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Sample records for archaeal orphans representing

  1. The Korarchaeota: Archaeal orphans representing an ancestral lineage of life

    Energy Technology Data Exchange (ETDEWEB)

    Elkins, James G.; Kunin, Victor; Anderson, Iain; Barry, Kerrie; Goltsman, Eugene; Lapidus, Alla; Hedlund, Brian; Hugenholtz, Phil; Kyrpides, Nikos; Graham, David; Keller, Martin; Wanner, Gerhard; Richardson, Paul; Stetter, Karl O.

    2007-05-01

    Based on conserved cellular properties, all life on Earth can be grouped into different phyla which belong to the primary domains Bacteria, Archaea, and Eukarya. However, tracing back their evolutionary relationships has been impeded by horizontal gene transfer and gene loss. Within the Archaea, the kingdoms Crenarchaeota and Euryarchaeota exhibit a profound divergence. In order to elucidate the evolution of these two major kingdoms, representatives of more deeply diverged lineages would be required. Based on their environmental small subunit ribosomal (ss RNA) sequences, the Korarchaeota had been originally suggested to have an ancestral relationship to all known Archaea although this assessment has been refuted. Here we describe the cultivation and initial characterization of the first member of the Korarchaeota, highly unusual, ultrathin filamentous cells about 0.16 {micro}m in diameter. A complete genome sequence obtained from enrichment cultures revealed an unprecedented combination of signature genes which were thought to be characteristic of either the Crenarchaeota, Euryarchaeota, or Eukarya. Cell division appears to be mediated through a FtsZ-dependent mechanism which is highly conserved throughout the Bacteria and Euryarchaeota. An rpb8 subunit of the DNA-dependent RNA polymerase was identified which is absent from other Archaea and has been described as a eukaryotic signature gene. In addition, the representative organism possesses a ribosome structure typical for members of the Crenarchaeota. Based on its gene complement, this lineage likely diverged near the separation of the two major kingdoms of Archaea. Further investigations of these unique organisms may shed additional light onto the evolution of extant life.

  2. ORPHANED PROTOSTARS

    International Nuclear Information System (INIS)

    We explore the origin of a population of distant companions (∼1000-5000 AU) to Class I protostellar sources recently found by Connelley and coworkers, who noted that the companion fraction diminished as the sources evolved. Here, we present N-body simulations of unstable triple systems embedded in dense cloud cores. Many companions are ejected into unbound orbits and quickly escape, but others are ejected with insufficient momentum to climb out of the potential well of the cloud core and associated binary. These loosely bound companions reach distances of many thousands of AU before falling back and eventually being ejected into escapes as the cloud cores gradually disappear. We use the term orphans to denote protostellar objects that are dynamically ejected from their placental cloud cores, either escaping or for a time being tenuously bound at large separations. Half of all triple systems are found to disintegrate during the protostellar stage, so if multiple systems are a frequent outcome of the collapse of a cloud core, then orphans should be common. Bound orphans are associated with embedded close protostellar binaries, but escaping orphans can travel as far as ∼0.2 pc during the protostellar phase. The steep climb out of a potential well ensures that orphans are not kinematically distinct from young stars born with a less violent pre-history. The identification of orphans outside their heavily extincted cloud cores will allow the detailed study of protostars high up on their Hayashi tracks at near-infrared and in some cases even at optical wavelengths.

  3. 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

  4. Orphaned Protostars

    CERN Document Server

    Reipurth, Bo; Connelley, Michael; Valtonen, Mauri

    2010-01-01

    We explore the origin of a population of distant companions (~1000 - 5000 AU) to Class I protostellar sources recently found by Connelley and co-workers, who noted that the companion fraction diminished as the sources evolved. Here we present N-body simulations of unstable triple systems embedded in dense cloud cores. Many companions are ejected into unbound orbits and quickly escape, but others are ejected with insufficient momentum to climb out of the potential well of the cloud core and associated binary. These loosely bound companions reach distances of many thousands of AU before falling back and eventually being ejected into escapes as the cloud cores gradually disappear. We use the term orphans to denote protostellar objects that are dynamically ejected from their placental cloud cores, either escaping or for a time being tenuously bound at large separations. Half of all triple systems are found to disintegrate during the protostellar stage, so if multiple systems are a frequent outcome of the collapse...

  5. Archaeal Enzymes and Applications in Industrial Biocatalysts.

    Science.gov (United States)

    Littlechild, Jennifer A

    2015-01-01

    Archaeal enzymes are playing an important role in industrial biotechnology. Many representatives of organisms living in "extreme" conditions, the so-called Extremophiles, belong to the archaeal kingdom of life. This paper will review studies carried by the Exeter group and others regarding archaeal enzymes that have important applications in commercial biocatalysis. Some of these biocatalysts are already being used in large scale industrial processes for the production of optically pure drug intermediates and amino acids and their analogues. Other enzymes have been characterised at laboratory scale regarding their substrate specificity and properties for potential industrial application. The increasing availability of DNA sequences from new archaeal species and metagenomes will provide a continuing resource to identify new enzymes of commercial interest using both bioinformatics and screening approaches.

  6. Archaeal Enzymes and Applications in Industrial Biocatalysts

    Directory of Open Access Journals (Sweden)

    Jennifer A. Littlechild

    2015-01-01

    Full Text Available Archaeal enzymes are playing an important role in industrial biotechnology. Many representatives of organisms living in “extreme” conditions, the so-called Extremophiles, belong to the archaeal kingdom of life. This paper will review studies carried by the Exeter group and others regarding archaeal enzymes that have important applications in commercial biocatalysis. Some of these biocatalysts are already being used in large scale industrial processes for the production of optically pure drug intermediates and amino acids and their analogues. Other enzymes have been characterised at laboratory scale regarding their substrate specificity and properties for potential industrial application. The increasing availability of DNA sequences from new archaeal species and metagenomes will provide a continuing resource to identify new enzymes of commercial interest using both bioinformatics and screening approaches.

  7. Archaeal extrachromosomal genetic elements

    DEFF Research Database (Denmark)

    Wang, Haina; Peng, Nan; Shah, Shiraz Ali;

    2015-01-01

    viruses and plasmids. In particular, it has been suggested that ECE-host interactions have shaped the coevolution of ECEs and their archaeal hosts. Furthermore, archaeal hosts have developed defense systems, including the innate restriction-modification (R-M) system and the adaptive CRISPR (clustered...

  8. Orphan Care in China

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    Meng, Liu

    2009-07-01

    Full Text Available Orphan care in China was once provided by the central government as a means of social control. The centralized welfare delivery guaranteed some of the poorest orphans to be protected by the government. Since the economic reform, the central government started to relinquish its control over social welfare delivery, new forms of orphan care were introduced into China, sharing the responsibilities and burdens for caring the orphans. Yet, many issues and problems exist in social delivery due to a lack of finances, professionals, and policy support. In this chapter, we will discuss the background of social welfare changes in China, as pertains to orphan care, focusing on the different types of orphans as a result of social issues, service delivery, barriers and solutions. It is claimed that during the reform, the burden of orphan care in China may not be reduced in the coming future, and we offer suggestions to cope with that.

  9. Archaeal DNA replication.

    Science.gov (United States)

    Kelman, Lori M; Kelman, Zvi

    2014-01-01

    DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed. PMID:25421597

  10. 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].

  11. Orphan Drug Expenditures In The United States: A Historical And Prospective Analysis, 2007-18.

    Science.gov (United States)

    Divino, Victoria; DeKoven, Mitch; Kleinrock, Michael; Wade, Rolin L; Kaura, Satyin

    2016-09-01

    The Orphan Drug Act of 1983 established incentives for the development of drugs that treat rare, or orphan, diseases. We used the IMS Health MIDAS database of audited biopharmaceutical sales to measure US annual spending on orphan drugs in the period 2007-13, and we estimated spending on the drugs for the period 2014-18. We identified 356 brand-name orphan drugs that were approved by the Food and Drug Administration in the period 1983-2013. While we included orphan drugs with both orphan and other indications, we adjusted spending to include only spending for orphan indications. In 2014 dollars, expenditures on orphan drugs totaled $15 billion in 2007 and $30 billion in 2013-representing 4.8 percent and 8.9 percent of total pharmaceutical expenditures, respectively. Our future trend analysis for the period 2014-18 suggests a slowing in the growth of orphan drug expenditures. The overall impact of orphan drugs on payers' drug budgets is relatively small, and spending on orphan drugs as a percentage of total pharmaceutical expenditures has remained fairly stable. Concerns that growth in orphan drug expenditures may lead to unsustainable drug expenditures do not appear to be justified. PMID:27605637

  12. 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.

  13. [Orphan diseases and orphan medicines: a Belgian and European study].

    Science.gov (United States)

    Denis, Alain; Mergaert, Lut; Fostier, Christel; Cleemput, Irina; Simoens, Steven

    2009-12-01

    The objective of this study is to analyze policies concerning orphan medicines, used to treat patients suffering from a rare disease. The decisions about orphan designation and marketing authorization of orphan medicines are taken at European level, but each Member State is responsible for decisions regarding reimbursement. The European measures to encourage the development of orphan medicines, such as market exclusivity for a period of ten years, seem to be successful. However, this market exclusivity should be revised once the profitability of such medicines has clearly been demonstrated. Our study recommends the implementation of patient registries at the European level in order to describe the natural evolution of rare diseases and the efficacy of orphan medicines, the majority of which are relatively expensive. In 2008, Belgian social security services reimbursed orphan medicines for an amount of 66 million euro, accounting for more than 5% of the hospital pharmaceutical budget. The reimbursement of an orphan medicine to an individual patient is subject to multiple conditions. Our study recommends that a unique counter within the NIHDI is created which centralizes all reimbursement requests. The reimbursement of an orphan medicine must be linked to the provision of standardized information needed for a patient register. The NIHDI administration could then, in collaboration with external experts, evaluate reimbursement requests and ensure a coherent application of reimbursement criteria. PMID:20183989

  14. Orphan regulations for orphan drug development in India

    Directory of Open Access Journals (Sweden)

    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.

  15. Drug repositioning for orphan diseases.

    Science.gov (United States)

    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 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.

  16. Orphan drugs: the regulatory environment.

    Science.gov (United States)

    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.

  17. Orphan penumbrae: Submerging horizontal fields

    Science.gov (United States)

    Jurčák, J.; Bellot Rubio, L. R.; Sobotka, M.

    2014-04-01

    Aims: We investigate the properties of orphan penumbrae, which are photospheric filamentary structures observed in active regions near polarity inversion lines that resemble the penumbra of regular sunspots but are not connected to any umbra. Methods: We use Hinode data from the Solar Optical Telescope to determine the properties of orphan penumbrae. Spectropolarimetric data are employed to obtain the vector magnetic field and line-of-sight velocities in the photosphere. Magnetograms are used to study the overall evolution of these structures, and G-band and Ca ii H filtergrams are to investigate their brightness and apparent horizontal motions. Results: Orphan penumbrae form between regions of opposite polarity in places with horizontal magnetic fields. Their magnetic configuration is that of Ω-shaped flux ropes. In the two cases studied here, the opposite-polarity regions approach each other with time and the whole structure submerges as the penumbral filaments disappear. Orphan penumbrae are very similar to regular penumbrae, including the existence of strong gas flows. Therefore, they could have a similar origin. The main difference between them is the absence of a "background" magnetic field in orphan penumbrae. This could explain most of the observed differences. Conclusions: The fast flows we detect in orphan penumbrae may be caused by the siphon flow mechanism. Based on the similarities between orphan and regular penumbrae, we propose that the Evershed flow is also a manifestation of siphon flows. A movie attached to Fig. 11 is available in electronic form at http://www.aanda.org

  18. The Orphan Lenses Project

    Science.gov (United States)

    Moustakas, Leonidas A.; Brownstein, J.; Fadely, R.; Fassnacht, C. D.; Gavazzi, R.; Goodsall, T.; Griffith, R. L.; Keeton, C. R.; Kneib, J. P.; Koekemoer, A.; Koopmans, L. V. E.; Marshall, P. J.; Merten, J.; Metcalf, R. B.; Oguri, M.; Papovich, C.; Rein, H.; Ryan, R.; Stewart, K. R.; Treu, T.

    2012-01-01

    Strong gravitational lenses are uniquely suited for the study of dark matter structure and substructure within massive halos of many scales, act as gravitational telescopes for distant faint objects, and can give powerful and competitive cosmological constraints. Some 300 lenses have been identified in the literature in one form or another; many others have been found, but perhaps have not warranted dedicated publications. The Orphan Lenses project aims to be a master compilation of all strong gravitational lenses that are known, and a community repository for candidate lenses. A clear and uniform database of basic properties and gravitational lens models is being developed, which will be available online and through a smartphone interactive application. I will present the project, and scientific highlights with this dataset.

  19. Archaeal viruses of the sulfolobales

    DEFF Research Database (Denmark)

    Erdmann, Susanne; Garrett, Roger Antony

    2015-01-01

    Infection of archaea with phylogenetically diverse single viruses, performed in different laboratories, has failed to activate spacer acquisition into host CRISPR loci. The first successful uptake of archaeal de novo spacers was observed on infection of Sulfolobus solfataricus P2 with an environm......Infection of archaea with phylogenetically diverse single viruses, performed in different laboratories, has failed to activate spacer acquisition into host CRISPR loci. The first successful uptake of archaeal de novo spacers was observed on infection of Sulfolobus solfataricus P2...... in CRISPR loci of Sulfolobus species from a second coinfecting conjugative plasmid or virus (Erdmann and Garrett, Mol Microbiol 85:1044-1056, 2012; Erdmann et al. Mol Microbiol 91:900-917, 2014). Here we describe, firstly, the isolation of archaeal virus mixtures from terrestrial hot springs...

  20. Orphan penumbrae: Submerging horizontal fields

    CERN Document Server

    Jurcak, J; Sobotka, M

    2014-01-01

    We investigate the properties of orphan penumbrae, which are photospheric filamentary structures observed in active regions near polarity inversion lines that resemble the penumbra of regular sunspots but are not connected to any umbra. We use Hinode data from the Solar Optical Telescope to determine the properties of orphan penumbrae. Spectropolarimetric data are employed to obtain the vector magnetic field and line-of-sight velocities in the photosphere. Magnetograms are used to study the overall evolution of these structures, and G-band and Ca II H filtergrams are to investigate their brightness and apparent horizontal motions. Orphan penumbrae form between regions of opposite polarity in places with horizontal magnetic fields. Their magnetic configuration is that of $\\Omega$-shaped flux ropes. In the two cases studied here, the opposite-polarity regions approach each other with time and the whole structure submerges as the penumbral filaments disappear. Orphan penumbrae are very similar to regular penumbr...

  1. Analyses of in vivo interactions between transcription factors and the archaeal RNA polymerase.

    Science.gov (United States)

    Walker, Julie E; Santangelo, Thomas J

    2015-09-15

    Transcription factors regulate the activities of RNA polymerase (RNAP) at each stage of the transcription cycle. Many basal transcription factors with common ancestry are employed in eukaryotic and archaeal systems that directly bind to RNAP and influence intramolecular movements of RNAP and modulate DNA or RNA interactions. We describe and employ a flexible methodology to directly probe and quantify the binding of transcription factors to RNAP in vivo. We demonstrate that binding of the conserved and essential archaeal transcription factor TFE to the archaeal RNAP is directed, in part, by interactions with the RpoE subunit of RNAP. As the surfaces involved are conserved in many eukaryotic and archaeal systems, the identified TFE-RNAP interactions are likely conserved in archaeal-eukaryal systems and represent an important point of contact that can influence the efficiency of transcription initiation.

  2. 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.

  3. The Detectability of Orphan Afterglows

    Science.gov (United States)

    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.

  4. Shaping the Archaeal Cell Envelope

    NARCIS (Netherlands)

    Ellen, Albert F.; Zolghadr, Behnam; Driessen, Arnold M. J.; Albers, Sonja-Verena

    2010-01-01

    Although archaea have a similar cellular organization as other prokaryotes, the lipid composition of their membranes and their cell surface is unique. Here we discuss recent developments in our understanding of the archaeal protein secretion mechanisms, the assembly of macromolecular cell surface st

  5. Archaeal virus-host interactions

    NARCIS (Netherlands)

    Quax, T.E.F.

    2013-01-01

      The work presented in this thesis provides novel insights in several aspects of the molecular biology of archaea, bacteria and their viruses. Three fundamentally different groups of viruses are associated with the three domains of life. Archaeal viruses are characterized by a particularly

  6. Orphan Care in Russia

    Directory of Open Access Journals (Sweden)

    Schmidt, Victoria

    2009-07-01

    Full Text Available Current public opinion about the residential care system in contemporary Russia is extremely negative. A majority of Russians, both citizens and professionals, consider that family placement is the best arrangement for orphaned children. The year 2007 was announced as the Year of the Child in Russia. The majority of officials interpreted it as the year of de-institutionalization of the residential care system for children in Russia. De-institutionalization is mostly identified as reform focused on family placement instead of placement in institutions. Vladimir Fridlyanov, the executive director of the Ministry of Science and Education, announced in May, 2007 that the government is going to transfer 120,000 children from institutions into families every year from 2007 until 2010 and reduce the number of residential care institutions by one-third (Nesterova 2007. But the likelihood of family placement is small, with the exception of the adoption of infants without serious pathologies, and the attempts of precipitant de-institutionalization (when children’s homes are closed and children are distributed among families have failed (children were returned into children homes. According to the opinion of the Ministry, the key obstacle to effective de-institutionalization is the lack of professionals in adoption and foster care (Vazhdaeva 2006.

  7. Magnetic Au Nanoparticles on Archaeal S-Layer Ghosts as Templates

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    Sonja Selenska-Pobell

    2011-10-01

    Full Text Available Cell‐ghosts representing empty cells of the archaeon Sulfolobus acidocaldarius, consisting only of their highly ordered and unusually stable outermost proteinaceous surface layer (S‐layer, were used as templates for Au nanoparticles fabrication. The properties of these archaeal Au nanoparticles differ significantly from those produced earlier by us onto bacterial S‐layer sheets. The archaeal Au nanoparticles, with a size of about 2.5 nm, consist exclusively of metallic Au(0, while those produced on the bacterial S‐layer had a size of about 4 nm and represented a mixture of Au(0 and Au(III in the ratio of 40 to 60 %. The most impressive feature of the archaeal Au nanoparticles is that they are strongly paramagnetic, in contrast to the bacterial ones and also to bulk gold. SQUID magnetometry and XMCD measurements demonstrated that the archaeal Au nanoparticles possess a rather large magnetic moment of about 0.1 µB/atom. HR‐ TEM‐EDX analysis revealed that the archaeal Au nanoparticles are linked to the sulfur atoms of the thiol groups of the amino acid cysteine, characteristic only for archaeal S‐layers. This is the first study demonstrating the formation of such unusually strong magnetic Au nanoparticles on a non‐modified archaeal S‐layer.

  8. 78 FR 35117 - Orphan Drug Regulations

    Science.gov (United States)

    2013-06-12

    ..., 2011 (76 FR 64868), FDA issued a proposed rule to amend the Orphan Drug Regulations (part 316 (21 CFR... orphan drug program. As described in the proposed rule (76 FR 64868), FDA believes these revisions will... serve the intent of the Orphan Drug Act, as explained in the proposed rule (76 FR 64868 at 64869...

  9. Orphan drugs: expensive yet necessary.

    Science.gov (United States)

    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.

  10. 21 CFR 316.24 - Granting orphan-drug designation.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Granting orphan-drug designation. 316.24 Section...) DRUGS FOR HUMAN USE ORPHAN DRUGS Designation of an Orphan Drug § 316.24 Granting orphan-drug designation. (a) FDA will grant the request for orphan-drug designation if none of the reasons described in §...

  11. Orphans as agents for change

    Directory of Open Access Journals (Sweden)

    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.

  12. Psychological health of orphan bonobos and chimpanzees in African sanctuaries.

    Directory of Open Access Journals (Sweden)

    Victoria Wobber

    Full Text Available BACKGROUND: Facilities across Africa care for apes orphaned by the trade for "bushmeat." These facilities, called sanctuaries, provide housing for apes such as bonobos (Pan paniscus and chimpanzees (Pan troglodytes who have been illegally taken from the wild and sold as pets. Although these circumstances are undoubtedly stressful for the apes, most individuals arrive at the sanctuaries as infants and are subsequently provided with rich physical and social environments that can facilitate the expression of species-typical behaviors. METHODS AND FINDINGS: We tested whether bonobo and chimpanzee orphans living in sanctuaries show any behavioral, physiological, or cognitive abnormalities relative to other individuals in captivity as a result of the early-life stress they experience. Orphans showed lower levels of aberrant behaviors, similar levels of average cortisol, and highly similar performances on a broad battery of cognitive tests in comparisons with individuals of the same species who were either living at a zoo or were reared by their mothers at the sanctuaries. CONCLUSION: Taken together, these results support the rehabilitation strategy used by sanctuaries in the Pan-African Sanctuary Alliance (PASA and suggest that the orphans we examined did not show long-term signs of stress as a result of their capture. Our findings also show that sanctuary apes are as psychologically healthy as apes in other captive settings and thus represent a valuable resource for non-invasive research.

