDS leaving a generation of orphans to be cared for within extended family systems and communities. The experiences of youth who have lost parents to the HIV/AIDS epidemic provide an important ingress into this complex, evolving, multi-dimensional phenomenon. A fundamental qualitative descriptive study was conducted to develop a culturally relevant and comprehensive description of the experiences of orphanhood from the perspectives of Ugandan youth. A purposeful sample of 13 youth who had lost one or both parents to HIV/AIDS and who were affiliated with a non-governmental organization providing support to orphans were interviewed. Youth orphaned by HIV/AIDS described the experience of orphanhood beginning with parental illness, not death. Several losses were associated with the death of a parent including lost social capitol, educational opportunities and monetary assets. Unique findings revealed that youth experienced culturally specific stigma and conflict which was distinctly related to their HIV/AIDS orphan status. Exploitation within extended cultural family systems was also reported. Results from this study suggest that there is a pressing need to identify and provide culturally appropriate services for these Ugandan youth prior to and after the loss of a parent(s.

  7. Molecular pharmacological phenotyping of EBI2. An orphan seven-transmembrane receptor with constitutive activity

    DEFF Research Database (Denmark)

    Rosenkilde, Mette M; Benned-Jensen, Tau; Holst, Peter J;

    2006-01-01

    Epstein-Barr virus (EBV)-induced receptor 2 (EBI2) is an orphan seven-transmembrane (7TM) receptor originally identified as the most up-regulated gene (>200-fold) in EBV-infected cells. Here we show that EBI2 signals with constitutive activity through Galpha(i) as determined by a receptor-mediate...

  8. Educating Orphaned and Vulnerable Children in Elgeyo-Marakwet County, Kenya

    Science.gov (United States)

    Jepkemboi, Grace; Jolly, Pauline; Gillyard, KaNesha; Lissanu, Lydia

    2016-01-01

    According to UNICEF, 13.3 million children (0-17 years) worldwide have lost one or both parents to AIDS. Nearly 12 million of these children live in sub-Saharan Africa. Together, with other children who have been severely impacted by the AIDS pandemic, these orphaned and vulnerable children (OVC) are at higher risk of missing out on schooling,…

  9. Educational Support for Orphans and Vulnerable Children in Primary Schools: Challenges and Interventions

    Science.gov (United States)

    Mwoma, Teresa; Pillay, Jace

    2016-01-01

    Educational status is an important indicator of children's wellbeing and future life opportunities. It can predict growth potential and economic viability of a state. While this is an ideal situation for all children, the case may be different for orphans and vulnerable children (OVC) due to the challenges they go through on a daily basis. This…

  10. "Orphan" $\\gamma$-ray Flares and Stationary Sheaths of Blazar Jets

    CERN Document Server

    MacDonald, Nicholas R; Marscher, Alan P

    2016-01-01

    Blazars exhibit flares across the entire electromagnetic spectrum. Many $\\gamma$-ray flares are highly correlated with flares detected at longer wavelengths; however, a small subset appears to occur in isolation, with little or no correlated variability at longer wavelengths. These "orphan" $\\gamma$-ray flares challenge current models of blazar variability, most of which are unable to reproduce this type of behavior. Macdonald et al. have developed the Ring of Fire model to explain the origin of orphan $\\gamma$-ray flares from within blazar jets. In this model, electrons contained within a blob of plasma moving relativistically along the spine of the jet inverse-Compton scatter synchrotron photons emanating off of a ring of shocked sheath plasma that enshrouds the jet spine. As the blob propagates through the ring, the scattering of the ring photons by the blob electrons creates an orphan $\\gamma$-ray flare. This model was successfully applied to modeling a prominent orphan $\\gamma$-ray flare observed in the ...

  11. Education and Nutritional Status of Orphans and Children of HIV-Infected Parents in Kenya

    Science.gov (United States)

    Mishra, Vinod; Arnold, Fred; Otieno, Fredrick; Cross, Anne; Hong, Rathavuth

    2007-01-01

    We examined whether orphaned and fostered children and children of HIV-infected parents are disadvantaged in schooling, nutrition, and health care. We analyzed data on 2,756 children aged 0-4 years and 4,172 children aged 6-14 years included in the 2003 Kenya Demographic and Health Survey, with linked anonymous HIV testing, using multivariate…

  12. Examining Why the Canadian Federal Government Placed an Orphan Drug Strategy on Their Decision Agenda Now

    Directory of Open Access Journals (Sweden)

    Mark Gary Embrett

    2014-02-01

    Full Text Available The Ministry of Health’s announcement of a National Orphan Drug Framework on 3 October 2012 was the first federal public acknowledgement of orphan drugs since the 1997 Drugs Directorate (DD policy statement. The reform primarily announced an Orphan Drug Policy for Canada. This paper explains why the government decided to make this announcement now. Media and Parliamentary documents were analyzed for their use of symbols, numbers, and language in causal stories told by political actors. The initial story was that Canada’s population was too small and the cost too high for an orphan drug policy. Over the next fifteen years, a powerful interest group, the Canadian Organization for Rare Disorders (CORD, mobilized the rare disease community into a cooperative effort that generated collective action. They redefined the DD story from one of natural causes, to inadvertence, and finally to intentional causation. Their story invoked a federal response because it blamed the government directly for not acting on behalf of the 3 million Canadians with rare diseases, when patients in other countries were receiving better care.

  13. Tracing the Orphan Stream to 55 kpc with RR Lyrae Stars

    CERN Document Server

    Sesar, Branimir; Cohen, Judith G; Bellm, Eric C; Bhalerao, Varun B; Levitan, David; Laher, Russ R; Ofek, Eran O; Surace, Jason A; Tang, Sumin; Waszczak, Adam; Kulkarni, Shrinivas R; Prince, Thomas A

    2013-01-01

    We report positions, velocities and metallicities of 50 ab-type RR Lyrae (RRab) stars observed in the vicinity of the Orphan stellar stream. Using about 30 RRab stars classified as being likely members of the Orphan stream, we study the metallicity and the spatial extent of the stream. We find that RRab stars in the Orphan stream have a wide range of metallicities, from -1.5 dex to -2.7 dex. The average metallicity of the stream is -2.1 dex, identical to the value obtained by Newberg et al. (2010) using blue horizontal branch stars. We find that the most distant parts of the stream (40-50 kpc from the Sun) are about 0.3 dex more metal-poor than the closer parts (within ~30 kpc), suggesting a possible metallicity gradient along the stream's length. We have extended the previous studies and have mapped the stream up to 55 kpc from the Sun. Even after a careful search, we did not identify any more distant RRab stars that could plausibly be members of the Orphan stream. If confirmed with other tracers, this resul...

  14. The influence of the European paediatric regulation on marketing authorisation of orphan drugs for children

    NARCIS (Netherlands)

    Kreeftmeijer-Vegter, Annemarie Rosan; de Boer, Anthonius; van der Vlugt-Meijer, Roselinda H; de Vries, Peter J; Dep Farmaceutische wetenschappen; Sub Pharmacotherapy, Theoretical

    2014-01-01

    BACKGROUND: Drug development for rare diseases is challenging, especially when these orphan drugs (OD) are intended for children. In 2007 the EU Paediatric Drug Regulation was enacted to improve the development of high quality and ethically researched medicines for children through the establishment

  15. Limitations of drug registries to evaluate orphan medicinal products for the treatment of lysosomal storage disorders

    NARCIS (Netherlands)

    Hollak, C.E.M.; Aerts, J.M.F.G.; Aymé, S.; Manuel, J.

    2011-01-01

    Orphan drugs are often approved under exceptional circumstances, requiring submission of additional data on safety and effectiveness through registries. These registries are mainly focused on one drug only and data is frequently incomplete. Some registries also address phenotypic heterogeneity and n

  16. Art Therapy with Orphaned Children: Dynamics of Early Relational Trauma and Repetition Compulsion

    Science.gov (United States)

    Meshcheryakova, Ksenia

    2012-01-01

    This article explores the dynamics of orphaned children's engagement with art therapy in a group of preadolescent children living in a Russian orphanage. The phenomenon of repetition compulsion (i.e., origins in past traumatic experiences, destructive consequences, and protective psychic function) is discussed with respect to the children's…

  17. A review and update on orphan drugs for the treatment of noninfectious uveitis

    Science.gov (United States)

    You, Caiyun; Sahawneh, Haitham F; Ma, Lina; Kubaisi, Buraa; Schmidt, Alexander; Foster, C Stephen

    2017-01-01

    Introduction Uveitis, a leading cause of preventable blindness around the world, is a critically underserved disease in regard to the medications approved for use. Multiple immunomodulatory therapy (IMT) drugs are appropriate for uveitis therapy but are still off-label. These IMT agents, including antimetabolites, calcineurin inhibitors, alkylating agents, and biologic agents, have been designated as “orphan drugs” and are widely used for systemic autoimmune diseases or organ transplantation. Area covered The purpose of this paper is to comprehensively review and summarize the approved orphan drugs and biologics that are being used to treat systemic diseases and to discuss drugs that have not yet received approval as an “orphan drug for treating uveitis” by the US Food and Drug Administration (FDA). Our perspective IMT, as a steroid-sparing agent for uveitis patients, has shown promising clinical results. Refractory and recurrent uveitis requires combination IMT agents. IMT is continued for a period of 2 years while the patient is in remission before considering tapering medication. Our current goals include developing further assessments regarding the efficacy, optimal dose, and safety in efforts to achieve FDA approval for “on-label” use of current IMT agents and biologics more quickly and to facilitate insurance coverage and expand access to the products for this orphan disease. PMID:28203051

  18. Exploring emerging technologies using metaphors--a study of orphan drugs and pharmacogenomics.

    Science.gov (United States)

    Boon, Wouter; Moors, Ellen

    2008-05-01

    Due to uncertainties of several aspects of emerging health technologies, there is a need to anticipate these developments early. A first step would be to gather information and develop future visions about the technology. This paper introduces metaphor analysis as a novel way to do this. Specifically, we study the future of pharmacogenomics by comparing this technology with orphan drugs, which are more established and often act as a model with comparable (economic, research organisation, etc.) characteristics. The analysis consists of describing the dominant metaphors used and structurally exploring (dis)similarities between pharmacogenomics and orphan drugs developments. This comparison leads to lessons that can be learnt for the emerging pharmacogenomics future. We carried out a comprehensive literature review, extracting metaphors in a structured way from different areas of the drug research and development pipeline. The paper argues that (1) there are many similarities between orphan drugs and pharmacogenomics, especially in terms of registration, and social and economic impacts; (2) pharmacogenomics developments are regarded both as a future 'poison' and a 'chance', whereas orphan drugs are seen as a 'gift', and at the same time as a large 'problem'; and (3) metaphor analysis proves to be a tool for creating prospective images of pharmacogenomics and other emerging technologies.

  19. Education and nutritional status of orphans and children of HIV-infected parents in Kenya.

    Science.gov (United States)

    Mishra, Vinod; Arnold, Fred; Otieno, Fredrick; Cross, Anne; Hong, Rathavuth

    2007-10-01

    We examined whether orphaned and fostered children and children of HIV-infected parents are disadvantaged in schooling, nutrition, and health care. We analyzed data on 2,756 children aged 0-4 years and 4,172 children aged 6-14 years included in the 2003 Kenya Demographic and Health Survey, with linked anonymous HIV testing, using multivariate logistic regression. Results indicate that orphans, fostered children, and children of HIV-infected parents are significantly less likely to attend school than non-orphaned/non-fostered children of HIV-negative parents. Children of HIV-infected parents are more likely to be underweight and wasted, and less likely to receive medical care for ARI and diarrhea. Children of HIV-negative single mothers are also disadvantaged on most indicators. The findings highlight the need to expand child welfare programs to include not only orphans but also fostered children, children of single mothers, and children of HIV-infected parents, who tend to be equally, if not more, disadvantaged.

  20. Children as Ethnographers: Reflections on the Importance of Participatory Research in Assessing Orphans' Needs

    Science.gov (United States)

    Cheney, Kristen E.

    2011-01-01

    Critiques of child participation within aid programming suggest that it is superficial and insubstantive for the fulfilment of children's rights. By employing former child research participants as youth research assistants, the collaborative research design developed for my research project on the survival strategies of African orphans and…

  1. The Socioemotional Development of Orphans in Orphanages and Traditional Foster Care in Iraqi Kurdistan.

    Science.gov (United States)

    Ahmad, Abdulbaghi; Mohamad, Kirmanj

    1996-01-01

    A one-year follow-up study of children who had lost both parents and were placed in orphanages (n=19) or foster homes (n=18) in Iraqi Kurdistan investigated the orphans' situation and development. The children in orphanages were found to have higher frequency of post-traumatic stress disorder than the foster care children. (Author/CR)

  2. The psychological well-being of children orphaned by AIDS in Cape Town, South Africa

    Directory of Open Access Journals (Sweden)

    Cluver Lucie

    2006-07-01

    Full Text Available Abstract Background An estimated 2 million children are parentally bereaved by AIDS in South Africa. Little is known about mental health outcomes for this group. Methods This study aimed to investigate mental health outcomes for urban children living in deprived settlements in Cape Town. 30 orphaned children and 30 matched controls were compared using standardised questionnaires (SDQ on emotional and behavioural problems, peer and attention difficulties, and prosocial behaviour. The orphan group completed a modified version of a standardised questionnaire (IES-8, measuring Post-Traumatic Stress symptoms. Group differences were tested using t-tests and Pearson's chi-square. Results Both groups scored highly for peer problems, emotional problems and total scores. However, orphans were more likely to view themselves as having no good friends (p = .002, to have marked concentration difficulties (p = .03, and to report frequent somatic symptoms (p = .05, but were less likely to display anger through loss of temper (p = .03. Orphans were more likely to have constant nightmares (p = .01, and 73% scored above the cut-off for Post-Traumatic Stress Disorder. Conclusion Findings suggest important areas for larger-scale research for parentally-bereaved children.

  3. Rare, Low-Frequency, and Common Variants in the Protein-Coding Sequence of Biological Candidate Genes from GWASs Contribute to Risk of Rheumatoid Arthritis

    Science.gov (United States)

    Diogo, Dorothée; Kurreeman, Fina; Stahl, Eli A.; Liao, Katherine P.; Gupta, Namrata; Greenberg, Jeffrey D.; Rivas, Manuel A.; Hickey, Brendan; Flannick, Jason; Thomson, Brian; Guiducci, Candace; Ripke, Stephan; Adzhubey, Ivan; Barton, Anne; Kremer, Joel M.; Alfredsson, Lars; Sunyaev, Shamil; Martin, Javier; Zhernakova, Alexandra; Bowes, John; Eyre, Steve; Siminovitch, Katherine A.; Gregersen, Peter K.; Worthington, Jane; Klareskog, Lars; Padyukov, Leonid; Raychaudhuri, Soumya; Plenge, Robert M.

    2013-01-01

    The extent to which variants in the protein-coding sequence of genes contribute to risk of rheumatoid arthritis (RA) is unknown. In this study, we addressed this issue by deep exon sequencing and large-scale genotyping of 25 biological candidate genes located within RA risk loci discovered by genome-wide association studies (GWASs). First, we assessed the contribution of rare coding variants in the 25 genes to the risk of RA in a pooled sequencing study of 500 RA cases and 650 controls of European ancestry. We observed an accumulation of rare nonsynonymous variants exclusive to RA cases in IL2RA and IL2RB (burden test: p = 0.007 and p = 0.018, respectively). Next, we assessed the aggregate contribution of low-frequency and common coding variants to the risk of RA by dense genotyping of the 25 gene loci in 10,609 RA cases and 35,605 controls. We observed a strong enrichment of coding variants with a nominal signal of association with RA (p A [p.His266Gln]), and a noncoding variant, rs624988, reside on distinct haplotypes and independently contribute to the risk of RA (p = 4.6 × 10−6). Overall, our results indicate that variants (distributed across the allele-frequency spectrum) within the protein-coding portion of a subset of biological candidate genes identified by GWASs contribute to the risk of RA. Further, we have demonstrated that very large sample sizes will be required for comprehensively identifying the independent alleles contributing to the missing heritability of RA. PMID:23261300

  4. TRACING THE ORPHAN STREAM TO 55 kpc WITH RR LYRAE STARS

    Energy Technology Data Exchange (ETDEWEB)

    Sesar, Branimir; Cohen, Judith G.; Bellm, Eric C.; Levitan, David; Tang, Sumin; Waszczak, Adam; Kulkarni, Shrinivas R.; Prince, Thomas A. [Division of Physics, Mathematics and Astronomy, California Institute of Technology, Pasadena, CA 91125 (United States); Grillmair, Carl J.; Laher, Russ R.; Surace, Jason A. [Spitzer Science Center, California Institute of Technology, Pasadena, CA 91125 (United States); Bhalerao, Varun B. [Inter-University Centre for Astronomy and Astrophysics, Post Bag 4, Ganeshkhind, Pune 411 007 (India); Ofek, Eran O., E-mail: bsesar@astro.caltech.edu [Benoziyo Center for Astrophysics, Weizmann Institute of Science, 76100 Rehovot (Israel)

    2013-10-10

    We report positions, velocities, and metallicities of 50 ab-type RR Lyrae (RRab) stars observed in the vicinity of the Orphan stellar stream. Using about 30 RRab stars classified as being likely members of the Orphan stream, we study the metallicity and the spatial extent of the stream. We find that RRab stars in the Orphan stream have a wide range of metallicities, from –1.5 dex to –2.7 dex. The average metallicity of the stream is –2.1 dex, identical to the value obtained by Newberg et al. using blue horizontal branch stars. We find that the most distant parts of the stream (40-50 kpc from the Sun) are about 0.3 dex more metal-poor than the closer parts (within ∼30 kpc), suggesting a possible metallicity gradient along the stream's length. We have extended the previous studies and have mapped the stream up to 55 kpc from the Sun. Even after a careful search, we did not identify any more distant RRab stars that could plausibly be members of the Orphan stream. If confirmed with other tracers, this result would indicate a detection of the end of the leading arm of the stream. We have compared the distances of Orphan stream RRab stars with the best-fit orbits obtained by Newberg et al. We find that model 6 of Newberg et al. cannot explain the distances of the most remote Orphan stream RRab stars, and conclude that the best fit to distances of Orphan stream RRab stars and to the local circular velocity is provided by potentials where the total mass of the Galaxy within 60 kpc is M{sub 60} ∼ 2.7 × 10{sup 11} M{sub ☉}, or about 60% of the mass found by previous studies. More extensive modeling that would consider non-spherical potentials and the possibility of misalignment between the stream and the orbit is highly encouraged.

  5. Psychosocial support and parents' social life determine the self-esteem of orphan children

    Directory of Open Access Journals (Sweden)

    Erango MA

    2015-10-01

    Full Text Available Markos Abiso Erango,1 Zikie Ataro Ayka2 1School of Mathematical and Statistical Sciences, Department of Applied Statistics, Hawassa University, Hawassa, 2Department of Biology, Arba Minch University, Arba Minch, Ethiopia Abstract: Parental death affects the life of children in many ways, one of which is self-esteem problems. Providing psychosocial support and equipping orphans play a vital role in their lifes. A cross-sectional study was conducted on 7–18-year-old orphans at 17 local districts of Gamo Gofa Zone, Southern Regional State of Ethiopia. From a total of 48,270 orphans in these areas, 4,368 were selected using stratified simple random sampling technique. Data were collected with a designed questionnaire based on the Rosenberg's rating scale to measure their self-esteem levels. Self-esteem with a score less than or equal to an average score was considered to be low self-esteem in the analysis. Binary logistic regression model was used to analyze the data using the SPSS software. The results of the study revealed that the probability of orphans suffering from low self-esteem was 0.59. Several risk factors were found to be significant at the level of 5%. Psychosocial support (good guidance, counseling and treatment, physical protection and amount of love shared, financial and material support, and fellowship with other children, parents living together before death, strong relationship between parents before death, high average monthly income, voluntary support, and consideration from the society are some of the factors that decrease the risk of being low in self-esteem. There are many orphans with low self-esteem in the study areas. The factors negatively affecting the self-esteem of orphans include the lack of psychosocial support, poor social life of parents, and death of parents due to AIDS. Society and parents should be aware of the consequences of these factors which can influence their children's future self

  6. An Arabidopsis callose synthase

    DEFF Research Database (Denmark)

    Ostergaard, Lars; Petersen, Morten; Mattsson, Ole

    2002-01-01

    in the Arabidopsis mpk4 mutant which exhibits systemic acquired resistance (SAR), elevated beta-1,3-glucan synthase activity, and increased callose levels. In addition, AtGsl5 is a likely target of salicylic acid (SA)-dependent SAR, since AtGsl5 mRNA accumulation is induced by SA in wild-type plants, while...... expression of the nahG salicylate hydroxylase reduces AtGsl5 mRNA levels in the mpk4 mutant. These results indicate that AtGsl5 is likely involved in callose synthesis in flowering tissues and in the mpk4 mutant....

  7. A review and update on orphan drugs for the treatment of noninfectious uveitis

    Directory of Open Access Journals (Sweden)

    You C

    2017-01-01

    Full Text Available Caiyun You,1–3 Haitham F Sahawneh,1,2 Lina Ma,1,2 Buraa Kubaisi,1,2 Alexander Schmidt,1,2 C Stephen Foster1,2,4 1Massachusetts Eye Research and Surgery Institution (MERSI, Waltham, 2Ocular Immunology and Uveitis Foundation, Weston, MA, USA; 3Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China; 4Harvard Medical School, Boston, MA, USA Introduction: Uveitis, a leading cause of preventable blindness around the world, is a critically underserved disease in regard to the medications approved for use. Multiple immunomodulatory therapy (IMT drugs are appropriate for uveitis therapy but are still off-label. These IMT agents, including antimetabolites, calcineurin inhibitors, alkylating agents, and biologic agents, have been designated as “orphan drugs” and are widely used for systemic autoimmune diseases or organ transplantation.Area covered: The purpose of this paper is to comprehensively review and summarize the approved orphan drugs and biologics that are being used to treat systemic diseases and to discuss drugs that have not yet received approval as an “orphan drug for treating uveitis” by the US Food and Drug Administration (FDA.Our perspective: IMT, as a steroid-sparing agent for uveitis patients, has shown promising clinical results. Refractory and recurrent uveitis requires combination IMT agents. IMT is continued for a period of 2 years while the patient is in remission before considering tapering medication. Our current goals include developing further assessments regarding the efficacy, optimal dose, and safety in efforts to achieve FDA approval for “on-label” use of current IMT agents and biologics more quickly and to facilitate insurance coverage and expand access to the products for this orphan disease. Keywords: immunomodulatory, orphan drug, steroid sparing, uveitis

  8. Thirty Years of Orphan Drug Legislation and the Development of Drugs to Treat Rare Seizure Conditions: A Cross Sectional Analysis

    Science.gov (United States)

    Hoffmann, Georg F.

    2016-01-01

    Background Epilepsy is a serious chronic health condition with a high morbidity impairing the life of patients and afflicted families. Many epileptic conditions, especially those affecting children, are rare disorders generating an urgent medical need for more efficacious therapy options. Therefore, we assessed the output of the US and European orphan drug legislations. Methods Quantitative analysis of the FDA and EMA databases for orphan drug designations according to STrengthening the Reporting of OBservational studies in Epidemiology (STROBE) criteria. Results Within the US Orphan Drug Act 40 designations were granted delivering nine approvals, i.e. clobazam, diazepam viscous solution for rectal administration, felbamate, fosphenytoin, lamotrigine, repository corticotropin, rufinamide, topiramate, and vigabatrin. Since 2000 the EMA granted six orphan drug designations whereof two compounds were approved, i.e. rufinamide and stiripentol. In the US, two orphan drug designations were withdrawn. Orphan drugs were approved for conditions including Lennox-Gastaut syndrome, infantile spasms, Dravet syndrome, and status epilepticus. Comparing time to approval for rufinamide, which was approved in the US and the EU to treat rare seizure conditions, the process seems faster in the EU (2.2 years) than in the US (4.3 years). Conclusion Orphan drug development in the US and in the EU delivered only few molecular entities to treat rare seizure disorders. The development programs focused on already approved antiepileptic drugs or alternative pharmaceutical formulations. Most orphan drugs approved in the US are not approved in the EU to treat rare seizures although some were introduced after 2000 when the EU adopted the Orphan Drug Regulation. PMID:27557111

  9. Multi-criteria decision analysis for assessment and appraisal of orphan drugs

    Directory of Open Access Journals (Sweden)

    Georgi Iskrov

    2016-09-01

    Full Text Available Background: Limited resources and expanding expectations push all countries and types of health systems to adopt new approaches in priority setting and resources allocation. Despite best efforts, it is difficult to reconcile all competing interests and trade-offs are inevitable. This is why multi-criteria decision analysis (MCDA has played a major role in recent uptake of value-based reimbursement. MCDA framework enables exploration of stakeholders’ preferences, as well as explicit organization of broad range of criteria on which real-world decisions are made.Assessment and appraisal of orphan drugs tend to be one of the most complicated health technology assessment (HTA tasks. Access to market approved orphan therapies remains an issue. Early constructive dialogue among rare disease stakeholders and elaboration of orphan drug-tailored decision support tools could set the scene for ongoing accumulation of evidence, as well as for proper reimbursement decision-making.Objective: The objective of this study was to create a MCDA value measurement model to assess and appraise orphan drugs. This was achieved by exploring the preferences on decision criteria’s weights and performance scores through a stakeholder-representative survey and a focus group discussion that were both organized in Bulgaria.Results/Conclusions: Decision criteria that describe the health technology’s characteristics were unanimously agreed as the most important group of reimbursement considerations. This outcome, combined with the high individual weight of disease severity and disease burden criteria underlined some of the fundamental principles of healthcare – equity and fairness. Our study proved that strength of evidence may be a key criterion in orphan drug assessment and appraisal. Evidence is not only used to shape reimbursement decision-making, but also to lend legitimacy to policies pursued. The need for real-world data on orphan drugs was largely stressed

  10. Anderson's disease/chylomicron retention disease in a Japanese patient with uniparental disomy 7 and a normal SAR1B gene protein coding sequence

    Directory of Open Access Journals (Sweden)

    Okada Tomoo

    2011-11-01

    Full Text Available Abstract Background Anderson's Disease (AD/Chylomicron Retention Disease (CMRD is a rare hereditary hypocholesterolemic disorder characterized by a malabsorption syndrome with steatorrhea, failure to thrive and the absence of chylomicrons and apolipoprotein B48 post-prandially. All patients studied to date exhibit a mutation in the SAR1B gene, which codes for an essential component of the vesicular coat protein complex II (COPII necessary for endoplasmic reticulum to Golgi transport. We describe here a patient with AD/CMRD, a normal SAR1B gene protein coding sequence and maternal uniparental disomy of chromosome 7 (matUPD7. Methods and Results The patient, one of two siblings of a Japanese family, had diarrhea and steatorrhea beginning at five months of age. There was a white duodenal mucosa upon endoscopy. Light and electron microscopy showed that the intestinal villi were normal but that they had lipid laden enterocytes containing accumulations of lipid droplets in the cytoplasm and lipoprotein-size particles in membrane bound structures. Although there were decreased amounts in plasma of total- and low-density lipoprotein cholesterol, apolipoproteins AI and B and vitamin E levels, the triglycerides were normal, typical of AD/CMRD. The presence of low density lipoproteins and apolipoprotein B in the plasma, although in decreased amounts, ruled out abetalipoproteinemia. The parents were asymptomatic with normal plasma cholesterol levels suggesting a recessive disorder and ruling out familial hypobetalipoproteinemia. Sequencing of genomic DNA showed that the 8 exons of the SAR1B gene were normal. Whole genome SNP analysis and karyotyping revealed matUPD7 with a normal karyotype. In contrast to other cases of AD/CMRD which have shown catch-up growth following vitamin supplementation and a fat restricted diet, our patient exhibits continued growth delay and other aspects of the matUPD7 and Silver-Russell Syndrome phenotypes. Conclusions This

  11. Reference: 774 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available an essential gene, the disruption of which causes embryonic lethality. Plants carrying a hypomorphic smg7 mu...e progression from anaphase to telophase in the second meiotic division in Arabidopsis. Arabidopsis SMG7 is

  12. Reference: 398 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available plays attenuated chloroplast movements under intermediate and high light intensitie...hese movements. In this work, we describe plastid movement impaired 2 (pmi2), a mutant in Arabidopsis (Arabidopsis thaliana) that dis

  13. Reference: 173 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available mical approaches to elucidate the action mechanisms of sirtinol in Arabidopsis. A...tic and chemical analyses of the action mechanisms of sirtinol in Arabidopsis. 8 3129-34 15710899 2005 Feb P

  14. Reference: 718 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available displayed a moderate but significant decrease in germination in the presence of D...NA damage. This report links Ubc13-Uev with functions in DNA damage response in Arabidopsis. Arabidopsis UEV

  15. Arabidopsis CDS blastp result: AK068856 [KOME

    Lifescience Database Archive (English)

    Full Text Available eme oxygenase (HY1) [Arabidopsis thaliana] GI:4877362, heme oxygenase 1 [Arabidopsis thaliana] GI:4530591 GB:AF132475; annotation upd...ated per Seth J. Davis at University of Wisconsin-Madison 3e-90 ...