  13. Saving orphan drug legislations: misconceptions and clarifications.

    Science.gov (United States)

    Hyry, Hanna I; Cox, Timothy M; Roos, Jonathan C P

    2016-01-01

    Orphan-drug sales are rocketing, with revenue expected to total $176 billion annually by 2020. As a share of the industry, orphan drugs now account for close to 15% of all prescription revenue globally (excluding generics) and the sector is set to grow at more than twice the rate (10.5%) of the overall prescription market (4.3%). But this success also equates to costs--borne by individual patients and cash-strapped health systems. Prices for orphan drugs can be 19 times higher than for other medications, hampering access for patients, many of whom are children. With ever more such expensive drugs reaching the market, the situation is becoming unsustainable and putting the survival of the orphan drug legislation itself at risk. Here the authors consider why there has been an increase in orphan drug designations, how orphan drug prices are set and regulated, before discussing proposals for how changes which could save the legislation. PMID:26768506

  14. Global analysis of viral infection in an archaeal model system

    Directory of Open Access Journals (Sweden)

    Walid S. Maaty

    2012-12-01

    Full Text Available The origin and evolutionary relationship of viruses is poorly understood. This makes archaeal virus-host of particular interest because the hosts generally root near the base of phylogenetic trees, while some of the viruses have clear structural similarities to those that infect prokaryotic and eukaryotic cells. Despite the advantageous position for use in evolutionary studies, little is known about archaeal viruses or how they interact with their hosts, compared to viruses of bacteria and eukaryotes. In addition, many archaeal viruses have been isolated from extreme environments and present a unique opportunity for elucidating factors that are important for existence at the extremes.. In this article we focus on virus-host interactions using a proteomics approach to study Sulfolobus Turreted Icosahedral Virus (STIV infection of Sulfolobus solfataricus P2. Using cultures grown from the ATCC cell stock, a single cycle of STIV infection was sampled 6 times over a 72 hr period. More than 700 proteins were identified throughout the course of the experiments. Seventy one host proteins were found to change by nearly two-fold (p<0.05 with 40 becoming more abundant and 31 less abundant. The modulated proteins represent 30 different cell pathways and 14 COG groups. 2D gel analysis showed that changes in post translational modifications were a common feature of the affected proteins. The results from these studies showed that the prokaryotic antiviral adaptive immune system CRISPR associated proteins (CAS proteins were regulated in response to the virus infection. It was found that regulated proteins come from mRNAs with a shorter than average half-life. In addition, activity-based protein profiling (ABPP profiling on 2D gels showed caspase, hydrolase and tyrosine phosphatase enzyme activity labeling at the protein isoform level. Together, this data provides a more detailed global view of archaeal cellular responses to viral infection, demonstrates the

  15. The UCSC Archaeal Genome Browser: 2012 update

    OpenAIRE

    Chan, Patricia P.; Holmes, Andrew D.; Smith, Andrew M.; Tran, Danny; Lowe, Todd M.

    2011-01-01

    The UCSC Archaeal Genome Browser (http://archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes. By bringing together existing gene annotations, gene expression data, multiple-genome alignments, pre-computed sequence comparisons and other specialized analysis tracks, the genome browser is a powerful aggregator of varied genomic information. The genome browser environment maintains the current look-and-feel of ...

  16. Post-authorisation assessment of orphan drugs

    NARCIS (Netherlands)

    C.E.M. Hollak; M. Biegstraaten; M. Levi; R. Hagendijk

    2015-01-01

    The EU regulation of orphan drugs has promoted the development of new treatments for rare disorders.1 However, the high cost of most orphan drugs threatens the sustainability of public health care. Unfortunately, the effectiveness of treatment is often unclear for part, if not all, of the patient po

  17. 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.

  18. The UCSC Archaeal Genome Browser: 2012 update.

    Science.gov (United States)

    Chan, Patricia P; Holmes, Andrew D; Smith, Andrew M; Tran, Danny; Lowe, Todd M

    2012-01-01

    The UCSC Archaeal Genome Browser (http://archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes. By bringing together existing gene annotations, gene expression data, multiple-genome alignments, pre-computed sequence comparisons and other specialized analysis tracks, the genome browser is a powerful aggregator of varied genomic information. The genome browser environment maintains the current look-and-feel of the vertebrate UCSC Genome Browser, but also integrates archaeal and bacterial-specific tracks with a few graphic display enhancements. The browser currently contains 115 archaeal genomes, plus 31 genomes of viruses known to infect archaea. Some of the recently developed or enhanced tracks visualize data from published high-throughput RNA-sequencing studies, the NCBI Conserved Domain Database, sequences from pre-genome sequencing studies, predicted gene boundaries from three different protein gene prediction algorithms, tRNAscan-SE gene predictions with RNA secondary structures and CRISPR locus predictions. We have also developed a companion resource, the Archaeal COG Browser, to provide better search and display of arCOG gene function classifications, including their phylogenetic distribution among available archaeal genomes.

  19. Orphan Stars Found in Long Galaxy Tail

    Science.gov (United States)

    2007-09-01

    ESO 137-001 and Tail in Abell 3627 H-alpha Image of ESO 137-001 and Tail in Abell 3627 "By our galactic standards, these are extremely lonely stars," said Mark Voit, another team member from MSU. "If life was to form out there on a planet a few billion years from now, they would have very dark skies." The gas that formed the orphan stars was stripped out of its parent galaxy by the pressure induced by the motion of the galaxy through the multimillion degree gas that pervades the intergalactic space of the galaxy cluster. Eventually most of the gas will be scoured from the galaxy, depleting the raw material for new stars, and effectively stopping further star formation in the galaxy. This process may represent an important but short-lived stage in the transformation of a galaxy. Although apparently rare in the present-day universe, galactic tails of gas and orphan stars may have been more common billions of years ago when galaxies were younger and richer in star-forming gas. These results will appear in the December 10th issue of The Astrophysical Journal. NASA's Marshall Space Flight Center, Huntsville, Ala., manages the Chandra program for the agency's Science Mission Directorate. The Smithsonian Astrophysical Observatory controls science and flight operations from the Chandra X-ray Center in Cambridge, Mass. The SOAR (Southern Astrophysical Research Telescope) is a joint project of Michigan State University, Conselho Nacional de Pesquisas Científicas e Tecnológicas (CNPq-Brazil), The University of North Carolina at Chapel Hill, and the National Optical Astronomy Observatory.

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

    Science.gov (United States)

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

    2014-09-26

    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

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

    Science.gov (United States)

    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

  2. Protein Adaptations in Archaeal Extremophiles

    Directory of Open Access Journals (Sweden)

    Christopher J. Reed

    2013-01-01

    Full Text Available Extremophiles, especially those in Archaea, have a myriad of adaptations that keep their cellular proteins stable and active under the extreme conditions in which they live. Rather than having one basic set of adaptations that works for all environments, Archaea have evolved separate protein features that are customized for each environment. We categorized the Archaea into three general groups to describe what is known about their protein adaptations: thermophilic, psychrophilic, and halophilic. Thermophilic proteins tend to have a prominent hydrophobic core and increased electrostatic interactions to maintain activity at high temperatures. Psychrophilic proteins have a reduced hydrophobic core and a less charged protein surface to maintain flexibility and activity under cold temperatures. Halophilic proteins are characterized by increased negative surface charge due to increased acidic amino acid content and peptide insertions, which compensates for the extreme ionic conditions. While acidophiles, alkaliphiles, and piezophiles are their own class of Archaea, their protein adaptations toward pH and pressure are less discernible. By understanding the protein adaptations used by archaeal extremophiles, we hope to be able to engineer and utilize proteins for industrial, environmental, and biotechnological applications where function in extreme conditions is required for activity.

  3. 21 CFR 316.36 - Insufficient quantities of orphan drugs.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Insufficient quantities of orphan drugs. 316.36... (CONTINUED) DRUGS FOR HUMAN USE ORPHAN DRUGS Orphan-drug Exclusive Approval § 316.36 Insufficient quantities of orphan drugs. (a) Under section 527 of the act, whenever the Director has reason to believe...

  4. Archaeal Nitrification in Hot Springs

    Science.gov (United States)

    Richter, A.; Daims, H.; Reigstad, L.; Wanek, W.; Wagner, M.; Schleper, C.

    2006-12-01

    Biological nitrification, i.e. the aerobic conversion of ammonia to nitrate via nitrite, is a major component of the global nitrogen cycle. Until recently, it was thought that the ability to aerobically oxidize ammonia was confined to bacteria of the phylum Proteobacteria. However, it has recently been shown that Archaea of the phylum Crenarchaeota are also capable of ammonia oxidation. As many Crenarchaeota are thermophilic or hyperthermophilic, and at least some of them are capable of ammonia oxidation we speculated on the existence of (hyper)thermophilic ammonia-oxidizing archaea (AOA). Using PCR primers specifically targeting the archaeal ammonia monooxygenase (amoA) gene, we were indeed able to confirm the presence of such organisms in several hot springs in Reykjadalur, Iceland. These hot springs exhibited temperatures well above 80 °C and pH values ranging from 2.0 to 4.5. To proof that nitrification actually took place under these extreme conditions, we measured gross nitrification rates by the isotope pool dilution method; we added 15N-labelled nitrate to the mud and followed the dilution of the label by nitrate production from ammonium either in situ (incubation in the hot spring) or under controlled conditions in the laboratory (at 80 °C). The nitrification rates in the hot springs ranged from 0.79 to 2.22 mg nitrate-N per L of mud and day. Controls, in which microorganisms were killed before the incubations, demonstrated that the nitrification was of biological origin. Addition of ammonium increased the gross nitrification rate approximately 3-fold, indicating that the nitrification was ammonium limited under the conditions used. Collectively, our study provides evidence that (1) AOA are present in hot springs and (2) that they are actively nitrifying. These findings have major implications for our understanding of nitrogen cycling of hot environments.

  5. Composition of bacterial and archaeal communities during landfill refuse decomposition processes.

    Science.gov (United States)

    Song, Liyan; Wang, Yangqing; Zhao, Heping; Long, David T

    2015-12-01

    Little is known about the archaeal and the bacterial diversities in a landfill during different phases of decomposition. In this study, the archaeal and the bacterial diversities of Laogang landfill (Shanghai, China) at two different decomposition phases (i.e., initial methanogenic phase (IMP) and stable methanogenic phase (SMP)), were culture-independently examined using PCR-based 454 pyrosequencing. A total of 47,753 sequences of 16S rRNA genes were retrieved from 69,954 reads and analyzed to evaluate the diversities of the archaeal and bacterial communities. The most predominant types of archaea were hydrogenotrophic Methanomicrobiales, and of bacteria were Proteobacteria, Firmicutes, and Bacteroidetes. As might be expected, their abundances varied at decomposition phases. Archaea Methanomicrobiales accounts for 97.6% of total archaeal population abundance in IMP and about 57.6% in SMP. The abundance of archaeal genus Halobacteriale was 0.1% in IMP and was 20.3% in the SMP. The abundance of Firmicutes was 21.3% in IMP and was 4.3% in SMP. The abundance of Bacteroidetes represented 11.5% of total bacterial in IMP and was dominant (49.4%) in SMP. Both the IMP and SMP had unique cellulolytic bacteria compositions. IMP consisted of members of Bacillus, Fibrobacter, and Eubacterium, while SMP harbored groups of Microbacterium. Both phases had Clostridium with different abundance, 4-5 folds higher in SMP.

  6. Orphans in the Dead Sea Scrolls

    Directory of Open Access Journals (Sweden)

    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

  7. Hyperthermophilic Archaeal Viruses as Novel Nanoplatforms

    DEFF Research Database (Denmark)

    Uldahl, Kristine Buch

    ; attachment, alignment, and fusion. Upon infection, the intracellular replication cycle lasts 8 h at which point the virus particles are released as spindle-shaped tailless particles. Chapter II builds on the replication and purification methods in Chapter I to study the interaction between the two...... nanoplatforms than mammalian viruses because they cannot proliferate in humans and hence are less likely to trigger adverse effects. Another group of viruses that fits this criterion is archaeal viruses yet their potential remains untapped. As a group, archaeal viruses offer distinct advantages such as unique...

  8. Bacterial and Archaeal Diversity From the Eastern Lau Spreading Center

    Science.gov (United States)

    Reysenbach, A.; Banta, A.; Kelly, S.; Kirshstein, J.; Voytek, M.

    2005-12-01

    Due to the diversity of venting styles, geological settings and variations in fluid geochemistry, the Valu Fa Ridge and Eastern Lau Spreading Center (ELSC) provide a unique opportunity to explore the effects geological and geochemical variables on patterns of microbial phylogenetic and metabolic diversity. High temperature sulfides, diffuse flow fluids and microbial mats were collected from six active vent fields on the Valu Fa Ridge and Eastern Lau Spreading Center during the R/V Melville cruise TUIM05MV. All samples were subsampled for molecular and microbial culturing purposes. The archaeal and bacterial 16S rRNA genes were amplified by PCR from a selection of samples. Additionally, the presence of Aquificales and an unidentified lineage, the DHVE archaeal group, was explored using PCR primers specific for these groups. A selection of DNAs were also screened for functional genes that are diagnostic for certain pathways, viz, aclB (reductive TCA cycle), mcrA (methanogenesis), nirS and nirK (nitrite reduction), amoA (ammonia oxidation). Culturing of thermophiles, both acidophiles and neutrophiles, was initiated. Over 20 hydrogen oxidizing (hydrogen and oxygen) or nitrate reducing (hydrogen and nitrate) chemolithoautotrophs were isolated as colonies and grow at 70 degrees C. All are related to Persephonella hydrogenophila, with the exception of 2 cultures that perhaps represent new species of Hydrogenivirga and Aquifex. Preliminary analysis of patterns of Aquificales diversity using both culturing and molecular approaches suggest that the distributions of this group alone are very different from that observed at other hydrothermal sites such as along the East Pacific Rise or Central Indian Ridge. As yet, the most commonly isolated Aquificales, P. marina, has not been detected in enrichment cultures from ELSC, and the diversity of Aquificales-related sequences is much greater than detected from sites along the EPR. It is therefore also likely, that patterns of

  9. The Orphan among Us: An Examination of Orphans in Newbery Award Winning Literature

    Science.gov (United States)

    Mattix, April A.

    2012-01-01

    Orphan stories in children's literature are rich and complex, and they have historically permeated the pages of children's books. The purpose of this study was to explore the use of orphans as protagonists in children's award-winning literature through content analysis. This study utilizes all the Newbery Award winning books…

  10. Searching for Orphan radiation sources

    International Nuclear Information System (INIS)

    Full text: The problem of orphan sources cannot be left unaddressed due high probability of accidental exposure and use of sources for terrorism. Search of objects of this kind is complex particularly when search territory is large. This requires devices capable of detecting sources, identifying their radionuclide composition, and correlating scan results to geographical coordinates and displaying results on a map. Spectral radiation scanner AT6101C can fulfill the objective of search for gamma and neutron radiation sources, radionuclide composition identification, correlation results to geographical coordinates and displaying results on a map. The scanner consists of gamma radiation scintillation detection unit based on NaI(Tl) crystal, neutron detection unit based on two He3 counters, GPS receiver and portable ruggedized computer. Built-in and application software automates entire scan process, saving all results to memory for further analysis with visual representation of results as spectral information diagrams, count rate profile and gamma radiation dose rates on a geographical map. The scanner informs operator with voice messages on detection of radiation sources, identification result and other events. Scanner detection units and accessories are packed in a backpack. Weighing 7 kg, the scanner is human portable and can be used for scan inside cars. The scanner can also be used for radiation mapping and inspections. (author)

  11. 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.

  12. Modelling the evolution of the archaeal tryptophan synthase

    Directory of Open Access Journals (Sweden)

    Merkl Rainer

    2007-04-01

    Full Text Available Abstract Background Microorganisms and plants are able to produce tryptophan. Enzymes catalysing the last seven steps of tryptophan biosynthesis are encoded in the canonical trp operon. Among the trp genes are most frequently trpA and trpB, which code for the alpha and beta subunit of tryptophan synthase. In several prokaryotic genomes, two variants of trpB (named trpB1 or trpB2 occur in different combinations. The evolutionary history of these trpB genes is under debate. Results In order to study the evolution of trp genes, completely sequenced archaeal and bacterial genomes containing trpB were analysed. Phylogenetic trees indicated that TrpB sequences constitute four distinct groups; their composition is in agreement with the location of respective genes. The first group consisted exclusively of trpB1 genes most of which belonged to trp operons. Groups two to four contained trpB2 genes. The largest group (trpB2_o contained trpB2 genes all located outside of operons. Most of these genes originated from species possessing an operon-based trpB1 in addition. Groups three and four pertain to trpB2 genes of those genomes containing exclusively one or two trpB2 genes, but no trpB1. One group (trpB2_i consisted of trpB2 genes located inside, the other (trpB2_a of trpB2 genes located outside the trp operon. TrpA and TrpB form a heterodimer and cooperate biochemically. In order to characterise trpB variants and stages of TrpA/TrpB cooperation in silico, several approaches were combined. Phylogenetic trees were constructed for all trp genes; their structure was assessed via bootstrapping. Alternative models of trpB evolution were evaluated with parsimony arguments. The four groups of trpB variants were correlated with archaeal speciation. Several stages of TrpA/TrpB cooperation were identified and trpB variants were characterised. Most plausibly, trpB2 represents the predecessor of the modern trpB gene, and trpB1 evolved in an ancestral bacterium

  13. Turnover of microbial lipids in the deep biosphere and growth of benthic archaeal populations.

    Science.gov (United States)

    Xie, Sitan; Lipp, Julius S; Wegener, Gunter; Ferdelman, Timothy G; Hinrichs, Kai-Uwe

    2013-04-01

    Deep subseafloor sediments host a microbial biosphere with unknown impact on global biogeochemical cycles. This study tests previous evidence based on microbial intact polar lipids (IPLs) as proxies of live biomass, suggesting that Archaea dominate the marine sedimentary biosphere. We devised a sensitive radiotracer assay to measure the decay rate of ([(14)C]glucosyl)-diphytanylglyceroldiether (GlcDGD) as an analog of archaeal IPLs in continental margin sediments. The degradation kinetics were incorporated in model simulations that constrained the fossil fraction of subseafloor IPLs and rates of archaeal turnover. Simulating the top 1 km in a generic continental margin sediment column, we estimated degradation rate constants of GlcDGD being one to two orders of magnitude lower than those of bacterial IPLs, with half-lives of GlcDGD increasing with depth to 310 ky. Given estimated microbial community turnover times of 1.6-73 ky in sediments deeper than 1 m, 50-96% of archaeal IPLs represent fossil signals. Consequently, previous lipid-based estimates of global subseafloor biomass probably are too high, and the widely observed dominance of archaeal IPLs does not rule out a deep biosphere dominated by Bacteria. Reverse modeling of existing concentration profiles suggest that archaeal IPL synthesis rates decline from around 1,000 pg⋅mL(-1) sediment⋅y(-1) at the surface to 0.2 pg⋅mL(-1)⋅y(-1) at 1 km depth, equivalent to production of 7 × 10(5) to 140 archaeal cells⋅mL(-1) sediment⋅y(-1), respectively. These constraints on microbial growth are an important step toward understanding the relationship between the deep biosphere and the carbon cycle.

  14. Environmental shaping of sponge associated archaeal communities.

    Directory of Open Access Journals (Sweden)

    Aline S Turque

    Full Text Available BACKGROUND: Archaea are ubiquitous symbionts of marine sponges but their ecological roles and the influence of environmental factors on these associations are still poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: We compared the diversity and composition of archaea associated with seawater and with the sponges Hymeniacidon heliophila, Paraleucilla magna and Petromica citrina in two distinct environments: Guanabara Bay, a highly impacted estuary in Rio de Janeiro, Brazil, and the nearby Cagarras Archipelago. For this we used metagenomic analyses of 16S rRNA and ammonia monooxygenase (amoA gene libraries. Hymeniacidon heliophila was more abundant inside the bay, while P. magna was more abundant outside and P. citrina was only recorded at the Cagarras Archipelago. Principal Component Analysis plots (PCA generated using pairwise unweighted UniFrac distances showed that the archaeal community structure of inner bay seawater and sponges was different from that of coastal Cagarras Archipelago. Rarefaction analyses showed that inner bay archaeaoplankton were more diverse than those from the Cagarras Archipelago. Only members of Crenarchaeota were found in sponge libraries, while in seawater both Crenarchaeota and Euryarchaeota were observed. Although most amoA archaeal genes detected in this study seem to be novel, some clones were affiliated to known ammonia oxidizers such as Nitrosopumilus maritimus and Cenarchaeum symbiosum. CONCLUSION/SIGNIFICANCE: The composition and diversity of archaeal communities associated with pollution-tolerant sponge species can change in a range of few kilometers, probably influenced by eutrophication. The presence of archaeal amoA genes in Porifera suggests that Archaea are involved in the nitrogen cycle within the sponge holobiont, possibly increasing its resistance to anthropogenic impacts. The higher diversity of Crenarchaeota in the polluted area suggests that some marine sponges are able to change the composition

  15. Structure and cell biology of archaeal virus STIV.

    Science.gov (United States)

    Fu, Chi-yu; Johnson, Johnson E

    2012-04-01

    Recent investigations of archaeal viruses have revealed novel features of their structures and life cycles when compared to eukaryotic and bacterial viruses, yet there are structure-based unifying themes suggesting common ancestral relationships among dsDNA viruses in the three kingdoms of life. Sulfolobus solfataricus and the infecting virus Sulfolobus turreted icosahedral virus (STIV) is one of the well-established model systems to study archaeal virus replication and viral-host interactions. Reliable laboratory conditions to propagate STIV and available genetic tools allowed structural characterization of the virus and viral components that lead to the proposal of common capsid ancestry with PRD1 (bacteriophage), Adenovirus (eukaryotic virus) and PBCV (chlorellavirus). Microarray and proteomics approaches systematically analyzed viral replication and the corresponding host responses. Cellular cryo-electron tomography and thin-section EM studies uncovered the assembly and maturation pathway of STIV and revealed dramatic cellular ultra-structure changes upon infection. The viral-induced pyramid-like protrusions on cell surfaces represent a novel viral release mechanism and previously uncharacterized functions in viral replication. PMID:22482708

  16. Family Contexts and Schooling Disruption among Orphans in Post-Genocide Rwanda

    OpenAIRE

    Kevin J.A. Thomas

    2009-01-01

    This study examines the relationship between orphan status and schooling disruption in post-genocide Rwanda. The results indicate that while non-orphans have more favorable schooling outcomes in two-parent than in single-parent families, the reverse is true among Rwandan orphans. In single-mother households, paternal orphans, i.e. orphans with only a living mother, have better outcomes than their orphan and non-orphan counterparts. In contrast, paternal orphans have worse outcomes than other ...

  17. Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours

    DEFF Research Database (Denmark)

    Yamada, Takuji; Waller, Alison S.; Raes, Jeroen;

    2012-01-01

    Despite the current wealth of sequencing data, one-third of all biochemically characterized metabolic enzymes lack a corresponding gene or protein sequence, and as such can be considered orphan enzymes. They represent a major gap between our molecular and biochemical knowledge, and consequently a...

  18. An Orphan No Longer? Detection of the Southern Orphan Stream and a Candidate Progenitor

    CERN Document Server

    Grillmair, Carl J; Carlberg, Raymond G; Willman, Beth

    2015-01-01

    Using a shallow, two-color survey carried out with the Dark Energy Camera, we detect the southern, possibly trailing arm of the Orphan Stream. The stream is reliably detected to a declination of $-38^\\circ$, bringing the total known length of the Orphan stream to $108^\\circ$. We find a slight offset or "S" shape in the stream at $\\delta \\simeq -14^\\circ$ that would be consistent with the transition from leading to trailing arms. This coincides with a moderate concentration of $137 \\pm 25$ stars (to $g = 21.6$) that we consider a possible remnant of the Orphan progenitor. The position of this feature is in agreement with previous predictions.