  16. Arabidopsis CDS blastp result: AK104955 [KOME

    Lifescience Database Archive (English)

    Full Text Available B:AF132475; annotation updated per Seth J. Davis at University of Wisconsin-Madison 3e-90 ... ...heme oxygenase (HY1) [Arabidopsis thaliana] GI:4877362, heme oxygenase 1 [Arabidopsis thaliana] GI:4530591 G

  17. Reference: 110 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available on process. Our study shows that an Arabidopsis SNM protein, although structurally closer to the SNM1/PSO2 members, shares some prope...rties with ARTEMIS but also has novel characteristics. Arabidopsis plants defective

  18. Poverty and psychological health among AIDS-orphaned children in Cape Town, South Africa.

    Science.gov (United States)

    Cluver, Lucie; Gardner, Frances; Operario, Don

    2009-06-01

    This study examined associations between AIDS-orphanhood status, poverty indicators, and psychological problems (depression, anxiety, post-traumatic stress, peer problems, delinquency, conduct problems) among children and adolescents in townships surrounding Cape Town, South Africa. One thousand and twenty-five children and adolescents completed standardized and culturally sensitive cross-sectional surveys. Children orphaned by AIDS had more psychological problems including depression, peer problems, post-traumatic stress, and conduct problems. Specific poverty indicators including food security, access to social welfare grants, employment in the household and access to school were associated with better psychological health. Poverty indicators mediated associations of AIDS-orphanhood with psychological problems. Food security showed the most consistent association with reduced psychological problems. Poverty alleviation measures have the potential to improve psychological health for AIDS-orphaned children in South African townships.

  19. Neotenic formation in laboratory colonies of the termite Coptotermes gestroi after orphaning

    Directory of Open Access Journals (Sweden)

    Ana Maria Costa-Leonardo

    2004-04-01

    Full Text Available The termite Coptotermes gestroi (Wasmann, 1896 (Rhinotermitidae: Coptotermitinae is an exotic species in Brazil and information concerning its reproductive developmental biology is scarce. We induced the formation of neotenics in laboratory colonies through orphaning experiments. Orphaning experiments were conducted in three-year old colonies of C. gestroi kept under laboratory conditions. After three months, eight nymphoid neotenics were observed in one colony after queen removal. Histological analysis showed that these neotenics were non-functional. The results suggest that these individuals may have arisen from the first nymphal instar (N1 or from an early N1 instar after one or two larval moults. Neotenics also were recorded on two incipient colonies of C. gestroi that lost the queen naturally.

  20. The health burden of orphan zoonotic disease in the United Kingdom, 2005-2009.

    Science.gov (United States)

    Halsby, K D; Walsh, A L; Smith, R; Said, B; Kirkbride, H; Smyth, B; Browning, L; Larkin, L; Morgan, D

    2014-02-01

    'Orphan' zoonotic diseases attract disproportionately low scientific and public health attention for the impact that they can have. This article pulls together information on their health burden in the UK from routine and enhanced data sources. These diseases are heterogeneous in nature; some have very low case numbers (e.g. hydatid disease), whilst others affect hundreds of patients each year (e.g. toxoplasmosis). The number of deaths attributed to orphan zoonoses is relatively low, and the majority recorded in this article were caused by toxoplasmosis. There is a clear issue of under-reporting and under-diagnosis in the data sets presented, and further work should be carried out to obtain more accurate estimates of the prevalence of zoonotic infections. Joint human and veterinary studies are especially important for these diseases.

  1. Orphan γ-ray flares from relativistic blobs encountering luminous stars

    Science.gov (United States)

    Banasiński, P.; Bednarek, W.; Sitarek, J.

    2016-11-01

    We propose that {\\gamma} -rays in blazars can be produced during encounters of relativistic blobs of plasma with radiation field produced by luminous stars within (or close to) the jet. The blob is expected to contain relativistic electrons which comptonize stellar radiation to the GeV-TeV energies. Produced {\\gamma} -rays can initiate the Inverse Compton e+/- pair cascade in the stellar radiation. We propose that such a scenario can be responsible for the appearance of the so-called orphan {\\gamma} -ray flares. We show that the relativistic blob/luminous star collision model can explain the appearance of the extreme orphan {\\gamma} -ray flare observed in the GeV and sub-TeV energy range from the flat spectrum radio quasar PKS 1222+21.

  2. Health promotion needs of Hammanskraal families with adolescents orphaned by HIV/AIDS

    OpenAIRE

    N.C. van Wyk; M.D. Peu; A DH Botha

    2008-01-01

    Health promotion is regarded as the cornerstone of good health. It is the action expected from individuals and families in order to better their own health situation. Health promotion is an art and science (Edelman & Mandle, 2002:16) that is integrated into the primary health care to reduce existing health problems. The purpose of the research on which this article is reporting, was to explore and describe the health promotion needs of families with adolescents orphaned by human immu...

  3. Child work and labour among orphaned and abandoned children in five low and middle income countries

    OpenAIRE

    Pence Brian; Whetten Kathryn; Ostermann Jan; Messer Lynne; Whetten Rachel; Buckner Megan; Thielman Nathan; O'Donnell Karen

    2011-01-01

    Abstract Background The care and protection of the estimated 143,000,000 orphaned and abandoned children (OAC) worldwide is of great importance to global policy makers and child service providers in low and middle income countries (LMICs), yet little is known about rates of child labour among OAC, what child and caregiver characteristics predict child engagement in work and labour, or when such work infers with schooling. This study examines rates and correlates of child labour among OAC and ...

  4. An orphan gyrB in the Mycobacterium smegmatis genome uncovered by comparative genomics

    Indian Academy of Sciences (India)

    P. Jain; V. Nagaraja

    2002-11-01

    DNA gyrase is an essential topoisomerase found in all bacteria. It is encoded by gyrB and gyrA genes. These genes are organized differently in different bacteria. Direct comparison of Mycobacterium tuberculosis and Mycobacterium smegmatis genomes reveals presence of an additional gyrB in M. smegmatis flanked by novel genes. Analysis of the amino acid sequence of GyrB from different organisms suggests that the orphan GyrB in M. smegmatis may have an important cellular role.

  5. Identification and functional analysis of acute myeloid leukemia susceptibility associated single nucleotide polymorphisms at non-protein coding regions of RUNX1.

    Science.gov (United States)

    Xu, Xin; Ren, Xiuyu; Wang, Haiying; Zhao, Yao; Yi, Zhengjun; Wang, Kaifeng; Zhang, Shizhuang; Wang, Lin; Samuelson, David J; Hu, Zhenbo

    2016-01-01

    Little is known about the susceptibility to acute myeloid leukemia. We aim to search non-protein coding regions of key hematopoiesis transcription factors for genetic variations associated with acute myeloid leukemia susceptibility. We genotyped SNPs of RUNX1 P1 promoter, P2 promoter, +23 enhancer, intron 5.2 enhancer, PU.1 promoter, CEBPA promoter, and CEBPE promoter from acute myeloid leukemia patients and healthy controls. Rs2249650 and rs2268276 at RUNX1 intron 5.2 enhancer were found to be associated with acute myeloid leukemia susceptibility. Artificial reporters containing different rs2249650 and rs2268276 alleles showed differential activities in the K562 cell line, a human immortalized myeloid leukemia line. Rs2249650 contributes to reporter activities more than rs2268276. Gel shift assay is consistent with the luciferase assay. Supershift assay indicated that one potential binding protein was PU.1. To sum up, rs2268276 and especially rs2249650 may be qualified as new acute myeloid leukemia susceptibility-associated SNPs.

  6. MALDI-TOF MS analysis of ribosomal proteins coded in S10 and spc operons rapidly classified the Sphingomonadaceae as alkylphenol polyethoxylate-degrading bacteria from the environment.

    Science.gov (United States)

    Hotta, Yudai; Sato, Hiroaki; Hosoda, Akifumi; Tamura, Hiroto

    2012-05-01

    Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) using ribosomal subunit proteins coded in the S10-spc-alpha operon as biomarkers was applied for the classification of the Sphingomonadaceae from the environment. To construct a ribosomal protein database, S10-spc-alpha operon of type strains of the Sphingomonadaceae and their related alkylphenol polyethoxylate (APEO(n) )-degrading bacteria were sequenced using specific primers designed based on nucleotide sequences of genome-sequenced strains. The observed MALDI mass spectra of intact cells were compared with the theoretical mass of the constructed ribosomal protein database. The nine selected biomarkers coded in the S10-spc-alpha operon, L18, L22, L24, L29, L30, S08, S14, S17, and S19, could successfully distinguish the Sphingopyxis terrae NBRC 15098(T) and APEO(n) -degrading bacteria strain BSN20, despite only one base difference in the 16S rRNA gene sequence. This method, named the S10-GERMS (S10-spc-alpha operon gene-encoded ribosomal protein mass spectrum) method, is a significantly useful tool for bacterial discrimination of the Sphingomonadaceae at the strain level and can detect and monitor the main APEO(n) -degrading bacteria in the environment.

  7. Classification of the genus Bacillus based on MALDI-TOF MS analysis of ribosomal proteins coded in S10 and spc operons.

    Science.gov (United States)

    Hotta, Yudai; Sato, Jun; Sato, Hiroaki; Hosoda, Akifumi; Tamura, Hiroto

    2011-05-25

    A rapid bacterial identification method by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) using ribosomal proteins coded in S10 and spc operons as biomarkers, named the S10-GERMS (the S10-spc-alpha operon gene encoded ribosomal protein mass spectrum) method, was applied for the genus Bacillus a Gram-positive bacterium. The S10-GERMS method could successfully distinguish the difference between B. subtilis subsp. subtilis NBRC 13719(T) and B. subtilis subsp. spizizenii NBRC 101239(T) because of the mass difference of 2 ribosomal subunit proteins, despite the difference of only 2 bases in the 16S rRNA gene between them. The 8 selected reliable and reproducible ribosomal subunit proteins without disturbance of S/N level on MALDI-TOF MS analysis, S10, S14, S19, L18, L22, L24, L29, and L30, coded in S10 and spc operons were significantly useful biomarkers for rapid bacterial classification at species and strain levels by the S10-GERMS method of genus Bacillus strains without purification of ribosomal proteins.

  8. The complete mitochondrial genome of the land snail Cornu aspersum (Helicidae: Mollusca: intra-specific divergence of protein-coding genes and phylogenetic considerations within Euthyneura.

    Directory of Open Access Journals (Sweden)

    Juan Diego Gaitán-Espitia

    Full Text Available The complete sequences of three mitochondrial genomes from the land snail Cornu aspersum were determined. The mitogenome has a length of 14050 bp, and it encodes 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. It also includes nine small intergene spacers, and a large AT-rich intergenic spacer. The intra-specific divergence analysis revealed that COX1 has the lower genetic differentiation, while the most divergent genes were NADH1, NADH3 and NADH4. With the exception of Euhadra herklotsi, the structural comparisons showed the same gene order within the family Helicidae, and nearly identical gene organization to that found in order Pulmonata. Phylogenetic reconstruction recovered Basommatophora as polyphyletic group, whereas Eupulmonata and Pulmonata as paraphyletic groups. Bayesian and Maximum Likelihood analyses showed that C. aspersum is a close relative of Cepaea nemoralis, and with the other Helicidae species form a sister group of Albinaria caerulea, supporting the monophyly of the Stylommatophora clade.

  9. An orphan LuxR homolog of Sinorhizobium meliloti affects stress adaptation and competition for nodulation.

    Science.gov (United States)

    Patankar, Arati V; González, Juan E

    2009-02-01

    The Sin/ExpR quorum-sensing system of Sinorhizobium meliloti plays an important role in the symbiotic association with its host plant, Medicago sativa. The LuxR-type response regulators of the Sin system include the synthase (SinI)-associated SinR and the orphan regulator ExpR. Interestingly, the S. meliloti Rm1021 genome codes for four additional putative orphan LuxR homologs whose regulatory roles remain to be identified. These response regulators contain the characteristic domains of the LuxR family of proteins, which include an N-terminal autoinducer/response regulatory domain and a C-terminal helix-turn-helix domain. This study elucidates the regulatory role of one of the orphan LuxR-type response regulators, NesR. Through expression and phenotypic analyses, nesR was determined to affect the active methyl cycle of S. meliloti. Moreover, nesR was shown to influence nutritional and stress response activities in S. meliloti. Finally, the nesR mutant was deficient in competing with the wild-type strain for plant nodulation. Taken together, these results suggest that NesR potentially contributes to the adaptability of S. meliloti when it encounters challenges such as high osmolarity, nutrient starvation, and/or competition for nodulation, thus increasing its chances for survival in the stressful rhizosphere.

  10. Inactivation of the Nuclear Orphan Receptor COUP-TFII by Small Chemicals.

    Science.gov (United States)

    Le Guével, Rémy; Oger, Frédérik; Martinez-Jimenez, Celia P; Bizot, Maud; Gheeraert, Céline; Firmin, François; Ploton, Maheul; Kretova, Miroslava; Palierne, Gaëlle; Staels, Bart; Barath, Peter; Talianidis, Iannis; Lefebvre, Philippe; Eeckhoute, Jérôme; Salbert, Gilles

    2017-01-13

    Chicken ovalbumin upstream promoter-transcription factor II (COUP-TFII/NR2F2) is an orphan member of the nuclear receptor family of transcription factors whose activities are modulated upon binding of small molecules into an hydrophobic ligand-binding pocket (LBP). Although the LBP of COUP-TFII is filled with aromatic amino-acid side chains, alternative modes of ligand binding could potentially lead to regulation of the orphan receptor. Here, we screened a synthetic and natural compound library in a yeast one-hybrid assay and identified 4-methoxynaphthol as an inhibitor of COUP-TFII. This synthetic inhibitor was able to counteract processes either positively or negatively regulated by COUP-TFII in different mammalian cell systems. Hence, we demonstrate that the true orphan receptor COUP-TFII can be targeted by small chemicals which could be used to study the physiological functions of COUP-TFII or to counteract detrimental COUP-TFII activities in various pathological conditions.

  11. Could the Wein fireball be associated to the "orphan" TeV flares ?

    CERN Document Server

    Fraija, Nissim

    2015-01-01

    TeV $\\gamma$-ray detections in flaring states without activity in X-rays from blazars have attracted much attention due to the irregularity of these "orphan" flares. Although the synchrotron self-Compton model has been very successful in explaining the spectral energy distribution and spectral variability of these sources, it has not been able to describe these atypical flaring events. On the other hand, an electron-positron pair plasma at the base of the AGN jet was proposed as the mechanism of bulk acceleration of relativistic outflows. This plasma in quasi-themal equilibrium called Wein fireball emits radiation at MeV-peak energies serving as target of accelerated protons. In this work we describe the "orphan" TeV flares presented in blazars 1ES 1959+650 and Mrk421 assuming geometrical considerations in the jet and evoking the interactions of Fermi-accelerated protons and MeV-peak target photons coming from the Wein fireball. After describing successfully these "orphan" TeV flares, we correlate the TeV $\\g...

  12. Orphans of the HIV epidemic: the challenges from toddlerhood to adolescence and beyond

    Directory of Open Access Journals (Sweden)

    Mamatha M Lala

    2014-11-01

    Full Text Available This presentation focuses on the challenges and practical issues faced each day by orphans of the HIV epidemic and the holistic care that can be provided, as they continue to grow from toddlerhood to adolescence and beyond. An HIV Research Trust Scholarship enabled me to spend quality time in a sub-Saharan African province worst hit by the HIV epidemic and to interact with local experts and learn from mutual clinical experience. It was an immensely useful exercise as the clinical spectra of the diseases are very similar to ours and they have ongoing active research programs very relevant to our setting. India is arguably home to the largest number of orphans of the HIV epidemic. The responsibility of caring for orphaned children overwhelms and pushes many extended families beyond their ability to cope. Many countries are experiencing large increases in the number of families headed by women and grandparents, or even young children. These households are often unable to meet basic needs, and so the number of children living on the streets is rising. Orphaned children are disadvantaged in many devastating ways. In addition to the trauma of witnessing the sickness and death of one or both parents and perhaps siblings, they lack the necessary parental guidance through crucial life-stages of identity formation and transition into adulthood. They are more likely to suffer damage to their cognitive and emotional development and be subjected to; exploitation in terms of labour, social exclusion, extreme economic uncertainty, physical and sexual abuse, illiteracy, malnutrition and illness. Education remains a distant dream. With stigma and discrimination, they lack legal protection, lose inheritance rights, access to essential services available to other community members and professional help from doctors, teachers and lawyers. The implications for these unfortunate children are extraordinarily grave but governments, international agencies, non

  13. Orphans of the HIV epidemic: the challenges from toddlerhood to adolescence and beyond.

    Science.gov (United States)

    Lala, Mamatha M

    2014-01-01

    This presentation focuses on the challenges and practical issues faced each day by orphans of the HIV epidemic and the holistic care that can be provided, as they continue to grow from toddlerhood to adolescence and beyond. An HIV Research Trust Scholarship enabled me to spend quality time in a sub-Saharan African province worst hit by the HIV epidemic and to interact with local experts and learn from mutual clinical experience. It was an immensely useful exercise as the clinical spectra of the diseases are very similar to ours and they have ongoing active research programs very relevant to our setting. India is arguably home to the largest number of orphans of the HIV epidemic. The responsibility of caring for orphaned children overwhelms and pushes many extended families beyond their ability to cope. Many countries are experiencing large increases in the number of families headed by women and grandparents, or even young children. These households are often unable to meet basic needs, and so the number of children living on the streets is rising. Orphaned children are disadvantaged in many devastating ways. In addition to the trauma of witnessing the sickness and death of one or both parents and perhaps siblings, they lack the necessary parental guidance through crucial life-stages of identity formation and transition into adulthood. They are more likely to suffer damage to their cognitive and emotional development and be subjected to; exploitation in terms of labour, social exclusion, extreme economic uncertainty, physical and sexual abuse, illiteracy, malnutrition and illness. Education remains a distant dream. With stigma and discrimination, they lack legal protection, lose inheritance rights, access to essential services available to other community members and professional help from doctors, teachers and lawyers. The implications for these unfortunate children are extraordinarily grave but governments, international agencies, non-governmental organizations

  14. LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock.

    Science.gov (United States)

    Helfer, Anne; Nusinow, Dmitri A; Chow, Brenda Y; Gehrke, Andrew R; Bulyk, Martha L; Kay, Steve A

    2011-01-25

    Circadian clocks provide an adaptive advantage by allowing organisms to anticipate daily and seasonal environmental changes [1, 2]. Eukaryotic oscillators rely on complex hierarchical networks composed of transcriptional and posttranslational regulatory circuits [3]. In Arabidopsis, current representations of the circadian clock consist of three or four interlocked transcriptional feedback loops [3, 4]. Although molecular components contributing to different domains of these circuits have been described, how the loops are connected at the molecular level is not fully understood. Genetic screens previously identified LUX ARRHYTHMO (LUX) [5], also known as PHYTOCLOCK1 (PCL1) [6], an evening-expressed putative transcription factor essential for circadian rhythmicity. We determined the in vitro DNA-binding specificity for LUX by using universal protein binding microarrays; we then demonstrated that LUX directly regulates the expression of PSEUDO RESPONSE REGULATOR9 (PRR9), a major component of the morning transcriptional feedback circuit, through association with the newly discovered DNA binding site. We also show that LUX binds to its own promoter, defining a new negative autoregulatory feedback loop within the core clock. These novel connections between the archetypal loops of the Arabidopsis clock represent a significant advance toward defining the molecular dynamics underlying the circadian network in plants and provide the first mechanistic insight into the molecular function of the previously orphan clock factor LUX.

  15. Arabidopsis thaliana peroxidase N

    DEFF Research Database (Denmark)

    Mirza, Osman Asghar; Henriksen, A; Ostergaard, L

    2000-01-01

    The structure of the neutral peroxidase from Arabidopsis thaliana (ATP N) has been determined to a resolution of 1.9 A and a free R value of 20.5%. ATP N has the expected characteristic fold of the class III peroxidases, with a C(alpha) r.m.s.d. of 0.82 A when compared with horseradish peroxidase C...... (HRP C). HRP C is 54% identical to ATP N in sequence. When the structures of four class III plant peroxidases are superimposed, the regions with structural differences are non-randomly distributed; all are located in one half of the molecule. The architecture of the haem pocket of ATP N is very similar...... to that of HRP C, in agreement with the low small-molecule substrate specificity of all class III peroxidases. The structure of ATP N suggests that the pH dependence of the substrate turnover will differ from that of HRP C owing to differences in polarity of the residues in the substrate-access channel. Since...

  16. Chromosomal proteins of Arabidopsis thaliana.

    Science.gov (United States)

    Moehs, C P; McElwain, E F; Spiker, S

    1988-07-01

    In plants with large genomes, each of the classes of the histones (H1, H2A, H2B, H3 and H4) are not unique polypeptides, but rather families of closely related proteins that are called histone variants. The small genome and preponderance of single-copy DNA in Arabidopsis thaliana has led us to ask if this plant has such families of histone variants. We have thus isolated histones from Arabidopsis and analyzed them on four polyacrylamide gel electrophoretic systems: an SDS system; an acetic acid-urea system; a Triton transverse gradient system; and a two-dimensional system combining SDS and Triton-acetic acid-urea systems. This approach has allowed us to identify all four of the nucleosomal core histones in Arabidopsis and to establish the existence of a set of H2A and H2B variants. Arabidopsis has at least four H2A variants and three H2B variants of distinct molecular weights as assessed by electrophoretic mobility on SDS-polyacrylamide gels. Thus, Arabidopsis displays a diversity in these histones similar to the diversity displayed by plants with larger genomes such as wheat.The high mobility group (HMG) non-histone chromatin proteins have attracted considerable attention because of the evidence implicating them as structural proteins of transcriptionally active chromatin. We have isolated a group of non-histone chromatin proteins from Arabidopsis that meet the operational criteria to be classed as HMG proteins and that cross-react with antisera to HMG proteins of wheat.

  17. Role of traditional healers in psychosocial support in caring for the orphans: A case of Dar-es Salaam City, Tanzania

    Directory of Open Access Journals (Sweden)

    Massila Mariam

    2005-07-01

    Full Text Available Abstract Orphans are an increasing problem in developing countries particularly in Africa; due to the HIV/AIDS pandemic; and needs collective effort in intervention processes by including all stakeholders right from the grass roots level. This paper attempts to present the role of traditional healers in psychosocial support for orphan children in Dar-es-Salaam City with special focus on those whose parents have died because of HIV/AIDS. Six traditional healers who were involved in taking care of orphans were visited at their "vilinge" (traditional clinics. In total they had 72 orphans, 31 being boys and 41 being girls with age range from 3 years to 19. It was learned that traditional healers, besides providing remedies for illnesses/diseases of orphans, they also provided other basic needs. Further, they even provided psychosocial support allowing children to cope with orphan hood life with ease. Traditional healers are living within communities at the grass roots level; and appear unnoticed hidden forces, which are involved in taking care of orphans. This role of traditional healers in taking care of orphans needs to be recognised and even scaling it up by empowering them both in financial terms and training in basic skills of psychosocial techniques in how to handle orphans, in order to reduce discrimination and stigmatisation in the communities where they live.

  18. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus.

    Science.gov (United States)

    Martin, William; Rujan, Tamas; Richly, Erik; Hansen, Andrea; Cornelsen, Sabine; Lins, Thomas; Leister, Dario; Stoebe, Bettina; Hasegawa, Masami; Penny, David

    2002-09-17

    Chloroplasts were once free-living cyanobacteria that became endosymbionts, but the genomes of contemporary plastids encode only approximately 5-10% as many genes as those of their free-living cousins, indicating that many genes were either lost from plastids or transferred to the nucleus during the course of plant evolution. Previous estimates have suggested that between 800 and perhaps as many as 2,000 genes in the Arabidopsis genome might come from cyanobacteria, but genome-wide phylogenetic surveys that could provide direct estimates of this number are lacking. We compared 24,990 proteins encoded in the Arabidopsis genome to the proteins from three cyanobacterial genomes, 16 other prokaryotic reference genomes, and yeast. Of 9,368 Arabidopsis proteins sufficiently conserved for primary sequence comparison, 866 detected homologues only among cyanobacteria and 834 other branched with cyanobacterial homologues in phylogenetic trees. Extrapolating from these conserved proteins to the whole genome, the data suggest that approximately 4,500 of Arabidopsis protein-coding genes ( approximately 18% of the total) were acquired from the cyanobacterial ancestor of plastids. These proteins encompass all functional classes, and the majority of them are targeted to cell compartments other than the chloroplast. Analysis of 15 sequenced chloroplast genomes revealed 117 nuclear-encoded proteins that are also still present in at least one chloroplast genome. A phylogeny of chloroplast genomes inferred from 41 proteins and 8,303 amino acids sites indicates that at least two independent secondary endosymbiotic events have occurred involving red algae and that amino acid composition bias in chloroplast proteins strongly affects plastid genome phylogeny.

  19. Genome-Wide Survey of Nuclear Protein-Coding Markers for Beetle Phylogenetics and Their Application in Resolving both Deep and Shallow-Level Divergences.

    Science.gov (United States)

    Che, Li-Heng; Zhang, Shao-Qian; Li, Yun; Liang, Dan; Pang, Hong; Ślipiński, Adam; Zhang, Peng

    2017-03-03

    Beetles (Coleoptera) are the most diverse and species-rich insect group, representing an impressive explosive radiation in the evolutionary history of insects, and their evolutionary relationships are often difficult to resolve. The amount of "traditional markers" (e.g., mitochondrial genes and nuclear rDNAs) for beetle phylogenetics is small and these markers often lack sufficient signals in resolving relationships for such a rapidly radiating lineage. Here, based on the available genome data of beetles and other related insect species, we performed a genome-wide survey to search nuclear protein-coding (NPC) genes suitable for research on beetle phylogenetics. As a result, we identified 1470 candidate loci, which provided a valuable data resource to the beetle evolutionary research community for NPC marker development. We randomly chose 180 candidate loci from the database to design primers and successfully developed 95 NPC markers which can be PCR amplified from standard genomic DNA extracts. These new nuclear markers are universally applicable across Coleoptera, with an average amplification success rate of 90%. To test the phylogenetic utility, we used them to investigate the backbone phylogeny of Coleoptera (18 families sampled) and the family Coccinellidae (39 species sampled). Both phylogenies are well resolved (average bootstrap support > 95%), showing that our markers can be used to address phylogenetic questions of various evolutionary depth (from species level to family level). In general, the newly developed nuclear markers are much easier to use and more phylogenetically informative than the "traditional markers", and show great potential to expedite resolution of many parts in the Beetle Tree of Life. This article is protected by copyright. All rights reserved.

  20. TYK2 Protein-Coding Variants Protect against Rheumatoid Arthritis and Autoimmunity, with No Evidence of Major Pleiotropic Effects on Non-Autoimmune Complex Traits

    Science.gov (United States)

    Diogo, Dorothée; Bastarache, Lisa; Liao, Katherine P.; Graham, Robert R.; Fulton, Robert S.; Greenberg, Jeffrey D.; Eyre, Steve; Bowes, John; Cui, Jing; Lee, Annette; Pappas, Dimitrios A.; Kremer, Joel M.; Barton, Anne; Coenen, Marieke J. H.; Franke, Barbara; Kiemeney, Lambertus A.; Mariette, Xavier; Richard-Miceli, Corrine; Canhão, Helena; Fonseca, João E.; de Vries, Niek; Tak, Paul P.; Crusius, J. Bart A.; Nurmohamed, Michael T.; Kurreeman, Fina; Mikuls, Ted R.; Okada, Yukinori; Stahl, Eli A.; Larson, David E.; Deluca, Tracie L.; O'Laughlin, Michelle; Fronick, Catrina C.; Fulton, Lucinda L.; Kosoy, Roman; Ransom, Michael; Bhangale, Tushar R.; Ortmann, Ward; Cagan, Andrew; Gainer, Vivian; Karlson, Elizabeth W.; Kohane, Isaac; Murphy, Shawn N.; Martin, Javier; Zhernakova, Alexandra; Klareskog, Lars; Padyukov, Leonid; Worthington, Jane; Mardis, Elaine R.; Seldin, Michael F.; Gregersen, Peter K.; Behrens, Timothy; Raychaudhuri, Soumya; Denny, Joshua C.; Plenge, Robert M.

    2015-01-01

    Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3x10-21), A928V (rs35018800, OR = 0.53, P = 1.2x10-9), and I684S (rs12720356, OR = 0.86, P = 4.6x10-7). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, Pomnibus = 6x10-18), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; Pomnibus = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases. PMID:25849893

  1. Characterization of the Lactobacillus casei group based on the profiling of ribosomal proteins coded in S10-spc-alpha operons as observed by MALDI-TOF MS.