  19. Enriching Orphans' Potentials through Interpersonal and Intrapersonal Intelligence Enrichment Activities

    Science.gov (United States)

    Azid, Nurulwahida Hj; Yaacob, Aizan

    2016-01-01

    Orphans are considered a minority and they should be given a greater emphasis so that they do not feel left out and can build their own lives without a sense of humility. This does not mean that the orphans should be pampered instead they should be given the confidence and motivation to strive for success in later life. Humility among orphans can…

  20. Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters.

    Science.gov (United States)

    Hugoni, Mylène; Taib, Najwa; Debroas, Didier; Domaizon, Isabelle; Jouan Dufournel, Isabelle; Bronner, Gisèle; Salter, Ian; Agogué, Hélène; Mary, Isabelle; Galand, Pierre E

    2013-04-01

    Marine Archaea are important players among microbial plankton and significantly contribute to biogeochemical cycles, but details regarding their community structure and long-term seasonal activity and dynamics remain largely unexplored. In this study, we monitored the interannual archaeal community composition of abundant and rare biospheres in northwestern Mediterranean Sea surface waters by pyrosequencing 16S rDNA and rRNA. A detailed analysis of the rare biosphere structure showed that the rare archaeal community was composed of three distinct fractions. One contained the rare Archaea that became abundant at different times within the same ecosystem; these cells were typically not dormant, and we hypothesize that they represent a local seed bank that is specific and essential for ecosystem functioning through cycling seasonal environmental conditions. The second fraction contained cells that were uncommon in public databases and not active, consisting of aliens to the studied ecosystem and representing a nonlocal seed bank of potential colonizers. The third fraction contained Archaea that were always rare but actively growing; their affiliation and seasonal dynamics were similar to the abundant microbes and could not be considered a seed bank. We also showed that the major archaeal groups, Thaumarchaeota marine group I and Euryarchaeota group II.B in winter and Euryarchaeota group II.A in summer, contained different ecotypes with varying activities. Our findings suggest that archaeal diversity could be associated with distinct metabolisms or life strategies, and that the rare archaeal biosphere is composed of a complex assortment of organisms with distinct histories that affect their potential for growth.

  1. Niche specialization of terrestrial archaeal ammonia oxidizers

    OpenAIRE

    Gubry-Rangin, Cécile; Hai, Brigitte; Quince, Christopher; Engel, Marion; Thomson, Bruce C.; James, Phillip; Schloter, Michael; Robert I. Griffiths; Prosser, James I.; Nicol, Graeme W.

    2011-01-01

    Soil pH is a major determinant of microbial ecosystem processes and potentially a major driver of evolution, adaptation, and diversity of ammonia oxidizers, which control soil nitrification. Archaea are major components of soil microbial communities and contribute significantly to ammonia oxidation in some soils. To determine whether pH drives evolutionary adaptation and community structure of soil archaeal ammonia oxidizers, sequences of amoA, a key functional gene of ammonia oxidation, were...

  2. Exploring the Relationship between Caregiving and Health: Perceptions among Orphaned and Non-Orphaned Adolescents in Tanzania

    Science.gov (United States)

    Mmari, Kristin

    2011-01-01

    The objectives of this study were to (1) explore the nature of caregiving for orphaned and non-orphaned adolescents; and (2), examine how changes in the caretaking roles, as a result of a parental loss, impact on an orphan's sexual behaviors. A total of 52 in-depth interviews and 11 focus group discussions (n = 83) were conducted among adolescent…

  3. TBP Domain Symmetry in Basal and Activated Archaeal Transcription

    OpenAIRE

    Ouhammouch, Mohamed; Hausner, Winfried; Geiduschek, E Peter

    2008-01-01

    The TATA-box binding protein (TBP) is the platform for assembly of archaeal and eukaryotic transcription preinitiation complexes. Ancestral gene duplication and fusion events have produced the saddle-shaped TBP molecule, with its two direct-repeat subdomains and pseudo-two-fold symmetry. Collectively, eukaryotic TBPs have diverged from their present-day archaeal counterparts, which remain highly symmetrical. The similarity of the N- and C-halves of archaeal TBPs is especially pronounced in th...

  4. 76 FR 64868 - Orphan Drug Regulations

    Science.gov (United States)

    2011-10-19

    ... preamble to the final rule, ``Orphan Drug Regulations'' (57 FR 62076 at 62084), FDA reiterated that it... Regulations in the Federal Register of December 29, 1992 (57 FR 62076), FDA has reviewed over 3,350 requests... Federal Register of January 29, 1991 (56 FR 3338 at 3339). Because the term ``medically plausible''...

  5. The African Orphan Crisis and International Adoption

    Science.gov (United States)

    Roby, Jini L.; Shaw, Stacey A.

    2006-01-01

    The plight of Africa's AIDS orphans has reached crisis proportions, and the international community is beginning to mobilize at the family, community, national, and international levels. Despite these encouraging efforts, the response is inadequate, and increased attention and action are needed. The authors suggest that international adoption,…

  6. A Routing Protocol Orphan-Leach to Join Orphan Nodes in Wireless Sensor Network

    Directory of Open Access Journals (Sweden)

    Wassim JERBI

    2016-04-01

    Full Text Available The hierarchical routing protocol LEACH (Low Energy Adaptive Clustering Hierarchy is referred to as the basic algorithm of distributed c lustering protocols. LEACH allows clusters formation. Each cluster has a leader called Cluster Head (CH. The selection of CHs is made with a probabilistic calculation. It is supposed th at each non-CH node join a cluster and becomes a cluster member. Nevertheless, some CHs ca n be concentrated in a specific part of the network. Thus several sensor nodes cannot reach any CH. As a result, the remaining part of the controlled field will not be covered; some sensor n odes will be outside the network. To solve this problem, we propose O-LEACH (Orphan Low Energy Adap tive Clustering Hierarchy a routing protocol that takes into account the orphan nodes. Indeed, a cluster member will be able to play the role of a gateway which allows the joining of o rphan nodes. If a gateway node has to connect a important number of orphan nodes, thus a sub-cluster is created and the gateway node is considered as a CH’ for connected orphans. As a result, orphan nodes become able to send their data messages to the CH which performs i n turn data aggregation and send aggregated data message to the CH. The WSN applicat ion receives data from the entire network including orphan nodes. The simulation results show that O-LEACH performs b etter than LEACH in terms of connectivity rate, energy, scalability and coverage .

  7. EU orphan regulation--ten years of application.

    Science.gov (United States)

    Michaux, Geneviève

    2010-01-01

    In April 2000, European Regulation (EC) No 141/2000 on Orphan Medicinal Products, which, following the U.S. example, had been adopted to boost the research, development, and marketing of medicinal products for rare diseases, became effective. Ten years later, figures prove that, with an average of more than 70 orphan designations per year, the European orphan regulation is a success. To date, the key issue is no longer research and development but effective market access. Less than 10% of the orphan designated products are approved for marketing and even less products are actually placed on the European national markets due to pricing and reimbursement obstacles. The article examines the European orphan regime, focusing on its two cornerstones--orphan designation and exclusivity--and highlighting the concepts that are still unclear and the issues that have not yet been addressed. The European Orphan Regulation has been proved to work well, but it would be even more successful if orphan designation was easier and orphan incentives were more attractive. The article concludes on the changes to be made to the European orphan legal regime that would encourage even more the research and development of orphan products. PMID:24479246

  8. Factors Controlling the Distribution of Archaeal Tetraethers in Terrestrial Hot Springs▿

    OpenAIRE

    Pearson, Ann; Pi, Yundan; Zhao, Weidong; Li, Wenjun; Li, Yiliang; Inskeep, William; Perevalova, Anna; Romanek, Christopher; Li, Shuguang; Zhang, Chuanlun L.

    2008-01-01

    Glycerol dialkyl glycerol tetraethers (GDGTs) found in hot springs reflect the abundance and community structure of Archaea in these extreme environments. The relationships between GDGTs, archaeal communities, and physical or geochemical variables are underexamined to date and when reported often result in conflicting interpretations. Here, we examined profiles of GDGTs from pure cultures of Crenarchaeota and from terrestrial geothermal springs representing a wide distribution of locations, i...

  9. Geochemical Approach to Archaeal Ecology: δ13C of GDGTs

    Science.gov (United States)

    Lichtin, S.; Warren, C.; Pearson, A.; Pagani, M.

    2015-12-01

    Over the last decade and a half, glycerol dialkyl glycerol tetraethers (GDGTs) have increasingly been used to reconstruct environmental temperatures; proxies like TEX86 that correlate the relative abundance of these archaeal cell membrane lipids to sea surface temperature are omnipresent in paleoclimatology literature. While it has become common to make claims about past temperatures using GDGTs, our present understanding of the organisms that synthesize the compounds is still quite limited. The generally accepted theory states that microorganisms like the Thaumarchaeota modify the structure of membrane lipids to increase intermolecular interactions, strengthening the membrane at higher temperatures. Yet to date, culture experiments have been largely restricted to a single species, Nitrosopumilus maritimes, and recent studies on oceanic archaeal rRNA have revealed that these biomarkers are produced in diverse, heterogeneous, and site-specific communities. This brings up questions as to whether different subclasses of GDGTs, and all subsequent proxies, represent adaptation within a single organismal group or a shift in community composition. To investigate whether GDGTs with different chain structures, from the simple isoprenoidal GDGT-0 to Crenarchaeol with its many cyclopentane groups, are sourced from archaea with similar or disparate metabolic pathways—and if that information is inherited in GDGTs trapped in marine sediments—this study examines the stable carbon isotope values (δ13C) of GDGTs extracted from the uppermost meters of sediment in the Orca Basin, Gulf of Mexico, using spooling-wire microcombustion isotope-ratio mass spectrometer (SWiM-IRMS), tackling a fundamental assumption of the TEX86 proxy that influences the way we perceive the veracity of existing temperature records.

  10. Archaeal CRISPR-based immune systems

    DEFF Research Database (Denmark)

    Garrett, Roger A; Vestergaard, Gisle Alberg; Shah, Shiraz Ali

    2011-01-01

    CRISPR (clustered regularly interspaced short palindromic repeats)-based immune systems are essentially modular with three primary functions: the excision and integration of new spacers, the processing of CRISPR transcripts to yield mature CRISPR RNAs (crRNAs), and the targeting and cleavage...... of foreign nucleic acid. The primary target appears to be the DNA of foreign genetic elements, but the CRISPR/Cmr system that is widespread amongst archaea also specifically targets and cleaves RNA in vitro. The archaeal CRISPR systems tend to be both diverse and complex. Here we examine evidence...... of CRISPR loci and the evidence for intergenomic exchange of CRISPR systems....

  11. 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.

  12. 21 CFR 316.26 - Amendment to orphan-drug designation.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Amendment to orphan-drug designation. 316.26... (CONTINUED) DRUGS FOR HUMAN USE ORPHAN DRUGS Designation of an Orphan Drug § 316.26 Amendment to orphan-drug designation. (a) At any time prior to approval of a marketing application for a designated orphan drug,...

  13. 21 CFR 316.25 - Refusal to grant orphan-drug designation.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Refusal to grant orphan-drug designation. 316.25... (CONTINUED) DRUGS FOR HUMAN USE ORPHAN DRUGS Designation of an Orphan Drug § 316.25 Refusal to grant orphan-drug designation. (a) FDA will refuse to grant a request for orphan-drug designation if any of...

  14. 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.

  15. Correlating Orphaned Windows Registry Data Structures

    Directory of Open Access Journals (Sweden)

    Damir Kahved

    2009-06-01

    Full Text Available Recently, it has been shown that deleted entries of the Microsoft Windows registry (keys may still reside in the system files once the entries have been deleted from the active database. Investigating the complete keys in context may be extremely important from both a Forensic Investigation point of view and a legal point of view where a lack of context can bring doubt to an argument. In this paper we formalise the registry behaviour and show how a retrieved value may not maintain a relation to the part of the registry it belonged to and hence lose that context. We define registry orphans and elaborate on how they can be created inadvertently during software uninstallation and other system processes. We analyse the orphans and attempt to reconstruct them automatically. We adopt a data mining approach and introduce a set of attributes that can be applied by the forensic investigator to match values to their parents. The heuristics are encoded in a Decision Tree that can discriminate between keys and select those which most likely owned a particular orphan value.

  16. Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes.

    Science.gov (United States)

    Saw, Jimmy H; Spang, Anja; Zaremba-Niedzwiedzka, Katarzyna; Juzokaite, Lina; Dodsworth, Jeremy A; Murugapiran, Senthil K; Colman, Dan R; Takacs-Vesbach, Cristina; Hedlund, Brian P; Guy, Lionel; Ettema, Thijs J G

    2015-09-26

    The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteobacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal 'dark matter', is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Korarchaeum-related lineage. The maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell. PMID:26323759

  17. Methanopyrus kandleri: an archaeal methanogen unrelated to all other known methanogens

    Science.gov (United States)

    Burggraf, S.; Stetter, K. O.; Rouviere, P.; Woese, C. R.

    1991-01-01

    Analysis of its 16S rRNA sequence shows that the newly discovered hyperthermophilic methanogen, Methanopryus kandleri, is phylogenetically unrelated to any other known methanogen. The organism represents a separate lineage originating near the root of the archaeal tree. Although the 16S rRNA sequence of Mp. kandleri resembles euryarchaeal 16S rRNAs more than it does crenarchaeal, it shows more crenarchaeal signature features than any known euryarchaeal rRNA. Attempts to place it in relation to the root of the archaeal tree show that the Mp. kandleri lineage likely arises from the euryarchaeal branch of the tree. While the existence of so deeply branching a methanogenic lineage brings into question the thesis that methanogenesis evolved from an earlier metabolism similar to that seen in Thermococcus, it at the same time reinforces the notion that the aboriginal [correction of aborginal] archaeon was a thermophile.

  18. An Orphan No Longer? Detection of the Southern Orphan Stream and a Candidate Progenitor

    Science.gov (United States)

    Grillmair, Carl J.; Hetherington, Lauren; Carlberg, Raymond G.; Willman, Beth

    2015-10-01

    Using a shallow, two-color survey carried out with the Dark Energy Camera, we detect the southern, possibly trailing arm of the Orphan Stream. The stream is reliably detected to a decl. of ‑38°, bringing the total known length of the Orphan Stream to 108°. We find a slight offset or “S” shape in the stream at δ ≃ ‑14° that would be consistent with the transition from leading to trailing arms. This coincides with a moderate concentration of 137 ± 25 stars (to g = 21.6) that we consider a possible remnant of the Orphan progenitor. The position of this feature is in agreement with previous predictions.

  19. 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

  20. Emerging roles of orphan nuclear receptors in cancer.

    Science.gov (United States)

    Baek, Sung Hee; Kim, Keun Il

    2014-01-01

    A growing body of evidence suggests that a subset of orphan nuclear receptors are amplified and prognostic for some human cancers. However, the specific roles of these orphan nuclear receptors in tumor progression and their utility as drug targets are not fully understood. In this review, we summarize recent progress in elucidating the direct and indirect involvement of orphan nuclear receptors in cancer as well as their therapeutic potential in a variety of human cancers. Furthermore, we contrast the role of orphan nuclear receptors in cancer with the known roles of estrogen receptor and androgen receptor in hormone-dependent cancers. PMID:24215441

  1. Factors Associated with Substance Use among Orphaned and Non-Orphaned Youth in South Africa

    Science.gov (United States)

    Meghdadpour, Susanne; Curtis, Sian; Pettifor, Audrey; MacPhail, Catherine

    2012-01-01

    Substance use is increasing among youth in South Africa, and may be contributing to transmission of HIV. As parental death often leaves youth with altered emotional and physical resources, substance use may be greater among orphaned adolescents. Utilizing data from a household survey of 15-24 year old South Africans (n = 11,904), multivariable…

  2. 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.

  3. Activation of archaeal transcription mediated by recruitment of transcription factor B.

    Science.gov (United States)

    Ochs, Simon M; Thumann, Sybille; Richau, Renate; Weirauch, Matt T; Lowe, Todd M; Thomm, Michael; Hausner, Winfried

    2012-05-25

    Archaeal promoters consist of a TATA box and a purine-rich adjacent upstream sequence (transcription factor B (TFB)-responsive element (BRE)), which are bound by the transcription factors TATA box-binding protein (TBP) and TFB. Currently, only a few activators of archaeal transcription have been experimentally characterized. The best studied activator, Ptr2, mediates activation by recruitment of TBP. Here, we present a detailed biochemical analysis of an archaeal transcriptional activator, PF1088, which was identified in Pyrococcus furiosus by a bioinformatic approach. Operon predictions suggested that an upstream gene, pf1089, is polycistronically transcribed with pf1088. We demonstrate that PF1088 stimulates in vitro transcription by up to 7-fold when the pf1089 promoter is used as a template. By DNase I and hydroxyl radical footprinting experiments, we show that the binding site of PF1088 is located directly upstream of the BRE of pf1089. Mutational analysis indicated that activation requires the presence of the binding site for PF1088. Furthermore, we show that activation of transcription by PF1088 is dependent upon the presence of an imperfect BRE and is abolished when the pf1089 BRE is replaced with a BRE from a strong archaeal promoter. Gel shift experiments showed that TFB recruitment to the pf1089 operon is stimulated by PF1088, and TFB seems to stabilize PF1088 operator binding even in the absence of TBP. Taken together, these results represent the first biochemical evidence for a transcriptional activator working as a TFB recruitment factor in Archaea, for which the designation TFB-RF1 is suggested. PMID:22496454

  4. Nitrification of archaeal ammonia oxidizers in a high- temperature hot spring

    Science.gov (United States)

    Chen, Shun; Peng, Xiaotong; Xu, Hengchao; Ta, Kaiwen

    2016-04-01

    The oxidation of ammonia by microbes has been shown to occur in diverse natural environments. However, the link of in situ nitrification activity to taxonomic identities of ammonia oxidizers in high-temperature environments remains poorly understood. Here, we studied in situ ammonia oxidation rates and the diversity of ammonia-oxidizing Archaea (AOA) in surface and bottom sediments at 77 °C in the Gongxiaoshe hot spring, Tengchong, Yunnan, China. The in situ ammonia oxidation rates measured by the 15N-NO3- pool dilution technique in the surface and bottom sediments were 4.80 and 5.30 nmol N g-1 h-1, respectively. Real-time quantitative polymerase chain reaction (qPCR) indicated that the archaeal 16S rRNA genes and amoA genes were present in the range of 0.128 to 1.96 × 108 and 2.75 to 9.80 × 105 gene copies g-1 sediment, respectively, while bacterial amoA was not detected. Phylogenetic analysis of 16S rRNA genes showed high sequence similarity to thermophilic Candidatus Nitrosocaldus yellowstonii, which represented the most abundant operational taxonomic units (OTU) in both surface and bottom sediments. The archaeal predominance was further supported by fluorescence in situ hybridization (FISH) visualization. The cell-specific rate of ammonia oxidation was estimated to range from 0.410 to 0.790 fmol N archaeal cell-1 h-1, higher than those in the two US Great Basin hot springs. These results suggest the importance of archaeal rather than bacterial ammonia oxidation in driving the nitrogen cycle in terrestrial geothermal environments.

  5. Bacterial and archaeal phylogenetic diversity associated with swine sludge from an anaerobic treatment lagoon.

    Science.gov (United States)

    Cardinali-Rezende, Juliana; Pereira, Zelina L; Sanz, José L; Chartone-Souza, Edmar; Nascimento, Andréa M A

    2012-11-01

    Over the last decades, the demand for pork products has increased significantly, along with concern about suitable waste management. Anaerobic-lagoon fermentation for swine-sludge stabilization is a good strategy, although little is known about the microbial communities in the lagoons. Here, we employed a cloning- and sequencing-based analysis of the 16S rRNA gene to characterize and quantify the prokaryotic community composition in a swine-waste-sludge anaerobic lagoon (SAL). DNA sequence analysis revealed that the SAL library harbored 15 bacterial phyla: Bacteroidetes, Cloroflexi, Proteobacteria, Firmicutes, Deinococcus-Thermus, Synergystetes, Gemmatimonadetes, Chlorobi, Fibrobacteres, Verrucomicrobia and candidates division OP5, OP8, WWE1, KSB1, WS6. The SAL library was generally dominated by carbohydrate-oxidizing bacteria. The archaeal sequences were related to the Crenarchaeota and Euryarchaeota phyla. Crenarchaeota predominated in the library, demonstrating that it is not restricted to high-temperature environments, being also responsible for ammonium oxidation in the anaerobic lagoon. Euryarchaeota sequences were associated with the hydrogenotrophic methanogens (Methanomicrobiales and Methanobacteriales). Quantitative PCR analysis revealed that the number of bacterial cells was at least three orders of magnitude higher than the number of archaeal cells in the SAL. The identified prokaryotic diversity was ecologically significant, particularly the archaeal community of hydrogenotrophic methanogens, which was responsible for methane production in the anaerobic lagoon. This study provided insight into the archaeal involvement in the overall oxidation of organic matter and the production of methane. Therefore, the treatment of swine waste in the sludge anaerobic lagoon could represent a potential inoculum for the start-up of municipal solid-waste digesters. PMID:22828793

  6. A Method for Identification of Selenoprotein Genes in Archaeal Genomes

    Institute of Scientific and Technical Information of China (English)

    Mingfeng Li; Yanzhao Huang; Yi Xiao

    2009-01-01

    The genetic codon UGA has a dual function: serving as a terminator and encoding selenocysteine. However, most popular gene annotation programs only take it as a stop signal, resulting in misannotation or completely missing selenoprotein genes. We developed a computational method named Asec-Prediction that is specific for the prediction of archaeal selenoprotein genes. To evaluate its effectiveness, we first applied it to 14 archaeal genomes with previously known selenoprotein genes, and Asec-Prediction identified all reported selenoprotein genes without redundant results. When we applied it to 12 archaeal genomes that had not been researched for selenoprotein genes, Asec-Prediction detected a novel selenoprotein gene in Methanosarcina acetivorans. Further evidence was also collected to support that the predicted gene should be a real selenoprotein gene. The result shows that Asec-Prediction is effective for the prediction of archaeal selenoprotein genes.

  7. Orphan Children: Adjusting to Life after the Boarding Institution

    Science.gov (United States)

    Prisiazhnaia, N. V.