    Science.gov (United States)

    Sato, Hiroaki; Torimura, Masaki; Kitahara, Maki; Ohkuma, Moriya; Hotta, Yudai; Tamura, Hiroto

    2012-10-01

    The taxonomy of the members of the Lactobacillus casei group is complicated because of their phylogenetic similarity and controversial nomenclatural status. In this study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of ribosomal proteins coded in the S10-spc-alpha operon, termed S10-GERMS, was applied in order to classify 33 sample strains belonging to the L. casei group. A total of 14 types of ribosomal protein genes coded in the operon were first sequenced from four type strains of the L. casei group (L. casei JCM 1134(T), L. paracasei subsp. paracasei JCM 8130(T), L. paracasei subsp. tolerans JCM 1171(T), and L. rhamnosus JCM 1136(T)) together with L. casei JCM 11302, which is the former type strain of 'L. zeae'. The theoretical masses of the 14 types of ribosomal proteins used as biomarkers were classified into five types and compiled into a ribosomal protein database. The observed ribosomal proteins of each strain, identified by MALDI-TOF MS, were categorized into types based on their masses, summarized as ribosomal protein profiles, and they were used to construct a phylogenetic tree. The 33 sample strains, together with seven genome-sequenced strains, could be classified into four major clusters, which coincided precisely with the taxa of the (sub)species within the L. casei group. Three "ancient" strains, identified as L. acidophilus and L. casei, were correctly re-identified as L. paracasei subsp. paracasei by S10-GERMS. S10-GERMS would thus appear to be a powerful tool for phylogenetic characterization, with considerable potential for management of culture collections.

  2. TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits.

    Directory of Open Access Journals (Sweden)

    Dorothée Diogo

    Full Text Available Despite the success of genome-wide association studies (GWAS in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples, Exomechip genotyping (n = 18,409 case/control samples and targeted exon-sequencing (n = 2,236 case/controls samples to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2 independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3 x 10(-21, A928V (rs35018800, OR = 0.53, P = 1.2 x 10(-9, and I684S (rs12720356, OR = 0.86, P = 4.6 x 10(-7. Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, Pomnibus = 6 x 10(-18, and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V may also protect against inflammatory bowel disease (IBD; P(omnibus = 0.005. Finally, in a phenome-wide association study (PheWAS assessing >500 phenotypes using electronic medical records (EMR in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases.

  3. High abundance of Serine/Threonine-rich regions predicted to be hyper-O-glycosylated in the secretory proteins coded by eight fungal genomes

    Directory of Open Access Journals (Sweden)

    González Mario

    2012-09-01

    Full Text Available Abstract Background O-glycosylation of secretory proteins has been found to be an important factor in fungal biology and virulence. It consists in the addition of short glycosidic chains to Ser or Thr residues in the protein backbone via O-glycosidic bonds. Secretory proteins in fungi frequently display Ser/Thr rich regions that could be sites of extensive O-glycosylation. We have analyzed in silico the complete sets of putatively secretory proteins coded by eight fungal genomes (Botrytis cinerea, Magnaporthe grisea, Sclerotinia sclerotiorum, Ustilago maydis, Aspergillus nidulans, Neurospora crassa, Trichoderma reesei, and Saccharomyces cerevisiae in search of Ser/Thr-rich regions as well as regions predicted to be highly O-glycosylated by NetOGlyc (http://www.cbs.dtu.dk. Results By comparison with experimental data, NetOGlyc was found to overestimate the number of O-glycosylation sites in fungi by a factor of 1.5, but to be quite reliable in the prediction of highly O-glycosylated regions. About half of secretory proteins have at least one Ser/Thr-rich region, with a Ser/Thr content of at least 40% over an average length of 40 amino acids. Most secretory proteins in filamentous fungi were predicted to be O-glycosylated, sometimes in dozens or even hundreds of sites. Residues predicted to be O-glycosylated have a tendency to be grouped together forming hyper-O-glycosylated regions of varying length. Conclusions About one fourth of secretory fungal proteins were predicted to have at least one hyper-O-glycosylated region, which consists of 45 amino acids on average and displays at least one O-glycosylated Ser or Thr every four residues. These putative highly O-glycosylated regions can be found anywhere along the proteins but have a slight tendency to be at either one of the two ends.

  4. Excluding Orphan Drugs from the 340B Drug Discount Program: the Impact on 18 Critical Access Hospitals

    Directory of Open Access Journals (Sweden)

    Madeline Carpinelli Wallack

    2012-01-01

    Full Text Available Purpose: The 340B Drug Pricing Program is a federal program designed to reduce the amount that safety net providers spend on outpatient drugs. The Patient Protection and Affordable Health Care Act of 2010 extended eligibility for 340B to critical access hospitals (CAHs for all drugs except those designated as “orphan.” Because this policy is unprecedented, this study quantifies the gross financial impact that this exemption has on a group of CAHs. Methods: Drug spending for 2010 from 18 CAHs in Minnesota and Wisconsin are reviewed to identify the prevalence of orphan drug purchases and to calculate the price differentials between the 340B price and the hospitals’ current cost. Results: The 18 CAHs’ purchases of orphan drugs comprise an average of 44% of the total annual drug budgets, but only 5% of units purchased, thus representing a very high proportion of their expenditures. In the aggregate, the 18 hospitals would have saved $3.1 million ($171,000 average per hospital had purchases of drugs with orphan designations been made at the 340B price. Because CAH claims for Medicare are reimbursed on a cost-basis, the Federal government is losing an opportunity for savings. Conclusion: The high prevalence of orphan drug use and considerable potential for cost reduction through the 340B program demonstrate the loss of benefit to the hospitals, Federal government and the states.

  5. Exploiting Natural Variation in Arabidopsis

    NARCIS (Netherlands)

    Molenaar, J.A.; Keurentjes, J.J.B.

    2014-01-01

    Natural variation for many traits is present within the species Arabidopsis thaliana . This chapter describes the use of natural variation to elucidate genes underlying the regulation of quantitative traits. It deals with the development and use of mapping populations, the detection and handling of

  6. Exploiting natural variation in Arabidopsis

    NARCIS (Netherlands)

    J.A. Molenaar; J.J.B. Keurentjes

    2014-01-01

    Natural variation for many traits is present within the species Arabidopsis thaliana. This chapter describes the use of natural variation to elucidate genes underlying the regulation of quantitative traits. It deals with the development and use of mapping populations, the detection and handling of g

  7. The salty tale of Arabidopsis.

    Science.gov (United States)

    Sanders, D

    2000-06-29

    High concentrations of sodium chloride are toxic to most plant species. New insights into the mechanisms by which plants tolerate salt have emerged from the identification of genes in Arabidopsis thaliana that play a critical part in physiological resistance to salt.

  8. The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation.

    Science.gov (United States)

    Mayer, Melanie G; Rödelsperger, Christian; Witte, Hanh; Riebesell, Metta; Sommer, Ralf J

    2015-06-01

    Many nematodes form dauer larvae when exposed to unfavorable conditions, representing an example of phenotypic plasticity and a major survival and dispersal strategy. In Caenorhabditis elegans, the regulation of dauer induction is a model for pheromone, insulin, and steroid-hormone signaling. Recent studies in Pristionchus pacificus revealed substantial natural variation in various aspects of dauer development, i.e. pheromone production and sensing and dauer longevity and fitness. One intriguing example is a strain from Ohio, having extremely long-lived dauers associated with very high fitness and often forming the most dauers in response to other strains' pheromones, including the reference strain from California. While such examples have been suggested to represent intraspecific competition among strains, the molecular mechanisms underlying these dauer-associated patterns are currently unknown. We generated recombinant-inbred-lines between the Californian and Ohioan strains and used quantitative-trait-loci analysis to investigate the molecular mechanism determining natural variation in dauer development. Surprisingly, we discovered that the orphan gene dauerless controls dauer formation by copy number variation. The Ohioan strain has one dauerless copy causing high dauer formation, whereas the Californian strain has two copies, resulting in strongly reduced dauer formation. Transgenic animals expressing multiple copies do not form dauers. dauerless is exclusively expressed in CAN neurons, and both CAN ablation and dauerless mutations increase dauer formation. Strikingly, dauerless underwent several duplications and acts in parallel or downstream of steroid-hormone signaling but upstream of the nuclear-hormone-receptor daf-12. We identified the novel or fast-evolving gene dauerless as inhibitor of dauer development. Our findings reveal the importance of gene duplications and copy number variations for orphan gene function and suggest daf-12 as major target for

  9. The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat

    Directory of Open Access Journals (Sweden)

    Clémence Plissonneau

    2016-10-01

    Full Text Available Fungal plant pathogens rapidly evolve virulence on resistant hosts through mutations in genes encoding proteins that modulate the host immune responses. The mutational spectrum likely includes chromosomal rearrangements responsible for gains or losses of entire genes. However, the mechanisms creating adaptive structural variation in fungal pathogen populations are poorly understood. We used complete genome assemblies to quantify structural variants segregating in the highly polymorphic fungal wheat pathogen Zymoseptoria tritici. The genetic basis of virulence in Z. tritici is complex, and populations harbor significant genetic variation for virulence; hence, we aimed to identify whether structural variation led to functional differences. We combined single-molecule real-time sequencing, genetic maps, and transcriptomics data to generate a fully assembled and annotated genome of the highly virulent field isolate 3D7. Comparative genomics analyses against the complete reference genome IPO323 identified large chromosomal inversions and the complete gain or loss of transposable-element clusters, explaining the extensive chromosomal-length polymorphisms found in this species. Both the 3D7 and IPO323 genomes harbored long tracts of sequences exclusive to one of the two genomes. These orphan regions contained 296 genes unique to the 3D7 genome and not previously known for this species. These orphan genes tended to be organized in clusters and showed evidence of mutational decay. Moreover, the orphan genes were enriched in genes encoding putative effectors and included a gene that is one of the most upregulated putative effector genes during wheat infection. Our study showed that this pathogen species harbored extensive chromosomal structure polymorphism that may drive the evolution of virulence.

  10. Child work and labour among orphaned and abandoned children in five low and middle income countries

    Directory of Open Access Journals (Sweden)

    Pence Brian

    2011-01-01

    Full Text Available Abstract Background The care and protection of the estimated 143,000,000 orphaned and abandoned children (OAC worldwide is of great importance to global policy makers and child service providers in low and middle income countries (LMICs, yet little is known about rates of child labour among OAC, what child and caregiver characteristics predict child engagement in work and labour, or when such work infers with schooling. This study examines rates and correlates of child labour among OAC and associations of child labour with schooling in a cohort of OAC in 5 LMICs. Methods The Positive Outcomes for Orphans (POFO study employed a two-stage random sampling survey methodology to identify 1480 single and double orphans and children abandoned by both parents ages 6-12 living in family settings in five LMICs: Cambodia, Ethiopia, India, Kenya, and Tanzania. Regression models examined child and caregiver associations with: any work versus no work; and with working Results The majority of OAC (60.7% engaged in work during the past week, and of those who worked, 17.8% (10.5% of the total sample worked 28 or more hours. More than one-fifth (21.9%; 13% of the total sample met UNICEF's child labour definition. Female OAC and those in good health had increased odds of working. OAC living in rural areas, lower household wealth and caregivers not earning an income were associated with increased child labour. Child labour, but not working fewer than 28 hours per week, was associated with decreased school attendance. Conclusions One in seven OAC in this study were reported to be engaged in child labour. Policy makers and social service providers need to pay close attention to the demands being placed on female OAC, particularly in rural areas and poor households with limited income sources. Programs to promote OAC school attendance may need to focus on the needs of families as well as the OAC.

  11. РSYCHOLOGICAL AND PSYCHOPHYSIOLOGICAL CHARACTERISTICS OF ORPHANS AND CHILDREN WITHOUT PARENTAL CARE

    Directory of Open Access Journals (Sweden)

    Н. А. Киселева

    2014-01-01

    Full Text Available The article analyzes the psychological and psychophy-siological characteristics of children living in the Children’s Village-SOS and in the Children’s Home. Particular emotional and cognitive areas, self image, creativity, mental stress and neurotic tendencies in orphans and children without parental care are characterized in the article. Age and gender differences in the parameters studied are detected.Purpose. The purpose is to discoverage and gender aspects of the psychological and psychophysiological characteristics of children of orphans and children without parental care living in the Children’s Village-SOS and in the Children’s Home.Methodology. Empirical research of gender particular features of psychic state of alarmness of adopted children with the help of testing.Results. The significant gender differences in terms of phobias and fears were revealed; the significant gender differences on the scale of the emotional content of images were revealed; the study revealed the trends toward significant difference by gender in the manifestation of sleep disorders and autonomic dysfunction;the significant age-related differences in terms of increased anxiety, autonomic dysfunction, eating disorders were revealed.Practical implications. The results are of interest to the science workers of age psychology, gender psychology, social psychology, to the workers of the children’s institutions and to the organizations occupied with medical-social-psychological-pedagogycal maintenance of orphans and children without parental care.Purchase on Elibrary.ru > Buy now

  12. Impact of domestic care environment on trauma and posttraumatic stress disorder among orphans in western Kenya.

    Directory of Open Access Journals (Sweden)

    Lukoye Atwoli

    Full Text Available The aim of this study was to determine the impact of the domestic care environment on the prevalence of potentially traumatic events (PTEs and posttraumatic stress disorder (PTSD among orphaned and separated children in Uasin Gishu County, western Kenya.A total of 1565 (55.5% male orphaned and separated adolescents aged 10-18 years (mean 13.8 years, sd 2.2, were assessed for PTSD and PTEs including bullying, physical abuse and sexual abuse. In this sample, 746 lived in extended family households, 746 in Charitable Children's Institutions (CCIs, and 73 on the street. Posttraumatic stress symptom (PTSS scores and PTSD were assessed using the Child PTSD Checklist.Bullying was the commonest PTE in all domestic care environments, followed by physical and sexual abuse. All PTEs were commonest among the street youth followed by CCIs. However, sexual abuse was more prevalent in households than in CCIs. Prevalence of PTSD was highest among street youth (28.8%, then households (15.0% and CCIs (11.5%. PTSS scores were also highest among street youth, followed by CCIs and households. Bullying was associated with higher PTSS scores and PTSD odds than either sexual or physical abuse.This study demonstrated differences in distribution of trauma and PTSD among orphaned and separated children in different domestic care environments, with street youth suffering more than those in CCIs or households. Interventions are needed to address bullying and sexual abuse, especially in extended family households. Street youth, a heretofore neglected population, are urgently in need of dedicated mental health services and support.

  13. The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation.

    Directory of Open Access Journals (Sweden)

    Melanie G Mayer

    2015-06-01

    Full Text Available Many nematodes form dauer larvae when exposed to unfavorable conditions, representing an example of phenotypic plasticity and a major survival and dispersal strategy. In Caenorhabditis elegans, the regulation of dauer induction is a model for pheromone, insulin, and steroid-hormone signaling. Recent studies in Pristionchus pacificus revealed substantial natural variation in various aspects of dauer development, i.e. pheromone production and sensing and dauer longevity and fitness. One intriguing example is a strain from Ohio, having extremely long-lived dauers associated with very high fitness and often forming the most dauers in response to other strains' pheromones, including the reference strain from California. While such examples have been suggested to represent intraspecific competition among strains, the molecular mechanisms underlying these dauer-associated patterns are currently unknown. We generated recombinant-inbred-lines between the Californian and Ohioan strains and used quantitative-trait-loci analysis to investigate the molecular mechanism determining natural variation in dauer development. Surprisingly, we discovered that the orphan gene dauerless controls dauer formation by copy number variation. The Ohioan strain has one dauerless copy causing high dauer formation, whereas the Californian strain has two copies, resulting in strongly reduced dauer formation. Transgenic animals expressing multiple copies do not form dauers. dauerless is exclusively expressed in CAN neurons, and both CAN ablation and dauerless mutations increase dauer formation. Strikingly, dauerless underwent several duplications and acts in parallel or downstream of steroid-hormone signaling but upstream of the nuclear-hormone-receptor daf-12. We identified the novel or fast-evolving gene dauerless as inhibitor of dauer development. Our findings reveal the importance of gene duplications and copy number variations for orphan gene function and suggest daf-12 as

  14. Role of Orphan Nuclear Receptor DAX-1/NR0B1 in Development, Physiology, and Disease

    Directory of Open Access Journals (Sweden)

    Enzo Lalli

    2014-01-01

    Full Text Available DAX-1/NR0B1 is an unusual orphan receptor that has a pivotal role in the development and function of steroidogenic tissues and of the reproductive axis. Recent studies have also indicated that this transcription factor has an important function in stem cell biology and in several types of cancer. Here I critically review the most important findings on the role of DAX-1 in development, physiology, and disease of endocrine tissues since the cloning of its gene twenty years ago.

  15. Determinants for successful marketing authorisation of orphan medicinal products in the EU.

    Science.gov (United States)

    Putzeist, Michelle; Heemstra, Harald E; Garcia, Jordi Llinares; Mantel-Teeuwisse, Aukje K; Gispen-De Wied, Christine C; Hoes, Arno W; Leufkens, Hubert G M

    2012-04-01

    In 2010, the European Regulation for Orphan Medicinal Products (OMPs) was in force for ten years. In this study we assessed possible determinants of applications for OMPs in the EU since 2000 that are associated with a successful marketing authorisation. Our analysis shows that clinical trial characteristics such as demonstrating convincing evidence of a beneficial effect on the primary endpoint, the selection of a clinically relevant endpoint, providing RCT data as pivotal study evidence and the submission of sound dose finding data are critical success factors. In addition, high medical need seems to counterweigh uncertainties about the scientific evidence in the benefit-risk assessment of OMPs.

  16. Are female orphans at risk for early marriage, early sexual debut, and teen pregnancy? Evidence from sub-Saharan Africa.

    Science.gov (United States)

    Palermo, Tia; Peterman, Amber

    2009-06-01

    Female orphans are widely cited as being at risk for early marriage, early childbearing, and risky sexual behavior; however, to date no studies have examined these linkages using population-level data across multiple countries. This study draws from recent Demographic and Health Surveys from ten sub-Saharan African countries to examine the relationship between orphanhood status and measures of early marriage, early sexual debut, and teen pregnancy among adolescent girls aged 15 to 17. Results indicate that, overall, little association is found between orphanhood and early marriage or teen pregnancy, whereas evidence from seven countries supports associations between orphanhood and early sexual debut. Findings are sensitive to the use of multivariate models, type of orphan, and country setting. Orphanhood status alone may not be a sufficient targeting mechanism for addressing these outcomes in many countries; a broader, multidimensional targeting scheme including orphan type, schooling, and poverty measures would be more robust in identifying and aiding young women at risk.

  17. An Orphan LuxR Homolog of Sinorhizobium meliloti Affects Stress Adaptation and Competition for Nodulation▿ †

    OpenAIRE

    Patankar, Arati V.; González, Juan E.

    2008-01-01

    The Sin/ExpR quorum-sensing system of Sinorhizobium meliloti plays an important role in the symbiotic association with its host plant, Medicago sativa. The LuxR-type response regulators of the Sin system include the synthase (SinI)-associated SinR and the orphan regulator ExpR. Interestingly, the S. meliloti Rm1021 genome codes for four additional putative orphan LuxR homologs whose regulatory roles remain to be identified. These response regulators contain the characteristic domains of the L...

  18. SOCIAL RIGHT AND ITS APPLICATION FOR MARTYR'S WIDOW, ORPHAN AND WAR VETERAN-VICTIM WHO NEEDED SPECIAL CARE AND PROTECTION

    Directory of Open Access Journals (Sweden)

    Bülent KARA

    2010-04-01

    Full Text Available In respect to social state principle, the 61’ st article of the Constitution is allocated for disadvantaged people. Because of special situations of Turkey, social rights of the casualties, the orphans and the widows, the handicapped and the veterans were determined and organized in this article. The main aim of this study is to evaluate the laws, policies and problems of the casualties, the orphans and the widows, the handicapped and the veterans who were preserved by the Constitution and some laws.

  19. Characterization of radioactive orphan sources by gamma spectrometry; Caracterizacion de fuentes huerfanas radiactivas por espectrometria gamma

    Energy Technology Data Exchange (ETDEWEB)

    Cruz W, H., E-mail: wcruz@ipen.gob.pe [Instituto Peruano de Energia Nuclear (PGRR/IPEN), Lima (Peru). Planta de Gestion de Residuos Radiactivos

    2013-07-01

    The sealed radioactive sources are widely applicable in industry. They must have a permanent control and must be registered with the Technical Office of the National Authority (OTAN). However, at times it has identified the presence of abandoned sealed sources unknown to the owner. These sources are called 'orphan sources'. Of course these sources represent a high potential risk because accidents can trigger dire consequences depending on your activity and chemical form in which it presents the radioisotope. This paper describes the process and the actions taken to characterize two orphan radioactive sources from the smelter a Aceros Arequipa. For characterization we used a gamma spectrometry system using a detector NaI(Tl) 3″ x 3″ with a multichannel analyzer Nucleus PCA-II. The radioisotope identified was cesium - 137 ({sup 137}Cs) in both cases. Fortunately, the sources maintained their integrity would otherwise have generated significant pollution considering the chemical form of the radioisotope and easy dispersion. (author)

  20. Government-NGO collaboration and sustainability of orphans and vulnerable children projects in southern Africa.

    Science.gov (United States)

    Rosenberg, Alana; Hartwig, Kari; Merson, Michael

    2008-02-01

    Given current donor attention to orphans and children made vulnerable by HIV/AIDS, and the need for a new framework that recognizes the complementary roles of nations and non-governmental organizations (NGOs), this analysis reviews NGO-operated community-based orphans and vulnerable children (OVC) projects in Botswana, Lesotho, Namibia, South Africa, and Swaziland. There has been a lack of attention within the field of evaluation to inter-organizational relationships, specifically those with government agencies, as a factor in sustainability. We analyzed evaluations of nine OVC projects funded by the Bristol-Myers Squibb Foundation for the influence of government-NGO collaboration on project sustainability. For eight of the nine projects, evaluations provided evidence of the importance of the government partnership for sustainability. Government collaboration was important in projects designed to help families access government grants, initiate community-based solutions, and advocate for OVC rights through legislation. Government partnerships were also critical to the sustainability of two projects involved in placing children in foster care, but these showed signs of tension with government partners. In addition to the more common factors associated with sustainability, such as organizational characteristics, donors and NGOs should concentrate on developing strong partnerships with local and national government agencies for the sustainability of their projects.

  1. The orphan nuclear receptor SHP regulates PGC-1alpha expression and energy production in brown adipocytes.

    Science.gov (United States)

    Wang, Li; Liu, Jun; Saha, Pradip; Huang, Jiansheng; Chan, Lawrence; Spiegelman, Bruce; Moore, David D

    2005-10-01

    Brown adipocytes increase energy production in response to induction of PGC-1alpha, a dominant regulator of energy metabolism. We have found that the orphan nuclear receptor SHP (NR0B2) is a negative regulator of PGC-1alpha expression in brown adipocytes. Mice lacking SHP show increased basal expression of PGC-1alpha, increased energy expenditure, and resistance to diet-induced obesity. Increased PGC-1alpha expression in SHP null brown adipose tissue is not due to beta-adrenergic activation, since it is also observed in primary cultures of SHP(-/-) brown adipocytes that are not exposed to such stimuli. In addition, acute inhibition of SHP expression in cultured wild-type brown adipocytes increases basal PGC-1alpha expression, and SHP overexpression in SHP null brown adipocytes decreases it. The orphan nuclear receptor ERRgamma is expressed in BAT and its transactivation of the PGC-1alpha promoter is potently inhibited by SHP. We conclude that SHP functions as a negative regulator of energy production in BAT.

  2. The small SLC43 family: facilitator system l amino acid transporters and the orphan EEG1.

    Science.gov (United States)

    Bodoy, Susanna; Fotiadis, Dimitrios; Stoeger, Claudia; Kanai, Yoshikatsu; Palacín, Manuel

    2013-01-01

    The SLC43 family is composed of only three genes coding for the plasma membrane facilitator system l amino acid transporters LAT3 (SLC43A1; TC 2.A.1.44.1) and LAT4 (SLC43A2; TC 2.A.1.44.2), and the orphan protein EEG1 (SLC43A3; TC 2.A.1.44.3). Besides the known mechanism of transport of LAT3 and LAT4, their physiological roles still remain quite obscure. Morphants suggested a role of LAT3 in renal podocyte development in zebrafish. Expression in liver and skeletal muscle, and up-regulation by starvation suggest a role of LAT3 in the flux of branched-chain amino acids (BCAAs) from liver and skeletal muscle to the bloodstream. Finally, LAT3 is up-regulated in androgen-dependent cancers, suggesting a role in mTORC1 signaling in this type of tumors. In addition, LAT4 might contribute to the transfer of BCAAs from mother to fetus. Unfortunately, the EEG1 mouse model (EEG1(Y221∗)) described here has not yet offered a clue to the physiological role of this orphan protein.

  3. Fatal herpesvirus hemorrhagic disease in wild and orphan asian elephants in southern India.

    Science.gov (United States)

    Zachariah, Arun; Zong, Jian-Chao; Long, Simon Y; Latimer, Erin M; Heaggans, Sarah Y; Richman, Laura K; Hayward, Gary S

    2013-04-01

    Up to 65% of deaths of young Asian elephants (Elephas maximus) between 3 mo and 15 yr of age in Europe and North America over the past 20 yr have been attributed to hemorrhagic disease associated with a novel DNA virus called elephant endotheliotropic herpesvirus (EEHV). To evaluate the potential role of EEHV in suspected cases of a similar lethal acute hemorrhagic disease occurring in southern India, we studied pathologic tissue samples collected from field necropsies. Nine cases among both orphaned camp and wild Asian elephants were identified by diagnostic PCR. These were subjected to detailed gene subtype DNA sequencing at multiple PCR loci, which revealed seven distinct strains of EEHV1A and one of EEHV1B. Two orphan calves that died within 3 days of one another at the same training camp had identical EEHV1A DNA sequences, indicating a common epidemiologic source. However, the high level of EEHV1 subtype genetic diversity found among the other Indian strains matches that among over 30 EEHV1 strains that have been evaluated from Europe and North America. These results argue against the previous suggestions that this is just a disease of captive elephants and that the EEHV1 virus has crossed recently from African elephant (Loxodonta africana) hosts to Asian elephants. Instead, both the virus and the disease are evidently widespread in Asia and, despite the disease severity, Asian elephants appear to be the ancient endogenous hosts of both EEHV1A and EEHV1B.

  4. Extremely Soft X-ray Flash as the indicator of off-axis orphan GRB afterglow

    CERN Document Server

    Urata, Yuji; Yamazaki, Ryo; Sakamoto, Takanori

    2015-01-01

    We verified the off-axis jet model of X-ray flashes (XRFs) and examined a discovery of off-axis orphan gamma-ray burst (GRBs) afterglows. The XRF sample was selected on the basis of the following three factors: (1) a constraint on the lower peak energy of the prompt spectrum $E^{src}_{obs}$, (2) redshift measurements, and (3) multi-color observations of an earlier (or brightening) phase. XRF020903 was the only sample selected basis of these criteria. A complete optical multi-color afterglow light curve of XRF020903 obtained from archived data and photometric results in literature showed an achromatic brightening around 0.7 days. An off-axis jet model with a large observing angle (0.21 rad, which is twice the jet opening half-angle, $\\theta_{jet}$) can naturally describe the achromatic brightening and the prompt X-ray spectral properties. This result indicates the existence of off-axis orphan GRB afterglow light curves. Events with a larger viewing angle ($>\\sim2\\theta_{jet}$) could be discovered using an 8-m ...

  5. The Orphan Nuclear Receptor TR4 Is a Vitamin A-activated Nuclear Receptor

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, X. Edward; Suino-Powell, Kelly M.; Xu, Yong; Chan, Cee-Wah; Tanabe, Osamu; Kruse, Schoen W.; Reynolds, Ross; Engel, James Douglas; Xu, H. Eric (Michigan-Med); (Van Andel)

    2015-11-30

    Testicular receptors 2 and 4 (TR2/4) constitute a subgroup of orphan nuclear receptors that play important roles in spermatogenesis, lipid and lipoprotein regulation, and the development of the central nervous system. Currently, little is known about the structural features and the ligand regulation of these receptors. Here we report the crystal structure of the ligand-free TR4 ligand binding domain, which reveals an autorepressed conformation. The ligand binding pocket of TR4 is filled by the C-terminal half of helix 10, and the cofactor binding site is occupied by the AF-2 helix, thus preventing ligand-independent activation of the receptor. However, TR4 exhibits constitutive transcriptional activity on multiple promoters, which can be further potentiated by nuclear receptor coactivators. Mutations designed to disrupt cofactor binding, dimerization, or ligand binding substantially reduce the transcriptional activity of this receptor. Importantly, both retinol and retinoic acid are able to promote TR4 to recruit coactivators and to activate a TR4-regulated reporter. These findings demonstrate that TR4 is a ligand-regulated nuclear receptor and suggest that retinoids might have a much wider regulatory role via activation of orphan receptors such as TR4.