    2008-01-01

    According to official statistics, in Russia there are over 800,000 orphans and children who are deprived of parental care; 260,000 are living and being taught in more than 4,000 state boarding institutions. The category "orphan child" consists of children up to the age of eighteen, one or both of whose parents have died. The term "social…

  8. Predictors of orphan drug approval in the European Union

    NARCIS (Netherlands)

    H.E. Heemstra (Harald); R.L.A. de Vrueh (Remco); S. van Weely (Sonja); H.A. Büller (Hans); H.G.M. Leufkens (Hubert)

    2008-01-01

    textabstractObjective: To encourage the development of drugs for rare diseases, orphan drug legislation has been introduced in the USA (1983) and in the EU (2000). Recent literature discusses factors that may influence the development of new orphan medicinal products in the EU. This study aims to id

  9. World and experiences of AIDS orphans in north central Namibia

    NARCIS (Netherlands)

    Brug, van der M.

    2007-01-01

    How do young AIDS orphans deal with the loss of their parents and their changed circumstances? This thesis discusses the social environment, experiences and perceptions of fourteen orphans in north central Namibia. The author followed the children for five months from September 2003 until March 2004

  10. Structure and Cell Biology of Archaeal Virus STIV

    OpenAIRE

    Fu, Chi-yu; Johnson, John E.

    2012-01-01

    Recent investigations of archaeal viruses have revealed novel features of their structures and life cycles when compared to eukaryotic and bacterial viruses, yet there are structure-based unifying themes suggesting common ancestral relationships among dsDNA viruses in the three kingdoms of life. Sulfolobus solfataricus and the infecting virus Sulfolobus turreted icosahedral virus (STIV) is one of the well-established model systems to study archaeal virus replication and viral-host interaction...

  11. The Orphan Drug Act: Restoring the Mission to Rare Diseases.

    Science.gov (United States)

    Daniel, Michael G; Pawlik, Timothy M; Fader, Amanda N; Esnaola, Nestor F; Makary, Martin A

    2016-04-01

    The Orphan Drug Act has fostered drug development for patients with rare cancers and other diseases; however, current data suggest that companies are gaming the system to use the law for mainstream drugs. We identify a pattern of pharmaceutical companies submitting drugs to the Food and Drug Administration (FDA) as orphan drugs but once approved, the drugs are used broadly off-label with the lucrative orphan drug protections and exclusivity benefits. Since the law was passed, the proportion of new FDA-approved drugs that were submitted as orphan drugs has increased with a peak last year of 41% of all FDA-approved drugs approved as orphan drugs. On the basis of the current data, we suggest that patients with rare cancers and other diseases may suffer due to dilution of the incentives and benefits. We propose reform to increase submission scrutiny, decrease benefits based on off-label use, and increase price transparency. PMID:26580246

  12. Exploring Responses to Transformative Group Therapy for Orphaned Children in the Context of Mass Orphaning in Botswana

    Science.gov (United States)

    Thamuku, Masego; Daniel, Marguerite

    2013-01-01

    In the context of AIDS, the Botswana Government has adopted a group therapy program to help large numbers of orphaned children cope with bereavement. This study explores the effectiveness of the therapy and examines how it interacts with cultural attitudes and practices concerning death. Ten orphaned children were involved in five rounds of data…

  13. 21 CFR 316.20 - Content and format of a request for orphan-drug designation.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Content and format of a request for orphan-drug... SERVICES (CONTINUED) DRUGS FOR HUMAN USE ORPHAN DRUGS Designation of an Orphan Drug § 316.20 Content and format of a request for orphan-drug designation. (a) A sponsor that submits a request for...

  14. 21 CFR 316.27 - Change in ownership of orphan-drug designation.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Change in ownership of orphan-drug designation... SERVICES (CONTINUED) DRUGS FOR HUMAN USE ORPHAN DRUGS Designation of an Orphan Drug § 316.27 Change in ownership of orphan-drug designation. (a) A sponsor may transfer ownership of or any beneficial interest...

  15. 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... SERVICES (CONTINUED) DRUGS FOR HUMAN USE ORPHAN DRUGS Designation of an Orphan Drug § 316.30 Annual reports of holder of orphan-drug designation. Within 14 months after the date on which a drug was...

  16. 21 CFR 316.31 - Scope of orphan-drug exclusive approval.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Scope of orphan-drug exclusive approval. 316.31... (CONTINUED) DRUGS FOR HUMAN USE ORPHAN DRUGS Orphan-drug Exclusive Approval § 316.31 Scope of orphan-drug exclusive approval. (a) After approval of a sponsor's marketing application for a designated...

  17. 21 CFR 316.28 - Publication of orphan-drug designations.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Publication of orphan-drug designations. 316.28... (CONTINUED) DRUGS FOR HUMAN USE ORPHAN DRUGS Designation of an Orphan Drug § 316.28 Publication of orphan-drug designations. Each month FDA will update a publically available list of drugs designated as...

  18. 21 CFR 316.40 - Treatment use of a designated orphan drug.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Treatment use of a designated orphan drug. 316.40... (CONTINUED) DRUGS FOR HUMAN USE ORPHAN DRUGS Open Protocols for Investigations § 316.40 Treatment use of a designated orphan drug. Prospective investigators seeking to obtain treatment use of designated orphan...

  19. Virus-mediated archaeal hecatomb in the deep seafloor

    Science.gov (United States)

    Danovaro, Roberto; Dell’Anno, Antonio; Corinaldesi, Cinzia; Rastelli, Eugenio; Cavicchioli, Ricardo; Krupovic, Mart; Noble, Rachel T.; Nunoura, Takuro; Prangishvili, David

    2016-01-01

    Viruses are the most abundant biological entities in the world’s oceans, and they play a crucial role in global biogeochemical cycles. In deep-sea ecosystems, archaea and bacteria drive major nutrient cycles, and viruses are largely responsible for their mortality, thereby exerting important controls on microbial dynamics. However, the relative impact of viruses on archaea compared to bacteria is unknown, limiting our understanding of the factors controlling the functioning of marine systems at a global scale. We evaluate the selectivity of viral infections by using several independent approaches, including an innovative molecular method based on the quantification of archaeal versus bacterial genes released by viral lysis. We provide evidence that, in all oceanic surface sediments (from 1000- to 10,000-m water depth), the impact of viral infection is higher on archaea than on bacteria. We also found that, within deep-sea benthic archaea, the impact of viruses was mainly directed at members of specific clades of Marine Group I Thaumarchaeota. Although archaea represent, on average, ~12% of the total cell abundance in the top 50 cm of sediment, virus-induced lysis of archaea accounts for up to one-third of the total microbial biomass killed, resulting in the release of ~0.3 to 0.5 gigatons of carbon per year globally. Our results indicate that viral infection represents a key mechanism controlling the turnover of archaea in surface deep-sea sediments. We conclude that interactions between archaea and their viruses might play a profound, previously underestimated role in the functioning of deep-sea ecosystems and in global biogeochemical cycles. PMID:27757416

  20. Orphans at risk in Sub-Saharan Africa : evidence on educational and health outcomes

    OpenAIRE

    Coneus, Katja; Mühlenweg, Andrea M.

    2011-01-01

    In this paper, we examine how orphanhood affects children’s educational and health outcomes in eleven sub-Saharan African countries. Our analysis is based on a comparison of orphans and non-orphaned children living under the same conditions. We also examine the impacts of various family structures and compare social orphans (non-orphaned children not living with a biological parent) to orphans. Using household fixed-effects estimation, we provide evidence that children not living with a biolo...

  1. Functional analysis of archaeal MBF1 by complementation studies in yeast

    Directory of Open Access Journals (Sweden)

    Siebers Bettina

    2011-03-01

    Full Text Available Abstract Background Multiprotein-bridging factor 1 (MBF1 is a transcriptional co-activator that bridges a sequence-specific activator (basic-leucine zipper (bZIP like proteins (e.g. Gcn4 in yeast or steroid/nuclear-hormone receptor family (e.g. FTZ-F1 in insect and the TATA-box binding protein (TBP in Eukaryotes. MBF1 is absent in Bacteria, but is well- conserved in Eukaryotes and Archaea and harbors a C-terminal Cro-like Helix Turn Helix (HTH domain, which is the only highly conserved, classical HTH domain that is vertically inherited in all Eukaryotes and Archaea. The main structural difference between archaeal MBF1 (aMBF1 and eukaryotic MBF1 is the presence of a Zn ribbon motif in aMBF1. In addition MBF1 interacting activators are absent in the archaeal domain. To study the function and therefore the evolutionary conservation of MBF1 and its single domains complementation studies in yeast (mbf1Δ as well as domain swap experiments between aMBF1 and yMbf1 were performed. Results In contrast to previous reports for eukaryotic MBF1 (i.e. Arabidopsis thaliana, insect and human the two archaeal MBF1 orthologs, TMBF1 from the hyperthermophile Thermoproteus tenax and MMBF1 from the mesophile Methanosarcina mazei were not functional for complementation of an Saccharomyces cerevisiae mutant lacking Mbf1 (mbf1Δ. Of twelve chimeric proteins representing different combinations of the N-terminal, core domain, and the C-terminal extension from yeast and aMBF1, only the chimeric MBF1 comprising the yeast N-terminal and core domain fused to the archaeal C-terminal part was able to restore full wild-type activity of MBF1. However, as reported previously for Bombyx mori, the C-terminal part of yeast Mbf1 was shown to be not essential for function. In addition phylogenetic analyses revealed a common distribution of MBF1 in all Archaea with available genome sequence, except of two of the three Thaumarchaeota; Cenarchaeum symbiosum A and Nitrosopumilus maritimus

  2. Crystal structure of an archaeal actin homolog.

    Science.gov (United States)

    Roeben, Annette; Kofler, Christine; Nagy, István; Nickell, Stephan; Hartl, F Ulrich; Bracher, Andreas

    2006-04-21

    Prokaryotic homologs of the eukaryotic structural protein actin, such as MreB and ParM, have been implicated in determination of bacterial cell shape, and in the segregation of genomic and plasmid DNA. In contrast to these bacterial actin homologs, little is known about the archaeal counterparts. As a first step, we expressed a predicted actin homolog of the thermophilic archaeon Thermoplasma acidophilum, Ta0583, and determined its crystal structure at 2.1A resolution. Ta0583 is expressed as a soluble protein in T.acidophilum and is an active ATPase at physiological temperature. In vitro, Ta0583 forms sheets with spacings resembling the crystal lattice, indicating an inherent propensity to form filamentous structures. The fold of Ta0583 contains the core structure of actin and clearly belongs to the actin/Hsp70 superfamily of ATPases. Ta0583 is approximately equidistant from actin and MreB on the structural level, and combines features from both eubacterial actin homologs, MreB and ParM. The structure of Ta0583 co-crystallized with ADP indicates that the nucleotide binds at the interface between the subdomains of Ta0583 in a manner similar to that of actin. However, the conformation of the nucleotide observed in complex with Ta0583 clearly differs from that in complex with actin, but closely resembles the conformation of ParM-bound nucleotide. On the basis of sequence and structural homology, we suggest that Ta0583 derives from a ParM-like actin homolog that was once encoded by a plasmid and was transferred into a common ancestor of Thermoplasma and Ferroplasma. Intriguingly, both genera are characterized by the lack of a cell wall, and therefore Ta0583 could have a function in cellular organization.

  3. 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

  4. Factors Controlling the Distribution of Archaeal Tetraethers in Terrestrial Hot Springs▿

    Science.gov (United States)

    Pearson, Ann; Pi, Yundan; Zhao, Weidong; Li, WenJun; Li, Yiliang; Inskeep, William; Perevalova, Anna; Romanek, Christopher; Li, Shuguang; Zhang, Chuanlun L.

    2008-01-01

    Glycerol dialkyl glycerol tetraethers (GDGTs) found in hot springs reflect the abundance and community structure of Archaea in these extreme environments. The relationships between GDGTs, archaeal communities, and physical or geochemical variables are underexamined to date and when reported often result in conflicting interpretations. Here, we examined profiles of GDGTs from pure cultures of Crenarchaeota and from terrestrial geothermal springs representing a wide distribution of locations, including Yellowstone National Park (United States), the Great Basin of Nevada and California (United States), Kamchatka (Russia), Tengchong thermal field (China), and Thailand. These samples had temperatures of 36.5 to 87°C and pH values of 3.0 to 9.2. GDGT abundances also were determined for three soil samples adjacent to some of the hot springs. Principal component analysis identified four factors that accounted for most of the variance among nine individual GDGTs, temperature, and pH. Significant correlations were observed between pH and the GDGTs crenarchaeol and GDGT-4 (four cyclopentane rings, m/z 1,294); pH correlated positively with crenarchaeol and inversely with GDGT-4. Weaker correlations were observed between temperature and the four factors. Three of the four GDGTs used in the marine TEX86 paleotemperature index (GDGT-1 to -3, but not crenarchaeol isomer) were associated with a single factor. No correlation was observed for GDGT-0 (acyclic caldarchaeol): it is effectively its own variable. The biosynthetic mechanisms and exact archaeal community structures leading to these relationships remain unknown. However, the data in general show promise for the continued development of GDGT lipid-based physiochemical proxies for archaeal evolution and for paleo-ecology or paleoclimate studies. PMID:18390673

  5. Factors controlling the distribution of archaeal tetraethers in terrestrial hot springs.

    Science.gov (United States)

    Pearson, Ann; Pi, Yundan; Zhao, Weidong; Li, WenJun; Li, Yiliang; Inskeep, William; Perevalova, Anna; Romanek, Christopher; Li, Shuguang; Zhang, Chuanlun L

    2008-06-01

    Glycerol dialkyl glycerol tetraethers (GDGTs) found in hot springs reflect the abundance and community structure of Archaea in these extreme environments. The relationships between GDGTs, archaeal communities, and physical or geochemical variables are underexamined to date and when reported often result in conflicting interpretations. Here, we examined profiles of GDGTs from pure cultures of Crenarchaeota and from terrestrial geothermal springs representing a wide distribution of locations, including Yellowstone National Park (United States), the Great Basin of Nevada and California (United States), Kamchatka (Russia), Tengchong thermal field (China), and Thailand. These samples had temperatures of 36.5 to 87 degrees C and pH values of 3.0 to 9.2. GDGT abundances also were determined for three soil samples adjacent to some of the hot springs. Principal component analysis identified four factors that accounted for most of the variance among nine individual GDGTs, temperature, and pH. Significant correlations were observed between pH and the GDGTs crenarchaeol and GDGT-4 (four cyclopentane rings, m/z 1,294); pH correlated positively with crenarchaeol and inversely with GDGT-4. Weaker correlations were observed between temperature and the four factors. Three of the four GDGTs used in the marine TEX(86) paleotemperature index (GDGT-1 to -3, but not crenarchaeol isomer) were associated with a single factor. No correlation was observed for GDGT-0 (acyclic caldarchaeol): it is effectively its own variable. The biosynthetic mechanisms and exact archaeal community structures leading to these relationships remain unknown. However, the data in general show promise for the continued development of GDGT lipid-based physiochemical proxies for archaeal evolution and for paleo-ecology or paleoclimate studies. PMID:18390673

  6. Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin.

    Science.gov (United States)

    Pérez-Rueda, Ernesto; Janga, Sarath Chandra

    2010-06-01

    Archaea, which represent a large fraction of the phylogenetic diversity of organisms, are prokaryotes with eukaryote-like basal transcriptional machinery. This organization makes the study of their DNA-binding transcription factors (TFs) and their transcriptional regulatory networks particularly interesting. In addition, there are limited experimental data regarding their TFs. In this work, 3,918 TFs were identified and exhaustively analyzed in 52 archaeal genomes. TFs represented less than 5% of the gene products in all the studied species comparable with the number of TFs identified in parasites or intracellular pathogenic bacteria, suggesting a deficit in this class of proteins. A total of 75 families were identified, of which HTH_3, AsnC, TrmB, and ArsR families were universally and abundantly identified in all the archaeal genomes. We found that archaeal TFs are significantly small compared with other protein-coding genes in archaea as well as bacterial TFs, suggesting that a large fraction of these small-sized TFs could supply the probable deficit of TFs in archaea, by possibly forming different combinations of monomers similar to that observed in eukaryotic transcriptional machinery. Our results show that although the DNA-binding domains of archaeal TFs are similar to bacteria, there is an underrepresentation of ligand-binding domains in smaller TFs, which suggests that protein-protein interactions may act as mediators of regulatory feedback, indicating a chimera of bacterial and eukaryotic TFs' functionality. The analysis presented here contributes to the understanding of the details of transcriptional apparatus in archaea and provides a framework for the analysis of regulatory networks in these organisms.

  7. Familial relationships in hyperthermo- and acidophilic archaeal viruses

    DEFF Research Database (Denmark)

    Happonen, Lotta Johanna; Redder, Peter; Peng, Xu;

    2010-01-01

    Archaea often live in extreme, harsh environments such as acidic hot springs and hypersaline waters. To date, only two icosahedrally symmetric, membrane-containing archaeal viruses, SH1 and Sulfolobus turreted icosahedral virus (STIV), have been described in detail. We report the sequence and three...

  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. Implementation of oral health education to orphan children

    International Nuclear Information System (INIS)

    To determine the knowledge and oral hygiene status of orphange children in apune and a changes in them after health education. Study Design: Interventional study. Place and Duration of Study: Centers for Orphan Children in Pune, India, from April to June 2014. Methodology: A specially designed questionnaire was used to assess the dental problems and existing oral hygiene maintenance practice among children between 5 - 12 years of age (n=100) in an orphanage center. Pre- and post interventional intra-oral examination was carried out to check their oral hygiene status which included DMFS (Decayed Missing Filled Tooth Surfaces index (for permanent teeth)), OHIS (Simplified Oral Hygiene Index) and gingival indices. Intervention was in the form of oral health education, demonstration of correct brushing technique, diet counselling and maintenance of overall oral hygiene. Results: Present study shows that the orphans had multiple dental problems along with improper oral hygiene practices and careless attitude towards oral health. Pre- and post-interventional DMFS was compared using Wilcoxon sign rank test, which was not significant; while OHIS and gingival indices were compared by using repeat measures ANOVA(p < 0.001) which was significant for each, respectively. Conclusion: There was considerable improvement in the oral hygiene status of orphans due to educational intervention. Oral health education at right age can help to cultivate healthy oral hygiene practices in orphans which will benefit them for lifelong. Caretakers should be educated and trained about oral hygiene practices so that they can implement it and supervise the orphan children. (author)

  10. Environmental and Genetic Influences of Archaeal Lipid Distribution in Natural and Artificial Marine Environments

    Science.gov (United States)

    Warren, C.; Pagani, M.

    2012-12-01

    TEX86 is a proxy of sea surface temperature based on refractory glycerol dibiphytanyl glycerol tetraethers (GDGT) in the cell membranes of low-temperature dwelling (non-hyperthermophilic) Archaea. The degree to which environmental signals other than temperature influence the distribution of GDGT compounds is poorly understood. Few representatives of the Thaumarchaeota — the clade to which the dominant GDGT production has been attributed — have been described or isolated in pure culture, and the role of genetic lineage in the synthesis and distribution of GDGTs is unknown. For this project we collected water, filter and substrate samples from tank systems in non-profit and commercial aquariums around the United States. This analysis compares GDGT core lipids and intact polar lipid distributions with Archaeal genetic sequence data processed using rRNA and 454 Pyrosequencing. Environmental attributes (such as dissolved oxygen concentration, salinity, organic density, etc.) specific to each tank are also compared to lipid analyses and the presence of specific lineages within select tank systems. Our preliminary results demonstrate that archaeal GDGTs are present and abundant within a range of environmental conditions, including artificial saline and brackish waters derived from municipal sources. Comparisons of existing TEX86 calibration values with known temperatures suggest that residuals vary based on non-temperature parameters. Branched compounds are absent in most aquarium systems, but dominate in systems prepared with municipal water.

  11. Insights into archaeal evolution and symbiosis from the genomes of a Nanoarchaeon and its crenarchaeal host from Yellowstone National Park

    Energy Technology Data Exchange (ETDEWEB)

    Podar, Mircea [ORNL; Graham, David E [ORNL; Reysenbach, Anna-Louise [Portland State University; Koonin, Eugene [National Center for Biotechnology Information; Wolf, Yuri [National Center for Biotechnology Information; Makarova, Kira S. [National Center for Biotechnology Information

    2013-01-01

    A hyperthemophilic member of the Nanoarchaeota from Obsidian Pool, a thermal feature in Yellowstone National Park was characterized using single cell isolation and sequencing, together with its putative host, a Sulfolobales archaeon. This first representative of a non-marine Nanoarchaeota (Nst1) resembles Nanoarchaeum equitans by lacking most biosynthetic capabilities, the two forming a deep-branching archaeal lineage. However, the Nst1 genome is over 20% larger, encodes a complete gluconeogenesis pathway and a full complement of archaeal flagellum proteins. Comparison of the two genomes suggests that the marine and terrestrial Nanoarchaeota lineages share a common ancestor that was already a symbiont of another archaeon. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales. The two distinct Nanoarchaeota-host genomic data sets offer insights into the evolution of archaeal symbiosis and parasitism and will further enable studies of the cellular and molecular mechanisms of these relationships.

  12. 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.

  13. Orphan caribou, Rangifer tarandus, calves: A re-evaluation of overwinter survival data

    Science.gov (United States)

    Joly, Kyle

    2000-01-01

    Low sample size and high variation within populations reduce power of statistical tests. These aspects of statistical power appear to have affected an analysis comparing overwinter survival rates of non-orphan and orphan Caribou (Rangifer tarandus) calves by an earlier study for the Porcupine Caribou Herd. A re-evaluation of the data revealed that conclusions about a lack of significant difference in the overwinter survival rates between orphan and non-orphan calves were premature.

  14. Evolution of an Orphaned Source Management Strategy: Canadian Experience

    International Nuclear Information System (INIS)

    During the course of providing regulatory control over nuclear substances, the Canadian Nuclear Safety Commission (CNSC) from time to time has identified sources without an owner or a responsible party. In 2011, after completing a review of its regulatory oversight with respect to orphan sources, the CNSC put in place a strategy that is based on promotion and communication, prevention, and response and recovery of orphan sources. The paper describes the challenges that have occurred during the development of the strategy and the lessons learned during the implementation phase. (author)

  15. Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water.