  6. The orphan nuclear receptor TR4 is a vitamin A-activated nuclear receptor.

    Science.gov (United States)

    Zhou, X Edward; Suino-Powell, Kelly M; Xu, Yong; Chan, Cee-Wah; Tanabe, Osamu; Kruse, Schoen W; Reynolds, Ross; Engel, James Douglas; Xu, H Eric

    2011-01-28

    Testicular receptors 2 and 4 (TR2/4) constitute a subgroup of orphan nuclear receptors that play important roles in spermatogenesis, lipid and lipoprotein regulation, and the development of the central nervous system. Currently, little is known about the structural features and the ligand regulation of these receptors. Here we report the crystal structure of the ligand-free TR4 ligand binding domain, which reveals an autorepressed conformation. The ligand binding pocket of TR4 is filled by the C-terminal half of helix 10, and the cofactor binding site is occupied by the AF-2 helix, thus preventing ligand-independent activation of the receptor. However, TR4 exhibits constitutive transcriptional activity on multiple promoters, which can be further potentiated by nuclear receptor coactivators. Mutations designed to disrupt cofactor binding, dimerization, or ligand binding substantially reduce the transcriptional activity of this receptor. Importantly, both retinol and retinoic acid are able to promote TR4 to recruit coactivators and to activate a TR4-regulated reporter. These findings demonstrate that TR4 is a ligand-regulated nuclear receptor and suggest that retinoids might have a much wider regulatory role via activation of orphan receptors such as TR4.

  7. Reference: 710 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available n factor family in Arabidopsis (Arabidopsis thaliana). Treatment with abscisic acid (ABA) induced AtMYB44 tr...anscript accumulation within 30 min. The gene was also activated under various abiotic stre...sses, such as dehydration, low temperature, and salinity. In transgenic Arabidopsis carrying an At...MYB44 promoter-driven beta-glucuronidase (GUS) construct, strong GUS activity was observed in the vasculature... and leaf epidermal guard cells. Transgenic Arabidopsis overexpressing AtMYB44 is more

  8. Strategies for Supporting Orphans and Vulnerable Children: An Exploratory Study of an Exemplary Model of Care in Kenya

    Science.gov (United States)

    Mears, Melynda; Singletary, Jon; Rogers, Rob

    2011-01-01

    This qualitative study explored the extent to which programs in a religiously affiliated agency in Kenya incorporate 12 internationally sanctioned strategies for supporting orphans and vulnerable children in Sub-Saharan Africa (Olson, Knight, & Foster, 2006). The results indicated that all 12 strategies were being employed, though to varying…

  9. Search campaign orphan sources conducted by Enresa; Campana de busqueda de fuentes huerfanas llevada a cabo por Enresa

    Energy Technology Data Exchange (ETDEWEB)

    Alcaide Tranas, E.; Ortiz Ramis, T.; Orta Navarro, M. C.; Rueda Fresnedo, C.

    2011-07-01

    This paper sets out the requirements for the control of high activity sources and the possibility of a campaign to recover orphan sources. National authorities undertook this campaign to the National Company for Radioactive Waste (ENRESA) and grown for three years (2007-2009).

  10. Differential transcription of the orphan receptor RORbeta in nuclear extracts derived from Neuro2A and HeLa cells.

    NARCIS (Netherlands)

    Gawlas, K.; Stunnenberg, H.G.

    2001-01-01

    An important model system for studying the process leading to productive transcription is provided by the superfamily of nuclear receptors, which are for the most part ligand-controlled transcription factors. Over the past years several 'orphan' nuclear receptors have been isolated for which no liga

  11. Hubble Space Telescope Proper Motions of Individual Stars in Stellar Streams: Orphan, Sagittarius, Lethe, and the New "Parallel’ Stream"

    Science.gov (United States)

    Sohn, Sangmo Tony; van der Marel, Roeland P.; Kallivayalil, Nitya; Majewski, Steven R.; Besla, Gurtina; Carlin, Jeffrey L.; Law, David R.; Siegel, Michael H.; Anderson, Jay

    2016-12-01

    We present a multi-epoch Hubble Space Telescope (HST) study of stellar proper motions (PMs) for four fields along the Orphan Stream. We determine absolute PMs of several individual stars per target field using established techniques that utilize distant background galaxies to define a stationary reference frame. Five Orphan Stream stars are identified in one of the four fields based on combined color-magnitude and PM information. The average PM is consistent with the existing model of the Orphan Stream by Newberg et al. In addition to the Orphan Stream stars, we detect stars that likely belong to other stellar streams. To identify which stellar streams these stars belong to, we examine the 2d bulk motion of each group of stars on the sky by subtracting the PM contribution of the solar motion (which is a function of position on the sky and distance) from the observed PMs, and comparing the vector of net motion with the spatial extent of known stellar streams. By doing this, we identify candidate stars in the Sagittarius and Lethe streams, and a newly found stellar stream at a distance of ˜17 kpc, which we tentatively name the “Parallel Stream.” Together with our Sagittarius stream study, this work demonstrates that even in the Gaia era, HST will continue to be advantageous in measuring PMs of old stellar populations on a star-by-star basis, especially for distances beyond ˜10 kpc.

  12. Grief-Processing-Based Psychological Intervention for Children Orphaned by AIDS in Central China: A Pilot Study

    Science.gov (United States)

    Lin, Xiuyun; Fang, Xiaoyi; Chi, Peilian; Li, Xiaoming; Chen, Wenrui; Heath, Melissa Allen

    2014-01-01

    A group of 124 children orphaned by AIDS (COA), who resided in two orphanages funded by the Chinese government, participated in a study investigating the efficacy of a grief-processing-based psychological group intervention. This psychological intervention program was designed to specifically help COA process their grief and reduce their…

  13. 78 FR 51732 - The Food and Drug Administration/European Medicines Agency Orphan Product Designation and Grant...

    Science.gov (United States)

    2013-08-21

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration The Food and Drug Administration/European Medicines Agency Orphan Product Designation and Grant Public Workshop AGENCY: Food and Drug Administration, HHS. ACTION: Notice of public workshop. The Food and...

  14. 77 FR 52744 - Food and Drug Administration/European Medicines Agency Orphan Product Designation and Grant Workshop

    Science.gov (United States)

    2012-08-30

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration Food and Drug Administration/European Medicines Agency Orphan Product Designation and Grant Workshop AGENCY: Food and Drug Administration, HHS. ACTION: Notice of meeting. The Food and Drug Administration's...

  15. Hubble Space Telescope Proper Motions of Individual Stars in Stellar Streams: Orphan, Sagittarius, Lethe, and the New "Parallel" Stream

    CERN Document Server

    Sohn, Sangmo Tony; Kallivayalil, Nitya; Majewski, Steven R; Besla, Gurtina; Carlin, Jeffrey L; Law, David R; Siegel, Michael H; Anderson, Jay

    2016-01-01

    We present a multi-epoch Hubble Space Telescope (HST) study of stellar proper motions (PMs) for four fields along the Orphan Stream. We determine absolute PMs of several individual stars per target field using established techniques that utilize distant background galaxies to define a stationary reference frame. Five Orphan Stream stars are identified in one of the four fields based on combined color-magnitude and PM information. The average PM is consistent with the existing model of the Orphan stream by Newberg et al. In addition to the Orphan stream stars, we detect stars that likely belong to other stellar streams. To identify which stellar streams these stars belong to, we examine the 2-d bulk motion of each group of stars on the sky by subtracting the PM contribution of the solar motion (which is a function of position on the sky and distance) from the observed PMs, and comparing the vector of net motion with the spatial extent of known stellar streams. By doing this, we identify candidate stars in the ...

  16. Novel Agonist Bioisosteres and Common Structure-Activity Relationships for The Orphan G Protein-Coupled Receptor GPR139

    DEFF Research Database (Denmark)

    Shehata, Mohamed A; Jensen, Anne Cathrine Nøhr; Lissa, Delphine;

    2016-01-01

    GPR139 is an orphan class A G protein-coupled receptor found mainly in the central nervous system. It has its highest expression levels in the hypothalamus and striatum, regions regulating metabolism and locomotion, respectively, and has therefore been suggested as a potential target for obesity...

  17. Orphan Sources and Fresh Fallout: Virtual Exercise in Mobile Measurement (ORPEX)

    Energy Technology Data Exchange (ETDEWEB)

    Dowdall, M. (Norwegian Radiation Protection Authority, OEsteraas (Norway)); Smethurst, M.A. (Univ. of Exeter and Avalonia Geophysics, Cornwall Campus, Penryn (United Kingdom)); Andersson, K. (Technical Univ. of Denmark. Risoe National Lab. for Sustainable Energy, Roskilde (Denmark)); Aage, H.K. (Danish Emergency Management Agency, Birkeroed (Denmark)); Palsson, S.E. (Icelandic Radiation Protection Institute, Reykjavik (Iceland))

    2011-10-15

    In recent years carborne gamma spectrometry has expanded from its role as a geological survey platform to serving as a useful asset in the field of emergency response to radiological and nuclear situations. Its two main applications are searching for orphan sources and for surveying in the aftermath of an accident involving the release of radioactive materials. Despite this expansion, the opportunities for gaining practical experience in the field are limited by cost considerations and practicability. These limitations are exacerbated by the fact that data generated and displayed in the field differ significantly from gamma spectral data generated in a laboratory environment. As a means of exercising existing emergency measuring/surveying capability and introducing carborne measurements to a larger group, a virtual exercise was devised. The exercise ORPEX (Orphan Sources and Fresh Fallout Virtual Exercise in Mobile Measurement) featured two typical emergency scenarios in which carborne measuring systems might be deployed: firstly a search for multiple orphan sources and secondly surveying to delineate patchy fallout from a local release point. In the first scenario, synthetic spectral data were generated for imaginary point sources and inserted into genuine carborne measurements from in the Trondheim area of Norway. Participants were presented with a typical software tool and data in a range of typical formats and asked to report the source locations and isotopes within a time limit. In the second scenario, synthetic spectral data representing fallout from a local fire involving radioactive material were added to real carborne data from the Trondheim area. Participants were asked to produce maps that identify and characterise the regions of contamination within the same time limit. Fourteen individual organisations from seven different countries supplied results. Results from participants indicate that for strong sources of isotopes with simple spectra featuring

  18. An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community

    Science.gov (United States)

    The future bioinformatics needs of the Arabidopsis community as well as those of other scientific communities that depend on Arabidopsis resources were discussed at a pair of recent meetings held by the Multinational Arabidopsis Steering Committee (MASC) and the North American Arabidopsis Steering C...

  19. Arabidopsis CDS blastp result: AK240652 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK240652 J023098G11 At5g63090.2 68418.m07919 LOB domain protein / lateral organ boundaries... protein (LOB) identical to LOBa [Arabidopsis thaliana] GI:17484100, SP|Q9FML4 LATERAL ORGAN BOUNDARIES protein {Arabidopsis thaliana} 1e-13 ...

  20. Arabidopsis CDS blastp result: AK241761 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241761 J065205C18 At5g63090.1 68418.m07918 LOB domain protein / lateral organ boundaries... protein (LOB) identical to LOBa [Arabidopsis thaliana] GI:17484100, SP|Q9FML4 LATERAL ORGAN BOUNDARIES protein {Arabidopsis thaliana} 5e-32 ...

  1. Arabidopsis CDS blastp result: AK240652 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK240652 J023098G11 At5g63090.1 68418.m07918 LOB domain protein / lateral organ boundaries... protein (LOB) identical to LOBa [Arabidopsis thaliana] GI:17484100, SP|Q9FML4 LATERAL ORGAN BOUNDARIES protein {Arabidopsis thaliana} 1e-13 ...

  2. Arabidopsis CDS blastp result: AK240652 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK240652 J023098G11 At5g63090.4 68418.m07921 LOB domain protein / lateral organ boundaries... protein (LOB) identical to LOBa [Arabidopsis thaliana] GI:17484100, SP|Q9FML4 LATERAL ORGAN BOUNDARIES protein {Arabidopsis thaliana} 1e-13 ...

  3. Arabidopsis CDS blastp result: AK241761 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241761 J065205C18 At5g63090.3 68418.m07920 LOB domain protein / lateral organ boundaries... protein (LOB) identical to LOBa [Arabidopsis thaliana] GI:17484100, SP|Q9FML4 LATERAL ORGAN BOUNDARIES protein {Arabidopsis thaliana} 5e-32 ...

  4. Arabidopsis CDS blastp result: AK241761 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241761 J065205C18 At5g63090.2 68418.m07919 LOB domain protein / lateral organ boundaries... protein (LOB) identical to LOBa [Arabidopsis thaliana] GI:17484100, SP|Q9FML4 LATERAL ORGAN BOUNDARIES protein {Arabidopsis thaliana} 5e-32 ...

  5. Arabidopsis CDS blastp result: AK241761 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241761 J065205C18 At5g63090.4 68418.m07921 LOB domain protein / lateral organ boundaries... protein (LOB) identical to LOBa [Arabidopsis thaliana] GI:17484100, SP|Q9FML4 LATERAL ORGAN BOUNDARIES protein {Arabidopsis thaliana} 5e-32 ...

  6. Arabidopsis CDS blastp result: AK240652 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK240652 J023098G11 At5g63090.3 68418.m07920 LOB domain protein / lateral organ boundaries... protein (LOB) identical to LOBa [Arabidopsis thaliana] GI:17484100, SP|Q9FML4 LATERAL ORGAN BOUNDARIES protein {Arabidopsis thaliana} 1e-13 ...

  7. Arabidopsis CDS blastp result: AK105527 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK105527 001-127-G05 At5g63090.4 LOB domain protein / lateral organ boundaries prot...ein (LOB) identical to LOBa [Arabidopsis thaliana] GI:17484100, SP|Q9FML4 LATERAL ORGAN BOUNDARIES protein {Arabidopsis thaliana} 3e-52 ...

  8. Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

    Science.gov (United States)

    Zhang, Xiaorong

    2009-01-01

    This article describes a new approach to teaching bioinformatics using "Arabidopsis" genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bioinformatics, using "Arabidopsis" leucine-rich repeat receptor-like kinase (LRR…

  9. Arabidopsis CDS blastp result: AK240730 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK240730 J043030K09 At2g32440.1 68415.m03963 ent-kaurenoic acid hydroxylase, putati...ve / cytochrome P450, putative identical to ent-kaurenoic acid hydroxylase / cytochrome P450 CYP88A (GI:1302...1856) [Arabidopsis thaliana]; similar to ent-kaurenoic acid hydroxylase [Arabidopsis thaliana] GI:13021853 2e-11 ...

  10. Arabidopsis CDS blastp result: AK288052 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK288052 J075151I09 At2g32440.1 68415.m03963 ent-kaurenoic acid hydroxylase, putati...ve / cytochrome P450, putative identical to ent-kaurenoic acid hydroxylase / cytochrome P450 CYP88A (GI:1302...1856) [Arabidopsis thaliana]; similar to ent-kaurenoic acid hydroxylase [Arabidopsis thaliana] GI:13021853 6e-14 ...

  11. Arabidopsis CDS blastp result: AK240911 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK240911 J065037E05 At2g32440.1 68415.m03963 ent-kaurenoic acid hydroxylase, putati...ve / cytochrome P450, putative identical to ent-kaurenoic acid hydroxylase / cytochrome P450 CYP88A (GI:1302...1856) [Arabidopsis thaliana]; similar to ent-kaurenoic acid hydroxylase [Arabidopsis thaliana] GI:13021853 4e-22 ...

  12. Arabidopsis CDS blastp result: AK241119 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241119 J065094C22 At2g32440.1 68415.m03963 ent-kaurenoic acid hydroxylase, putati...ve / cytochrome P450, putative identical to ent-kaurenoic acid hydroxylase / cytochrome P450 CYP88A (GI:1302...1856) [Arabidopsis thaliana]; similar to ent-kaurenoic acid hydroxylase [Arabidopsis thaliana] GI:13021853 2e-13 ...

  13. Arabidopsis CDS blastp result: AK243149 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK243149 J100032I21 At2g32440.1 68415.m03963 ent-kaurenoic acid hydroxylase, putati...ve / cytochrome P450, putative identical to ent-kaurenoic acid hydroxylase / cytochrome P450 CYP88A (GI:1302...1856) [Arabidopsis thaliana]; similar to ent-kaurenoic acid hydroxylase [Arabidopsis thaliana] GI:13021853 7e-12 ...

  14. Arabidopsis CDS blastp result: AK241581 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241581 J065181K09 At2g32440.1 68415.m03963 ent-kaurenoic acid hydroxylase, putati...ve / cytochrome P450, putative identical to ent-kaurenoic acid hydroxylase / cytochrome P450 CYP88A (GI:1302...1856) [Arabidopsis thaliana]; similar to ent-kaurenoic acid hydroxylase [Arabidopsis thaliana] GI:13021853 4e-15 ...

  15. Arabidopsis CDS blastp result: AK287479 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287479 J043023O14 At2g32440.1 68415.m03963 ent-kaurenoic acid hydroxylase, putati...ve / cytochrome P450, putative identical to ent-kaurenoic acid hydroxylase / cytochrome P450 CYP88A (GI:1302...1856) [Arabidopsis thaliana]; similar to ent-kaurenoic acid hydroxylase [Arabidopsis thaliana] GI:13021853 1e-17 ...

  16. Reference: 631 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ggest that atRZ-1a has a negative impact on seed germination and seedling growth of Arabidopsis under salt o...binding protein, atRZ-1a, has a negative impact on seed germination and seedling growth of Arabidopsis thali

  17. Rates of trauma spectrum disorders and risks of posttraumatic stress disorder in a sample of orphaned and widowed genocide survivors

    Directory of Open Access Journals (Sweden)

    Susanne Schaal

    2011-06-01

    Full Text Available During the Rwandan genocide of 1994, nearly one million people were killed within a period of 3 months.The objectives of this study were to investigate the levels of trauma exposure and the rates of mental health disorders and to describe risk factors of posttraumatic stress reactions in Rwandan widows and orphans who had been exposed to the genocide.Trained local psychologists interviewed orphans (n=206 and widows (n=194. We used the PSS-I to assess posttraumatic stress disorder (PTSD, the Hopkins Symptom Checklist to assess depression and anxiety symptoms, and the M.I.N.I. to assess risk of suicidality.Subjects reported having been exposed to a high number of different types of traumatic events with a mean of 11 for both groups. Widows displayed more severe mental health problems than orphans: 41% of the widows (compared to 29% of the orphans met symptom criteria for PTSD and a substantial proportion of widows suffered from clinically significant depression (48% versus 34% and anxiety symptoms (59% versus 42% even 13 years after the genocide. Over one-third of respondents of both groups were classified as suicidal (38% versus 39%. Regression analysis indicated that PTSD severity was predicted mainly by cumulative exposure to traumatic stressors and by poor physical health status. In contrast, the importance given to religious/spiritual beliefs and economic variables did not correlate with symptoms of PTSD.While a significant portion of widows and orphans continues to display severe posttraumatic stress reactions, widows seem to constitute a particularly vulnerable survivor group. Our results point to the chronicity of mental health problems in this population and show that PTSD may endure over time if not addressed by clinical intervention. Possible implications of poor mental health and the need for psychological intervention are discussed.

  18. Relationship Between Family Economic Resources, Psychosocial Well-being, and Educational Preferences of AIDS-Orphaned Children in Southern Uganda: Baseline Findings.

    Science.gov (United States)

    Ssewamala, Fred M; Nabunya, Proscovia; Ilic, Vilma; Mukasa, Miriam N; Ddamulira, Christopher

    2015-06-01

    This study examines the relationship between economic resources, psychosocial well-being, and educational preferences of AIDS-orphaned children in southern Uganda. We use baseline data from a sample of 1410 AIDS-orphaned children (defined as children who have lost one or both biological parents to AIDS) enrolled in the Bridges to the Future study, a National Institute of Child Health and Human Development (NICHD) funded study. Analyses from both bivariate and multiple regression analyses indicate the following: 1) despite the well-documented economic and psychosocial challenges AIDS-orphaned children face, many of these children have high educational plans and aspirations; 2) educational aspirations differ by orphanhood status (double orphan vs. single orphan); 3) regardless of orphanhood status, children report similar levels of psychosocial well-being; 4) high levels of family cohesion, positive perceptions of the future, school satisfaction, and lower levels of hopelessness (hopefulness) are associated with high educational aspirations; and 5) reported family economic resources at baseline, all seem to play a role in predicting children's educational preferences and psychosocial well-being. These findings suggest that the focus for care and support of orphaned children should not be limited to addressing their psychosocial needs. Addressing the economic needs of the households in which orphaned children live is equally important. Indeed, in the context of extreme poverty-in which most of the children represented in this study live-addressing structural factors, including poverty, may be a key driver in addressing their psychosocial functioning.

  19. The paediatric rheumatologist and orphan disease - a story without happy ending.

    Science.gov (United States)

    Roszkiewicz, Justyna; Biernacka-Zielińska, Małgorzata; Smolewska, Elżbieta

    2016-01-01

    Orphan diseases are not a common challenge in the everyday practice of the rheumatologist. Despite their extremely rare occurrence one of the patients under our care developed one of them - neuronal ceroid lipofuscinosis, the most frequent neurodegenerative disease observed in the paediatric population. We report a case of 2-year-old girl diagnosed with oligoarticular form of juvenile idiopathic arthritis treated in our Department with steroids and methotrexate and staying in the stage of disease remission. During routine checkups at Outpatient Clinic we observed progressive deterioration of girls neurological condition resulting in ataxia, gait disturbances with no rheumatological cause behind and speech impairment. The appearance of the symptoms was accompanied by frequent episodes of epileptic seizures, with little clinical improvement on combined antiepileptic treatment. Magnetic resonance imaging that we performed showed a picture highly suggestive of neuronal ceroid lipofuscinosis - atrophy of the patients cerebrum and cerebellum. Genetic testing conducted resulted in the diagnosis of late infantile neuronal ceroid lipofuscinosis (LINCL).

  20. Essential Regulation of Lung Surfactant Homeostasis by the Orphan G Protein-Coupled Receptor GPR116

    Directory of Open Access Journals (Sweden)

    Mi Young Yang

    2013-05-01

    Full Text Available GPR116 is an orphan seven-pass transmembrane receptor whose function has been unclear. Global disruption of the Gpr116 gene in mice revealed an unexpected, critical role for this receptor in lung surfactant homeostasis, resulting in progressive accumulation of surfactant lipids and proteins in the alveolar space, labored breathing, and a reduced lifespan. GPR116 expression analysis, bone marrow transplantation studies, and characterization of conditional knockout mice revealed that GPR116 expression in ATII cells is required for maintaining normal surfactant levels. Aberrant packaging of surfactant proteins with lipids in the Gpr116 mutant mice resulted in compromised surfactant structure, function, uptake, and processing. Thus, GPR116 plays an indispensable role in lung surfactant homeostasis with important ramifications for the understanding and treatment of lung surfactant disorders.

  1. Cbln1 is a ligand for an orphan glutamate receptor delta2, a bidirectional synapse organizer.

    Science.gov (United States)

    Matsuda, Keiko; Miura, Eriko; Miyazaki, Taisuke; Kakegawa, Wataru; Emi, Kyoichi; Narumi, Sakae; Fukazawa, Yugo; Ito-Ishida, Aya; Kondo, Tetsuro; Shigemoto, Ryuichi; Watanabe, Masahiko; Yuzaki, Michisuke

    2010-04-16

    Cbln1, secreted from cerebellar granule cells, and the orphan glutamate receptor delta2 (GluD2), expressed by Purkinje cells, are essential for synapse integrity between these neurons in adult mice. Nevertheless, no endogenous binding partners for these molecules have been identified. We found that Cbln1 binds directly to the N-terminal domain of GluD2. GluD2 expression by postsynaptic cells, combined with exogenously applied Cbln1, was necessary and sufficient to induce new synapses in vitro and in the adult cerebellum in vivo. Further, beads coated with recombinant Cbln1 directly induced presynaptic differentiation and indirectly caused clustering of postsynaptic molecules via GluD2. These results indicate that the Cbln1-GluD2 complex is a unique synapse organizer that acts bidirectionally on both pre- and postsynaptic components.

  2. X-ray Observations of Disrupted Recycled Pulsars: No Refuge for Orphaned Central Compact Objects

    CERN Document Server

    Gotthelf, E V; Allen, B; Knispel, B

    2013-01-01

    We present a Chandra X-ray survey of the disrupted recycled pulsars (DRPs), isolated radio pulsars with P > 20 ms and B_s 1E4 - 1E5 yr, roughly 10 times the ages of the approximately 10 known CCOs in a similar volume of the Galaxy. The order of a hundred CCO descendants that could be detected by this method are thus either intrinsically radio quiet, or occupy a different region of (P,B_s) parameter space from the DRPs. This motivates a new X-ray search for orphaned CCOs among radio pulsars with larger B-fields, which could verify the theory that their fields are buried by fall-back of supernova ejecta, but quickly regrow to join the normal pulsar population.

  3. FROM UNREAL TO POETIC: AZARIAS, AN ORPHAN CHILD ON THE WINGS OF THE NDLATI

    Directory of Open Access Journals (Sweden)

    Elizabeth da Silva Mendonça

    2014-11-01

    Full Text Available The breadth of the concept of post-colonialism welcome some literary crit­icism made from the productions of Nations previously colonized by West­ern metropolises. Thinking in the formulations of Appiah (2007, on the plea that the post-colonial narratives earlier, in name of an ethical-human­ist universalism, we can observe the literature of Mia Couto, in the story “O dia em que explodiu Mabata-bata” from the book Vozes Anoitecidas, as a literary project that can unite the aesthetic and the politician. The entire southern Mozambican cultural tradition is presented to narrate the story of an orphaned child, abandoned by his relative and rescued by their own imagination, a brutal death.

  4. Development of novel silicon-containing inverse agonists of retinoic acid receptor-related orphan receptors.

    Science.gov (United States)

    Toyama, Hirozumi; Nakamura, Masaharu; Nakamura, Masahiko; Matsumoto, Yotaro; Nakagomi, Madoka; Hashimoto, Yuichi

    2014-03-15

    Retinoic acid receptor (RAR)-related orphan receptors (RORs) regulate a variety of physiological processes, including hepatic gluconeogenesis, lipid metabolism, circadian rhythm and immune function. The RAR agonist: all-trans retinoic acid was reported to be an RORβ inverse agonist, but no information is available regarding ROR activity of its synthetic analogue Am580. Therefore, we screened Am580 and some related tetramethyltetrahydronaphthalene derivatives and carried out structural development studies, including substitution of carbon atoms with silicon, with the aim of creating a potent ROR transcriptional inhibitor. The phenyl amide disila compound 22 showed the most potent ROR-inhibitory activity among the compounds examined. Its activity towards RORα, RORβ and RORγ was increased compared to that of Am580. The IC₅₀ values for RORα, RORβ and RORγ are 1.3, >10 and 4.5 μM, respectively.

  5. Identification and evolution of the orphan genes in the domestic silkworm, Bombyx mori.

    Science.gov (United States)

    Sun, Wei; Zhao, Xin-Wei; Zhang, Ze

    2015-09-14

    Orphan genes (OGs) which have no recognizable homology to any sequences in other species could contribute to the species specific adaptations. In this study, we identified 738 OGs in the silkworm genome. About 31% of the silkworm OGs is derived from transposable elements, and 5.1% of the silkworm OGs emerged from gene duplication followed by divergence of paralogs. Five de novo silkworm OGs originated from non-coding regions. Microarray data suggested that most of the silkworm OGs were expressed in limited tissues. RNA interference experiments suggested that five de novo OGs are not essential to the silkworm, implying that they may contribute to genetic redundancy or species-specific adaptation. Our results provide some new insights into the evolutionary significance of the silkworm OGs.

  6. Searching for a family of orphan sequences with SAMBA, a parallel hardware dedicated to biological applications.

    Science.gov (United States)

    Guerdoux-Jamet, P; Risler, J L

    1996-01-01

    A significant proportion of coding sequences or open reading frames discovered in the course of sequencing projects do not show any similarity with other sequences deposited with the protein databanks. In such cases the search for similarities must be performed with as many comparison algorithms as possible, so as to increase the chance of finding weak relationships. A specialised parallel hardware (SAMBA) implementing the Smith & Waterman algorithm has been developed at the 'Institut de Recherche en Informatique et Systèmes Aléatoìres' (IRISA). It makes it possible to scan protein databanks at a speed comparable with that of BLAST or FASTA. We report here a study performed with SAMBA on 814 orphan sequences from S cerevisiae and compare the results with those from BLAST and FASTA.

  7. Orphan G protein receptor GPR55 as an emerging target in cancer therapy and management

    Directory of Open Access Journals (Sweden)

    Leyva-Illades D

    2013-07-01

    Full Text Available Dinorah Leyva-Illades,1–3 Sharon DeMorrow1–3 1Digestive Disease Research Center, Scott and White Hospital, Temple, TX, USA; 2Department of Internal MedicineTexas A&M Health Science Center, Temple, TX, USA; 3Research Service, Central Texas Veterans Health Care System, Temple, TX, USA Abstract: G protein-coupled receptors (GPCRs modulate a vast array of cellular processes. The current review gives an overview of the general characteristics of GPCRs and their role in physiological conditions. In addition, it describes the current knowledge of the physiological and pathophysiological functions of GPR55, an orphan GPCR, and how it can be exploited as a therapeutic target to combat various cancers. Keywords: GPR55, cancer, GPCR, endocannabinoids

  8. An orphan gene is necessary for preaxial digit formation during salamander limb development.

    Science.gov (United States)

    Kumar, Anoop; Gates, Phillip B; Czarkwiani, Anna; Brockes, Jeremy P

    2015-10-26

    Limb development in salamanders differs from other tetrapods in that the first digits to form are the two most anterior (preaxial dominance). This has been proposed as a salamander novelty and its mechanistic basis is unknown. Salamanders are the only adult tetrapods able to regenerate the limb, and the contribution of preaxial dominance to limb regeneration is unclear. Here we show that during early outgrowth of the limb bud, a small cohort of cells express the orphan gene Prod1 together with Bmp2, a critical player in digit condensation in amniotes. Disruption of Prod1 with a gene-editing nuclease abrogates these cells, and blocks formation of the radius and ulna, and outgrowth of the anterior digits. Preaxial dominance is a notable feature of limb regeneration in the larval newt, but this changes abruptly after metamorphosis so that the formation of anterior and posterior digits occurs together within the autopodium resembling an amniote-like pattern.

  9. Psychological characteristics of adolescent orphans with no experience of socialization in the family

    Directory of Open Access Journals (Sweden)

    T.I. Shulga

    2013-07-01

    Full Text Available We present the study results of psychological characteristics of adolescent orphans living outside the family and having a violation of socialization at the micro level. It was assumed that children experiencing total maternal deprivation from birth, have difficulties in adapting to life. It was revealed that in this group of adolescents the level of motivational tendencies is higher, reflecting a fear of rejection, and the level of suspicion. They are more than their peers convinced that other people are plotting something evil and can cause harm to demonstrate high degree of irritability, ready to show negative feelings at the slightest excitation (short temper, rudeness, stress, anger. These features are important to understand by specialists to create an educational system that allows to correct the negative aspects, prepare the child for substitute family, provide support and maintenance for a period of adaptation, to help prospective parents.

  10. On the Origin of De Novo Genes in Arabidopsis thaliana Populations.

    Science.gov (United States)

    Li, Zi-Wen; Chen, Xi; Wu, Qiong; Hagmann, Jörg; Han, Ting-Shen; Zou, Yu-Pan; Ge, Song; Guo, Ya-Long

    2016-08-03

    De novo genes, which originate from ancestral nongenic sequences, are one of the most important sources of protein-coding genes. This origination process is crucial for the adaptation of organisms. However, how de novo genes arise and become fixed in a population or species remains largely unknown. Here, we identified 782 de novo genes from the model plant Arabidopsis thaliana and divided them into three types based on the availability of translational evidence, transcriptional evidence, and neither transcriptional nor translational evidence for their origin. Importantly, by integrating multiple types of omics data, including data from genomes, epigenomes, transcriptomes, and translatomes, we found that epigenetic modifications (DNA methylation and histone modification) play an important role in the origination process of de novo genes. Intriguingly, using the transcriptomes and methylomes from the same population of 84 accessions, we found that de novo genes that are transcribed in approximately half of the total accessions within the population are highly methylated, with lower levels of transcription than those transcribed at other frequencies within the population. We hypothesized that, during the origin of de novo gene alleles, those neutralized to low expression states via DNA methylation have relatively high probabilities of spreading and becoming fixed in a population. Our results highlight the process underlying the origin of de novo genes at the population level, as well as the importance of DNA methylation in this process.

  11. Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome[W][OA

    Science.gov (United States)

    Li, Fan; Zheng, Qi; Vandivier, Lee E.; Willmann, Matthew R.; Chen, Ying; Gregory, Brian D.

    2012-01-01

    The secondary structure of an RNA molecule plays an integral role in its maturation, regulation, and function. However, the global influence of this feature on plant gene expression is still largely unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach in conjunction with transcriptome-wide sequencing of rRNA-depleted (RNA sequencing), small RNA, and ribosome-bound RNA populations to investigate the impact of RNA secondary structure on gene expression regulation in Arabidopsis thaliana. From this analysis, we find that highly unpaired and paired RNAs are strongly correlated with euchromatic and heterochromatic epigenetic histone modifications, respectively, providing evidence that secondary structure is necessary for these RNA-mediated posttranscriptional regulatory pathways. Additionally, we uncover key structural patterns across protein-coding transcripts that indicate RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in this model plant. We further reveal that RNA folding is significantly anticorrelated with overall transcript abundance, which is often due to the increased propensity of highly structured mRNAs to be degraded and/or processed into small RNAs. Finally, we find that secondary structure affects mRNA translation, suggesting that this feature regulates plant gene expression at multiple levels. These findings provide a global assessment of RNA folding and its significant regulatory effects in a plant transcriptome. PMID:23150631

  12. The RdDM Pathway Is Required for Basal Heat Tolerance in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Olga V.Popova; Huy Q.Dinh; Werner Aufsatz; Claudia Jonak

    2013-01-01

    Heat stress affects epigenetic gene silencing in Arabidopsis.To test for a mechanistic involvement of epigenetic regulation in heat-stress responses,we analyzed the heat tolerance of mutants defective in DNA methylation,histone modifications,chromatin-remodeling,or siRNA-based silencing pathways.Plants deficient in NRPD2,the common second-largest subunit of RNA polymerases Ⅳ and V,and in the Rpd3-type histone deacetylase HDA6 were hypersensitive to heat exposure.Microarray analysis demonstrated that NRPD2 and HDA6 have independent roles in transcriptional reprogramming in response to temperature stress.The misexpression of protein-coding genes in nrpd2 mutants recovering from heat correlated with defective epigenetic regulation of adjacent transposon remnants which involved the loss of control of heat-stress-induced read-through transcription.We provide evidence that the transcriptional response to temperature stress,at least partially,relies on the integrity of the RNA-dependent DNA methylation pathway.

  13. SUPERMAN attenuates positive INNER NO OUTER autoregulation to maintain polar development of Arabidopsis ovule outer integuments.

    Science.gov (United States)

    Meister, Robert J; Kotow, Louren M; Gasser, Charles S

    2002-09-01

    The outer integument of Arabidopsis ovules exhibits marked polarity in its development, growing extensively from the abaxial side, but only to a very limited extent from the adaxial side of the ovule. Mutations in two genes affect this asymmetric growth. In strong inner no outer (ino) mutants outer integument growth is eliminated, whereas in superman (sup) mutants integument growth on the adaxial side is nearly equal to wild-type growth on the abaxial side. Through complementation and reporter gene analysis, a region of INO 5'-flanking sequences was identified that contains sufficient information for appropriate expression of INO. Using this INO promoter (P-INO) we show that INO acts as a positive regulator of transcription from P-INO, but is not sufficient for de novo initiation of transcription in other plant parts. Protein fusions demonstrate nuclear localization of INO, consistent with a proposed role as a transcription factor for this member of the YABBY protein family. Through its ability to inhibit expression of the endogenous INO gene and transgenes driven by P-INO, SUP is shown to be a negative regulator of INO transcription. Substitution of another YABBY protein coding region (CRABS CLAW) for INO overcomes this negative regulation, indicating that SUP suppresses INO transcription through attenuation of the INO positive autoregulatory loop.

  14. Endogenous TasiRNAs mediate non-cell autonomous effects on gene regulation in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Rebecca Schwab

    Full Text Available BACKGROUND: Different classes of small RNAs (sRNAs refine the expression of numerous genes in higher eukaryotes by directing protein partners to complementary nucleic acids, where they mediate gene silencing. Plants encode a unique class of sRNAs, called trans-acting small interfering RNAs (tasiRNAs, which post-transcriptionally regulate protein-coding transcripts, as do microRNAs (miRNAs, and both sRNA classes control development through their targets. TasiRNA biogenesis requires multiple components of the siRNA pathway and also miRNAs. But while 21mer siRNAs originating from transgenes can mediate silencing across several cell layers, miRNA action seems spatially restricted to the producing or closely surrounding cells. PRINCIPAL FINDINGS: We have previously described the isolation of a genetrap reporter line for TAS3a, the major locus producing AUXIN RESPONS FACTOR (ARF-regulating tasiRNAs in the Arabidopsis shoot. Its activity is limited to the adaxial (upper side of leaf primordia, thus spatially isolated from ARF-activities, which are located in the abaxial (lower side. We show here by in situ hybridization and reporter fusions that the silencing activities of ARF-regulating tasiRNAs are indeed manifested non-cell autonomously to spatially control ARF activities. CONCLUSIONS/SIGNIFICANCE: Endogenous tasiRNAs are thus mediators of a mobile developmental signal and might provide effective gene silencing at a distance beyond the reach of most miRNAs.

  15. Cost-effectiveness of school support for orphan girls to prevent HIV infection in Zimbabwe.

    Science.gov (United States)

    Miller, Ted; Hallfors, Denise; Cho, Hyunsan; Luseno, Winnie; Waehrer, Geetha

    2013-10-01

    This cost-effectiveness study analyzes the cost per quality-adjusted life year (QALY) gained in a randomized controlled trial that tested school support as a structural intervention to prevent HIV risk factors among Zimbabwe orphan girl adolescents. The intervention significantly reduced early marriage, increased years of schooling completed, and increased health-related quality of life. By reducing early marriage, the literature suggests the intervention reduced HIV infection. The intervention yielded an estimated US$1,472 in societal benefits and an estimated gain of 0.36 QALYs per orphan supported. It cost an estimated US$6/QALY gained, about 1 % of annual per capita income in Zimbabwe. That is well below the maximum price that the World Health Organization (WHO) Commission on Macroeconomics and Health recommends paying for health gains in low and middle income countries. About half the girls in the intervention condition were boarded when they reached high school. For non-boarders, the intervention's financial benefits exceeded its costs, yielding an estimated net cost savings of $502 per pupil. Without boarding, the intervention would yield net savings even if it were 34 % less effective in replication. Boarding was not cost-effective. It cost an additional $1,234 per girl boarded (over the 3 years of the study, discounted to present value at a 3 % discount rate) but had no effect on any of the outcome measures relative to girls in the treatment group who did not board. For girls who did not board, the average cost of approximately 3 years of school support was US$973.

  16. Community interventions providing care and support to orphans and vulnerable children: a review of evaluation evidence.

    Science.gov (United States)

    Schenk, Katie D

    2009-07-01

    Children affected by HIV in their families and communities face multiple risks to their health, education and psychosocial wellbeing. Community interventions for children who have been orphaned or rendered vulnerable take many forms, including educational assistance, home-based care, legal protection and psychosocial support. Despite a recent influx of funding for programme implementation, there exists little evidence to inform policymakers about whether their investments are improving the lives of vulnerable children and meeting key benchmarks including the Millennium Development Goals. This paper reviews the current evidence base on evaluations of community interventions for orphans and vulnerable children (OVC) in high HIV-prevalence African settings, focusing on studies' methodologies. Sources reviewed include published research studies and evidence from the unpublished programmatic "grey literature" located through database and internet searches. A total of 21 studies, varying in scope and generalisability, were identified. Interventions reviewed address children's wellbeing through various strategies within their communities. Evaluation methodologies reflect quantitative and qualitative approaches, including surveys (with and without baseline or comparison data), costing studies, focus groups, interviews, case studies, and participatory review techniques. Varied study methodologies reflect diverse research questions, various intervention types, and the challenges associated with evaluating complex interventions; highlighting the need to broaden the research paradigm in order to build the evidence base by including quasi-experimental and process evaluation approaches, and seeking further insights through participatory qualitative methodologies and costing studies. Although findings overall indicate the value of community interventions in effecting measurable improvements in child and family wellbeing, the quality and rigour of evidence is varied. A strategic

  17. Do ultra-orphan medicinal products warrant ultra-high prices? A review

    Directory of Open Access Journals (Sweden)

    Picavet E

    2013-06-01

    Full Text Available Eline Picavet,1 David Cassiman,2 Steven Simoens1 1Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium; 2Department of Hepatology, University Hospital Leuven, Leuven, Belgium Abstract: Ultra-orphan medicinal products (ultra-OMPs are intended for the treatment, prevention, or diagnosis of ultra-rare diseases, ie, life-threatening or chronically debilitating diseases that affect less than one per 50,000 individuals. Recently, high prices for ultra-OMPs have given rise to debate on the sustainability and justification of these prices. The aim of this article is to review the international scientific literature on the pricing of ultra-OMPs and to provide an overview of the current knowledge on the drivers of ultra-OMP pricing. The pricing process of ultra-OMPs is a complex and nontransparent issue. Evidence in the literature seems to indicate that ultra-OMPs are priced according to rarity and what the manufacturer believes the market will bear. Additionally, there appears to be a trend between the price of an ultra-OMP and the number of available alternatives. Patients, third-party payers, and pharmaceutical companies could benefit from more transparent pricing strategies. With a view to containing health care costs, it is likely that cost-sharing strategies, such as performance-based risk sharing arrangements, will become increasingly more important. However, it is vital that any measures for price control are consistent with the intended goals of the incentives to promote the development of new OMPs. Ideally, a balance must be struck between attaining affordable prices for ultra-OMPs and securing a realistic return on investment for the pharmaceutical industry. Keywords: ultra-orphan medicinal product, ultra-rare disease, pricing

  18. Orphan receptor GPR15/BOB is up-regulated in rheumatoid arthritis.

    Science.gov (United States)

    Cartwright, Alison; Schmutz, Caroline; Askari, Ayman; Kuiper, Jan-Herman; Middleton, Jim

    2014-06-01

    Chemokine receptors on leukocytes mediate the recruitment and accumulation of these cells within affected joints in chronic inflammatory diseases such as rheumatoid arthritis (RA). Identification of involved receptors offers potential for development of therapeutic interventions. The objective of this study was to investigate the expression of orphan receptor GPR15/BOB in the synovium of RA and non-RA patients and in peripheral blood of RA patients and healthy donors. GPR15/BOB protein and messenger RNA expression were examined in RA and non-RA synovium by immunofluorescence and reverse-transcription polymerase chain reaction (RT-PCR) respectively. GPR15/BOB expression on peripheral blood leukocytes was analysed by flow cytometry and GPR15/BOB messenger RNA was examined in peripheral blood monocytes by RT-PCR. GPR15/BOB protein was observed in CD68+ and CD14+ macrophages in synovia, with greater expression in RA synovia. GPR15/BOB protein was expressed in all patient synovia whereas in non-RA synovia expression was low or absent. Similarly GPR15/BOB messenger RNA was detected in all RA and a minority of non-RA synovia. GPR15/BOB protein was expressed on peripheral blood leukocytes from RA and healthy individuals with increased expression by monocytes and neutrophils in RA. GPR15/BOB messenger RNA expression was confirmed in peripheral blood monocytes. In conclusion GPR15/BOB is expressed by macrophages in synovial tissue and on monocytes and neutrophils in peripheral blood, and expression is up-regulated in RA patients compared to non-RA controls. This orphan receptor on monocytes/macrophages and neutrophils may play a role in RA pathophysiology.

  19. Jasmonate Signal Pathway in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Xiao-Yi Shan; Zhi-Long Wang; Daoxin Xie

    2007-01-01

    Jasmonates (JAs), which include jasmonic acid and its cyclopentane derivatives are synthesized from the octadecanoid pathway and widely distributed throughout the plant kingdom. JAs modulate the expression of numerous genes and mediate responses to stress, wounding, insect attack, pathogen infection, and UV damage. They also affect a variety of processes in many plant developmental processes. The JA signal pathway involves two important events: the biosynthesis of JA and the transduction of JA signal. Several important Arabidopsis mutants in jasmonate signal pathway were described in this review.

  20. Reference: 572 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available et al. 2007 May. Plant J. 50(3):439-51. Although glycine-rich RNA-binding protein 2 (GRP2) has been implicated in plant re...sponses to environmental stresses, the function and importance of GRP2 in stress responses are largely unknown. Here...haliana under high-salinity, cold or osmotic stress. GRP2 affects seed germination of Arabidopsis plants under salt stre...ss, but does not influence seed germination and seedling growth of Arabidopsis plants under osmotic stre...ss. GRP2 accelerates seed germination and seedling growth in Arabidopsis plants under cold stre

  1. Reference: 446 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available rk E et al. 2006 Nov. Plant Physiol. 142(3):1004-13. Arabidopsis (Arabidopsis thaliana) QUARTET (QRT) genes are require...d for pollen separation during normal floral development. In qrt mutants, the four products of microsporogenesis re...main fused and pollen grains are released as tetrads. In Arabid...opsis, tetrad analysis in qrt mutants has been used to map all five centromeres, easily distinguish sporophy...tic from gametophytic mutations, and accurately assess crossover interference. Using a combination of forward and re

  2. The role of globalization in drug development and access to orphan drugs: orphan drug legislation in the US/EU and in Latin America [v1; ref status: indexed, http://f1000r.es/3ix

    Directory of Open Access Journals (Sweden)

    Renée J.G. Arnold

    2015-02-01

    Full Text Available Compared to a decade ago, nearly three times as many drugs for rare diseases are slated for development. This article addresses the market access issues associated with orphan drug status in Europe and the United States in contrast to the legislation in five Latin American (LA countries that have made strides in this regard--Mexico, Brazil, Colombia, Chile and Argentina. Based on the success of orphan drug legislation in the EU and US, LA countries should strive to adopt similar strategies with regard to rare diseases and drug development. With the implementation of new targeted regulations, reimbursement strategies, and drug approvals, accessibility to treatment will be improved for people afflicted with rare diseases in these developing countries.

  3. The potential impact of a cataract surgery programme on the care of orphans and vulnerable children in Swaziland.

    Science.gov (United States)

    Pons, J; Mapham, W E; Newsome, B; Myer, L; Anderson, R; Courtright, P; Cook, C

    2012-02-23

    We aimed to evaluate the potential impact of a cataract surgery programme at the Good Shepherd Hospital, Siteki, Swaziland, on the care of orphans and vulnerable children in Swaziland. We studied consecutive patients aged 50 years and older undergoing surgery for age-related cataract who reported having children living in their household. Of 131 subjects recruited, 65 (49.6%) were the primary caregivers for the child(ren) in their household. Visual acuities measured 2 weeks after surgery significantly improved. Four weeks after surgery, there was a sizable increase in the proportions of subjects who were able to undertake self-care activities, attend to activities of daily living, undertake income-generating activities and care for children. Cataract surgery on elderly visually impaired patients has the potential to impact positively on the care of orphans and vulnerable children.

  4. Improving the lives of vulnerable children: implications of Horizons research among orphans and other children affected by AIDS.

    Science.gov (United States)

    Schenk, Katie D; Michaelis, Annie; Sapiano, Tobey Nelson; Brown, Lisanne; Weiss, Ellen

    2010-01-01

    From 1997 through 2007, the Horizons program conducted research to inform the care and support of children who had been orphaned and rendered vulnerable by acquired immunodeficiency syndrome in sub-Saharan Africa. Horizons conducted studies in Kenya, Malawi, Rwanda, South Africa, Uganda, Zambia, and Zimbabwe. Research included both diagnostic studies exploring the circumstances of families and communities affected by human immunodeficiency virus (HIV) and evaluations of pioneering intervention strategies. Interventions found to be supportive of families included succession planning for families with an HIV-positive parent, training and supporting youth as caregivers, and youth mentorship for child-headed households. Horizons researchers developed tools to assess the psychosocial well-being of children affected by HIV and outlined key ethical guidelines for conducting research among children. The design, implementation, and evaluation of community-based interventions for orphans and vulnerable children continue to be a key gap in the evidence base.

  5. Community-based mental health support for orphans and vulnerable children in South Africa: A triangulation study.

    Science.gov (United States)

    Marais, Lochner; Sharp, Carla; Pappin, Michelle; Rani, Kholisa; Skinner, Donald; Lenka, Molefi; Cloete, Jan; Serekoane, Joe

    2014-01-01

    Community-based care is receiving increasing global attention as a way to support children who are orphaned or vulnerable due to the HIV/AIDS pandemic. Using both qualitative and quantitative methodology, this study assesses community-based responses to the well-being of orphans and vulnerable children (OVC) and compares these responses with the actual mental health of OVC in order to evaluate the South African government's approach of funding community-based organisations (CBOs) that support and care for OVC. The study results show that the activities of CBOs mainly extend government services and address poverty. Although this should not be seen as insignificant, the paper argues that CBOs give very little attention to the mental health of OVC.

  6. Arabidopsis CDS blastp result: AK065259 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK065259 J013002J18 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  7. Arabidopsis CDS blastp result: AK102134 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK102134 J033085F12 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  8. Arabidopsis CDS blastp result: AK066835 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK066835 J013087I16 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 1e-171 ...

  9. Arabidopsis CDS blastp result: AK100523 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK100523 J023100P04 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  10. Arabidopsis CDS blastp result: AK102695 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK102695 J033103F21 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  11. Reference: 488 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available Inactivation of ATAB2 strongly affects Arabidopsis development and thylakoid mem...n center subunits is decreased and the association of their mRNAs with polysomes is affected. ATAB2 is a chl

  12. Reference: 212 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available identified in pea (Pisum sativum) using biochemical approaches. The Arabidopsis (...C75-IV, which we studied using a range of molecular, genetic, and biochemical techniques. Expression of atTO

  13. Reference: 480 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available activity was analyzed. Compared to all other Suc transporters, AtSUC9 had an ult...abidopsis (Arabidopsis thaliana) L. Heynh., was expressed in Xenopus (Xenopus laevis) oocytes, and transport

  14. Reference: 507 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available een them. However, little is known about the mechanisms that regulate the two pathways and the metabolic cro...ss-talk. To identify such regulatory mechanisms, we isolated and characterized the Arabidopsis T-DNA inserti

  15. Reference: 278 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available functional ERA1 gene, which encodes the beta-subunit of protein farnesyltransferase (PFT), exhibit pleiotropic effects...gnaling and meristem development. Here, we report the effects of T-DNA insertion mutations in the Arabidopsi

  16. Reference: 185 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available organisms, we suggest that AtARP4 is likely to exert its effects on plant develop...nuclear actin-related protein AtARP4 in Arabidopsis has multiple effects on plant development, including ear

  17. Arabidopsis CDS blastp result: AK069960 [KOME

    Lifescience Database Archive (English)

    Full Text Available thyltransferase 1 / caffeic acid/5-hydroxyferulic acid O-methyltransferase (OMT1) identical to O-methyltrans...T1) (Flavonol 3- O-methyltransferase 1) (Caffeic acid/5-hydroxyferulic acid O- methyltransferase) {Arabidopsis thaliana} 5e-60 ...

  18. Arabidopsis CDS blastp result: AK064768 [KOME

    Lifescience Database Archive (English)

    Full Text Available thyltransferase 1 / caffeic acid/5-hydroxyferulic acid O-methyltransferase (OMT1) identical to O-methyltrans...T1) (Flavonol 3- O-methyltransferase 1) (Caffeic acid/5-hydroxyferulic acid O- methyltransferase) {Arabidopsis thaliana} 1e-112 ...

  19. Arabidopsis CDS blastp result: AK061551 [KOME

    Lifescience Database Archive (English)

    Full Text Available ethyltransferase 1 / caffeic acid/5-hydroxyferulic acid O-methyltransferase (OMT1) identical to O-methyltran...MT1) (Flavonol 3- O-methyltransferase 1) (Caffeic acid/5-hydroxyferulic acid O- methyltransferase) {Arabidopsis thaliana} 2e-67 ...

  20. Arabidopsis CDS blastp result: AK104764 [KOME

    Lifescience Database Archive (English)

    Full Text Available ethyltransferase 1 / caffeic acid/5-hydroxyferulic acid O-methyltransferase (OMT1) identical to O-methyltran...MT1) (Flavonol 3- O-methyltransferase 1) (Caffeic acid/5-hydroxyferulic acid O- methyltransferase) {Arabidopsis thaliana} 2e-67 ...

  1. Arabidopsis CDS blastp result: AK098998 [KOME

    Lifescience Database Archive (English)

    Full Text Available thyltransferase 1 / caffeic acid/5-hydroxyferulic acid O-methyltransferase (OMT1) identical to O-methyltrans...T1) (Flavonol 3- O-methyltransferase 1) (Caffeic acid/5-hydroxyferulic acid O- methyltransferase) {Arabidopsis thaliana} 8e-57 ...

  2. Arabidopsis CDS blastp result: AK061859 [KOME

    Lifescience Database Archive (English)

    Full Text Available ethyltransferase 1 / caffeic acid/5-hydroxyferulic acid O-methyltransferase (OMT1) identical to O-methyltran...MT1) (Flavonol 3- O-methyltransferase 1) (Caffeic acid/5-hydroxyferulic acid O- methyltransferase) {Arabidopsis thaliana} 1e-100 ...

  3. Arabidopsis CDS blastp result: AK103387 [KOME

    Lifescience Database Archive (English)

    Full Text Available ntical to SC35-like splicing factor SCL28, 28 kD [Arabidopsis thaliana] GI:9843655; contains Pfam profile PF00076: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 2e-34 ...

  4. Reference: 564 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 39-44 17360695 2007 Feb Proceedings of the National Academy of Sciences of the Un...tion in plants. Arabidopsis plasma membrane protein crucial for Ca2+ influx and touch sensing in roots. 9 36

  5. Reference: 796 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ceedings of the National Academy of Sciences of the United States of America DeBolt...required for normal microtubule dynamics and organization in Arabidopsis. 46 18064-9 19004800 2008 Nov Pro

  6. Reference: 67 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available A complete knockout of AGD2 renders embryos inviable. We suggest that AGD2 synthesizes an important amino a...no acid-derived molecule important for activating defense signaling. Divergent roles in Arabidopsis thaliana

  7. Reference: 420 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available are found in various compartments in plant cells. The cytosolic and chloroplast APXs appear to play important...d development, suggesting that APX3 may not be an important antioxidant enzyme in Arabidopsis, at least unde

  8. Reference: 771 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available RCADIAN TIMEKEEPER (XCT), an Arabidopsis thaliana gene important for light regula...l elongation in xct is hyposensitive to red light but hypersensitive to blue light. Finally, XCT is important

  9. Reference: 797 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available that the level of GMPase activity regulates Arabidopsis sensitivity to NH(4)(+). Further analysis showed that defective N-glycosylati...on of proteins, unfolded protein response, and cell death in the roots are likely i

  10. Arabidopsis CDS blastp result: AK241712 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241712 J065197H24 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 6e-27 ...

  11. Arabidopsis CDS blastp result: AK242957 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242957 J090089I15 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 1e-28 ...

  12. Arabidopsis CDS blastp result: AK287726 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287726 J065138E17 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 1e-88 ...

  13. Arabidopsis CDS blastp result: AK242387 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242387 J080051E14 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 2e-45 ...

  14. Arabidopsis CDS blastp result: AK106306 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK106306 002-101-C10 At4g37750.1 ovule development protein aintegumenta (ANT) ident...ical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 3e-89 ...

  15. Arabidopsis CDS blastp result: AK241272 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241272 J065132I19 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 1e-88 ...

  16. Arabidopsis CDS blastp result: AK240892 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK240892 J065030K10 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 5e-88 ...

  17. Arabidopsis CDS blastp result: AK109848 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK109848 002-148-F05 At4g37750.1 ovule development protein aintegumenta (ANT) ident...ical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 5e-73 ...

  18. Arabidopsis CDS blastp result: AK287673 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287673 J065121E18 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 6e-17 ...

  19. Arabidopsis CDS blastp result: AK287621 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287621 J065066I09 At4g37750.1 68417.m05344 ovule development protein aintegumenta... (ANT) identical to ovule development protein aintegumenta (ANT) (GI:1244708) ) [Arabidopsis thaliana] 5e-85 ...

  20. Reference: 142 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available te S-glucosyltransferase, UGT74B1, to determine its role in the Arabidopsis glucosinolate pathway. Biochem...ical analyses demonstrate that recombinant UGT74B1 specifically glucosylates the th

  1. Reference: 522 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available tol phosphate (InsP) and phosphoinositide phosphate (PtdInsP) substrates. Arabidopsis thaliana has 15 genes encoding 5PTases. Biochem...ical analyses of a subgroup of 5PTase enzymes suggest th

  2. Reference: 459 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available plants. These results suggest an additive contribution of AMT1;1 and AMT1;3 to the overall ammonium uptake ...capacity in Arabidopsis roots under nitrogen-deficiency conditions. Additive contribution

  3. Arabidopsis CDS blastp result: AK288065 [KOME

    Lifescience Database Archive (English)

    Full Text Available al to sulfate tansporter Sultr1;3 [Arabidopsis thaliana] GI:10716805; contains Pfam profile PF00916: Sulfate... transporter family; contains Pfam profile PF01740: STAS domain; contains TIGRfam profile TIGR00815: sulfate permease 1e-145 ...

  4. Reference: 645 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available rter AtDUR3 in nitrogen nutrition in Arabidopsis. In transgenic lines expressing ... impaired growth on urea as a sole nitrogen source were used to investigate a role of the H+/urea co-transpo

  5. The fifth international conference on Arabidopsis research

    Energy Technology Data Exchange (ETDEWEB)

    Hangarter, R.; Scholl, R.; Davis, K.; Feldmann, K.

    1993-12-31

    This volume contains abstracts of oral and poster presentations made in conjunction with the Fifth International Conference on Arabidopsis Research held August 19--22, 1993 at the Ohio State University, Columbus, Ohio.

  6. Reference: 711 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available of the RLK signaling pathway, which also mediates adaptation to Na(+) stress. RLK pathway components, known... The Arabidopsis kinase-associated protein phosphatase regulates adaptation to Na+ stress. 2 612-22 18162596

  7. Reference: 734 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available umi et al. 2008 Apr. Development 135(7):1335-45. CAPRICE (CPC) encodes a small protein with an R3 MYB motif ...doreduplication. Arabidopsis CAPRICE-LIKE MYB 3 (CPL3) controls endoreduplication and flowering development

  8. Arabidopsis CDS blastp result: AK101526 [KOME

    Lifescience Database Archive (English)

    Full Text Available ucosaminyltransferase, putative similar to N-acetylglucosaminyltransferase I from Arabidopsis thaliana [gi:5139335]; contains AT-AC non-consensus splice sites at intron 13 1e-179 ...