    Science.gov (United States)

    Long, Yan; Yi, Hao; Chen, Sili; Zhang, Zhengke; Cui, Kai; Bing, Yongxin; Zhuo, Qiongfang; Li, Bingxin; Xie, Shuguang; Guo, Qingwei

    2016-10-01

    Both bacteria and archaeal communities can play important roles in biogeochemical processes in constructed wetland (CW) system. However, the influence of plant type on microbial community in surface water CW remains unclear. The present study investigated bacterial and archaeal communities in five surface water CW systems with different plant species. The abundance, richness, and diversity of both bacterial and archaeal communities considerably differed in these five CW systems. Compared with the other three CW systems, the CW systems planted with Vetiveria zizanioides or Juncus effusus L. showed much higher bacterial abundance but lower archaeal abundance. Bacteria outnumbered archaea in each CW system. Moreover, the CW systems planted with V. zizanioides or J. effusus L. had relatively lower archaeal but higher bacterial richness and diversity. In each CW system, bacterial community displayed much higher richness and diversity than archaeal community. In addition, a remarkable difference of both bacterial and archaeal community structures was observed in the five studied CW systems. Proteobacteria was the most abundant bacterial group (accounting for 33-60 %). Thaumarchaeota organisms (57 %) predominated in archaeal communities in CW systems planted with V. zizanioides or J. effusus L., while Woesearchaeota (23 or 24 %) and Euryarchaeota (23 or 15 %) were the major archaeal groups in CW systems planted with Cyperus papyrus or Canna indica L. Archaeal community in CW planted with Typha orientalis Presl was mainly composed of unclassified archaea. Therefore, plant type exerted a considerable influence on microbial community in surface water CW system. PMID:27392623

  16. 77 FR 71452 - Extension of Comment Period: Orphan Works and Mass Digitization

    Science.gov (United States)

    2012-11-30

    ... Copyright Office Extension of Comment Period: Orphan Works and Mass Digitization AGENCY: Copyright Office... issues relating to orphan works and mass digitization under U.S. copyright law. DATES: Comments are due... relating to orphan works and mass digitization under U.S. copyright law. Due to the number and...

  17. 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

  18. 76 FR 3910 - Agency Information Collection Activities; Proposed Collection; Comment Request; Orphan Drugs...

    Science.gov (United States)

    2011-01-21

    ... Collection; Comment Request; Orphan Drugs; Common European Medicines Agency/Food and Drug Administration Application Form for Orphan Medicinal Product Designation (Form FDA 3671) AGENCY: Food and Drug Administration... solicits comments on the procedures by which sponsors of orphan drugs may request eligibility for...

  19. 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…

  20. 78 FR 35277 - Agency Information Collection Activities; Proposed Collection; Comment Request; Orphan Drugs...

    Science.gov (United States)

    2013-06-12

    ... Collection; Comment Request; Orphan Drugs; Common European Medicines Agency/Food and Drug Administration Application Form for Orphan Medicinal Product Designation (Form FDA 3671) AGENCY: Food and Drug Administration... solicits comments on ] the procedures by which sponsors of orphan drugs may request eligibility for...

  1. 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. PMID:22293040

  2. Insights into orphan nuclear receptors as prognostic markers and novel therapeutic targets for breast cancer

    OpenAIRE

    Reidun eAesoy; Colin D Clyne; Ashwini eChand

    2015-01-01

    The roles of orphan nuclear receptors in breast cancer development and progression are not well understood. In this review, we correlate orphan nuclear receptor expression in breast cancer tumour subtypes with patient outcomes and provide an overview of functional evidence that identifies candidate orphan nuclear receptors as prognostic markers or as therapeutic targets in breast cancer.

  3. The Therapeutic Potential of Orphan GPCRs, GPR35 and GPR55

    Directory of Open Access Journals (Sweden)

    Patricia Hodapp Reggio

    2015-04-01

    Full Text Available The G protein-coupled receptor (GPCR superfamily of integral proteins is the largest family of signal transducers, comprised of ~1000 members. Considering their prevalence and functional importance, it’s not surprising that ~60% of drugs target GPCRs. Regardless, there exists a subset of the GPCR superfamily that is largely uncharacterized and poorly understood; specifically, more than 140 GPCRs have unknown endogenous ligands—the so-called orphan GPCRs. Orphan GPCRs offer tremendous promise, as they may provide novel therapeutic targets that may be more selective than currently known receptors, resulting in the potential reduction in side effects. In addition, they may provide access to signal transduction pathways currently unknown, allowing for new strategies in drug design. Regardless, orphan GPCRs are an important area of inquiry, as they represent a large gap in our understanding of signal transduction at the cellular level. Here, we focus on the therapeutic potential of two recently-deorphanized GPCRs: GPR35/CXCR8 and GPR55. First, GPR35/CXCR8 has been observed in numerous tissues/organ systems, including the gastrointestinal tract, liver, immune system, central nervous system, and cardiovascular system. Not surprisingly, GPR35/CXCR8 has been implicated in numerous pathologies involving these tissues/systems. While several endogenous ligands have been identified, GPR35/CXCR8 has recently been observed to bind the chemokine CXCL17. Second, GPR55 has been observed to be expressed in the central nervous system, adrenal glands, gastrointestinal tract, lung, liver, uterus, bladder, kidney and bone, as well as, other tissues/organ systems. Likewise, it is not surprising that GPR55 has been implicated in pathologies involving these tissues/systems. GPR55 was initially deorphanized as a cannabinoid receptor and this receptor does bind many cannabinoid compounds. However, the GPR55 endogenous ligand has been found to be a non

  4. Distribution of Archaeal and Bacterial communities in a subtropical reservoir

    Directory of Open Access Journals (Sweden)

    Laís Américo Soares

    2015-12-01

    Full Text Available Abstract Aim: Microbial communities play a central role in environmental process such as organic matter mineralization and the nutrient cycling process in aquatic ecosystems. Despite their ecological importance, variability of the structure of archaeal and bacterial communities in freshwater remains understudied. Methods In the present study we investigated the richness and density of archaea and bacteria in the water column and sediments of the Itupararanga Reservoir. We also evaluated the relationship between the communities and the biotic and abiotic characteristics. Samples were taken at five depths in the water column next to the dam and three depths next to the reservoir entrance. Results PCR-DGGE evaluation of the archaeal and bacterial communities showed that both were present in the water column, even in oxygenated conditions. Conclusions The density of the bacteria (qPCR was greater than that of the archaea, a result of the higher metabolic plasticity of bacteria compared with archaea.

  5. Prediction of novel archaeal enzymes from sequence-derived features

    DEFF Research Database (Denmark)

    Jensen, Lars Juhl; Skovgaard, Marie; Brunak, Søren

    2002-01-01

    The completely sequenced archaeal genomes potentially encode, among their many functionally uncharacterized genes, novel enzymes of biotechnological interest. We have developed a prediction method for detection and classification of enzymes from sequence alone (available at http://www.cbs.dtu.dk/......The completely sequenced archaeal genomes potentially encode, among their many functionally uncharacterized genes, novel enzymes of biotechnological interest. We have developed a prediction method for detection and classification of enzymes from sequence alone (available at http......://www.cbs.dtu.dk/services/ArchaeaFun/). The method does not make use of sequence similarity; rather, it relies on predicted protein features like cotranslational and posttranslational modifications, secondary structure, and simple physical/chemical properties....

  6. Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil

    Directory of Open Access Journals (Sweden)

    Yendi E. Navarro-Noya

    2015-01-01

    Full Text Available In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic Candidatus Nitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5, indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils. Halobiforma, Halostagnicola, Haloterrigena, and Natronomonas were found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances clearly clustered the communities by pH.

  7. Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil.

    Science.gov (United States)

    Navarro-Noya, Yendi E; Valenzuela-Encinas, César; Sandoval-Yuriar, Alonso; Jiménez-Bueno, Norma G; Marsch, Rodolfo; Dendooven, Luc

    2015-01-01

    In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC) ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic Candidatus Nitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5), indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils. Halobiforma, Halostagnicola, Haloterrigena, and Natronomonas were found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances) clearly clustered the communities by pH.

  8. Ribonucleoproteins in Archaeal Pre-rRNA Processing and Modification

    Directory of Open Access Journals (Sweden)

    W. S. Vincent Yip

    2013-01-01

    Full Text Available Given that ribosomes are one of the most important cellular macromolecular machines, it is not surprising that there is intensive research in ribosome biogenesis. Ribosome biogenesis is a complex process. The maturation of ribosomal RNAs (rRNAs requires not only the precise cleaving and folding of the pre-rRNA but also extensive nucleotide modifications. At the heart of the processing and modifications of pre-rRNAs in Archaea and Eukarya are ribonucleoprotein (RNP machines. They are called small RNPs (sRNPs, in Archaea, and small nucleolar RNPs (snoRNPs, in Eukarya. Studies on ribosome biogenesis originally focused on eukaryotic systems. However, recent studies on archaeal sRNPs have provided important insights into the functions of these RNPs. This paper will introduce archaeal rRNA gene organization and pre-rRNA processing, with a particular focus on the discovery of the archaeal sRNP components, their functions in nucleotide modification, and their structures.

  9. Bombesin-Like Receptor 3: Physiology of a Functional Orphan.

    Science.gov (United States)

    Xiao, Cuiying; Reitman, Marc L

    2016-09-01

    Bombesin-like receptor 3 (BRS-3) is an X-linked orphan Gq-coupled receptor that regulates food intake, metabolic rate, body temperature, heart rate, blood pressure, and insulin secretion. Most BRS-3 actions occur via the brain, through mechanisms including regulating sympathetic outflow. Ablation of Brs3 causes obesity, while synthetic agonists produce weight loss. PMID:27055378

  10. Control of transboundary movement of orphan radioactive source in Lithuania

    International Nuclear Information System (INIS)

    The problem of transboundary movement of orphan radioactive sources needs a prompt solution. For clearance of Lithuanian competent authorities activities in case of detecting, at the state border, an illegal radioactive source a new legislative act is now being created. Although this problem needs much more attention, this is a step towards its solution. (author)

  11. Motives for Taking Orphan Children into a Foster (Guardian) Family

    Science.gov (United States)

    Kozlova, T. Z.

    2013-01-01

    Research in Russia on the opinions of guardians and experts of the department of guardianship examines the motives that people have for taking orphan children into their homes. The data indicate that about 80 percent of the guardians are grandmothers taking care of their grandchildren, whose parents have been stripped of their parental rights.…

  12. An Analysis of How Multicultural Adult Orphans Achieve Economic Success

    Science.gov (United States)

    Simonee, Saundra W.

    2014-01-01

    Successful multicultural adult orphans who were not adopted pose an interesting challenge in their history, their physical, psychological, social emotional and personal identity development. One must understand their journey from orphanhood to adulthood and their current prominent status in life to build a contextualized personal story (Banks,…

  13. The Social and Pedagogical Protection of Orphans in Russia

    Science.gov (United States)

    Pantiukhina, E. N.

    2009-01-01

    This article discusses the history of the provision of children's care ("prizrenie") in Russia which provides evidence that the desire to help those close to one, especially orphans and the poor, was a traditional trait of the Russian national character. The system of children's welfare as it took shape over many centuries is unique in its own…

  14. Family and Nation: Cherokee Orphan Care, 1835-1903

    Science.gov (United States)

    Reed, Julie L.

    2010-01-01

    On November 17, 1903, fifteen miles from the nearest railway station and fifty miles northwest of the capital of the Cherokee Nation in Tahlequah, a fire engulfed the Cherokee Orphan Asylum. After the fire the Cherokee Nation relocated the homeless children to the nation's Insane Asylum in Tahlequah, where Sequoyah School stands today. The…

  15. 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.

  16. Distribution and Diversity of Archaeal Ammonia Monooxygenase Genes Associated with Corals▿ †

    OpenAIRE

    Beman, J. Michael; Roberts, Kathryn J.; Wegley, Linda; Rohwer, Forest; Francis, Christopher A.

    2007-01-01

    Corals are known to harbor diverse microbial communities of Bacteria and Archaea, yet the ecological role of these microorganisms remains largely unknown. Here we report putative ammonia monooxygenase subunit A (amoA) genes of archaeal origin associated with corals. Multiple DNA samples drawn from nine coral species and four different reef locations were PCR screened for archaeal and bacterial amoA genes, and archaeal amoA gene sequences were obtained from five different species of coral coll...

  17. 21 CFR 316.23 - Timing of requests for orphan-drug designation; designation of already approved drugs.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Timing of requests for orphan-drug designation..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS FOR HUMAN USE ORPHAN DRUGS Designation of an Orphan Drug § 316.23 Timing of requests for orphan-drug designation; designation of already approved drugs....

  18. 76 FR 53912 - FDA's Public Database of Products With Orphan-Drug Designation: Replacing Non-Informative Code...

    Science.gov (United States)

    2011-08-30

    ...The Food and Drug Administration (FDA), Office of Orphan Products Development, is announcing that it has replaced non- informative code names with descriptive identifiers on its public database of products that have received orphan-drug designation. The Orphan Drug Act mandates that FDA provide notice to the public respecting the designation of a drug as an orphan-drug. FDA typically provides......

  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. 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

  1. Representing dispositions

    Directory of Open Access Journals (Sweden)

    Röhl Johannes

    2011-08-01

    Full Text Available Abstract Dispositions and tendencies feature significantly in the biomedical domain and therefore in representations of knowledge of that domain. They are not only important for specific applications like an infectious disease ontology, but also as part of a general strategy for modelling knowledge about molecular interactions. But the task of representing dispositions in some formal ontological systems is fraught with several problems, which are partly due to the fact that Description Logics can only deal well with binary relations. The paper will discuss some of the results of the philosophical debate about dispositions, in order to see whether the formal relations needed to represent dispositions can be broken down to binary relations. Finally, we will discuss problems arising from the possibility of the absence of realizations, of multi-track or multi-trigger dispositions and offer suggestions on how to deal with them.

  2. Bacterial and archaeal resistance to ionizing radiation

    Energy Technology Data Exchange (ETDEWEB)

    Confalonieri, F; Sommer, S, E-mail: fabrice.confalonieri@u-psud.fr, E-mail: suzanne.sommer@u-psud.fr [University Paris-Sud, CNRS UMR8621, Institut de Genetique et Microbiologie, Batiments 400-409, Universite Paris-Sud, 91405 Orsay (France)

    2011-01-01

    Organisms living in extreme environments must cope with large fluctuations of temperature, high levels of radiation and/or desiccation, conditions that can induce DNA damage ranging from base modifications to DNA double-strand breaks. The bacterium Deinococcus radiodurans is known for its resistance to extremely high doses of ionizing radiation and for its ability to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments. Recently, extreme ionizing radiation resistance was also generated by directed evolution of an apparently radiation-sensitive bacterial species, Escherichia coli. Radioresistant organisms are not only found among the Eubacteria but also among the Archaea that represent the third kingdom of life. They present a set of particular features that differentiate them from the Eubacteria and eukaryotes. Moreover, Archaea are often isolated from extreme environments where they live under severe conditions of temperature, pressure, pH, salts or toxic compounds that are lethal for the large majority of living organisms. Thus, Archaea offer the opportunity to understand how cells are able to cope with such harsh conditions. Among them, the halophilic archaeon Halobacterium sp and several Pyrococcus or Thermococcus species, such as Thermococcus gammatolerans, were also shown to display high level of radiation resistance. The dispersion, in the phylogenetic tree, of radioresistant prokaryotes suggests that they have independently acquired radioresistance. Different strategies were selected during evolution including several mechanisms of radiation byproduct detoxification and subtle cellular metabolism modifications to help cells recover from radiation-induced injuries, protection of proteins against oxidation, an efficient DNA repair tool box, an original pathway of DNA double-strand break repair, a condensed nucleoid that may prevent the dispersion of the DNA fragments and specific radiation-induced proteins involved in

  3. Electroporation of archaeal lipid membranes using MD simulations.

    Science.gov (United States)

    Polak, Andraž; Tarek, Mounir; Tomšič, Matija; Valant, Janez; Ulrih, Nataša Poklar; Jamnik, Andrej; Kramar, Peter; Miklavčič, Damijan

    2014-12-01

    Molecular dynamics (MD) simulations were used to investigate the electroporation of archaeal lipid bilayers when subjected to high transmembrane voltages induced by a charge imbalance, mimicking therefore millisecond electric pulse experiments. The structural characteristics of the bilayer, a 9:91 mol% 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-myo-inositol (AI) and 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-1'(2'-O-α-D-glucosyl)-myo-inositol (AGI) were compared to small angle X-ray scattering data. A rather good agreement of the electron density profiles at temperatures of 298 and 343 K was found assessing therefore the validity of the protocols and force fields used in simulations. Compared to dipalmitoyl-phosphatidylcholine (DPPC), the electroporation threshold for the bilayer was found to increase from ~2 V to 4.3 V at 323 K, and to 5.2 V at 298 K. Comparing the electroporation thresholds of the archaeal lipids to those of simple diphytanoyl-phosphatidylcholine (DPhPC) bilayers (2.5 V at 323 K) allowed one to trace back the stability of the membranes to the structure of their lipid head groups. Addition of DPPC in amounts of 50 mol% to the archaeal lipid bilayers decreases their stability and lowers the electroporation thresholds to 3.8 V and 4.1 V at respectively 323 and 298 K. The present study therefore shows how membrane compositions can be selected to cover a wide range of responses to electric stimuli. This provides new routes for the design of liposomes that can be efficiently used as drug delivery carriers, as the selection of their composition allows one to tune in their electroporation threshold for subsequent release of their load.

  4. Factors affecting Archaeal Lipid Compositions of the Sulfolobus Species

    Science.gov (United States)

    He, L.; Han, J.; Wei, Y.; Lin, L.; Wei, Y.; Zhang, C.

    2010-12-01

    Temperature is the best known variable affecting the distribution of the archaeal glycerol dibiphytanyl glycerol tetraethers (GDGTs) in marine and freshwater systems. Other variables such as pH, ionic strength, or bicarbonate concentration may also affect archaeal GDGTs in terrestrial systems. Studies of pure cultures can help us pinpoint the specific effects these variables may have on archaeal lipid distribution in natural environments. In this study, three Sulfolobus species (HG4, HB5-2, HB9-6) isolated from Tengchong hot springs (pH 2-3, temperature 73-90°C) in China were used to investigate the effects of temperature, pH, substrate, and type of strain on the composition of GDGTs. Results showed that increase in temperature had negative effects on the relative contents of GDGT-0 (no cyclopentyl rings), GDGT-1 (one cyclopentyl ring), GDGT-2 and GDGT-3 but positive effects on GDGT-4, GDGT-4', GDGT-5 and GDGT-5'. Increase in pH, on the other hand, had negative effects on GDGT-0, GDGT-1, GDGT-4', GDGT-5 and GDGT-5', and positive effects on GDGT-3 and GDGT-4. GDGT-2 remained relatively constant with changing pH. When the HG4 was grown on different substrates, GDGT-5 was five time more abundant in sucrose-grown cultures than in yeast extract- or sulfur- grown cultures, suggesting that carbohydrates may stimulate the production of GDGT-5. For all three species, the ring index (average number of rings) of GDGTs correlated positively with incubation temperature. In HG4, ring index was much lower at optimal pH (3.5) than at other pH values. Ring index of HB5-2 or HB9-6 is higher than that of HG4, suggesting that speciation may affect the degree of cyclization of GDGT of the Sulfolobus. These results indicate that individual archaeal lipids respond differently to changes in environmental variables, which may be also species specific.

  5. 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.

  6. The archaeal TFIIE homologue facilitates transcription initiation by enhancing TATA-box recognition

    NARCIS (Netherlands)

    Bell, S.D.; Brinkman, A.B.; Oost, van der J.; Jackson, S.P.

    2001-01-01

    Transcription from many archaeal promoters can be reconstituted in vitro using recombinant TATA-box binding protein (TBP) and transcription factor B (TFB)—homologues of eukaryal TBP and TFIIB—together with purified RNA polymerase (RNAP). However, all archaeal genomes sequenced to date reveal the pre

  7. Haitian orphan population and protective factors against caries

    OpenAIRE

    Madelyn Rea

    2016-01-01

    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 ...

  8. 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.

  9. Energy for two: New archaeal lineages and the origin of mitochondria.

    Science.gov (United States)

    Martin, William F; Neukirchen, Sinje; Zimorski, Verena; Gould, Sven B; Sousa, Filipa L

    2016-09-01

    Metagenomics bears upon all aspects of microbiology, including our understanding of mitochondrial and eukaryote origin. Recently, ribosomal protein phylogenies show the eukaryote host lineage - the archaeal lineage that acquired the mitochondrion - to branch within the archaea. Metagenomic studies are now uncovering new archaeal lineages that branch more closely to the host than any cultivated archaea do. But how do they grow? Carbon and energy metabolism as pieced together from metagenome assemblies of these new archaeal lineages, such as the Deep Sea Archaeal Group (including Lokiarchaeota) and Bathyarchaeota, do not match the physiology of any cultivated microbes. Understanding how these new lineages live in their environment is important, and might hold clues about how mitochondria arose and how the eukaryotic lineage got started. Here we look at these exciting new metagenomic studies, what they say about archaeal physiology in modern environments, how they impact views on host-mitochondrion physiological interactions at eukaryote origin. PMID:27339178

  10. Extending stellar density maps of the Orphan Tidal Stream

    Science.gov (United States)

    Varilly, Taylor; Carlin, J. L.; Newberg, H. J.; Beaton, R.; Majewski, S. R.

    2014-01-01

    This project involves analyzing data directly off the footprint of the Sloan Digital Sky Survey in order to find the progenitor of the Orphan tidal stream. This stream of stellar debris, known to span distances 20 to 47 kpc from the Sun, is believed to be the remnants of a small dwarf galaxy that is largely disrupted. Images were obtained in the vicinity of this stream from the MOSAIC1.1 camera on the 4-meter Mayall telescope at the Kitt Peak National Observatory. The region observed covers 11 square degrees of sky, approximately 7 square degrees of which have no SDSS data. The area outside the SDSS was selected to explore the increase in density of Orphan stars in this location, discussed in Newberg et al. 2010. The positions and magnitudes of stars outside of the SDSS were calculated and calibrated with both data from the SDSS itself, as well as the USNOB-1 catalog. The resulting Orphan candidates selected from this catalog were used to explore the stellar densities along this stream, providing insight into the nature of its progenitor. This research was supported by NSF grant AST 09-37523.

  11. Methanobacterium Dominates Biocathodic Archaeal Communities in Methanogenic Microbial Electrolysis Cells

    KAUST Repository

    Siegert, Michael

    2015-07-06

    © 2015 American Chemical Society. Methane is the primary end product from cathodic current in microbial electrolysis cells (MECs) in the absence of methanogenic inhibitors, but little is known about the archaeal communities that develop in these systems. MECs containing cathodes made from different materials (carbon brushes, or plain graphite blocks or blocks coated with carbon black and platinum, stainless steel, nickel, ferrihydrite, magnetite, iron sulfide, or molybdenum disulfide) were inoculated with anaerobic digester sludge and acclimated at a set potential of -600 mV (versus a standard hydrogen electrode). The archaeal communities on all cathodes, except those coated with platinum, were predominated by Methanobacterium (median 97% of archaea). Cathodes with platinum contained mainly archaea most similar to Methanobrevibacter. Neither of these methanogens were abundant (<0.1% of archaea) in the inoculum, and therefore their high abundance on the cathode resulted from selective enrichment. In contrast, bacterial communities on the cathode were more diverse, containing primarily δ-Proteobacteria (41% of bacteria). The lack of a consistent bacterial genus on the cathodes indicated that there was no similarly selective enrichment of bacteria on the cathode. These results suggest that the genus Methanobacterium was primarily responsible for methane production in MECs when cathodes lack efficient catalysts for hydrogen gas evolution. (Figure Presented).