  9. Reference: 733 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available role in this transition. Specifically, two autonomous factors in the Arabidopsis...tes FCA alternative polyadenylation and promotes flowering as a novel factor in the autonomous pathway. Firs

  10. Reference: 343 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available the characterization of a T-DNA insertion mutant of the Arabidopsis CAP-C gene. Analysis of the progeny of selfe...matin was observed between segregating mitotic chromosomes in pollen produced by selfed heterozygotes. Addit

  11. Arabidopsis CDS blastp result: AK241281 [KOME

    Lifescience Database Archive (English)

    Full Text Available 2 protein) [Arabidopsis thaliana]; a false single bp exon was added to circumvent a single basepair insertion in the genomic sequence, supported by cDNA/genome alignment. 3e-19 ...

  12. Arabidopsis CDS blastp result: AK241243 [KOME

    Lifescience Database Archive (English)

    Full Text Available 2 protein) [Arabidopsis thaliana]; a false single bp exon was added to circumvent a single basepair insertion in the genomic sequence, supported by cDNA/genome alignment. 6e-11 ...

  13. Arabidopsis CDS blastp result: AK243188 [KOME

    Lifescience Database Archive (English)

    Full Text Available 2 protein) [Arabidopsis thaliana]; a false single bp exon was added to circumvent a single basepair insertion in the genomic sequence, supported by cDNA/genome alignment. 8e-23 ...

  14. Arabidopsis CDS blastp result: AK242986 [KOME

    Lifescience Database Archive (English)

    Full Text Available 2 protein) [Arabidopsis thaliana]; a false single bp exon was added to circumvent a single basepair insertion in the genomic sequence, supported by cDNA/genome alignment. 1e-17 ...

  15. Reference: 30 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ponse to various biotic and abiotic stresses. However the physiological role of t...his pathway remains obscure. To elucidate its role in plants, we analyzed Arabidopsis T-DNA knockout mutants

  16. Arabidopsis CDS blastp result: AK062082 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK062082 001-044-F11 At3g59970.3 methylenetetrahydrofolate reductase 1 (MTHFR1) ide...ntical to methylenetetrahydrofolate reductase MTHFR1 [Arabidopsis thaliana] GI:5911425 4e-81 ...

  17. Reference: 783 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available sis ACBP6 was confirmed by analyses of transgenic Arabidopsis expressing autofluorescence-tagged ACBP6 and w... mRNA encoding phospholipase Ddelta. Lipid profiling analyses of rosettes from co

  18. Reference: 789 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ylakoid membranes. Microarray analysis of the chl27-t mutant showed repression of numerous nuclear genes involved in photosynthesis...d CHL27 proteins. Role of Arabidopsis CHL27 protein for photosynthesis, chloroplast development and gene exp

  19. Reference: 352 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available em II and has a specific function distinct from 2-Cys peroxiredoxin in protecting photosynthesis. Its absenc...f Arabidopsis thaliana is attached to the thylakoids and functions in context of photosynthesis

  20. Reference: 21 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ication of a number of mutant lines with altered Chl fluorescence characteristics. Analysis of photosynthesis...cation of mutants of Arabidopsis defective in acclimation of photosynthesis to th

  1. Reference: 413 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ollination and fertilization, and, in the absence of fertilization, flowers senesce. In the Arabidopsis thal...ARF8 acts as an inhibitor to stop further carpel development in the absence of fertilization and the generat

  2. Reference: 405 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available as previously thought. These mutants will prove to be valuable resources for understanding laccase functions in vivo. Mutant identifi...cation and characterization of the laccase gene family in Arabidopsis. 11 2563-9 16

  3. Reference: 263 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available idopsis leaves GLB1 expression and PII protein levels were not significantly affected by either the day/nigh...bolism. Physiological characterisation of Arabidopsis mutants affected in the expression of the putative reg

  4. Reference: 160 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available excessive accumulation of these toxic compounds impairs cell death containment and counteracts the effect...iveness of the plant defenses to restrict pathogen infection. Arabidopsis SHMT1, a

  5. Arabidopsis CDS blastp result: AK242550 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242550 J080319D10 At2g35630.1 68415.m04369 microtubule organization 1 protein (MO...R1) identical to microtubule organization 1 protein GI:14317953 from [Arabidopsis thaliana] 5e-44 ...

  6. Reference: 301 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available n phosphatidylinositol metabolism and is encoded by an At5PTase gene family in Arabidopsis thaliana. A previous study...ntracellular calcium levels. In this study, we provide evidence that At5PTase13 m

  7. Reference: 724 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available is required in the roots during early signaling steps of rhizobacteria-mediated ...ISR. MYB72 is required in early signaling steps of rhizobacteria-induced systemic resistance in Arabidopsis.

  8. Reference: 289 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available f flavonoids in Arabidopsis seed coat. 11 2966-80 16243908 2005 Nov The Plant cell Caboche Michel|Debeaujon Isabelle|Kerhoas Lucien|Lepiniec Loïc|Pourcel Lucille|Routaboul Jean-Marc

  9. Reference: 684 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available cellular proliferation and expansion at nanomolar concentrations. PSY1 is widely expressed in various Arabi...ulfated glycopeptide involved in cellular proliferation and expansion in Arabidopsis. 46 18333-8 17989228 20

  10. Reference: 147 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available the region-specific control of trichome development of Arabidopsis. 3 389-98 15604688 2004 May Plant molecular biology Hulskamp Mart...in|Kirik Victor|Schiefelbein John|Simon Marissa|Wester Katja

  11. Arabidopsis CDS blastp result: AK241043 [KOME

    Lifescience Database Archive (English)

    Full Text Available upted by a stop codon, creating non-consensus donor and acceptor splice sites. 2e-41 ... ...tical to SP|P92997 Germin-like protein subfamily 1 member 13 precursor {Arabidopsis thaliana}; exon 2 interr

  12. Arabidopsis CDS blastp result: AK243135 [KOME

    Lifescience Database Archive (English)

    Full Text Available upted by a stop codon, creating non-consensus donor and acceptor splice sites. 7e-43 ... ...tical to SP|P92997 Germin-like protein subfamily 1 member 13 precursor {Arabidopsis thaliana}; exon 2 interr

  13. Reference: 798 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available iption factors, control the delicately tuned reorientation and timing of cell div...EZ and SOMBRERO control the orientation of cell division plane in Arabidopsis root stem cells. 6 913-22 1908

  14. Health promotion needs of Hammanskraal families with adolescents orphaned by HIV/AIDS

    Directory of Open Access Journals (Sweden)

    N C van Wyk

    2008-01-01

    Full Text Available Health promotion is regarded as the cornerstone of good health. It is the action expected from individuals and families in order to better their own health situation. Health promotion is an art and science (Edelman & Mandle, 2002:16 that is integrated into the primary health care to reduce existing health problems. The purpose of the research on which this article is reporting, was to explore and describe the health promotion needs of families with adolescents orphaned by human immunodeficiency virus or acquired immune deficiency syndrome (HIV/AIDS. The research was located within a qualitative paradigm that is both exploratory and descriptive. Eight families who were purposely selected participated in the research process. Qualitative methods, such as group interviews and field notes were utilised to collect data. The health promotion needs of the families with adolescents orphaned by HIV/AIDS were explored and described. Tesch’s analysis process, which entails a series of steps, was followed (Creswell, 2003:192. Themes, categories and subcategories that form the central focus of health promotion needs emerged during the data analysis. These themes,categories and subcategories are used to develop guidelines for health promotion. Opsomming Die bevordering van gesondheid is die hoeksteen van gesondheid. Dit is die aksie wat van individue en familie verwag word, sodat hulle hul eie gesondheidstoestand kan verbeter. Die bevordering van gesondheid is ‘n kuns en ‘n wetenskap, wat geïntegreer is in primêre gesondheidsorg, om bestaande gesondheidsprobleme te verminder (Edelman & Mandle, 2002:16. Die doel van die navorsing, waarna in hierdie artikel verwys word, was om uit te vind wat die gesondheidsorgbehoeftes van families, met adolessente wat wees gelaat is as gevolg van menslike immunogebrek virus of verworve immuungebrek sindroom (MIV/VIGS, is, en dit te beskryf. Die navorsing was binne die raamwerk van ‘n kwalitatiewe paradigma, wat

  15. Orphan receptor GPR110, an oncogene overexpressed in lung and prostate cancer

    Directory of Open Access Journals (Sweden)

    Channa Namitha

    2010-02-01

    Full Text Available Abstract Background GPR110 is an orphan G protein-coupled receptor--a receptor without a known ligand, a known signaling pathway, or a known function. Despite the lack of information, one can assume that orphan receptors have important biological roles. In a retroviral insertion mutagenesis screen in the mouse, we identified GPR110 as an oncogene. This prompted us to study the potential isoforms that can be gleaned from known GPR110 transcripts, and the expression of these isoforms in normal and transformed human tissues. Methods Various epitope-tagged isoforms of GPR110 were expressed in cell lines and assayed by western blotting to determine cleavage, surface localization, and secretion patterns. GPR110 transcript and protein levels were measured in lung and prostate cancer cell lines and clinical samples, respectively, by quantitative PCR and immunohistochemistry. Results We found four potential splice variants of GPR110. Of these variants, we confirmed three as being expressed as proteins on the cell surface. Isoform 1 is the canonical form, with a molecular mass of about 100 kD. Isoforms 2 and 3 are truncated products of isoform 1, and are 25 and 23 kD, respectively. These truncated isoforms lack the seven-span transmembrane domain characteristic of GPR proteins and thus are not likely to be membrane anchored; indeed, isoform 2 can be secreted. Compared with the median gene expression of ~200 selected genes, GPR110 expression was low in most tissues. However, it had higher than average gene expression in normal kidney tissue and in prostate tissues originating from older donors. Although identified as an oncogene in murine T lymphomas, GPR110 is greatly overexpressed in human lung and prostate cancers. As detected by immunohistochemistry, GPR110 was overexpressed in 20 of 27 (74% lung adenocarcinoma tissue cores and in 17 of 29 (59% prostate adenocarcinoma tissue cores. Additionally, staining with a GPR110 antibody enabled us to

  16. Health information, what happens when there isn't any? Information literacy and the challenges for rare and orphan diseases.

    Science.gov (United States)

    Spring, Hannah

    2014-09-01

    This feature looks at the challenges for information literacy in rare and orphan diseases. In particular, it focuses on the information difficulties faced by those living with a rare condition or awaiting a diagnosis, and also those of the health professionals in charge of their care. The feature also highlights some of the key issues that library and information professionals need to be aware of when providing information support in such circumstances.

  17. Securing the metal recycling chain for the steel industry by detecting orphan radioactive sources in scrap metal

    Science.gov (United States)

    Pesente, S.; Vanini, S.; Benettoni, M.; Bonomi, G.; Calvini, P.; Checchia, P.; Conti, E.; Gonella, F.; Nebbia, G.; Squarcia, S.; Viesti, G.; Zenoni, A.; Zumerle, G.

    2010-08-01

    Experimental tests are reported for the detection of the heavy metal shielding of orphan sources hidden inside scrap metal by using a recently developed muon tomography system. Shielded sources do not trigger alarm in radiation portal commonly employed at the entrance of steel industry using scrap metal. Future systems integrating radiation portals with muon tomography inspection gates will substantially reduce the possibility of accidental melting of radioactive sources securing the use of recycled metal.

  18. Arabidopsis CDS blastp result: AK071710 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK071710 J023110L07 At4g14030.1 selenium-binding protein, putative contains Pfam profile PF05694: 56kDa sele...nium binding protein (SBP56); identical to Putative selenium-binding protein (Swiss...-Prot:O23264) [Arabidopsis thaliana]; similar to selenium binding protein (GI:15485232) [Arabidopsis thalian...a]; identical to cDNA from partial mRNA for selenium binding protein (sbp gene) GI:15485231 1e-162 ...

  19. Reference: 221 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ell cycle. In addition, RAD51 is required for meiosis and its Arabidopsis (Arabidopsis thaliana) ortholog is important... cell cultures, the RAD51 paralog RAD51C is also important for mitotic homologous...ortant for recombination and DNA repair in the mitotic c...chromosome (homolog) pairing, synapsis, and recombination. The budding yeast (Saccharomyces cerevisiae) RAD51 gene is known to be imp

  20. Reference: 598 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available omoter is markedly reduced in the cdkc;2 and cyct1;5 mutants, indicating that the kinase complexes are important... flowering. These results establish Arabidopsis CDKC kinase complexes as important...T1;4 and CYCT1;5, play important roles in infection with Cauliflower mosaic virus...hat Arabidopsis thaliana CDK9-like proteins, CDKC;1 and CDKC;2, and their interacting cyclin T partners, CYC

  1. Ugandan HIV/AIDS orphans in charge of their households speak out: a study of their health-related worries.

    Science.gov (United States)

    Satzinger, F; Kipp, W; Rubaale, T

    2012-01-01

    The number of children orphaned due to HIV/AIDS in sub-Saharan Africa was estimated in 2007 by UNAIDS at upwards of 12 million. In Uganda alone, 800,000 of the estimated 1.6 million orphans are said to be orphaned due to this cause. These children suffer life-long consequences from the loss of their parents. This study explores the situation of children living in child-headed households in Uganda's western Kabarole district. Through qualitative research, including in-depth interviews with 20 child heads of households, the health concerns of these children are documented. The interview data were analysed using qualitative research techniques. The study reveals that the psychological and physical effects of orphanhood are magnified for those living in child-headed households. In particular, it highlights the fears of theft and abuse which are a constant source of anxiety for these children. It reports that illness episodes among younger siblings are also particularly worrisome for child heads of households. The article concludes with recommendations for addressing this urgent problem in sub-Saharan Africa.

  2. ONRLDB--manually curated database of experimentally validated ligands for orphan nuclear receptors: insights into new drug discovery.

    Science.gov (United States)

    Nanduri, Ravikanth; Bhutani, Isha; Somavarapu, Arun Kumar; Mahajan, Sahil; Parkesh, Raman; Gupta, Pawan

    2015-01-01

    Orphan nuclear receptors are potential therapeutic targets. The Orphan Nuclear Receptor Ligand Binding Database (ONRLDB) is an interactive, comprehensive and manually curated database of small molecule ligands targeting orphan nuclear receptors. Currently, ONRLDB consists of ∼11,000 ligands, of which ∼6500 are unique. All entries include information for the ligand, such as EC50 and IC50, number of aromatic rings and rotatable bonds, XlogP, hydrogen donor and acceptor count, molecular weight (MW) and structure. ONRLDB is a cross-platform database, where either the cognate small molecule modulators of a receptor or the cognate receptors to a ligand can be searched. The database can be searched using three methods: text search, advanced search or similarity search. Substructure search, cataloguing tools, and clustering tools can be used to perform advanced analysis of the ligand based on chemical similarity fingerprints, hierarchical clustering, binning partition and multidimensional scaling. These tools, together with the Tree function provided, deliver an interactive platform and a comprehensive resource for identification of common and unique scaffolds. As demonstrated, ONRLDB is designed to allow selection of ligands based on various properties and for designing novel ligands or to improve the existing ones. Database URL: http://www.onrldb.org/.

  3. Discussion on the Tragic Pleasure of Zhao's Orphan%论《赵氏孤儿》的悲剧快感

    Institute of Scientific and Technical Information of China (English)

    陈小刚

    2014-01-01

    《赵氏孤儿》是著名的古典悲剧,给人带来悲的世界,但这种悲不是绝望的悲,是一种给人奋发向上的悲。悲剧中既有痛感的体现,也有一种快感在其中。讨论《赵氏孤儿》戏剧的悲剧快感,主要从韩厥两难处境、屠岸贾的过场作用对《赵氏孤儿》加以审美的分析和提炼,从艺术自身的角度看待《赵氏孤儿》方能体会到它长久不衰的魅力。%Zhao's Orphan is a famous classical tragedy,which brings us a world of huge grief. However,the grief is not a despair but an inspiration. The tragedy is a mixture of the pain and the pleasure. This paper discusses the tragic pleasure of Zhao's Orphan, mainly from the dilemma of Han Jue and the interlude role of Tu An-gu. Only by analyzing and refining the text from aesthetic vision and loo-king on Zhao's Orphan from art perspective, can we experience its everlasting charm.

  4. Nonsense-Mediated Decay of Alternative Precursor mRNA Splicing Variants Is a Major Determinant of the Arabidopsis Steady State Transcriptome[C][W

    Science.gov (United States)

    Drechsel, Gabriele; Kahles, André; Kesarwani, Anil K.; Stauffer, Eva; Behr, Jonas; Drewe, Philipp; Rätsch, Gunnar; Wachter, Andreas

    2013-01-01

    The nonsense-mediated decay (NMD) surveillance pathway can recognize erroneous transcripts and physiological mRNAs, such as precursor mRNA alternative splicing (AS) variants. Currently, information on the global extent of coupled AS and NMD remains scarce and even absent for any plant species. To address this, we conducted transcriptome-wide splicing studies using Arabidopsis thaliana mutants in the NMD factor homologs UP FRAMESHIFT1 (UPF1) and UPF3 as well as wild-type samples treated with the translation inhibitor cycloheximide. Our analyses revealed that at least 17.4% of all multi-exon, protein-coding genes produce splicing variants that are targeted by NMD. Moreover, we provide evidence that UPF1 and UPF3 act in a translation-independent mRNA decay pathway. Importantly, 92.3% of the NMD-responsive mRNAs exhibit classical NMD-eliciting features, supporting their authenticity as direct targets. Genes generating NMD-sensitive AS variants function in diverse biological processes, including signaling and protein modification, for which NaCl stress–modulated AS-NMD was found. Besides mRNAs, numerous noncoding RNAs and transcripts derived from intergenic regions were shown to be NMD responsive. In summary, we provide evidence for a major function of AS-coupled NMD in shaping the Arabidopsis transcriptome, having fundamental implications in gene regulation and quality control of transcript processing. PMID:24163313

  5. Nuclear orphan receptor TLX affects gene expression, proliferation and cell apoptosis in beta cells.

    Science.gov (United States)

    Shi, Xiaoli; Xiong, Xiaokan; Dai, Zhe; Deng, Haohua; Sun, Li; Hu, Xuemei; Zhou, Feng; Xu, Yancheng

    Nuclear orphan receptor TLX is an essential regulator of the growth of neural stem cells. However, its exact function in pancreatic islet cells is still unknown. In the present study, gene expression profiling analysis revealed that overexpression of TLX in beta cell line MIN6 causes suppression of 176 genes and upregulation of 49 genes, including a cadre of cell cycle, cell proliferation and cell death control genes, such as Btg2, Ddit3 and Gadd45a. We next examined the effects of TLX overexpression on proliferation, apoptosis and insulin secretion in MIN6 cells. Proliferation analysis using EdU assay showed that overexpression of TLX increased percentage of EdU-positive cells. Cell cycle and apoptosis analysis revealed that overexpression of TLX in MIN6 cells resulted in higher percentage of cells exiting G1 into S-phase, and a 58.8% decrease of cell apoptosis induced by 0.5 mM palmitate. Moreover, TLX overexpression did not cause impairment of insulin secretion. Together, we conclude that TLX is among factors capable of controlling beta cell proliferation and survival, which may serve as a target for the development of novel therapies for diabetes.

  6. The oncoprotein BCL11A binds to orphan nuclear receptor TLX and potentiates its transrepressive function.

    Directory of Open Access Journals (Sweden)

    Sara B Estruch

    Full Text Available Nuclear orphan receptor TLX (NR2E1 functions primarily as a transcriptional repressor and its pivotal role in brain development, glioblastoma, mental retardation and retinopathologies make it an attractive drug target. TLX is expressed in the neural stem cells (NSCs of the subventricular zone and the hippocampus subgranular zone, regions with persistent neurogenesis in the adult brain, and functions as an essential regulator of NSCs maintenance and self-renewal. Little is known about the TLX social network of interactors and only few TLX coregulators are described. To identify and characterize novel TLX-binders and possible coregulators, we performed yeast-two-hybrid (Y2H screens of a human adult brain cDNA library using different TLX constructs as baits. Our screens identified multiple clones of Atrophin-1 (ATN1, a previously described TLX interactor. In addition, we identified an interaction with the oncoprotein and zinc finger transcription factor BCL11A (CTIP1/Evi9, a key player in the hematopoietic system and in major blood-related malignancies. This interaction was validated by expression and coimmunoprecipitation in human cells. BCL11A potentiated the transrepressive function of TLX in an in vitro reporter gene assay. Our work suggests that BCL11A is a novel TLX coregulator that might be involved in TLX-dependent gene regulation in the brain.

  7. The paediatric rheumatologist and orphan disease – a story without happy ending

    Science.gov (United States)

    Roszkiewicz, Justyna; Biernacka-Zielińska, Małgorzata

    2016-01-01

    Orphan diseases are not a common challenge in the everyday practice of the rheumatologist. Despite their extremely rare occurrence one of the patients under our care developed one of them – neuronal ceroid lipofuscinosis, the most frequent neurodegenerative disease observed in the paediatric population. We report a case of 2-year-old girl diagnosed with oligoarticular form of juvenile idiopathic arthritis treated in our Department with steroids and methotrexate and staying in the stage of disease remission. During routine checkups at Outpatient Clinic we observed progressive deterioration of girls neurological condition resulting in ataxia, gait disturbances with no rheumatological cause behind and speech impairment. The appearance of the symptoms was accompanied by frequent episodes of epileptic seizures, with little clinical improvement on combined antiepileptic treatment. Magnetic resonance imaging that we performed showed a picture highly suggestive of neuronal ceroid lipofuscinosis – atrophy of the patients cerebrum and cerebellum. Genetic testing conducted resulted in the diagnosis of late infantile neuronal ceroid lipofuscinosis (LINCL). PMID:27504025

  8. Social interactions and their connection to aggression and ovarian development in orphaned worker bumblebees (Bombus impatiens).

    Science.gov (United States)

    Sibbald, E D; Plowright, C M S

    2014-03-01

    This study examines the social dynamics of reproductive conflict. Orphaned worker bumblebees (Bombus impatiens) with comparatively high or low levels of social activity were paired to determine whether aggression and reproduction could be traced to earlier social interactions. The workers were paired according to their levels of social activity (a socially active+another socially active worker, socially active+socially inactive, and two socially inactive workers). The presence or absence of brood was also manipulated. The absence of brood increased both aggression and ovarian development, suggesting that aggression and reproduction are associated or that there is a third variable that affects both. Socially active pairs were significantly more aggressive: here, social activity can be taken as an early indicator of aggression. No such effect, however, was obtained on ovarian development as the socially active pairs did not differ on their degree of ovarian development compared to the others. Within the socially active+socially inactive pairs, the socially active worker did not have more developed ovaries and was not more aggressive than her socially inactive partner. Results highlight that environmental conditions (the absence of brood) can predict ovarian development and although social activity can be observed prior to aggression, differences in aggression do not translate into differences in ovarian development under these conditions.

  9. Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions.

    Science.gov (United States)

    Ekman, Diana; Björklund, Asa K; Frey-Skött, Johannes; Elofsson, Arne

    2005-04-22

    Comparative studies of the proteomes from different organisms have provided valuable information about protein domain distribution in the kingdoms of life. Earlier studies have been limited by the fact that only about 50% of the proteomes could be matched to a domain. Here, we have extended these studies by including less well-defined domain definitions, Pfam-B and clustered domains, MAS, in addition to Pfam-A and SCOP domains. It was found that a significant fraction of these domain families are homologous to Pfam-A or SCOP domains. Further, we show that all regions that do not match a Pfam-A or SCOP domain contain a significantly higher fraction of disordered structure. These unstructured regions may be contained within orphan domains or function as linkers between structured domains. Using several different definitions we have re-estimated the number of multi-domain proteins in different organisms and found that several methods all predict that eukaryotes have approximately 65% multi-domain proteins, while the prokaryotes consist of approximately 40% multi-domain proteins. However, these numbers are strongly dependent on the exact choice of cut-off for domains in unassigned regions. In conclusion, all eukaryotes have similar fractions of multi-domain proteins and disorder, whereas a high fraction of repeating domain is distinguished only in multicellular eukaryotes. This implies a role for repeats in cell-cell contacts while the other two features are important for intracellular functions.

  10. The orphan nuclear receptor SHP is a positive regulator of osteoblastic bone formation.

    Science.gov (United States)

    Jeong, Byung-Chul; Lee, Yong-Soo; Bae, In-Ho; Lee, Chul-Ho; Shin, Hong-In; Ha, Hyun Jung; Franceschi, Renny T; Choi, Hueng-Sik; Koh, Jeong-Tae

    2010-02-01

    The orphan nuclear receptor small heterodimer partner (SHP; NR0B2) interacts with a diverse array of transcription factors and regulates a variety of cellular events such as cell proliferation, differentiation, and metabolism. However, the role of SHP in bone formation has not yet been elucidated. SHP expression is significantly increased during osteoblast differentiation, and its expression is partially regulated by bone morphogenetic protein 2 (BMP-2), which plays an important role in bone formation. In our study, inhibition of SHP expression significantly repressed BMP-2-induced osteoblast differentiation and ectopic bone formation. In accordance with these in vitro and in vivo results, osteoblast differentiation in SHP(-/-) mice primary osteoblasts was significantly repressed, and the mice showed decreased bone mass resulting from decreased numbers of osteoblasts. Finally, SHP physically interacts and forms a complex with runt-related transcription factor 2 (Runx2) on the osteocalcin gene promoter, and overexpression of SHP increased Runx2 transactivity via competition with histone deacetylase 4 (HDAC4), an enzyme that inhibits DNA binding of Runx2 to its target genes. Taken together, these results indicate that SHP acts as a novel positive regulator of bone formation by augmenting osteoblast differentiation through regulation of the transcriptional activity of Runx2.

  11. Regioselective oxidation of lauric acid by CYP119, an orphan cytochrome P450 from Sulfolobus acidocaldarius.

    Science.gov (United States)

    Lim, Young-Ran; Eun, Chang-Yong; Park, Hyoung-Goo; Han, Songhee; Han, Jung-Soo; Cho, Kyoung Sang; Chun, Young-Jin; Kim, Donghak

    2010-03-01

    Archaebacteria Sulfolobus acidocaldarius contains the highly thermophilic cytochrome P450 enzyme (CYP119). CYP119 possesses stable enzymatic activity at up to 85 degrees C. However, this enzyme is still considered as an orphan P450 without known physiological function with endogenous or xenobiotic substrates. We characterized the regioselectivity of lauric acid by CYP119 using the auxiliary redox partner proteins putidaredoxin (Pd) and putidaredoxin reductase (PdR). Purified CYP119 protein showed a tight binding affinity to lauric acid (K(d)=1.1+/-0.1 microM) and dominantly hydroxylated (omega-1) position of lauric acid. We determined the steady-state kinetic parameters; k(cat) was 10.8 min(-1) and K(m) was 12 microM. The increased ratio to omega-hydroxylated production of lauric acid catalyzed by CYP119 was observed with increase in the reaction temperature. These studies suggested that the regioselectivity of CYP119 provide the critical clue for the physiological enzyme function in this thermophilic archaebacteria. In addition, regioselectivity control of CYP119 without altering its thermostability can lead to the development of novel CYP119-based catalysts through protein engineering.

  12. Citric acid cycle intermediates as ligands for orphan G-protein-coupled receptors.

    Science.gov (United States)

    He, Weihai; Miao, Frederick J-P; Lin, Daniel C-H; Schwandner, Ralf T; Wang, Zhulun; Gao, Jinhai; Chen, Jin-Long; Tian, Hui; Ling, Lei

    2004-05-13

    The citric acid cycle is central to the regulation of energy homeostasis and cell metabolism. Mutations in enzymes that catalyse steps in the citric acid cycle result in human diseases with various clinical presentations. The intermediates of the citric acid cycle are present at micromolar concentration in blood and are regulated by respiration, metabolism and renal reabsorption/extrusion. Here we show that GPR91 (ref. 3), a previously orphan G-protein-coupled receptor (GPCR), functions as a receptor for the citric acid cycle intermediate succinate. We also report that GPR99 (ref. 4), a close relative of GPR91, responds to alpha-ketoglutarate, another intermediate in the citric acid cycle. Thus by acting as ligands for GPCRs, succinate and alpha-ketoglutarate are found to have unexpected signalling functions beyond their traditional roles. Furthermore, we show that succinate increases blood pressure in animals. The succinate-induced hypertensive effect involves the renin-angiotensin system and is abolished in GPR91-deficient mice. Our results indicate a possible role for GPR91 in renovascular hypertension, a disease closely linked to atherosclerosis, diabetes and renal failure.