  12. Formation of a solar Hα filament from orphan penumbrae

    Science.gov (United States)

    Buehler, D.; Lagg, A.; van Noort, M.; Solanki, S. K.

    2016-05-01

    Aims: The formation and evolution of an Hα filament in active region (AR) 10953 is described. Methods: Observations from the Solar Optical Telescope (SOT) aboard the Hinode satellite starting from UT 18:09 on 27th April 2007 until UT 06:08 on 1st May 2007 were analysed. 20 scans of the 6302 Å Fe I line pair recorded by SOT/SP were inverted using the spatially coupled version of the SPINOR code. The inversions were analysed together with co-spatial SOT/BFI G-band and Ca II H and SOT/NFI Hα observations. Results: Following the disappearance of an initial Hα filament aligned along the polarity inversion line (PIL) of the AR, a new Hα filament formed in its place some 20 h later, which remained stable for, at least, another 1.5 days. The creation of the new Hα 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 Hα filament and formed orphan penumbrae already aligned along the Hα filament channel. The 700 G orphan penumbrae were stable and trapped in the photosphere until the disappearance of the overlying initial Hα filament, after which they started to ascend into the chromosphere at 10 ± 5 m/s. Each ascent was associated with a simultaneous magnetic flux reduction of up to 50% in the photosphere. The ascended orphan penumbrae formed dark seed structures in Hα in parallel with the PIL, which elongated and merged to form an Hα filament. The filament channel featured horizontal magnetic fields of on average 260 G at log (τ) = -2 suspended above the nearly field-free lower photosphere. The fields took on an overall inverse configuration at log (τ) = -2 suggesting a flux rope topology for the new Hα filament. The destruction of the initial Hα filament was likely caused by the flux emergence at the third location along the PIL. Conclusions: We present a new

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

    OpenAIRE

    Abdel-Hady El-Gilany; El-Bilsha, Mona A.; Azza Ibrahim

    2013-01-01

    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 se...

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

    OpenAIRE

    EL-GILANY, ABDEL-HADY; El-Bilsha, Mona A.; Ibrahim, Azza

    2013-01-01

    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 sel...

  15. 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.

  16. 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

  17. RNA-Based Assessment of Diversity and Composition of Active Archaeal Communities in the German Bight

    Directory of Open Access Journals (Sweden)

    Bernd Wemheuer

    2012-01-01

    Full Text Available Archaea play an important role in various biogeochemical cycles. They are known extremophiles inhabiting environments such as thermal springs or hydrothermal vents. Recent studies have revealed a significant abundance of Archaea in moderate environments, for example, temperate sea water. Nevertheless, the composition and ecosystem function of these marine archaeal communities is largely unknown. To assess diversity and composition of active archaeal communities in the German Bight, seven marine water samples were taken and studied by RNA-based analysis of ribosomal 16S rRNA. For this purpose, total RNA was extracted from the samples and converted to cDNA. Archaeal community structures were investigated by pyrosequencing-based analysis of 16S rRNA amplicons generated from cDNA. To our knowledge, this is the first study combining next-generation sequencing and metatranscriptomics to study archaeal communities in marine habitats. The pyrosequencing-derived dataset comprised 62,045 archaeal 16S rRNA sequences. We identified Halobacteria as the predominant archaeal group across all samples with increased abundance in algal blooms. Thermoplasmatales (Euryarchaeota and the Marine Group I (Thaumarchaeota were identified in minor abundances. It is indicated that archaeal community patterns were influenced by environmental conditions.

  18. Archaeal promoter architecture and mechanism of gene activation

    DEFF Research Database (Denmark)

    Peng, Nan; Ao, Xiang; Liang, Yun Xiang;

    2011-01-01

    Sulfolobus solfataricus and Sulfolobus islandicus contain several genes exhibiting D-arabinose-inducible expression and these systems are ideal for studying mechanisms of archaeal gene expression. At sequence level, only two highly conserved cis elements are present on the promoters: a regulatory...... element named ara box directing arabinose-inducible expression and the basal promoter element TATA, serving as the binding site for the TATA-binding protein. Strikingly, these promoters possess a modular structure that allows an essentially inactive basal promoter to be strongly activated. The invoked...... mechanisms include TFB (transcription factor B) recruitment by the ara-box-binding factor to activate gene expression and modulation of TFB recruitment efficiency to yield differential gene expression....

  19. Archaeal promoter architecture and mechanism of gene activation.

    Science.gov (United States)

    Peng, Nan; Ao, Xiang; Liang, Yun Xiang; She, Qunxin

    2011-01-01

    Sulfolobus solfataricus and Sulfolobus islandicus contain several genes exhibiting D-arabinose-inducible expression and these systems are ideal for studying mechanisms of archaeal gene expression. At sequence level, only two highly conserved cis elements are present on the promoters: a regulatory element named ara box directing arabinose-inducible expression and the basal promoter element TATA, serving as the binding site for the TATA-binding protein. Strikingly, these promoters possess a modular structure that allows an essentially inactive basal promoter to be strongly activated. The invoked mechanisms include TFB (transcription factor B) recruitment by the ara-box-binding factor to activate gene expression and modulation of TFB recruitment efficiency to yield differential gene expression. PMID:21265754

  20. Useful scars: Physics of the capsids of archaeal viruses

    Science.gov (United States)

    Perotti, L. E.; Dharmavaram, S.; Klug, W. S.; Marian, J.; Rudnick, J.; Bruinsma, R. F.

    2016-07-01

    We propose a physical model for the capsids of tailed archaeal viruses as viscoelastic membranes under tension. The fluidity is generated by thermal motion of scarlike structures that are an intrinsic feature of the ground state of large particle arrays covering surfaces with nonzero Gauss curvature. The tension is generated by a combination of the osmotic pressure of the enclosed genome and an extension force generated by filamentous structure formation that drives the formation of the tails. In continuum theory, the capsid has the shape of a surface of constant mean curvature: an unduloid. Particle arrays covering unduloids are shown to exhibit pronounced subdiffusive and diffusive single-particle transport at temperatures that are well below the melting temperature of defect-free particle arrays on a surface with zero Gauss curvature.

  1. Characterization of Olkiluoto bacterial and archaeal communities by 454 pyrosequencing

    Energy Technology Data Exchange (ETDEWEB)

    Bomberg, M.; Nyyssoenen, M.; Itaevaara, M. [VTT Technical Research Centre of Finland, Espoo (Finland)

    2012-06-15

    Recent advancement in sequencing technologies, 'Next Generation Sequencing', such as FLX 454 pyrosequencing has made it possible to obtain large amounts of sequence data where previously only few sequences could be obtained. This technique is especially useful for the study of community composition of uncultured microbial populations in environmental samples. In this project, the FLX 454 pyrosequencing technique was used to obtain up to 20 000 16S rRNA sequences or 10 000 mRNA sequences from each sample for identification of the microbial species composition as well as for comparison of the microbial communities between different samples. This project focused on the characterization of active microbial communities in the groundwater at the final disposal site of high radioactive wastes in Olkiluoto by FLX 454 pyrosequencing of the bacterial and archaeal ribosomal RNA as well as of the mRNA transcripts of the dsrB gene and mcrA gene of sulphate reducing bacteria and methanogenic archaea, respectively. Specific emphasis was put on studying the relationship of active and latent sulphate reducers and methanogens by qPCR due to their important roles in deep geobiochemical processes connected to copper corrosion. Seven packered boreholes were sampled anaerobically in Olkiluoto during 2009-2010. Groundwater was pumped from specific depths and the microbial cells werecollected by filtration on a membrane. Active microbial communities were studied based on RNA extracted from the membranes and translated to copy DNA, followed by sequencing by 454 Tag pyrosequencing. A total of 27 different bacterial and 17 archaeal taxonomic groups were detected.

  2. The Role of Multiple Transcription Factors In Archaeal Gene Expression

    Energy Technology Data Exchange (ETDEWEB)

    Charles J. Daniels

    2008-09-23

    Since the inception of this research program, the project has focused on two central questions: What is the relationship between the 'eukaryal-like' transcription machinery of archaeal cells and its counterparts in eukaryal cells? And, how does the archaeal cell control gene expression using its mosaic of eukaryal core transcription machinery and its bacterial-like transcription regulatory proteins? During the grant period we have addressed these questions using a variety of in vivo approaches and have sought to specifically define the roles of the multiple TATA binding protein (TBP) and TFIIB-like (TFB) proteins in controlling gene expression in Haloferax volcanii. H. volcanii was initially chosen as a model for the Archaea based on the availability of suitable genetic tools; however, later studies showed that all haloarchaea possessed multiple tbp and tfb genes, which led to the proposal that multiple TBP and TFB proteins may function in a manner similar to alternative sigma factors in bacterial cells. In vivo transcription and promoter analysis established a clear relationship between the promoter requirements of haloarchaeal genes and those of the eukaryal RNA polymerase II promoter. Studies on heat shock gene promoters, and the demonstration that specific tfb genes were induced by heat shock, provided the first indication that TFB proteins may direct expression of specific gene families. The construction of strains lacking tbp or tfb genes, coupled with the finding that many of these genes are differentially expressed under varying growth conditions, provided further support for this model. Genetic tools were also developed that led to the construction of insertion and deletion mutants, and a novel gene expression scheme was designed that allowed the controlled expression of these genes in vivo. More recent studies have used a whole genome array to examine the expression of these genes and we have established a linkage between the expression of

  3. 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...

  4. Review of regulatory recommendations for orphan drug submissions in the Netherlands and Scotland : focus on the underlying pharmacoeconomic evaluations

    NARCIS (Netherlands)

    Vegter, Stefan; Rozenbaum, Mark H.; Postema, Roelien; Tolley, Keith; Postma, Maarten J.

    2010-01-01

    Background: Pharmacoeconomic evaluations of new drug therapies are often required for reimbursement or guidance decisions. However, for orphan drugs, country-specific requirements exist. In the Netherlands, orphan drug developers can be exempted from providing a full pharmacoeconomic evaluation, whe

  5. HIV Orphanhood Research and the Representation of Older Orphans in Sub-Saharan Africa: A Literature Review.

    Science.gov (United States)

    Popoola, Tosin; Mchunu, Gugu

    2016-01-01

    One impact of incurable HIV infection is the large number of orphans and vulnerable children (OVC) who are affected by HIV. The age-based criteria used to determine support eligibility for HIV orphans, however, exclude older orphans (≥18 years of age) from support. We conducted a literature survey in order to explore possible inclusion of older orphans (ages 18-24 years) in HIV orphanhood research. We found 17 studies conducted in eight countries that met the review inclusion criteria. Findings from the review revealed that older HIV orphans are underrepresented in the OVC literature. The emerging, but limited, evidence suggests that older orphans are at risk for poorer psychosocial and reproductive outcomes. We recommend increasing inclusion of older orphans in HIV orphan research because of their complex physical, reproductive, and psychosocial needs. This inclusion is necessary to allow their experiences and needs to become clearer. PMID:26482073

  6. Non-extremophilic 'extremophiles' - Archaeal dominance in the subsurface and their implication for life

    Science.gov (United States)

    Reitschuler, Christoph; Lins, Philipp; Illmer, Paul

    2014-05-01

    Archaea - besides bacteria and eukaryota constituting the third big domain of life - were so far regarded as typical inhabitants of extreme environments, as indicated by the name (Archaeon, Greek: 'original', 'primal'). Previous research and cultivation successes were basically carried out in habitats characterized by extreme temperature, pH and salinity regimes. Such extreme conditions, as expected at the beginning of the Earth's evolution, are occasionally also prevalent on extraterrestrial planets and moons and make the Archaeal domain a key group to be studied concerning life's evolution and the most likely pioneer organisms to colonize environments that are regarded as hostile. However, in recent years it became obvious that Archaea, in particular non-extremophilic species, can be found almost ubiquitously in marine, freshwater, terrestrial and also subsurface habitats and occasionally outnumber other microbial domains and hold key positions in globally relevant energy and nutrient cycles. Besides extreme environments - the big question remains how to define a parameter as extreme - subsurface and cave environments present a window to the past, where adaptions to early life's conditions can be studied and how microbiomes may be structured in a habitat that represents a refugium on extraterrestrial celestial bodies, were surface conditions might be at first sight too extreme for life. The lower part of the alpine Hundsalm cave in Tyrol (Austria) offered a unique opportunity to study an almost pristine cave habitat, which is separated from the touristic part of the ice cave. The main focus of our research was laid on the microbial communities that were supposed to be in connection with secondary carbonate precipitations ('moonmilk'). For the ascertainment of these so far poorly evaluated structures a multiple approach assessment was chosen to generate a virtually complete picture of these subsurface microbiomes. Thereby, a combination of different cultivation

  7. Use of biomarkers in the context of orphan medicines designation in the European Union.

    Science.gov (United States)

    Tsigkos, Stelios; Llinares, Jordi; Mariz, Segundo; Aarum, Stiina; Fregonese, Laura; Dembowska-Baginska, Bozenna; Elbers, Rembert; Evers, Pauline; Foltanova, Tatiana; Lhoir, Andre; Corrêa-Nunes, Ana; O'Connor, Daniel; Voordouw, Albertha; Westermark, Kerstin; Sepodes, Bruno

    2014-01-01

    The use of biomarkers within the procedures of the Committee of Orphan Medicinal Products (COMP) of the European Medicines Agency (EMA) is discussed herein. The applications for Orphan Medicinal Product designation in the EU are evaluated at two stages. At the time of orphan designation application, the file undergoes an assessment to establish whether the proposed condition is a distinct and serious condition affecting not more than 5 in 10,000 people in the EU, and whether the product is plausible as a therapy for that condition. In cases where therapies already exist, the significant benefit of the candidate product over existing therapies is also evaluated. The orphan criteria are reassessed at the time of marketing authorisation, so that marketing exclusivity for the product in the orphan medical condition can be granted. Within this context, biomarkers have been used in submissions in order to define an orphan condition and to justify that the criteria for orphan designation are met. The current work discusses specific examples from the experience of the COMP, where biomarkers have played a decisive role. Importantly, it identifies the proposal of sub-sets of non-rare conditions based on biomarkers as a challenging issue in the evaluation of applications. In particular two specific requirements for the candidate orphan medicines in relation to the biomarker-based subsets are highlighted: the "plausible link to the condition" and the "exclusion of effects outside the subset". PMID:24461084

  8. Recommendations for orphan drugs in two eu member states - a focus on the underlying pharmoeconomic evaluations

    NARCIS (Netherlands)

    Vegter, S.; Postema, R.; Tolley, K.H.; Postma, M.J.

    2009-01-01

    OBJECTIVES: In the Netherlands, orphan drug developers can be exempted from providing a full phwhereas in Scotland no such exceptions can be made. METHODS: All orphan drug reimbursement reports from the Dutch reimbursement institution (CFH) and guidance issued by the Scottish Medicines ConsoRESULTS:

  9. Between Charity and Education: Orphans and Orphanages in Early Modern Times

    Science.gov (United States)

    Jacobi, Juliane

    2009-01-01

    In early modern times orphans have been children who could not expect sufficient support from their family because of lack of at least one parent, in most cases the father. This article will clarify of whom we are talking if we talk about orphans and what have been the conditions of living in a society which was organised by a high variety of…

  10. Educational Inequalities and Ukrainian Orphans' Future Pathways: Social Reproduction or Transformation through the Hidden Curriculum?

    Science.gov (United States)

    Korzh, Alla

    2013-01-01

    This qualitative multi-site case study, situated in the context of Ukraine's post-Soviet political economy, examined how orphanage educators' expectations and beliefs about orphans' academic abilities and potential, curriculum, peer relationships, and education policy shaped orphans' post-secondary education decisions and trajectories. Examination…

  11. U.S. Department of Energy (DOE) Nuclear Material Disposal Orphans

    Energy Technology Data Exchange (ETDEWEB)

    Chambers, B.; Gillas, D.; Kiess, T.

    2002-02-26

    The DOE-EM nuclear material orphan identification initiative was established in December 2000. The goals of this paper are to: (1) describe recent DOE efforts in the definition, categorization and identification of disposal orphan materials, and (2) describe the DOE actions to evaluate suitable disposition plans and select disposal options.

  12. 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

  13. Risk and Resilience in Orphaned Adolescents Living in a Community Affected by AIDS

    Science.gov (United States)

    Wild, Lauren G.; Flisher, Alan J.; Robertson, Brian A.

    2013-01-01

    The AIDS pandemic has resulted in a dramatic rise in the number of orphans in South Africa. This study was designed to investigate the associations between family, peer, and community factors and resilience in orphaned adolescents. Self-report questionnaires were administered verbally to 159 parentally bereaved adolescents (aged 10-19) in an…

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    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...

  15. FMRFamide related peptide ligands activate the Caenorhabditis elegans orphan GPCR Y59H11AL.1

    Science.gov (United States)

    G-protein coupled receptors (GPCRs) are ancient molecules that sense environmental and physiological signals. Currently, the majority of the predicted Caenorhabditis elegans GPCRs are orphan. Here, we describe the characterization of such an orphan C. elegans GPCR, which is categorized in the tachyk...

  16. 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.

  17. Persisting Mental Health Problems among AIDS-Orphaned Children in South Africa

    Science.gov (United States)

    Cluver, Lucie D.; Orkin, Mark; Gardner, Frances; Boyes, Mark E.

    2012-01-01

    Background: By 2008, 12 million children in sub-Saharan Africa were orphaned by AIDS. Cross-sectional studies show psychological problems for AIDS-orphaned children, but until now no longitudinal study has explored enduring psychological effects of AIDS-orphanhood in the developing world. Methods: A 4-year longitudinal follow-up of AIDS-orphaned…

  18. Social Support Disparities for Caregivers of AIDS-Orphaned Children in South Africa

    Science.gov (United States)

    Kuo, Caroline; Fitzgerald, Jane; Operario, Don; Casale, Marisa

    2012-01-01

    Drawing upon a sample of 1,599 adults caring for children in HIV-endemic Umlazi Township in South Africa, this cross-sectional survey investigated whether perceived social support varied among caregivers of AIDS-orphaned children (n = 359) as compared with caregivers of children orphaned by other causes (n = 171) and caregivers of nonorphaned…

  19. The identification of factors contributing to the vulnerability to sexual abuse of orphans in a rural area / Nomakubenje Agnes Ncanywa

    OpenAIRE

    Ncanywa, Nomakubenje Agnes

    2014-01-01

    Sexual abuse of children is a major problem in South Africa. There is an increasing number of orphans in urban but also in rural areas of children and orphans who are sexually abused. The researcher experienced in her daily work as social worker in the rural area of the Oliver Tambo district Municipality children and orphans who are sexually abused. The aim of this study is to identify the risks factors contributing to the vulnerability of orphans towards sexual abuse. Purposive sampling w...

  20. 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.

  1. 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. 

  2. 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.

  3. Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor

    Directory of Open Access Journals (Sweden)

    Takano Eriko

    2011-09-01

    Full Text Available Abstract Background Streptomyces coelicolor, a model organism of antibiotic producing bacteria, has one of the largest genomes of the bacterial kingdom, including 7825 predicted protein coding genes. A large number of these genes, nearly 34%, are functionally orphan (hypothetical proteins with unknown function. However, in gene expression time course data, many of these functionally orphan genes show interesting expression patterns. Results In this paper, we analyzed all functionally orphan genes of Streptomyces coelicolor and identified a list of "high priority" orphans by combining gene expression analysis and additional phylogenetic information (i.e. the level of evolutionary conservation of each protein. Conclusions The prioritized orphan genes are promising candidates to be examined experimentally in the lab for further characterization of their function.

  4. Gender differences in maladaptive cognitive schema in orphans in Dakahlia, Egypt.

    Science.gov (United States)

    El-Gilany, Abdel-Hady; El-Bilsha, Mona A; Ibrahim, Azza

    2013-01-01

    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. PMID:24453839

  5. Orphans in Nyanza, Kenya: Coping with the Struggles of Everyday Life in the Context of the HIV/AIDS Pandemic

    Science.gov (United States)

    Landry, Tamara; Luginaah, Isaac; Maticka-Tyndale, Eleanor; Elkins, David

    2007-01-01

    This paper examined the everyday challenges, stressors and coping strategies of orphans affected by HIV/AIDS in Nyanza, Kenya. A thematic analysis of six focus group discussions with orphans was guided by Stress and Coping Theoretical Framework. The orphans reported intense stress at the time of their parents' death with their immediate concern…

  6. 77 FR 46764 - Clinical Studies of Safety and Effectiveness of Orphan Products Research Project Grant (R01)

    Science.gov (United States)

    2012-08-06

    ... HUMAN SERVICES Food and Drug Administration Clinical Studies of Safety and Effectiveness of Orphan... of FDA's Office of Orphan Products Development (OPD) grant program. The goal of FDA's OPD grant... Needleman, Office of Orphan Products Development, Food and Drug Administration, 10903 New Hampshire...

  7. The orphan works problem: the copyright conundrum of digitizing large-scale audiovisual archives, and how to solve it

    NARCIS (Netherlands)

    S. van Gompel; P.B. Hugenholtz

    2010-01-01

    This article examines the problem of "orphan works" against the background of various projects for mass-digitization of audiovisual content. Orphan works are works for which the copyright owners cannot be identified or located. The fact that a particular work is "orphaned" makes it impossible to cle

  8. 75 FR 47602 - Clinical Studies of Safety and Effectiveness of Orphan Products Research Project Grant (R01)

    Science.gov (United States)

    2010-08-06

    ... HUMAN SERVICES Food and Drug Administration Clinical Studies of Safety and Effectiveness of Orphan... of FDA's Office of Orphan Products Development (OPD) grant program. The goal of FDA's OPD grant... Background and Significance section documentation to support the estimated prevalence of the orphan...

  9. Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia

    Science.gov (United States)

    Biogeochemical changes in marine sediments during coastal water hypoxia are well described, but less is known about underlying changes in microbial communities. Bacterial and archaeal communities in Louisiana continental shelf (LCS) hypoxic zone sediments were characterized by py...