  13. The nuclear orphan receptor COUP-TFII is required for limb and skeletal muscle development.

    Science.gov (United States)

    Lee, Christopher T; Li, Luoping; Takamoto, Norio; Martin, James F; Demayo, Francesco J; Tsai, Ming-Jer; Tsai, Sophia Y

    2004-12-01

    The nuclear orphan receptor COUP-TFII is widely expressed in multiple tissues and organs throughout embryonic development, suggesting that COUP-TFII is involved in multiple aspects of embryogenesis. Because of the early embryonic lethality of COUP-TFII knockout mice, the role of COUP-TFII during limb development has not been determined. COUP-TFII is expressed in lateral plate mesoderm of the early embryo prior to limb bud formation. In addition, COUP-TFII is also expressed in the somites and skeletal muscle precursors of the limbs. Therefore, in order to study the potential role of COUP-TFII in limb and skeletal muscle development, we bypassed the early embryonic lethality of the COUP-TFII mutant by using two methods. First, embryonic chimera analysis has revealed an obligatory role for COUP-TFII in limb bud outgrowth since mutant cells are unable to contribute to the distally growing limb mesenchyme. Second, we used a conditional-knockout approach to ablate COUP-TFII specifically in the limbs. Loss of COUP-TFII in the limbs leads to hypoplastic skeletal muscle development, as well as shorter limbs. Taken together, our results demonstrate that COUP-TFII plays an early role in limb bud outgrowth but not limb bud initiation. Also, COUP-TFII is required for appropriate development of the skeletal musculature of developing limbs.

  14. Lessons from writing sessions: a school-based randomized trial with adolescent orphans in Rwanda

    Directory of Open Access Journals (Sweden)

    Johanna Unterhitzenberger

    2014-12-01

    Full Text Available Background: Treatments for adolescents affected by long-term loss in low- and middle-income countries are lacking. As school-based interventions are cost-efficient and easy to disseminate, an evaluation of this treatment setting for adolescents is worthwhile. Objective: Examining the effect of a school-based unstructured emotional writing intervention (sensu Pennebaker, group 1 about the loss of a parent to reduce adaptation problems to loss, compared to writing about a hobby (group 2, and non-writing (group 3. Method: We randomly assigned 14–18-year-old Rwandan orphans to one of the three conditions (n=23 per condition. Before and after the intervention, subjects completed the Prolonged Grief Questionnaire for Adolescents and the Mini International Neuropsychiatric Interview for Children and Adolescents, Part A, on depression as self-report measures of long-term effects of early parental loss. Results: Repeated measures analyses of variance showed no differential effect for any of the three conditions but revealed a significant effect of time at posttest regarding grief severity. Reduction of grief symptoms was significantly higher in subjects with elevated grief. Depressive symptoms showed no significant change from pre- to posttest in the emotional writing condition, whereas they significantly decreased in the control condition. Conclusions: Results imply that unstructured, brief emotional writing might not be indicated in adolescents affected by early parental loss who show severe and long-term distress; a more structured approach seems recommendable.

  15. An orphan chemotaxis sensor regulates virulence and antibiotic tolerance in the human pathogen Pseudomonas aeruginosa.

    Directory of Open Access Journals (Sweden)

    Heather Pearl McLaughlin

    Full Text Available The synthesis of virulence factors by pathogenic bacteria is highly regulated and occurs in response to diverse environmental cues. An array of two component systems (TCSs serves to link perception of different cues to specific changes in gene expression and/or bacterial behaviour. Those TCSs that regulate functions associated with virulence represent attractive targets for interference in anti-infective strategies for disease control. We have previously identified PA2572 as a putative response regulator required for full virulence of Pseudomonas aeruginosa, the opportunistic human pathogen, to Galleria mellonella (Wax moth larvae. Here we have investigated the involvement of candidate sensors for signal transduction involving PA2572. Mutation of PA2573, encoding a probable methyl-accepting chemotaxis protein, gave rise to alterations in motility, virulence, and antibiotic resistance, functions which are also controlled by PA2572. Comparative transcriptome profiling of mutants revealed that PA2572 and PA2573 regulate expression of a common set of 49 genes that are involved in a range of biological functions including virulence and antibiotic resistance. Bacterial two-hybrid analysis indicated a REC-dependent interaction between PA2572 and PA2573 proteins. Finally expression of PA2572 in the PA2573 mutant background restored virulence to G. mellonella towards wild-type levels. The findings indicate a role for the orphan chemotaxis sensor PA2573 in the regulation of virulence and antibiotic tolerance in P. aeruginosa and indicate that these effects are exerted in part through signal transduction involving PA2572.

  16. The GA5 locus of Arabidopsis thaliana encodes a multifunctional gibberellin 20-oxidase: Molecular cloning and functional expression

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Yun-Ling; Li, Li; Wu, Keqiang [Michigan State Univ., East Lansing, MI (United States)] [and others

    1995-07-03

    The biosynthesis of gibberellins (GAs) after GA{sub 12}-aldehyde involves a series of oxidative steps that lead to the formation of bioactive GAs. Previously, a cDNA clone encoding a GA 20-oxidase [gibberellin, 2-oxoglutarate:oxygen oxidoreductase (20-hydroxylating, oxidizing), EC 1.14.11-] was isolated by immunoscreening a cDNA library from liquid endosperm of pumpkin (Cucurbita maxima L.) with antibodies against partially purified GA 20-oxidase. Here, we report isolation of a genomic clone for GA 20-oxidase from a genomic library of the long-day species Arabidopsis thaliana Heynh., strain Columbia, by using the pumpkin cDNA clone as a heterologous probe. This genomic clone contains a GA 20-oxidase gene that consists of three exons and two introns. The three exons are 1131-bp long and encode 377 amino acid residues. A cDNA clone corresponding to the putative GA 20-oxidase genomic sequence was constructed with the reverse transcription-PCR method, and the identity of the cDNA clone was confirmed by analyzing the capability of the fusion protein expressed in Escherichia coli to convert GA{sub 53} to GA{sub 44} and GA{sub 19} to GA{sub 20}. The Arabidopsis GA 20-oxidase shares 55% identity and >80% similarity with the pumpkin GA 20-oxidase at the derived amino acid level. Both GA 20-oxidases share high homology with other 2-oxoglutarate-dependent dioxygenases (2-ODDs), but the highest homology was found between the two GA 20-oxidases. Mapping results indicated tight linkage between the cloned GA 20-oxidase and the GA locus of Arabidopsis. The ga5 semidwarf mutant contains a G {yields} A point mutation that inserts a translational stop codon in the protein-coding sequence, thus confirming that the GA5 locus encodes GA 20-oxidase. Expression of the GA5 gene in Arabidopsis leaves was enhanced after plants were transferred from short to long days; it was reduced by GA{sub 4} treatment, suggesting end-product repression in the GA biosynthetic pathway. 28 refs., 6 figs.

  17. Paying for the Orphan Drug System: break or bend? Is it time for a new evaluation system for payers in Europe to take account of new rare disease treatments?

    OpenAIRE

    Hughes-Wilson Wills; Palma Ana; Schuurman Ad; Simoens Steven

    2012-01-01

    Abstract Since its enactment in 2000, the European Orphan Medicinal Products Regulation has allowed the review and approval of approaching 70 treatments for some 55 different conditions in Europe. Success does not come without a price, however. Many of these so-called “orphan drugs” have higher price points than treatments for more common diseases. This has been raising debate as to whether the treatments are worth it, which, in turn risks blocking patient access to treatment. To date, orphan...

  18. AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data

    KAUST Repository

    Zhang, Runxuan

    2016-05-06

    Background Alternative splicing is the major post-transcriptional mechanism by which gene expression is regulated and affects a wide range of processes and responses in most eukaryotic organisms. RNA-sequencing (RNA-seq) can generate genome-wide quantification of individual transcript isoforms to identify changes in expression and alternative splicing. RNA-seq is an essential modern tool but its ability to accurately quantify transcript isoforms depends on the diversity, completeness and quality of the transcript information. Results We have developed a new Reference Transcript Dataset for Arabidopsis (AtRTD2) for RNA-seq analysis containing over 82k non-redundant transcripts, whereby 74,194 transcripts originate from 27,667 protein-coding genes. A total of 13,524 protein-coding genes have at least one alternatively spliced transcript in AtRTD2 such that about 60% of the 22,453 protein-coding, intron-containing genes in Arabidopsis undergo alternative splicing. More than 600 putative U12 introns were identified in more than 2,000 transcripts. AtRTD2 was generated from transcript assemblies of ca. 8.5 billion pairs of reads from 285 RNA-seq data sets obtained from 129 RNA-seq libraries and merged along with the previous version, AtRTD, and Araport11 transcript assemblies. AtRTD2 increases the diversity of transcripts and through application of stringent filters represents the most extensive and accurate transcript collection for Arabidopsis to date. We have demonstrated a generally good correlation of alternative splicing ratios from RNA-seq data analysed by Salmon and experimental data from high resolution RT-PCR. However, we have observed inaccurate quantification of transcript isoforms for genes with multiple transcripts which have variation in the lengths of their UTRs. This variation is not effectively corrected in RNA-seq analysis programmes and will therefore impact RNA-seq analyses generally. To address this, we have tested different genome

  19. Advances in Arabidopsis research in China from 2006 to 2007

    Institute of Scientific and Technical Information of China (English)

    LIANG Yan; ZUO JianRu; YANG WeiCai

    2007-01-01

    @@ Arabidopsis thaliana, a model plant species, has a number of advantages over other plant species as an experimental organism due to many of its genetic and genomic features. The Chinese Arabidopsis community has made significant contributions to plant biology research in recent years[1,2]. In 2006, studies of plant biology in China received more attention than ever before, especially those pertaining to Arabidopsis research. Here we briefly summarize recent advances in Arabidopsis research in China.

  20. Mining the active proteome of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Renier A. L. Van Der Hoorn

    2011-11-01

    Full Text Available Assigning functions to the >30.000 proteins encoded by the Arabidopsis genome is a challenging task of the Arabidopsis Functional Genomics Network. Although genome-wide technologies like proteomics and transcriptomics have generated a wealth of information that significantly accelerated gene annotation, protein activities are poorly predicted by transcript or protein levels as protein activities are post-translationally regulated. To directly display protein activities in Arabidopsis proteomes, we developed and applied Activity-based Protein Profiling (ABPP. ABPP is based on the use of small molecule probes that react with the catalytic residues of distinct protein classes in an activity-dependent manner. Labeled proteins are separated and detected from proteins gels and purified and identified by mass spectrometry. Using probes of six different chemotypes we have displayed of activities of 76 Arabidopsis proteins. These proteins represent over ten different protein classes that contain over 250 Arabidopsis proteins, including cysteine- serine- and metallo-proteases, lipases, acyltransferases, and the proteasome. We have developed methods for identification of in vivo labeled proteins using click-chemistry and for in vivo imaging with fluorescent probes. In vivo labeling has revealed novel protein activities and unexpected subcellular activities of the proteasome. Labeling of extracts displayed several differential activities e.g. of the proteasome during immune response and methylesterases during infection. These studies illustrate the power of ABPP to display the functional proteome and testify to a successful interdisciplinary collaboration involving chemical biology, organic chemistry and proteomics.

  1. Plant insecticide L-canavanine repels Drosophila via the insect orphan GPCR DmX.

    Directory of Open Access Journals (Sweden)

    Christian Mitri

    2009-06-01

    Full Text Available For all animals, the taste sense is crucial to detect and avoid ingesting toxic molecules. Many toxins are synthesized by plants as a defense mechanism against insect predation. One example of such a natural toxic molecule is L-canavanine, a nonprotein amino acid found in the seeds of many legumes. Whether and how insects are informed that some plants contain L-canavanine remains to be elucidated. In insects, the taste sense relies on gustatory receptors forming the gustatory receptor (Gr family. Gr proteins display highly divergent sequences, suggesting that they could cover the entire range of tastants. However, one cannot exclude the possibility of evolutionarily independent taste receptors. Here, we show that L-canavanine is not only toxic, but is also a repellent for Drosophila. Using a pharmacogenetic approach, we find that flies sense food containing this poison by the DmX receptor. DmXR is an insect orphan G-protein-coupled receptor that has partially diverged in its ligand binding pocket from the metabotropic glutamate receptor family. Blockade of DmXR function with an antagonist lowers the repulsive effect of L-canavanine. In addition, disruption of the DmXR encoding gene, called mangetout (mtt, suppresses the L-canavanine repellent effect. To avoid the ingestion of L-canavanine, DmXR expression is required in bitter-sensitive gustatory receptor neurons, where it triggers the premature retraction of the proboscis, thus leading to the end of food searching. These findings show that the DmX receptor, which does not belong to the Gr family, fulfills a gustatory function necessary to avoid eating a natural toxin.

  2. Saving lives for a lifetime: supporting orphans and vulnerable children impacted by HIV/AIDS.

    Science.gov (United States)

    Nyberg, Beverly J; Yates, Dee Dee; Lovich, Ronnie; Coulibaly-Traore, Djeneba; Sherr, Lorraine; Thurman, Tonya Renee; Sampson, Anita; Howard, Brian

    2012-08-15

    President's Emergency Plan for AIDS Relief (PEPFAR's) response to the millions of children impacted by HIV/AIDS was to designate 10% of its budget to securing their futures, making it the leading supporter of programs reaching orphan and vulnerable children (OVC) programs globally. This article describes the evolution of PEPFAR's OVC response based on programmatic lessons learned and an evergrowing understanding of the impacts of HIV/AIDS. In launching this international emergency effort and transitioning it toward sustainable local systems, PEPFAR helped establish both the technical content and the central importance of care and support for OVC as a necessary complement to biomedical efforts to end the HIV/AIDS epidemic. Critical services are reaching millions of HIV-affected children and families through vast networks of community-based responders and strengthened national systems of care. But rapid program scale-up has at times resulted in inconsistent responses, failure to match resources to properly assessed needs, and a dearth of rigorous program evaluations. Key investments should continue to be directed toward more sustainable and effective responses. These include greater attention to children's most significant developmental stages, a focus on building the resilience of families and communities, a proper balance of government and civil society investments, and more rigorous evaluation and research to ensure evidence-based programming. Even as HIV prevalence declines and medical treatment improves and expands, the impacts of HIV/AIDS on children, families, communities, economies, and societies will continue to accumulate for generations. Protecting the full potential of children-and thus of societies-requires sustained and strategic global investments aligned with experience and science.

  3. ORPHANS IN EASTERN AZOV DURING WORLD WAR II AND THE EARLY POSTWAR YEARS

    Directory of Open Access Journals (Sweden)

    E. A. CHAIKA

    2016-01-01

    Full Text Available The article is devoted to one of the most important problems, the elimination of child homelessness in the Krasnodar Territory in 1941-1950 years. It was found that the Kuban from the first months of the war was one of the regions where the population is evacuated from the occupied territories of the USSR. Analyze the process of evacuation of children in orphanages in the summer of 1942 it demonstrated that even before the complete liberation of Krasnodar region from the Nazi invaders in its territory began to revive children's institutions. The author investigated the damage caused to children's homes occupiers of their financial situation during the war years; it showed the difficulties faced by students in the study period. The researcher concluded that during the war the main form of struggle against children's homelessness in the East Sea of Azov and other areas of the Krasnodar Territory was an orphanage. The country's leaders, using pre-war forms and methods of elimination of child neglect. In the early postwar years, financial status of children's institutions in the Kuban region in comparison with the military over the years has improved somewhat. Funding for children's homes was carried out in full, improved nutrition students. Despite the presence of local constraints on material maintenance of children's homes. In general, the existing system of social protection of orphans has fulfilled its function in the short term has been eliminated homeless children throughout the territory of Krasnodar region. The article shows the role of the party and government bodies in ensuring the conditions for the functioning of orphanages. For the opening theme used a variety of sources, some of which are introduced into scientific circulation for the first time.

  4. Comparative Analysis of the Orphan CRISPR2 Locus in 242 Enterococcus faecalis Strains.

    Directory of Open Access Journals (Sweden)

    Karthik Hullahalli

    Full Text Available Clustered, Regularly Interspaced Short Palindromic Repeats and their associated Cas proteins (CRISPR-Cas provide prokaryotes with a mechanism for defense against mobile genetic elements (MGEs. A CRISPR locus is a molecular memory of MGE encounters. It contains an array of short sequences, called spacers, that generally have sequence identity to MGEs. Three different CRISPR loci have been identified among strains of the opportunistic pathogen Enterococcus faecalis. CRISPR1 and CRISPR3 are associated with the cas genes necessary for blocking MGEs, but these loci are present in only a subset of E. faecalis strains. The orphan CRISPR2 lacks cas genes and is ubiquitous in E. faecalis, although its spacer content varies from strain to strain. Because CRISPR2 is a variable locus occurring in all E. faecalis, comparative analysis of CRISPR2 sequences may provide information about the clonality of E. faecalis strains. We examined CRISPR2 sequences from 228 E. faecalis genomes in relationship to subspecies phylogenetic lineages (sequence types; STs determined by multilocus sequence typing (MLST, and to a genome phylogeny generated for a representative 71 genomes. We found that specific CRISPR2 sequences are associated with specific STs and with specific branches on the genome tree. To explore possible applications of CRISPR2 analysis, we evaluated 14 E. faecalis bloodstream isolates using CRISPR2 analysis and MLST. CRISPR2 analysis identified two groups of clonal strains among the 14 isolates, an assessment that was confirmed by MLST. CRISPR2 analysis was also used to accurately predict the ST of a subset of isolates. We conclude that CRISPR2 analysis, while not a replacement for MLST, is an inexpensive method to assess clonality among E. faecalis isolates, and can be used in conjunction with MLST to identify recombination events occurring between STs.

  5. ANTIOXIDANT ENZYME ACTIVITY AMONG ORPHANS INFECTED WITH INTESTINAL PARASITES IN PATHUM THANI PROVINCE, THAILAND.

    Science.gov (United States)

    Mahittikorn, Aongart; Prasertbun, Rapeepan; Mori, Hirotake; Popruk, Supaluk

    2014-11-01

    Intestinal parasitic infections can negatively impact growth and nutrition in children. The infections can induce oxidative stress, resulting in a variety of illnesses. We measured antioxidant enzyme levels in orphan children infected with intestinal parasites to investigate the influence of nutritional status on antioxidant enzymes. This cross sectional study was conducted at an orphanage in Thailand. Stool samples were obtained from each subject and examined for intestinal parasites. Anthropometric measurements, complete blood count and biochemical parameters, including serum superoxide dismutase (SOD) and glutathione peroxidase (GPx) levels, were obtained from studied subjects. One hundred twenty-eight children were included in the study. Intestinal parasites were found on microscopic examination of the stools in 36.7% (47/128); 18% (23/128) had a mixed parasite infection. Intestinal protozoa were found in 34.4% of subjects and intestinal helminthes were found in 2.3%. The median GPx level in children infected with intestinal parasites (2.3 ng/ml) was significantly lower than in non-infected children (7.7 ng/ml) (p parasites, 2) non-pathogenic parasites and 3) no intestinal parasite infection, GPx levels differed significantly among three groups (2.2 ng/ml, 2.4 ng/ml and 7.7 ng/ml, respectively) (p parasites (107.2 ng/ml) was significantly higher than in underweight children infected with non-pathogenic parasites (68.6 ng/ml) and without intestinal parasite infections (72.2 ng/ml). The present study identified two key findings: low GPx levels in children with intestinal parasitic infections, and the potential impact of malnutrition on some antioxidants.

  6. Regulation of sialidase production in Clostridium perfringens by the orphan sensor histidine kinase ReeS.

    Directory of Open Access Journals (Sweden)

    Thomas J Hiscox

    Full Text Available Clostridium perfringens is ubiquitous in nature and is often found as a commensal of the human and animal gastrointestinal tract. It is the primary etiological agent of clostridial myonecrosis, or gas gangrene, a serious infection that results in extensive tissue necrosis due to the action of one or more potent extracellular toxins. α-toxin and perfringolysin O are the major extracellular toxins involved in the pathogenesis of gas gangrene, but histotoxic strains of C. perfringens, such as strain 13, also produce many degradative enzymes such as collagenases, hyaluronidases, sialidases and the cysteine protease, α-clostripain. The production of many of these toxins is regulated either directly or indirectly by the global VirSR two-component signal transduction system. By isolating a chromosomal mutant and carrying out microarray analysis we have identified an orphan sensor histidine kinase, which we have named ReeS (regulator of extracellular enzymes sensor. Expression of the sialidase genes nanI and nanJ was down-regulated in a reeS mutant. Since complementation with the wild-type reeS gene restored nanI and nanJ expression to wild-type levels, as shown by quantitative reverse transcription-PCR and sialidase assays we concluded that ReeS positively regulates the expression of these sialidase genes. However, mutation of the reeS gene had no significant effect on virulence in the mouse myonecrosis model. Sialidase production in C. perfringens has been previously shown to be regulated by both the VirSR system and RevR. In this report, we have analyzed a previously unknown sensor histidine kinase, ReeS, and have shown that it also is involved in controlling the expression of sialidase genes, adding further complexity to the regulatory network that controls sialidase production in C. perfringens.

  7. Neuroanatomical distribution of the orphan GPR50 receptor in adult sheep and rodent brains.

    Science.gov (United States)

    Batailler, M; Mullier, A; Sidibe, A; Delagrange, P; Prévot, V; Jockers, R; Migaud, M

    2012-05-01

    GPR50, formerly known as melatonin-related receptor, is one of three subtypes of the melatonin receptor subfamily, together with the MT(1) and MT(2) receptors. By contrast to these two high-affinity receptor subtypes and despite its high identity with the melatonin receptor family, GPR50 does not bind melatonin or any other known ligand. Specific and reliable immunological tools are therefore needed to be able to elucidate the physiological functions of this orphan receptor that are still largely unknown. We have generated and validated a new specific GPR50 antibody against the ovine GPR50 and used it to analyse the neuroanatomical distribution of the GPR50 in sheep, rat and mouse whole brain. We demonstrated that GPR50-positive cells are widely distributed in various regions, including the hypothalamus and the pars tuberalis of the pituitary, in all the three species studied. GPR50 expressing cells are abundant in the dorsomedial nucleus of the hypothalamus, the periventricular nucleus and the median eminence. In rodents, immunohistochemical studies revealed a broader distribution pattern for the GPR50 protein. GPR50 immunoreactivity is found in the medial preoptic area (MPA), the lateral septum, the lateral hypothalamic area, the bed nucleus of the stria terminalis, the vascular organ of the laminae terminalis and several regions of the amygdala, including the medial nuclei of amygdala. Additionally, in the rat brain, GPR50 protein was localised in the CA1 pyramidal cell layer of the dorsal hippocampus. In mice, moderate to high numbers of GPR50-positive cells were also found in the subfornical organ. Taken together, these results provide an enlarged distribution of GPR50 protein, give further insight into the organisation of the melatoninergic system, and may lay the framework for future studies on the role of the GPR50 in the brain.

  8. Molecular pathways: the role of NR4A orphan nuclear receptors in cancer.

    LENUS (Irish Health Repository)

    Mohan, Helen M

    2012-06-15

    Nuclear receptors are of integral importance in carcinogenesis. Manipulation of classic ligand-activated nuclear receptors, such as estrogen receptor blockade in breast cancer, is an important established cancer therapy. Orphan nuclear receptors, such as nuclear family 4 subgroup A (NR4A) receptors, have no known natural ligand(s). These elusive receptors are increasingly recognized as molecular switches in cell survival and a molecular link between inflammation and cancer. NR4A receptors act as transcription factors, altering expression of downstream genes in apoptosis (Fas-ligand, TRAIL), proliferation, DNA repair, metabolism, cell migration, inflammation (interleukin-8), and angiogenesis (VEGF). NR4A receptors are modulated by multiple cell-signaling pathways, including protein kinase A\\/CREB, NF-κB, phosphoinositide 3-kinase\\/AKT, c-jun-NH(2)-kinase, Wnt, and mitogen-activated protein kinase pathways. NR4A receptor effects are context and tissue specific, influenced by their levels of expression, posttranslational modification, and interaction with other transcription factors (RXR, PPAR-Υ). The subcellular location of NR4A "nuclear receptors" is also important functionally; novel roles have been described in the cytoplasm where NR4A proteins act both indirectly and directly on the mitochondria to promote apoptosis via Bcl-2. NR4A receptors are implicated in a wide variety of malignancies, including breast, lung, colon, bladder, and prostate cancer; glioblastoma multiforme; sarcoma; and acute and\\/or chronic myeloid leukemia. NR4A receptors modulate response to conventional chemotherapy and represent an exciting frontier for chemotherapeutic intervention, as novel agents targeting NR4A receptors have now been developed. This review provides a concise clinical overview of current knowledge of NR4A signaling in cancer and the potential for therapeutic manipulation.

  9. Analysis and Comparison of Foreign and Domestic Orphan Drug Registration Policies%国内外孤儿药注册制度比较研究

    Institute of Scientific and Technical Information of China (English)

    信枭雄; 管晓东; 陈敬; 史录文

    2013-01-01

    目的 借鉴部分发达国家与地区针对孤儿药注册管理的先进经验,探求适用于我国的孤儿药注册制度.方法 对美国、日本、欧盟、澳大利亚、中国台湾等地所采取的孤儿药注册制度进行研究和对比,并且对我国孤儿药注册管理的历史和现状进行总结.结果 国际上针对孤儿药注册普遍采用“身份认定+上市审批”的方式,这种方式切实有效地推动了各国及地区孤儿药产业的发展,提高了孤儿药的可及性.结论 我国有关部门应借鉴先进经验,尽快建立起孤儿药制度体系并不断完善其注册制度.%OBJECTIVE To learn from several developed countries and regions about their experience of orphan drug registration management and to explore appropriate orphan drug registration policy for China.METHODS The orphan drug registration policies of America,Japan,EU,Australia and Taiwan were analyze and compared,and the history and current situation of the orphan drug registration in China were summarized.RESULTS It has been a common trend in the world to use "designation of drugs + market approval" pattern for orphan drug registration,which has promoted the development of orphan drugs and increased the accessibility of orphan drugs in the above-mentioned countries and regions.CONCLUSION Related government departments in China should learn the advanced experience and establish our orphan drug system as soon as possible,at the same time,we should keep improving the orphan drug registration policy in China.

  10. Promoting uptake of child HIV testing: an evaluation of the role of a home visiting program for orphans and vulnerable children in South Africa.

    Science.gov (United States)

    Thurman, Tonya R; Luckett, Brian; Taylor, Tory; Carnay, Melissa

    2016-03-01

    HIV counseling and testing (HCT) is critical for children in generalized epidemic settings, but significant shortfalls in coverage persist, notably among orphans and others at disproportionate risk of infection. This study investigates the impact of a home visiting program in South Africa on orphaned and vulnerable children's uptake of HCT. Using propensity score matching, survey data for children receiving home visits from trained community-based care workers were compared to data from children living in similar households that had not yet received home visits (n = 1324). Home visits by community-based care workers increased the odds of a child being tested by 97% (OR = 1.97, 95% CI = 1.34-2.92). The home visitation program had an especially pronounced effect on orphans, more than doubling their odds of being tested (OR = 2.12, 95% CI = 1.00-4.47) compared to orphans living in similar households that did not receive home visits. Orphan status alone had no effect on HCT independent of program exposure, suggesting that the program was uniquely able to increase testing in this subgroup. Results highlight the potential for increasing HCT access among children at high risk through targeted community-based initiatives.

  11. [Shift of focus in the financing of Hungarian drugs. Reimbursement for orphan drugs for treating rare diseases: financing of enzyme replacement therapy in Hungary].

    Science.gov (United States)

    Szegedi, Márta; Molnár, Mária Judit; Boncz, Imre; Kosztolányi, György

    2014-11-01

    Focusing on the benefits of patients with rare disease the authors analysed the aspects of orphan medicines financed in the frame of the Hungarian social insurance system in 2012 in order to make the consumption more rational, transparent and predictable. Most of the orphan drugs were financed in the frame of compassionate use by the reimbursement system. Consequently, a great deal of crucial problems occurred in relation to the unconventional subsidized method, especially in the case of the highest cost enzyme replacement therapies. On the base of the findings, proposals of the authors are presented for access to orphan drugs, fitting to the specific professional, economical and ethical aspects of this unique field of the health care system. The primary goal is to provide a suitable subsidized method for the treatment of rare disease patients with unmet medical needs. The financial modification of orphans became indispensible in Hungary. Professionals from numerous fields dealing with rare disease patients' care expressed agreement on the issue. Transforming the orphan medicines' financial structure has been initiated according to internationally shared principles.

  12. The Formation of the Dilemma and Resolution Path of Orphan Works' Copyright%孤儿作品的版权困境及解决路径

    Institute of Scientific and Technical Information of China (English)

    马海群; 高思静

    2011-01-01

    解析孤儿作品的含义和形成原因,指出解决孤儿作品版权困境的必要性,在此基础上介绍分析国外解决孤儿作品版权问题的方案,最后提出版权管理信息、认证许可模式、延伸性集体管理、强制许可模式、责任限制制度、版权例外模式的6项建议,以期更好地解决我国孤儿作品的版权困境问题。%By analyzing the definition of orphan works and discussing the formation of orphan works, this paper proposes the necessity of solutions to the dilemma of orphan works, and then analyzes programs of solving orphan works' copyright issues from ahroad. This paper expects to resolve the orphan werks' copyright dilemma by proposing the following six adviees, including to rights management information,creative commons license, extended collective licensing,compulsory license,limited liability and statutory limitation.

  13. Recent Progress in Arabidopsis Research in China: A Preface

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hong Xu

    2006-01-01

    @@ In 2002, a workshop on Arabidopsis research in China was held in Shanghai, when a small group of Chinese plant scientists was working on this model species. Since then, we have witnessed the rapid growth of Arabidopsis research in China. This special issue of Journal of Integrative Plant Biology is dedicated exclusively to the Fourth Workshop on Arabidopsis Research in China, scheduled on November 30, 2005, in Beijing. In addition to reports collected in this special issue, the Chinese Arabidopsis community has been able to make significant contributions to many research fields. Here, I briefly summarize recent advances in Arabidopsis research in China.

  14. The arabidopsis cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara

    2016-05-11

    Background Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals. Methods An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling. Results A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment. Conclusions We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.

  15. Correlates of poor health among orphans and abandoned children in less wealthy countries: the importance of caregiver health.

    Directory of Open Access Journals (Sweden)

    Nathan Thielman

    Full Text Available BACKGROUND: More than 153 million children worldwide have been orphaned by the loss of one or both parents, and millions more have been abandoned. We investigated relationships between the health of orphaned and abandoned children (OAC and child, caregiver, and household characteristics among randomly selected OAC in five countries. METHODOLOGY: Using a two-stage random sampling strategy in 6 study areas in Cambodia, Ethiopia, India, Kenya, and Tanzania, the Positive Outcomes for Orphans (POFO study identified 1,480 community-living OAC ages 6 to 12. Detailed interviews were conducted with 1,305 primary caregivers at baseline and after 6 and 12 months. Multivariable logistic regression models describe associations between the characteristics of children, caregivers, and households and child health outcomes: fair or poor child health; fever, cough, or diarrhea within the past two weeks; illness in the past 6 months; and fair or poor health on at least two assessments. PRINCIPAL FINDINGS: Across the six study areas, 23% of OAC were reported to be in fair or poor health; 19%, 18%, and 2% had fever, cough, or diarrhea, respectively, within the past two weeks; 55% had illnesses within the past 6 months; and 23% were in fair or poor health on at least two assessments. Female gender, suspected HIV infection, experiences of potentially traumatic events, including the loss of both parents, urban residence, eating fewer than 3 meals per day, and low caregiver involvement were associated with poorer child health outcomes. Particularly strong associations were observed between child health measures and the health of their primary caregivers. CONCLUSIONS: Poor caregiver health is a strong signal for poor health of OAC. Strategies to support OAC should target the caregiver-child dyad. Steps to ensure food security, foster gender equality, and prevent and treat traumatic events are needed.

  16. Platelet function and Isoprostane biology. Should Isoprostanes be the newest member of the Orphan-ligand family?

    Directory of Open Access Journals (Sweden)

    Khasawneh Fadi T

    2010-04-01

    Full Text Available Abstract While there have been many reports investigating the biological activity and signaling mechanisms of isoprostanes, their role in biology, particularly in platelets, appears to still be underestimated. Moreover, whether these lipids have their own receptors is still debated, despite multiple reports that discrete receptors for isporpstanes do exist on platelets, vascular tissues, amongst others. This paper provides a review of the important literature of isoprostanes and provides reasoning that isoprostanes should be classified as orphan ligands until their receptor(s is/are identified.

  17. Cloning and characterization of a human orphan family C G-protein coupled receptor GPRC5D

    DEFF Research Database (Denmark)

    Bräuner-Osborne, H; Jensen, A A; Sheppard, P O

    2001-01-01

    predicted to encode an additional subtype. The full length coding regions of mouse mGprc5d and human GPRC5D were cloned and shown to contain predicted open reading frames of 300 and 345 amino acids, respectively. GPRC5D has seven putative transmembrane segments and is expressed in the cell membrane...... intestine, whereas other organs only express a subset of the genes. In an attempt to delineate the signal transduction pathway(s) of the orphan receptors, a series of chimeric receptors containing the amino terminal domain of the calcium sensing receptor or metabotropic glutamate receptor subtype 1...

  18. Role of G protein-coupled orphan receptors in intestinal inflammation: novel targets in inflammatory bowel diseases.

    Science.gov (United States)

    Wasilewski, Andrzej; Storr, Martin; Zielińska, Marta; Fichna, Jakub

    2015-03-01

    A large number of proteins were classified into the family of G protein-coupled receptors (GPCRs). Based on their characteristic serpentine domain, they are called 7 TM receptors. Presently, their ligands and physiological functions remain unknown. In this review, we summarize what is known on these receptors and discuss the potential use of these orphan GPCRs (GPRs) in the induction or maintenance of remission in inflammatory bowel diseases. We focus on GPRs 30, 41, 43, 55, 119, and 120, where scientific evidence supports a potential role in intestinal inflammation.

  19. Reference: 510 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ch stabilizes the water-oxidizing complex, is represented in Arabidopsis thaliana (Arabidopsis) by two isofo...rms. Two T-DNA insertion mutant lines deficient in either the PsbO1 or the PsbO2 protein were re...ally. Both PsbO proteins were able to support the oxygen evolution activity of PSII, although PsbO2 was less... efficient than PsbO1 under photoinhibitory conditions. Prolonged high light stress led to re...duced growth and fitness of the mutant lacking PsbO2 as compared with the wild type and the muta

  20. Reference: 600 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available n M et al. 2007 Jun. Plant J. 50(5):810-24. A novel abscisic acid (ABA)-deficient mutant, aba4, was identified in a scre...en for paclobutrazol-resistant germination. Compared with wild-type, the mutant showed reduced e...by map-based cloning, and found to be a unique gene in the Arabidopsis genome. The predicted protein has fou...r putative helical transmembrane domains and shows significant similarity to pred...icted proteins from tomato, rice and cyanobacteria. Constitutive expression of the ABA4 gene in Arabidopsis

  1. Reference: 59 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 59 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u4ria224u14563930i Kaczorowski Kare...naling network in Arabidopsis, we used a sensitized genetic screen for deetiolation-defective seedlings. Two allelic mutants were... isolated that exhibited reduced sensitivity to both continuous red and far-re...d light, suggesting involvement in both phyA and phyB signaling. The molecular lesions res...ponsible for the phenotype were shown to be mutations in the Arabidopsis PSEUDO-RESPONSE REGULATOR7 (PRR7) g

  2. Reference: 640 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available er Alois et al. 2007 Jul. Plant Cell 19(7):2213-24. Wound signaling pathways in plants are mediated by mitog...en-activated protein kinases (MAPKs) and stress hormones, such as ethylene and jasmonates. In Arabidopsis th...ed investigations; however, the involvement of specific phosphatases in wound signaling is not known. Here, ...we show that AP2C1, an Arabidopsis Ser/Thr phosphatase of type 2C, is a novel stress signal regulator that inactivates the stress-re... significantly higher amounts of jasmonate upon wounding and are more resistant to phytophagous mites (Tetra

  3. Reference: 756 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available elle et al. 2008 Jun. Plant Physiol. 147(2):595-610. Treatment of Arabidopsis (Arabidopsis thaliana) alterna...tive oxidase1a (aox1a) mutant plants with moderate light under drought conditions resulted in a phenotypic difference compare...d with ecotype Columbia (Col-0), as evidenced by a 10-fold incre...ase in the accumulation of anthocyanins in leaves, alterations in photosynthetic efficiency, and increased superoxide radical and re...duced root growth at the early stages of seedling growth. Analysis of metabolite profiles re

  4. Reference: 457 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available n et al. 2006 Oct. Plant J. 48(2):238-48. The Arabidopsis BAP1 gene encodes a small protein with a C2-like domain. Here...er and is associated with membranes in vivo. We identify multiple roles of BAP1 in negatively re...gulating defense responses and cell death in Arabidopsis thaliana. The loss of BAP1 function ...confers an enhanced disease resistance to virulent bacterial and oomycete pathogens. The enhanced resistance... is mediated by salicylic acid, PAD4 and a disease resistance gene SNC1. BAP1 is

  5. Gibberellins control fruit patterning in Arabidopsis thaliana.

    Science.gov (United States)

    Arnaud, Nicolas; Girin, Thomas; Sorefan, Karim; Fuentes, Sara; Wood, Thomas A; Lawrenson, Tom; Sablowski, Robert; Østergaard, Lars

    2010-10-01

    The Arabidopsis basic helix-loop-helix (bHLH) proteins INDEHISCENT (IND) and ALCATRAZ (ALC) specify tissues required for fruit opening that have major roles in seed dispersal and plant domestication. Here, we show that synthesis of the phytohormone gibberellin is a direct and necessary target of IND, and that ALC interacts directly with DELLA repressors, which antagonize ALC function but are destabilized by gibberellin. Thus, the gibberellin/DELLA pathway has a key role in patterning the Arabidopsis fruit, and the interaction between DELLA and bHLH proteins, previously shown to connect gibberellin and light responses, is a versatile regulatory module also used in tissue patterning.

  6. Unexpected Diversity of Chloroplast Noncoding RNAs as Revealed by Deep Sequencing of the Arabidopsis Transcriptome.

    Science.gov (United States)

    Hotto, Amber M; Schmitz, Robert J; Fei, Zhangjun; Ecker, Joseph R; Stern, David B

    2011-12-01

    Noncoding RNAs (ncRNA) are widely expressed in both prokaryotes and eukaryotes. Eukaryotic ncRNAs are commonly micro- and small-interfering RNAs (18-25 nt) involved in posttranscriptional gene silencing, whereas prokaryotic ncRNAs vary in size and are involved in various aspects of gene regulation. Given the prokaryotic origin of organelles, the presence of ncRNAs might be expected; however, the full spectrum of organellar ncRNAs has not been determined systematically. Here, strand-specific RNA-Seq analysis was used to identify 107 candidate ncRNAs from Arabidopsis thaliana chloroplasts, primarily encoded opposite protein-coding and tRNA genes. Forty-eight ncRNAs were shown to accumulate by RNA gel blot as discrete transcripts in wild-type (WT) plants and/or the pnp1-1 mutant, which lacks the chloroplast ribonuclease polynucleotide phosphorylase (cpPNPase). Ninety-eight percent of the ncRNAs detected by RNA gel blot had different transcript patterns between WT and pnp1-1, suggesting cpPNPase has a significant role in chloroplast ncRNA biogenesis and accumulation. Analysis of materials deficient for other major chloroplast ribonucleases, RNase R, RNase E, and RNase J, showed differential effects on ncRNA accumulation and/or form, suggesting specificity in RNase-ncRNA interactions. 5' end mapping demonstrates that some ncRNAs are transcribed from dedicated promoters, whereas others result from transcriptional read-through. Finally, correlations between accumulation of some ncRNAs and the symmetrically transcribed sense RNA are consistent with a role in RNA stability. Overall, our data suggest that this extensive population of ncRNAs has the potential to underpin a previously underappreciated regulatory mode in the chloroplast.

  7. CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes

    Directory of Open Access Journals (Sweden)

    Moreau Yves

    2007-10-01

    Gène genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family Tags or GFTs to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition. Conclusion To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA repertoire is available through the CATMA database http://www.catma.org.

  8. 罕用药新品种开发及临床评价%Development and clinical evaluation of orphan drugs

    Institute of Scientific and Technical Information of China (English)

    袁芳; 沈舜义

    2011-01-01

    The research and development of orphan drugs has been concerned gradually in recent years. The experience of developed countries in this field is a good reference to our country. This review describes the orphan drugs development policy in the United States and other developed countries, especially focuses on the recent listed orphan drugs and their clinical evaluation.%我国罕用药的研发近年逐步引起关注,目前我国对于罕见病的研究以及罕用药的开发主要参照国际发达因家的经验.本义简要回顾美国等发达国家鼓励罕用药开发的相关政策,重点介绍近期上市的儿种罕用药新品种及其临床评价.

  9. 欧美孤儿药的研究与开发现状%Current situation of orphan drug research and development in the Europe and America

    Institute of Scientific and Technical Information of China (English)

    田圆圆; 张象麟; 董江萍

    2012-01-01

    This paper analyzed the current situation of the orphan drug development in the Europe and A-merica. There are many difficulties in orphan drug research and development; however, current regulations, stimulating measures and other opportunity give the orphan drug impetus to develop, and promote the treatment of the patients with rare diseases. In fact, the perfect policies and reasonable measures of the government can solve the barriers of the orphan drug and ensure availability of new treatment to patients. The successful experience of orphan drug development in Europe and America can contribute to the establishment of the orphan drug management policies in China.%文中对欧美孤儿药开发现状进行了分析.孤儿药研发尽管面临众多困难,但在欧美孤儿药现有制度法规、优惠措施及其他机遇的推动下,取得了较好的成果,促进了对罕见病患者的医疗救治.事实证明,政府完善的政策和采取合理的措施和方法,可解决当前孤儿药研发面临的诸多障碍,保证患者对新治疗方法的可获得性.欧美孤儿药的研发成功经验可为我国孤儿药管理政策和制度的建立提供一定的借鉴.

  10. The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes.

    Directory of Open Access Journals (Sweden)

    Adam Alexander Thil Smith

    2012-05-01

    Full Text Available Of all biochemically characterized metabolic reactions formalized by the IUBMB, over one out of four have yet to be associated with a nucleic or protein sequence, i.e. are sequence-orphan enzymatic activities. Few bioinformatics annotation tools are able to propose candidate genes for such activities by exploiting context-dependent rather than sequence-dependent data, and none are readily accessible and propose result integration across multiple genomes. Here, we present CanOE (Candidate genes for Orphan Enzymes, a four-step bioinformatics strategy that proposes ranked candidate genes for sequence-orphan enzymatic activities (or orphan enzymes for short. The first step locates "genomic metabolons", i.e. groups of co-localized genes coding proteins catalyzing reactions linked by shared metabolites, in one genome at a time. These metabolons can be particularly helpful for aiding bioanalysts to visualize relevant metabolic data. In the second step, they are used to generate candidate associations between un-annotated genes and gene-less reactions. The third step integrates these gene-reaction associations over several genomes using gene families, and summarizes the strength of family-reaction associations by several scores. In the final step, these scores are used to rank members of gene families which are proposed for metabolic reactions. These associations are of particular interest when the metabolic reaction is a sequence-orphan enzymatic activity. Our strategy found over 60,000 genomic metabolons in more than 1,000 prokaryote organisms from the MicroScope platform, generating candidate genes for many metabolic reactions, of which more than 70 distinct orphan reactions. A computational validation of the approach is discussed. Finally, we present a case study on the anaerobic allantoin degradation pathway in Escherichia coli K-12.

  11. Safety and Security of Radioactive Sealed and Disused/Orphan Sources in Ukraine - German Contribution - 13359

    Energy Technology Data Exchange (ETDEWEB)

    Brasser, Thomas; Hertes, Uwe; Meyer, Thorsten; Uhlenbruck, Hermann [Gesellschaft fuer Anlagen- und Reaktorsicherheit - GRS mbH, Theodor-Heuss-Str. 4, 38122 Braunschweig (Germany); Shevtsov, Alexey [Ukrainian State Production Company IZOTOP 152, Gorky str., 03680 Kiev (Ukraine)

    2013-07-01

    cell to reduce the number of transports of radioactive sources within the city of Kiev. In future, the new established hot cell at IZOTOP's transport and storage facility will be useful for identification and characterization of orphan/disused radioactive sources. The projects implemented are performed in accordance with international recommendations (e. g. IAEA) and national normative documents and will make a crucial contribution towards an improved safety and security management of radioactive sources in Ukraine. (authors)

  12. PEPFAR's support for orphans and vulnerable children: some beneficial effects, but too little data, and programs spread thin.

    Science.gov (United States)

    Bryant, Malcolm; Beard, Jennifer; Sabin, Lora; Brooks, Mohamad I; Scott, Nancy; Larson, Bruce A; Biemba, Godfrey; Miller, Candace; Simon, Jonathon

    2012-07-01

    Sixteen million children in developing and middle-income countries have been orphaned by HIV/AIDS, and at least another million children per year are rendered vulnerable by parental HIV/AIDS-related illness. Since 2003 the US government has provided approximately $1.6 billion to give four million of these children care and support through the President's Emergency Plan for AIDS Relief (PEPFAR). We conducted five studies to evaluate the effectiveness of PEPFAR's interventions for such children in East Africa and southern Africa. We found evidence of beneficial changes in school enrollment rates and on the psychosocial well-being of children. However, we could not demonstrate empirically the impact of most of the PEPFAR initiatives that we examined, primarily because of a lack of baseline data and clear outcome and impact indicators. We also found that many programs were spread so thin across a vulnerable population that little in the way of services actually reached beneficiaries, which raises questions about whether PEPFAR funds are sufficient, or if the program is attempting to do much with too few resources. We offer several recommendations, including better measuring the effect of programs for orphans and vulnerable children by collecting baseline data and conducting well-designed, rigorous outcome and impact evaluations.

  13. Orphans of the AIDS epidemic? The extent, nature and circumstances of child-headed households in South Africa.

    Science.gov (United States)

    Meintjes, Helen; Hall, Katharine; Marera, Double-Hugh; Boulle, Andrew

    2010-01-01

    There is widespread concern that the number of children living in "child-headed households" is rapidly increasing as a result of AIDS-related adult mortality in much of sub-Saharan Africa. Based on analyses of data from several representative national surveys over the period 2000-2007, this paper examines the extent to which this is the case in South Africa. It explores trends in the number of children living in child-only households and characterises these children relative to children living in households with adults (mixed-generation households). The findings indicate that the proportion of child-only households is relatively small (0.47% in 2006) and does not appear to be increasing. In addition, the vast majority (92.1%) of children resident in child-only households have a living parent. The findings raise critical questions about the circumstances leading to the formation of child-only households and highlight that they cannot for the main part be ascribed to HIV orphaning. Nonetheless, the number of children living in this household form is not insignificant, and their circumstances, when compared with children in mixed-generation households, indicate a range of challenges, including greater economic vulnerability and inadequate service access. We argue that a solitary focus on the HIV epidemic and its related orphaning as the cause of child-only households masks other important issues for consideration in addressing their needs, and risks the development of inappropriate policies, programmes and interventions.

  14. Orphan Toxin OrtT (YdcX of Escherichia coli Reduces Growth during the Stringent Response

    Directory of Open Access Journals (Sweden)

    Sabina Islam

    2015-01-01

    Full Text Available Toxin/antitoxin (TA systems are nearly universal in prokaryotes; toxins are paired with antitoxins which inactivate them until the toxins are utilized. Here we explore whether toxins may function alone; i.e., whether a toxin which lacks a corresponding antitoxin (orphan toxin is physiologically relevant. By focusing on a homologous protein of the membrane-damaging toxin GhoT of the Escherichia coli GhoT/GhoS type V TA system, we found that YdcX (renamed OrtT for orphan toxin related to tetrahydrofolate is toxic but is not part of TA pair. OrtT is not inactivated by neighboring YdcY (which is demonstrated to be a protein, nor is it inactivated by antitoxin GhoS. Also, OrtT is not inactivated by small RNA upstream or downstream of ortT. Moreover, screening a genomic library did not identify an antitoxin partner for OrtT. OrtT is a protein and its toxicity stems from membrane damage as evidenced by transmission electron microscopy and cell lysis. Furthermore, OrtT reduces cell growth and metabolism in the presence of both antimicrobials trimethoprim and sulfamethoxazole; these antimicrobials induce the stringent response by inhibiting tetrahydrofolate synthesis. Therefore, we demonstrate that OrtT acts as an independent toxin to reduce growth during stress related to amino acid and DNA synthesis.

  15. Arabidopsis CDS blastp result: AK242890 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242890 J090079L19 At2g32540.1 68415.m03975 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 4e-47 ...

  16. Arabidopsis CDS blastp result: AK242585 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242585 J090010M20 At5g16910.1 68418.m01982 cellulose synthase family protein similar to gi:2827143 cellulo...se synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 1e-28 ...

  17. Arabidopsis CDS blastp result: AK242601 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242601 J090014G03 At4g23990.1 68417.m03448 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 2e-26 ...

  18. Arabidopsis CDS blastp result: AK242601 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242601 J090014G03 At2g32540.1 68415.m03975 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 2e-45 ...

  19. Arabidopsis CDS blastp result: AK242601 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242601 J090014G03 At5g16910.1 68418.m01982 cellulose synthase family protein similar to gi:2827143 cellulo...se synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  20. Arabidopsis CDS blastp result: AK242585 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242585 J090010M20 At1g32180.1 68414.m03958 cellulose synthase family protein similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose synthase-9 (gi:9622890) from Zea mays 1e-24 ...

  1. Arabidopsis CDS blastp result: AK242585 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242585 J090010M20 At5g16910.1 68418.m01982 cellulose synthase family protein similar to gi:2827143 cellulo...se synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 2e-65 ...

  2. Arabidopsis CDS blastp result: AK110534 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK110534 002-168-A07 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 1e-114 ...

  3. Arabidopsis CDS blastp result: AK242890 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242890 J090079L19 At2g32530.1 68415.m03974 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 4e-50 ...

  4. Arabidopsis CDS blastp result: AK242601 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242601 J090014G03 At4g38190.1 68417.m05391 cellulose synthase family protein similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose synthase-5 (gi:9622882) from Zea mays 0.0 ...

  5. Arabidopsis CDS blastp result: AK242601 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242601 J090014G03 At4g23990.1 68417.m03448 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 5e-25 ...

  6. Arabidopsis CDS blastp result: AK242585 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242585 J090010M20 At2g32530.1 68415.m03974 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 8e-98 ...

  7. Arabidopsis CDS blastp result: AK061162 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK061162 006-209-A01 At2g32540.1 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 3e-35 ...

  8. Arabidopsis CDS blastp result: AK242601 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242601 J090014G03 At1g32180.1 68414.m03958 cellulose synthase family protein similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose synthase-9 (gi:9622890) from Zea mays 0.0 ...

  9. Arabidopsis CDS blastp result: AK242585 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242585 J090010M20 At1g32180.1 68414.m03958 cellulose synthase family protein similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose synthase-9 (gi:9622890) from Zea mays 3e-66 ...

  10. Arabidopsis CDS blastp result: AK069071 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK069071 J023010H01 At2g32540.1 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 1e-167 ...

  11. Arabidopsis CDS blastp result: AK121003 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK121003 J023045B21 At2g32540.1 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 1e-167 ...

  12. Arabidopsis CDS blastp result: AK242890 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242890 J090079L19 At4g23990.1 68417.m03448 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 1e-45 ...

  13. Arabidopsis CDS blastp result: AK242585 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242585 J090010M20 At2g32540.1 68415.m03975 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 4e-98 ...

  14. Arabidopsis CDS blastp result: AK060286 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK060286 001-006-C08 At2g32540.1 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 6e-78 ...

  15. Arabidopsis CDS blastp result: AK242890 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242890 J090079L19 At4g38190.1 68417.m05391 cellulose synthase family protein similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose synthase-5 (gi:9622882) from Zea mays 1e-125 ...

  16. Arabidopsis CDS blastp result: AK242601 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242601 J090014G03 At4g23990.1 68417.m03448 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 8e-25 ...

  17. Arabidopsis CDS blastp result: AK242601 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242601 J090014G03 At2g32540.1 68415.m03975 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 3e-31 ...

  18. Arabidopsis CDS blastp result: AK242890 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242890 J090079L19 At5g16910.1 68418.m01982 cellulose synthase family protein similar to gi:2827143 cellulo...se synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 1e-130 ...

  19. Arabidopsis CDS blastp result: AK105393 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK105393 001-123-B04 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  20. Arabidopsis CDS blastp result: AK242601 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242601 J090014G03 At2g32530.1 68415.m03974 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 5e-48 ...

  1. Arabidopsis CDS blastp result: AK242601 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242601 J090014G03 At2g32530.1 68415.m03974 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 2e-29 ...

  2. Arabidopsis CDS blastp result: AK109812 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK109812 002-147-H02 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 5e-90 ...

  3. Arabidopsis CDS blastp result: AK242585 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242585 J090010M20 At4g38190.1 68417.m05391 cellulose synthase family protein similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose synthase-5 (gi:9622882) from Zea mays 8e-63 ...

  4. Arabidopsis CDS blastp result: AK242890 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242890 J090079L19 At1g32180.1 68414.m03958 cellulose synthase family protein similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose synthase-9 (gi:9622890) from Zea mays 1e-126 ...

  5. Arabidopsis CDS blastp result: AK242585 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242585 J090010M20 At4g23990.1 68417.m03448 cellulose synthase family protein similar to cellulose... synthase catalytic subunit from Arabidopsis thaliana [gi:5230423], cellulose synthase-5 from Zea mays [gi:9622882] 1e-124 ...

  6. Arabidopsis CDS blastp result: AK242585 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242585 J090010M20 At4g38190.1 68417.m05391 cellulose synthase family protein similar to cellulose... synthase catalytic subunit gi:2827143 from [Arabidopsis thaliana], cellulose synthase-5 (gi:9622882) from Zea mays 4e-27 ...

  7. Reference: 415 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available study focuses on the seven other Arabidopsis CAD for which functions are not yet elucidated. Their expression patterns were determine...ession of CAD 1, B1, and G genes was determined using their promoters fused to the GUS reporter gene. CAD 1

  8. Arabidopsis CDS blastp result: AK243408 [KOME

    Lifescience Database Archive (English)

    Full Text Available subunit ClpX, putative similar to CLP protease regulatory subunit CLPX GI:2674203 from [Arabidopsis thaliana]; non-consensus... splice donor GC at exon 4; non-consensus splice donor AA at exon 7 1e-151 ...

  9. Arabidopsis CDS blastp result: AK242797 [KOME

    Lifescience Database Archive (English)

    Full Text Available subunit ClpX, putative similar to CLP protease regulatory subunit CLPX GI:2674203 from [Arabidopsis thaliana]; non-consensus... splice donor GC at exon 4; non-consensus splice donor AA at exon 7 2e-23 ...

  10. Arabidopsis CDS blastp result: AK243408 [KOME

    Lifescience Database Archive (English)

    Full Text Available subunit ClpX, putative similar to CLP protease regulatory subunit CLPX GI:2674203 from [Arabidopsis thaliana]; non-consensus... splice donor GC at exon 4; non-consensus splice donor AA at exon 7 2e-12 ...

  11. Reference: 767 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available Arabidopsis thaliana genome. Mutation analysis of 25 of the 27 member genes representing 13 of the 14 sub-families... of the UBP gene family revealed that single-gene mutants of three genes in two sub-families exhibit v

  12. Reference: 158 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available onika et al. 2005 Feb. Plant J. 41(3):386-99. Cullin proteins, which belong to multigenic families in all eu...ic search revealed the existence of at least 76 BTB-domain proteins in Arabidopsis belonging to 11 major families.... Yeast two-hybrid experiments indicate that representative members of certain families are able to phy

  13. Reference: 456 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available h other Spo11/topo VIA proteins, but their functional relationship during meiosis or other processes is not ...s. Thus, the three Arabidopsis Spo11 homologues appear to function in two discrete processes, i.e. AtSPO11-1

  14. Reference: 412 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available the tobacco arcA gene, mediates hormone responses and plays a regulatory role in multiple developmental processes...in RACK1A confer defects in multiple developmental processes including seed germination, leaf production, an...ltiple hormone responsiveness and developmental processes in Arabidopsis. 11 2697-708 16829549 2006 Journal

  15. Reference: 51 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available urce of acetyl-CoA formation in the plastids of plants and is composed of multiple copies of four different ...astidic E2 (dihydrolipoyl acetyltransferase) subunit, plE2, of the complex in Arabidopsis destroys the expre

  16. Reference: 567 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ith findings that noxy2 and mutants with defective 9-LOX activity showed increased numbers of lateral roots,...or of lateral root formation. Histochemical and molecular analyses revealed that 9-HOT activated events comm...in Arabidopsis regulate lateral root development and defense responses through a specific signaling cascade.

  17. Arabidopsis CDS blastp result: AK287911 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287911 J065213B08 At1g12110.1 68414.m01402 nitrate/chlorate transporter (NRT1.1) ...(CHL1) identical to nitrate/chlorate transporter SP:Q05085 from [Arabidopsis thaliana]; contains Pfam profile: PF00854 POT family 3e-85 ...

  18. Arabidopsis CDS blastp result: AK318551 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK318551 J075138M12 At1g12110.1 68414.m01402 nitrate/chlorate transporter (NRT1.1) ...(CHL1) identical to nitrate/chlorate transporter SP:Q05085 from [Arabidopsis thaliana]; contains Pfam profile: PF00854 POT family 4e-27 ...

  19. Arabidopsis CDS blastp result: AK241823 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241823 J065212G21 At1g12110.1 68414.m01402 nitrate/chlorate transporter (NRT1.1) ...(CHL1) identical to nitrate/chlorate transporter SP:Q05085 from [Arabidopsis thaliana]; contains Pfam profile: PF00854 POT family 1e-150 ...

  20. Arabidopsis CDS blastp result: AK243378 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK243378 J100063A13 At1g12110.1 68414.m01402 nitrate/chlorate transporter (NRT1.1) ...(CHL1) identical to nitrate/chlorate transporter SP:Q05085 from [Arabidopsis thaliana]; contains Pfam profile: PF00854 POT family 5e-18 ...