  10. The essence of being extremophilic : the role of the unique archaeal membrane lipids

    NARCIS (Netherlands)

    Vossenberg, Jack L.C.M. van de; Driessen, Arnold J.M.; Konings, Wil N.

    1998-01-01

    In extreme environments, mainly Archaea are encountered. The archaeal cytoplasmic membrane contains unique ether lipids that cannot easily be degraded, are temperature- and mechanically resistant, and highly salt tolerant. Moreover, thermophilic and extreme acidophilic Archaea possess membrane-spann

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

    International Nuclear Information System (INIS)

    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)

  12. 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...

  13. 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 ...

  14. 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)

  15. Clinical and psychosocial profile of HIV orphans in Northern Karnataka – a longitudinal study

    Directory of Open Access Journals (Sweden)

    Mahesh.V

    2013-07-01

    Full Text Available Background India currently has an estimated 220,000 children infected by HIV/AIDS and is home to the largest number of AIDS Orphans only next to South Africa in the world. The pandemic not only deprives Orphans of their rights to enjoy a good or a normal childhood, but it also has deleterious effects on their chances of survival or well-being. Thus the future of these children orphaned by the AIDS epidemic addresses a key social issue. Hence this study was done with the objectives, to assess the Demographic profile, Clinical profile and psycho-social profile of HIV Orphans. Methods A Longitudinal study on 82 HIV orphans in the age group 5 to 15yrs was conducted after obtaining informed consent from their caregivers for duration of one year from at Anti retroviral therapy (ART centre KIMS, Hubli. Clinical profile was assessed by WHO staging of HIV, Child Behavior Checklist (CBCL was used to assess Psycho-Social Profile. Chi-square test, paired t test are the tests of significance for qualitative and quantitative variables respectively. Results Mother to Child was the most common mode of transmission in majority of cases i.e 97%. Among the orphans 60% of them were deprived of mother’s care i.e Double orphans and maternal orphans. Majority of subjects i.e 29 (35.4% were in stage 2 of WHO clinical staging. 27(32.9% were in mild immunosuppression at 350 to 499 Absolute lymphocytic count and CD4% in the range of 20 to 25% in 26(31.7%. A statistically significant increase of psychosocial problem in orphans was observed during the follow-up. Conclusion It can be concluded that during the follow-up Psycho-social problems increased in Orphans significantly.

  16. 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.

  17. 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.

  18. Response of Archaeal Communities in Beach Sediments to Spilled Oil and Bioremediation

    OpenAIRE

    Röling, Wilfred F. M.; Couto de Brito, Ivana R.; Swannell, Richard P. J.; Head, Ian M.

    2004-01-01

    While the contribution of Bacteria to bioremediation of oil-contaminated shorelines is well established, the response of Archaea to spilled oil and bioremediation treatments is unknown. The relationship between archaeal community structure and oil spill bioremediation was examined in laboratory microcosms and in a bioremediation field trial. 16S rRNA gene-based PCR and denaturing gradient gel analysis revealed that the archaeal community in oil-free laboratory microcosms was stable for 26 day...

  19. Identification of an archaeal mercury regulon by chromatin immunoprecipitation.

    Science.gov (United States)

    Rudrappa, Deepak; Yao, Andrew I; White, Derrick; Pavlik, Benjamin J; Singh, Raghuveer; Facciotti, Marc T; Blum, Paul

    2015-12-01

    Mercury is a heavy metal and toxic to all forms of life. Metal exposure can invoke a response to improve survival. In archaea, several components of a mercury response system have been identified, but it is not known whether metal transport is a member of this system. To identify such missing components, a peptide-tagged MerR transcription factor was used to localize enriched chromosome regions by chromosome immunoprecipitation combined with DNA sequence analysis. Such regions could serve as secondary regulatory binding sites to control the expression of additional genes associated with mercury detoxification. Among the 31 highly enriched loci, a subset of five was pursued as potential candidates based on their current annotations. Quantitative reverse transcription-PCR analysis of these regions with and without mercury treatment in WT and mutant strains lacking merR indicated significant regulatory responses under these conditions. Of these, a Family 5 extracellular solute-binding protein and the MarR transcription factor shown previously to control responses to oxidation were most strongly affected. Inactivation of the solute-binding protein by gene disruption increased the resistance of mutant cells to mercury challenge. Inductively coupled plasma-MS analysis of the mutant cell line following metal challenge indicated there was less intracellular mercury compared with the isogenic WT strain. Together, these regulated genes comprise new members of the archaeal MerR regulon and reveal a cascade of transcriptional control not previously demonstrated in this model organism.

  20. Protein phosphorylation and its role in archaeal signal transduction.

    Science.gov (United States)

    Esser, Dominik; Hoffmann, Lena; Pham, Trong Khoa; Bräsen, Christopher; Qiu, Wen; Wright, Phillip C; Albers, Sonja-Verena; Siebers, Bettina

    2016-09-01

    Reversible protein phosphorylation is the main mechanism of signal transduction that enables cells to rapidly respond to environmental changes by controlling the functional properties of proteins in response to external stimuli. However, whereas signal transduction is well studied in Eukaryotes and Bacteria, the knowledge in Archaea is still rather scarce. Archaea are special with regard to protein phosphorylation, due to the fact that the two best studied phyla, the Euryarchaeota and Crenarchaeaota, seem to exhibit fundamental differences in regulatory systems. Euryarchaeota (e.g. halophiles, methanogens, thermophiles), like Bacteria and Eukaryotes, rely on bacterial-type two-component signal transduction systems (phosphorylation on His and Asp), as well as on the protein phosphorylation on Ser, Thr and Tyr by Hanks-type protein kinases. Instead, Crenarchaeota (e.g. acidophiles and (hyper)thermophiles) only depend on Hanks-type protein phosphorylation. In this review, the current knowledge of reversible protein phosphorylation in Archaea is presented. It combines results from identified phosphoproteins, biochemical characterization of protein kinases and protein phosphatases as well as target enzymes and first insights into archaeal signal transduction by biochemical, genetic and polyomic studies.

  1. Protein phosphorylation and its role in archaeal signal transduction

    Science.gov (United States)

    Esser, Dominik; Hoffmann, Lena; Pham, Trong Khoa; Bräsen, Christopher; Qiu, Wen; Wright, Phillip C.; Albers, Sonja-Verena; Siebers, Bettina

    2016-01-01

    Reversible protein phosphorylation is the main mechanism of signal transduction that enables cells to rapidly respond to environmental changes by controlling the functional properties of proteins in response to external stimuli. However, whereas signal transduction is well studied in Eukaryotes and Bacteria, the knowledge in Archaea is still rather scarce. Archaea are special with regard to protein phosphorylation, due to the fact that the two best studied phyla, the Euryarchaeota and Crenarchaeaota, seem to exhibit fundamental differences in regulatory systems. Euryarchaeota (e.g. halophiles, methanogens, thermophiles), like Bacteria and Eukaryotes, rely on bacterial-type two-component signal transduction systems (phosphorylation on His and Asp), as well as on the protein phosphorylation on Ser, Thr and Tyr by Hanks-type protein kinases. Instead, Crenarchaeota (e.g. acidophiles and (hyper)thermophiles) only depend on Hanks-type protein phosphorylation. In this review, the current knowledge of reversible protein phosphorylation in Archaea is presented. It combines results from identified phosphoproteins, biochemical characterization of protein kinases and protein phosphatases as well as target enzymes and first insights into archaeal signal transduction by biochemical, genetic and polyomic studies. PMID:27476079

  2. 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.

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

    DEFF Research Database (Denmark)

    Rennard, Stephen I; Vestbo, Jørgen

    2008-01-01

    are prospectively monitored, assuring that rigorous longitudinal data are generated. This approach could encourage the pharmaceutical industry to stratify studies based on a more detailed characterization of study subjects at baseline, thus approaching "many small COPDs" instead of a single large and heterogeneous...... 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...... COPD. This strategy may help to address the increasing burden that COPD presents and for which no novel clinical class of treatment has been introduced for 30 years....

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

    DEFF Research Database (Denmark)

    Rennard, Stephen I; Vestbo, Jørgen

    2008-01-01

    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...... of costs to be recovered during the patent life of a product. COPD should qualify for the first criterion if the various conditions that comprise COPD are regarded separately. The subphenotyping of COPD into separate...... are prospectively monitored, assuring that rigorous longitudinal data are generated. This approach could encourage the pharmaceutical industry to stratify studies based on a more detailed characterization of study subjects at baseline, thus approaching "many small COPDs" instead of a single large and heterogeneous...

  5. Unveiling the population of orphan γ-ray bursts

    Science.gov (United States)

    Ghirlanda, G.; Salvaterra, R.; 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.

    2015-06-01

    Gamma-ray bursts (GRBs) are detectable in the γ-ray band if their jets are oriented toward the observer. However, for each GRB with a typical θjet, there should be ~2/θ2jet bursts whose emission cone is oriented elsewhere in space. These off-axis bursts can eventually be detected when, due to the deceleration of their relativistic jets, the beaming angle becomes comparable to the viewing angle. Orphan afterglows (OAs) should outnumber the current population of bursts detected in the γ-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 OAs with ongoing and forthcoming surveys. The average duration of OAs as transients above a given limiting flux is derived and described with analytical expressions: in general OAs should appear as daily transients in optical surveys and as monthly/yearly transients in the mm/radio band. We find that ~2 OA yr-1 could already be detected by Gaia and up to 20 OA yr-1 could be observed by the ZTF survey. A larger number of 50 OA yr-1 should be detected by LSST in the optical band. For the X-ray band, ~26 OA yr-1 could be detected by the eROSITA. For the large population of OA detectable by LSST, the X-ray and optical follow up of the light curve (for the brightest cases) and/or the extensive follow up of their emission in the mm and radio band could be the key to disentangling their GRB nature from other extragalactic transients of comparable flux density.

  6. Evolution and Cultural Significance of "Orphan" Story%论“赵氏孤儿”故事演变及其文化意义

    Institute of Scientific and Technical Information of China (English)

    刘玉

    2012-01-01

    从《左传》、《史记》开始,至元杂剧、明传奇、各地方剧种、当代戏剧和电影,"赵氏孤儿"的故事一直被当作经典题材而改编。由于时代和作者的不同,"赵氏孤儿"故事在流传发展过程中也产生了不同程度的变化。以若干具有代表性的历史和文学作品为对象,考察"赵氏孤儿"故事的演变及其文化意义。%"Zuo Zhuan", "Historical Records", Yuan Dynasty, Ming legend of local operas, contemporary theaterand film, the story of "Orphan" has always been as a classic theme and adapted. "Orphan" story spread development process due to the times of the different changes of varying degrees. This paper tries to historical and literaryworks of several representative objects to study the evolution and cultural significance of the "orphan" story.

  7. Abundance and diversity of archaeal accA gene in hot springs in Yunnan Province, China.

    Science.gov (United States)

    Song, Zhao-Qi; Wang, Li; Wang, Feng-Ping; Jiang, Hong-Chen; Chen, Jin-Quan; Zhou, En-Min; Liang, Feng; Xiao, Xiang; Li, Wen-Jun

    2013-09-01

    It has been suggested that archaea carrying the accA gene, encoding the alpha subunit of the acetyl CoA carboxylase, autotrophically fix CO2 using the 3-hydroxypropionate/4-hydroxybutyrate pathway in low-temperature environments (e.g., soils, oceans). However, little new information has come to light regarding the occurrence of archaeal accA genes in high-temperature ecosystems. In this study, we investigated the abundance and diversity of archaeal accA gene in hot springs in Yunnan Province, China, using DNA- and RNA-based phylogenetic analyses and quantitative polymerase chain reaction. The results showed that archaeal accA genes were present and expressed in the investigated Yunnan hot springs with a wide range of temperatures (66-96 °C) and pH (4.3-9.0). The majority of the amplified archaeal accA gene sequences were affiliated with the ThAOA/HWCG III [thermophilic ammonia-oxidizing archaea (AOA)/hot water crenarchaeotic group III]. The archaeal accA gene abundance was very close to that of AOA amoA gene, encoding the alpha subunit of ammonia monooxygenase. These data suggest that AOA in terrestrial hot springs might acquire energy from ammonia oxidation coupled with CO2 fixation using the 3-hydroxypropionate/4-hydroxybutyrate pathway.

  8. Eukaryotic and archaeal TBP and TFB/TF(II)B follow different promoter DNA bending pathways.

    Science.gov (United States)

    Gietl, Andreas; Holzmeister, Phil; Blombach, Fabian; Schulz, Sarah; von Voithenberg, Lena Voith; Lamb, Don C; Werner, Finn; Tinnefeld, Philip; Grohmann, Dina

    2014-06-01

    During transcription initiation, the promoter DNA is recognized and bent by the basal transcription factor TATA-binding protein (TBP). Subsequent association of transcription factor B (TFB) with the TBP-DNA complex is followed by the recruitment of the ribonucleic acid polymerase resulting in the formation of the pre-initiation complex. TBP and TFB/TF(II)B are highly conserved in structure and function among the eukaryotic-archaeal domain but intriguingly have to operate under vastly different conditions. Employing single-pair fluorescence resonance energy transfer, we monitored DNA bending by eukaryotic and archaeal TBPs in the absence and presence of TFB in real-time. We observed that the lifetime of the TBP-DNA interaction differs significantly between the archaeal and eukaryotic system. We show that the eukaryotic DNA-TBP interaction is characterized by a linear, stepwise bending mechanism with an intermediate state distinguished by a distinct bending angle. TF(II)B specifically stabilizes the fully bent TBP-promoter DNA complex and we identify this step as a regulatory checkpoint. In contrast, the archaeal TBP-DNA interaction is extremely dynamic and TBP from the archaeal organism Sulfolobus acidocaldarius strictly requires TFB for DNA bending. Thus, we demonstrate that transcription initiation follows diverse pathways on the way to the formation of the pre-initiation complex. PMID:24744242

  9. pH dominates variation in tropical soil archaeal diversity and community structure.

    Science.gov (United States)

    Tripathi, Binu M; Kim, Mincheol; Lai-Hoe, Ang; Shukor, Nor A A; Rahim, Raha A; Go, Rusea; Adams, Jonathan M

    2013-11-01

    Little is known of the factors influencing soil archaeal community diversity and composition in the tropics. We sampled soils across a range of forest and nonforest environments in the equatorial tropics of Malaysia, covering a wide range of pH values. DNA was PCR-amplified for the V1-V3 region of the 16S rRNA gene, and 454-pyrosequenced. Soil pH was the best predictor of diversity and community composition of Archaea, being a stronger predictor than land use. Archaeal OTU richness was highest in the most acidic soils. Overall archaeal abundance in tropical soils (determined by qPCR) also decreased at higher pH. This contrasts with the opposite trend previously found in temperate soils. Thaumarcheota group 1.1b was more abundant in alkaline soils, whereas group 1.1c was only detected in acidic soils. These results parallel those found in previous studies in cooler climates, emphasizing niche conservatism among broad archaeal groups. Among the most abundant operational taxonomic units (OTUs), there was clear evidence of niche partitioning by pH. No individual OTU occurred across the entire range of pH values. Overall, the results of this study show that pH plays a major role in structuring tropical soil archaeal communities.

  10. 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

  11. Geographical Distribution of Methanogenic Archaea in Nine Representative Paddy Soils in China

    Science.gov (United States)

    Zu, Qianhui; Zhong, Linghao; Deng, Ye; Shi, Yu; Wang, Baozhan; Jia, Zhongjun; Lin, Xiangui; Feng, Youzhi

    2016-01-01

    Paddy field methanogenic archaea are responsible for methane (CH4) production and contribute significantly to climate change. The information regarding the spatial variations in the abundance, the diversity and the composition of such ecologically important microbes, however, is quite limited at large scale. In this investigation, we studied the abundance, alpha diversity and geographical distribution of methanogenic archaeal communities in nine representative paddy sites, along a large latitudinal gradient in China, using pyrosequencing and real-time quantitative PCR. It is found that all paddy soils harbor constant methanogenic archaeal constituents, which is dominated by family Methanocellaceae (37.3%), Methanobacteriaceae (22.1%), Methanosaetaceae (17.2%), and Methanosarcinaceae (9.8%). Methanogenic archaeal abundance is primarily influenced by soil C (R = 0.612, P = 0.001) and N (R = 0.673, P = 0.001) contents, as well as alpha diversity by soil pH (PD: R = -0.552, P = 0.006; Chao1: R = -0.615, P = 0.002). Further exploration revealed that both spatial distance (R = 0.3469, P = 0.001, partial mental test) and soil chemical variables mainly about soil C and N (R = 0.2847, P = 0.001) are the two major factors affecting methanogenic archaeal community composition distribution in paddy soils. This finding will allow us to develop a better picture of the biogeographic ranges of these ecologically important microbes and get deeper insights into their ecology. PMID:27679621

  12. Geographical Distribution of Methanogenic Archaea in Nine Representative Paddy Soils in China.

    Science.gov (United States)

    Zu, Qianhui; Zhong, Linghao; Deng, Ye; Shi, Yu; Wang, Baozhan; Jia, Zhongjun; Lin, Xiangui; Feng, Youzhi

    2016-01-01

    Paddy field methanogenic archaea are responsible for methane (CH4) production and contribute significantly to climate change. The information regarding the spatial variations in the abundance, the diversity and the composition of such ecologically important microbes, however, is quite limited at large scale. In this investigation, we studied the abundance, alpha diversity and geographical distribution of methanogenic archaeal communities in nine representative paddy sites, along a large latitudinal gradient in China, using pyrosequencing and real-time quantitative PCR. It is found that all paddy soils harbor constant methanogenic archaeal constituents, which is dominated by family Methanocellaceae (37.3%), Methanobacteriaceae (22.1%), Methanosaetaceae (17.2%), and Methanosarcinaceae (9.8%). Methanogenic archaeal abundance is primarily influenced by soil C (R = 0.612, P = 0.001) and N (R = 0.673, P = 0.001) contents, as well as alpha diversity by soil pH (PD: R = -0.552, P = 0.006; Chao1: R = -0.615, P = 0.002). Further exploration revealed that both spatial distance (R = 0.3469, P = 0.001, partial mental test) and soil chemical variables mainly about soil C and N (R = 0.2847, P = 0.001) are the two major factors affecting methanogenic archaeal community composition distribution in paddy soils. This finding will allow us to develop a better picture of the biogeographic ranges of these ecologically important microbes and get deeper insights into their ecology. PMID:27679621

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

    OpenAIRE

    Erango MA; Ayka ZA

    2015-01-01

    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 di...

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

    OpenAIRE

    Erango, Markos

    2015-01-01

    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 loca...

  15. Constitutive Activity among Orphan Class-A G Protein Coupled Receptors

    OpenAIRE

    Martin, Adam L.; Michael A Steurer; Aronstam, Robert S.

    2015-01-01

    The purpose of this study was to evaluate the extent of constitutive activity among orphan class-A G protein coupled receptors within the cAMP signaling pathway. Constitutive signaling was revealed by changes in gene expression under control of the cAMP response element. Gene expression was measured in Chinese hamster ovary cells transiently co-transfected with plasmids containing a luciferase reporter and orphan receptor. Criteria adopted for defining constitutive activation were: 1) 200% el...

  16. 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.

  17. 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.

  18. Reproductive potential and its behavioural consequences in orphaned bumblebee workers (Bombus impatiens)

    OpenAIRE

    Sibbald, Emily D.; Plowright, Catherine M. S.

    2015-01-01

    AbstractThe supposition that aggression in orphaned workers is used in a battle over reproductive rights was evaluated for Bombus impatiens. Ovarian development was experimentally stimulated or inhibited in orphaned sisters. The manipulation translated into differences in egg laying. Two groups of pairs differed as to whether both or just one of the workers had developed ovaries. The prediction that workers with higher reproductive potential in the unmatched groups would show less aggression ...

  19. Causes and consequences of psychological distress among orphans in eastern Zimbabwe

    OpenAIRE

    Nyamukapa, C. A.; Gregson, S.; Wambe, M; Mushore, P.; Lopman, B.; Mupambireyi, Z.; Nhongo, K.; Jukes, Matthew

    2010-01-01

    Abstract Substantial resources are invested in psychological support for children orphaned or otherwise made vulnerable in the context HIV/AIDS (OVC). However, there is still only limited scientific evidence for greater psychological distress amongst orphans and even less evidence for the effectiveness of current support strategies. Furthermore, programmes that address established mechanisms through which orphanhood can lead to greater psychological distress should be more effectiv...

  20. Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs

    NARCIS (Netherlands)

    Frade, P.R.; Roll, K.; Bergauer, K.; Herndl, G.

    2016-01-01

    Comparative studies on the distribution of archaeal versus bacterial communities associatedwith the surface mucus layer of corals have rarely taken place. It has thereforeremained enigmatic whether mucus-associated archaeal and bacterial communities exhibita similar specificity towards coral hosts a

  1. 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.

  2. Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters.

    Science.gov (United States)

    Wilms, Reinhard; Sass, Henrik; Köpke, Beate; Köster, Jürgen; Cypionka, Heribert; Engelen, Bert

    2006-04-01

    The subsurface of a tidal-flat sediment was analyzed down to 360 cm in depth by molecular and geochemical methods. A community structure analysis of all three domains of life was performed using domain-specific PCR followed by denaturing gradient gel electrophoresis analysis and sequencing of characteristic bands. The sediment column comprised horizons easily distinguishable by lithology that were deposited in intertidal and salt marsh environments. The pore water profile was characterized by a subsurface sulfate peak at a depth of about 250 cm. Methane and sulfate profiles were opposed, showing increased methane concentrations in the sulfate-free layers. The availability of organic carbon appeared to have the most pronounced effect on the bacterial community composition in deeper sediment layers. In general, the bacterial community was dominated by fermenters and syntrophic bacteria. The depth distribution of methanogenic archaea correlated with the sulfate profile and could be explained by electron donor competition with sulfate-reducing bacteria. Sequences affiliated with the typically hydrogenotrophic Methanomicrobiales were present in sulfate-free layers. Archaea belonging to the Methanosarcinales that utilize noncompetitive substrates were found along the entire anoxic-sediment column. Primers targeting the eukaryotic 18S rRNA gene revealed the presence of a subset of archaeal sequences in the deeper part of the sediment cores. The phylogenetic distance to other archaeal sequences indicates that these organisms represent a new phylogenetic group, proposed as "tidal-flat cluster 1." Eukarya were still detectable at 360 cm, even though their diversity decreased with depth. Most of the eukaryotic sequences were distantly related to those of grazers and deposit feeders.

  3. 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.

  4. Liquid but Durable: Molecular Dynamics Simulations Explain the Unique Properties of Archaeal-Like Membranes

    Science.gov (United States)

    Chugunov, Anton O.; Volynsky, Pavel E.; Krylov, Nikolay A.; Boldyrev, Ivan A.; Efremov, Roman G.

    2014-12-01

    Archaeal plasma membranes appear to be extremely durable and almost impermeable to water and ions, in contrast to the membranes of Bacteria and Eucaryota. Additionally, they remain liquid within a temperature range of 0-100°C. These are the properties that have most likely determined the evolutionary fate of Archaea, and it may be possible for bionanotechnology to adopt these from nature. In this work, we use molecular dynamics simulations to assess at the atomistic level the structure and dynamics of a series of model archaeal membranes with lipids that have tetraether chemical nature and ``branched'' hydrophobic tails. We conclude that the branched structure defines dense packing and low water permeability of archaeal-like membranes, while at the same time ensuring a liquid-crystalline state, which is vital for living cells. This makes tetraether lipid systems promising in bionanotechnology and material science, namely for design of new and unique membrane nanosystems.

  5. Differences in the Composition of Archaeal Communities in Sediments from Contrasting Zones of Lake Taihu

    Science.gov (United States)

    Fan, Xianfang; Xing, Peng

    2016-01-01

    In shallow lakes, different primary producers might impact the physiochemical characteristics of the sediment and the associated microbial communities. Until now, little was known about the features of sediment Archaea and their variation across different primary producer-dominated ecosystems. Lake Taihu provides a suitable study area with cyanobacteria- and macrophyte-dominated zones co-occurring in one ecosystem. The composition of the sediment archaeal community was assessed using 16S rRNA gene amplicon sequencing technology, based on which the potential variation with respect to the physiochemical characteristics of the sediment was analyzed. Euryarchaeota (30.19% of total archaeal sequences) and Bathyarchaeota (28.00%) were the two most abundant phyla, followed by Crenarchaeota (11.37%), Aigarchaeota (10.24%) and Thaumarchaeota (5.98%). The differences found in the composition of the archaeal communities between the two zones was significant (p = 0.005). Sediment from macrophyte-dominated zones had high TOC and TN content and an abundance of archaeal lineages potentially involved in the degradation of complex organic compounds, such as the order Thermoplasmatales. In the area dominated by Cyanobacteria, archaeal lineages related to sulfur metabolism, for example, Sulfolobales and Desulfurococcales, were significantly enriched. Among Bathyarchaeota, subgroups MCG-6 and MCG-15 were significantly accumulated in the sediment of areas dominated by macrophytes whereas MCG-4 was consistently dominant in both type of sediments. The present study contributes to the knowledge of sediment archaeal communities with different primary producers and their possible biogeochemical functions in sediment habitats. PMID:27708641

  6. Pyrosequencing-derived bacterial, archaeal, and fungal diversity of spacecraft hardware destined for Mars.

    Science.gov (United States)

    La Duc, Myron T; Vaishampayan, Parag; Nilsson, Henrik R; Torok, Tamas; Venkateswaran, Kasthuri

    2012-08-01

    Spacecraft hardware and assembly cleanroom surfaces (233 m(2) in total) were sampled, total genomic DNA was extracted, hypervariable regions of the 16S rRNA gene (bacteria and archaea) and ribosomal internal transcribed spacer (ITS) region (fungi) were subjected to 454 tag-encoded pyrosequencing PCR amplification, and 203,852 resulting high-quality sequences were analyzed. Bioinformatic analyses revealed correlations between operational taxonomic unit (OTU) abundance and certain sample characteristics, such as source (cleanroom floor, ground support equipment [GSE], or spacecraft hardware), cleaning regimen applied, and location about the facility or spacecraft. National Aeronautics and Space Administration (NASA) cleanroom floor and GSE surfaces gave rise to a larger number of diverse bacterial communities (619 OTU; 20 m(2)) than colocated spacecraft hardware (187 OTU; 162 m(2)). In contrast to the results of bacterial pyrosequencing, where at least some sequences were generated from each of the 31 sample sets examined, only 13 and 18 of these sample sets gave rise to archaeal and fungal sequences, respectively. As was the case for bacteria, the abundance of fungal OTU in the GSE surface samples dramatically diminished (9× less) once cleaning protocols had been applied. The presence of OTU representative of actinobacteria, deinococci, acidobacteria, firmicutes, and proteobacteria on spacecraft surfaces suggests that certain bacterial lineages persist even following rigorous quality control and cleaning practices. The majority of bacterial OTU observed as being recurrent belonged to actinobacteria and alphaproteobacteria, supporting the hypothesis that the measures of cleanliness exerted in spacecraft assembly cleanrooms (SAC) inadvertently select for the organisms which are the most fit to survive long journeys in space.

  7. Metagenomic analysis of bacterial and archaeal assemblages in the soil-mousse surrounding a geothermal spring

    Directory of Open Access Journals (Sweden)

    Sonu Bhatia

    2015-09-01

    Full Text Available The soil-mousse surrounding a geothermal spring was analyzed for bacterial and archaeal diversity using 16S rRNA gene amplicon metagenomic sequencing which revealed the presence of 18 bacterial phyla distributed across 109 families and 219 genera. Firmicutes, Actinobacteria, and the Deinococcus-Thermus group were the predominant bacterial assemblages with Crenarchaeota and Thaumarchaeota as the main archaeal assemblages in this largely understudied geothermal habitat. Several metagenome sequences remained taxonomically unassigned suggesting the presence of a repertoire of hitherto undescribed microbes in this geothermal soil-mousse econiche.

  8. The detection of orphan radioactive sources and the regulatory attitude

    International Nuclear Information System (INIS)

    In the last decade, the appearance of orphan control radioactive sources has been one constant restlessness in the environment of the regulatory control. Of the well-known cases in the world the more common have been the appearance of type sources or industrial use, which by control lack, by negligence or abandonment were without the due protection and receipt. It is presented in this work the detection of a radioactive source of Cs-137 pickup among the scrap that entered to an important steelworks of the country, by a detector of portal type. Starting from there, Ia Nuclear Regulatory Authority (ARN) it carried out a deep investigation to determine the origin of the radioactive source, which drove to detect and to put low control to other three radioactive sources of the same type used in level measurement, originally housed in a tank of daily consumption of gas-oil, inside a craft that it was broken up for it sale like scrap. During the execution of these tasks they took the regulatory collection, chord to what indicates the normative of the Argentine Republic, harmonized by the international requirements as for the control of radioactive material. (Author)

  9. 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.

  10. 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.

  11. GRB orphan afterglows in present and future radio transient surveys

    CERN Document Server

    Ghirlanda, G; Ghisellini, G; Salvaterra, R; Bernardini, M G; Campana, S; Covino, S; D'Avanzo, P; D'Elia, V; Melandri, A; Murphy, T; Nava, L; Vergani, S D; Tagliaferri, G

    2014-01-01

    Orphan Afterglows (OA) are slow transients produced by Gamma Ray Bursts seen off-axis that become visible on timescales of days/years at optical/NIR and radio frequencies, when the prompt emission at high energies (X and gamma rays) has already ceased. Given the typically estimated jet opening angle of GRBs theta_jet ~ 3 deg, for each burst pointing to the Earth there should be a factor ~ 700 more GRBs pointing in other directions. Despite this, no secure OAs have been detected so far. Through a population synthesis code we study the emission properties of the population of OA at radio frequencies. OAs reach their emission peak on year-timescales and they last for a comparable amount of time. The typical peak fluxes (which depend on the observing frequency) are of few micro Jy in the radio band with only a few OA reaching the mJy level. These values are consistent with the upper limits on the radio flux of SN Ib/c observed at late times. We find that the OA radio number count distribution has a typical slope ...

  12. 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

  13. 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

  14. Correlates of Poor Health among Orphans and Abandoned Children in Less Wealthy Countries: The Importance of Caregiver Health

    OpenAIRE

    Nathan Thielman; Jan Ostermann; Kathryn Whetten; Rachel Whetten; Karen O'Donnell

    2012-01-01

    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 (PO...

  15. A novel chemogenomics analysis of G protein-coupled receptors (GPCRs and their ligands: a potential strategy for receptor de-orphanization

    Directory of Open Access Journals (Sweden)

    Emmerich Michael TM

    2010-06-01

    Full Text Available Abstract Background G protein-coupled receptors (GPCRs represent a family of well-characterized drug targets with significant therapeutic value. Phylogenetic classifications may help to understand the characteristics of individual GPCRs and their subtypes. Previous phylogenetic classifications were all based on the sequences of receptors, adding only minor information about the ligand binding properties of the receptors. In this work, we compare a sequence-based classification of receptors to a ligand-based classification of the same group of receptors, and evaluate the potential to use sequence relatedness as a predictor for ligand interactions thus aiding the quest for ligands of orphan receptors. Results We present a classification of GPCRs that is purely based on their ligands, complementing sequence-based phylogenetic classifications of these receptors. Targets were hierarchically classified into phylogenetic trees, for both sequence space and ligand (substructure space. The overall organization of the sequence-based tree and substructure-based tree was similar; in particular, the adenosine receptors cluster together as well as most peptide receptor subtypes (e.g. opioid, somatostatin and adrenoceptor subtypes. In ligand space, the prostanoid and cannabinoid receptors are more distant from the other targets, whereas the tachykinin receptors, the oxytocin receptor, and serotonin receptors are closer to the other targets, which is indicative for ligand promiscuity. In 93% of the receptors studied, de-orphanization of a simulated orphan receptor using the ligands of related receptors performed better than random (AUC > 0.5 and for 35% of receptors de-orphanization performance was good (AUC > 0.7. Conclusions We constructed a phylogenetic classification of GPCRs that is solely based on the ligands of these receptors. The similarities and differences with traditional sequence-based classifications were investigated: our ligand

  16. Care arrangements of AIDS orphans and their relationship with children's psychosocial well-being in rural China.

    Science.gov (United States)

    Hong, Yan; Li, Xiaoming; Fang, Xiaoyi; Zhao, Guoxiang; Zhao, Junfeng; Zhao, Qun; Lin, Xiuyun; Zhang, Liying; Stanton, Bonita

    2011-03-01

    There is an estimated 100,000 children orphaned by AIDS in China, but data on the care arrangement of these orphans are limited. In this study, we examine the relationship between AIDS orphans' care arrangement and their psychosocial well-being among a sample of AIDS orphans in rural China. A total of 296 children who lost both parents to AIDS participated in the study, including 176 in orphanages, 90 in kinship care and 30 in community-based group homes. All participants completed a cross-sectional survey assessing their traumatic symptoms, physical health and schooling. Data reveal that the AIDS orphans in group homes reported the best outcomes in three domains of psychosocial well-being, followed by those in the orphanages and then the kinship care. The differences in psychosocial well-being among the three groups of children persist after controlling for key demographic characteristics. The findings suggest that the appropriate care arrangement for AIDS orphans should be evaluated within the specific social and cultural context where the orphans live. In resource-poor regions or areas stricken hardest by the AIDS epidemic, kinship care may not sufficiently serve the needs of AIDS orphans. Community-based care models, with appropriate government and community support preserving the family style and low child-to-caregiver ratio may constitute an effective and sustainable care model for the best interest of the AIDS orphans in developing countries. PMID:20587602

  17. Orphan Basin crustal structure from a dense wide-angle seismic profile - layered modeling

    Science.gov (United States)

    Lau, K. W. Helen; Watremez, Louise; Louden, Keith E.; Nedimović, Mladen R.; Karner, Garry D.

    2014-05-01

    The Orphan Basin is a large, deep water basin to the east of Newfoundland and northwest of Flemish Cap, Canada. It contains a considerably wide series of rift basins that provides an excellent opportunity to study continental crustal deformations under varying degrees of extension. We present a 500-km-long P-wave velocity model across the complete rift system of the Orphan Basin, from Flemish Cap to the Bonavista Platform, using high-resolution refraction and wide-angle reflection data from 89 ocean-bottom seismometers (OBS). This layered model builds on a first-arrival traveltime tomography model (Watremez et al., this session) and is formed using additional constraints from a coincident multichannel seismic reflection profile, gravity data and borehole data from three wells. The layered model helps detail deep sediment and crustal variations across this wide region of extended continental crust. The sedimentary section contains post-rift Tertiary (vp~1.7-3.5 km/s) and syn-rift Cretaceous and Jurassic (vp~4-5.4 km/s) layers within both the eastern and the western sub-basins, separated by three basement highs, suggesting that the two sub-basins may have opened during a single, extended rifting event. The crust is composed of three layers with vp of 5.4-6.1, 6.1-6.5 and 6.3-7.1 km/s of highly variable combined thicknesses, from 32 km beneath Flemish Cap and the Bonavista Platform to Orphan Basin, Porcupine Bank and the East Orphan Basin, and the Central Orphan High and Porcupine Bank. Unlike the Rockall and Porcupine Basins, no evidence for partial serpentinization of the upper mantle is observed beneath the E. Orphan trough. However, hyperextension (crustal thickness Orphan trough, which might have allowed the basement to have been covered by syn-rift sediment that inhibited the flow of water down the faults.

  18. 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.

  19. 国外孤儿药管理制度对比研究及对我国的政策建议%Contrastive analysis of abroad orphan drug management systems and suggestions for China

    Institute of Scientific and Technical Information of China (English)

    唐健元; 赵夏茵

    2013-01-01

    以美国FDA为代表的欧美发达国家均建立完善针对罕见病和孤儿药的专门监管机构和措施,而我国罕见病的防治没有得到足够重视,甚至被边缘化,我国孤儿药管理制度较欧美国家存在明显欠缺.本文通过文献研究法对比分析各国孤儿药管理制度,根据中国国情提出促进我国孤儿药政策建设的建议.为国家孤儿药政策的建设提供参考,以促进我国孤儿药管理制度的实施.%Special regulators have been established in many developed countries with the representative as FDA in the United States.Special regulative department took measures to completely manage rare diseases and orphan drugs.However,Chinese regulatory has not paid much attention to prevention and treatment of rare disease,so even been marginalized.China is obviously defective in orphan drug management.In this paper,we contrastively analyzed orphan drug management systems in several other countries by literature research method.According to Chinese national conditions,we put forward some suggestions as references for the development of orphan drug policy for promoting the implementation of orphan drug management system in China.

  20. Planktonic Euryarchaeota are a significant source of archaeal tetraether lipids in the ocean

    Science.gov (United States)

    Lincoln, Sara A.; Wai, Brenner; Eppley, John M.; Church, Matthew J.; Summons, Roger E.; DeLong, Edward F.

    2014-01-01

    Archaea are ubiquitous in marine plankton, and fossil forms of archaeal tetraether membrane lipids in sedimentary rocks document their participation in marine biogeochemical cycles for >100 million years. Ribosomal RNA surveys have identified four major clades of planktonic archaea but, to date, tetraether lipids have been characterized in only one, the Marine Group I Thaumarchaeota. The membrane lipid composition of the other planktonic archaeal groups—all uncultured Euryarchaeota—is currently unknown. Using integrated nucleic acid and lipid analyses, we found that Marine Group II Euryarchaeota (MG-II) contributed significantly to the tetraether lipid pool in the North Pacific Subtropical Gyre at shallow to intermediate depths. Our data strongly suggested that MG-II also synthesize crenarchaeol, a tetraether lipid previously considered to be a unique biomarker for Thaumarchaeota. Metagenomic datasets spanning 5 y indicated that depth stratification of planktonic archaeal groups was a stable feature in the North Pacific Subtropical Gyre. The consistent prevalence of MG-II at depths where the bulk of exported organic matter originates, together with their ubiquitous distribution over diverse oceanic provinces, suggests that this clade is a significant source of tetraether lipids to marine sediments. Our results are relevant to archaeal lipid biomarker applications in the modern oceans and the interpretation of these compounds in the geologic record. PMID:24946804

  1. The effect of maturity and depositional redox conditions on archaeal tetraether lipid palaeothermometry

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Schouten, S.; Hopmans, E.C.

    2004-01-01

    Recently we proposed a new organic sea surface temperature proxy, TEX86, based on the distribution of archaeal tetraether lipids. Here, we have examined the effect of oxic degradation and maturity on this new temperature proxy. Our results show that oxic degradation does not appear to affect the TEX

  2. Effect of soil properties and hydrology on Archaeal community composition in three temperate grasslands on peat

    DEFF Research Database (Denmark)

    Görres, Carolyn-Monika; Conrad, Ralf; Petersen, Søren O

    2013-01-01

    Grasslands established on drained peat soils are regarded as negligible methane (CH4) sources; however, they can still exhibit considerable soil CH4 dynamics. We investigated archaeal community composition in two different fen peat soils and one bog peat soil under permanent grassland in Denmark...

  3. Archaeal and bacterial diversity in hot springs on the Tibetan Plateau, China.

    Science.gov (United States)

    Huang, Qiuyuan; Dong, Christina Z; Dong, Raymond M; Jiang, Hongchen; Wang, Shang; Wang, Genhou; Fang, Bin; Ding, Xiaoxue; Niu, Lu; Li, Xin; Zhang, Chuanlun; Dong, Hailiang

    2011-09-01

    The diversity of archaea and bacteria was investigated in ten hot springs (elevation >4600 m above sea level) in Central and Central-Eastern Tibet using 16S rRNA gene phylogenetic analysis. The temperature and pH of these hot springs were 26-81°C and close to neutral, respectively. A total of 959 (415 and 544 for bacteria and archaea, respectively) clone sequences were obtained. Phylogenetic analysis showed that bacteria were more diverse than archaea and that these clone sequences were classified into 82 bacterial and 41 archaeal operational taxonomic units (OTUs), respectively. The retrieved bacterial clones were mainly affiliated with four known groups (i.e., Firmicutes, Proteobacteria, Cyanobacteria, Chloroflexi), which were similar to those in other neutral-pH hot springs at low elevations. In contrast, most of the archaeal clones from the Tibetan hot springs were affiliated with Thaumarchaeota, a newly proposed archaeal phylum. The dominance of Thaumarchaeota in the archaeal community of the Tibetan hot springs appears to be unique, although the exact reasons are not yet known. Statistical analysis showed that diversity indices of both archaea and bacteria were not statistically correlated with temperature, which is consistent with previous studies.

  4. Metagenomic evaluation of bacterial and archaeal diversity in the geothermal hot springs of manikaran, India.

    Science.gov (United States)

    Bhatia, Sonu; Batra, Navneet; Pathak, Ashish; Green, Stefan J; Joshi, Amit; Chauhan, Ashvini

    2015-02-19

    Bacterial and archaeal diversity in geothermal spring water were investigated using 16S rRNA gene amplicon metagenomic sequencing. This revealed the dominance of Firmicutes, Aquificae, and the Deinococcus-Thermus group in this thermophilic environment. A number of sequences remained taxonomically unresolved, indicating the presence of potentially novel microbes in this unique habitat.

  5. CrAgDb--a database of annotated chaperone repertoire in archaeal genomes.

    Science.gov (United States)

    Rani, Shikha; Srivastava, Abhishikha; Kumar, Manish; Goel, Manisha

    2016-03-01

    Chaperones are a diverse class of ubiquitous proteins that assist other cellular proteins in folding correctly and maintaining their native structure. Many different chaperones cooperate to constitute the 'proteostasis' machinery in the cells. It has been proposed earlier that archaeal organisms could be ideal model systems for deciphering the basic functioning of the 'protein folding machinery' in higher eukaryotes. Several chaperone families have been characterized in archaea over the years but mostly one protein at a time, making it difficult to decipher the composition and mechanistics of the protein folding system as a whole. In order to deal with these lacunae, we have developed a database of all archaeal chaperone proteins, CrAgDb (Chaperone repertoire in Archaeal genomes). The data have been presented in a systematic way with intuitive browse and search facilities for easy retrieval of information. Access to these curated datasets should expedite large-scale analysis of archaeal chaperone networks and significantly advance our understanding of operation and regulation of the protein folding machinery in archaea. Researchers could then translate this knowledge to comprehend the more complex protein folding pathways in eukaryotic systems. The database is freely available at http://14.139.227.92/mkumar/cragdb/. PMID:26862144

  6. Identification of archaeal proteins that affect the exosome function in vitro

    Directory of Open Access Journals (Sweden)

    Palhano Fernando L

    2010-05-01

    Full Text Available Abstract Background The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors. Results Here, we show that the proteins PaSBDS and PaNip7, which bind preferentially to poly-A and AU-rich RNAs, respectively, affect the Pyrococcus abyssi exosome activity in vitro. PaSBDS inhibits slightly degradation of a poly-rA substrate, while PaNip7 strongly inhibits the degradation of poly-A and poly-AU by the exosome. The exosome inhibition by PaNip7 appears to depend at least partially on its interaction with RNA, since mutants of PaNip7 that no longer bind RNA, inhibit the exosome less strongly. We also show that FITC-labeled PaNip7 associates with the exosome in the absence of substrate RNA. Conclusions Given the high structural homology between the archaeal and eukaryotic proteins, the effect of archaeal Nip7 and SBDS on the exosome provides a model for an evolutionarily conserved exosome control mechanism.

  7. Seasonal Effects in a Lake Sediment Archaeal Community of the Brazilian Savanna

    Directory of Open Access Journals (Sweden)

    Thiago Rodrigues

    2014-01-01

    Full Text Available The Cerrado is a biome that corresponds to 24% of Brazil’s territory. Only recently microbial communities of this biome have been investigated. Here we describe for the first time the diversity of archaeal communities from freshwater lake sediments of the Cerrado in the dry season and in the transition period between the dry and rainy seasons, when the first rains occur. Gene libraries were constructed, using Archaea-specific primers for the 16S rRNA and amoA genes. Analysis revealed marked differences between the archaeal communities found in the two seasons. I.1a and I.1c Thaumarchaeota were found in greater numbers in the transition period, while MCG Archaea was dominant on the dry season. Methanogens were only found in the dry season. Analysis of 16S rRNA sequences revealed lower diversity on the transition period. We detected archaeal amoA sequences in both seasons, but there were more OTUs during the dry season. These sequences were within the same cluster as Nitrosotalea devanaterra’s amoA gene. The principal coordinate analysis (PCoA test revealed significant differences between samples from different seasons. These results provide information on archaeal diversity in freshwater lake sediments of the Cerrado and indicates that rain is likely a factor that impacts these communities.

  8. Archaeal communities associated with roots of the common reed (Phragmites australis) in Beijing Cuihu Wetland.

    Science.gov (United States)

    Liu, Yin; Li, Hong; Liu, Qun Fang; Li, Yan Hong

    2015-05-01

    The richness, phylogeny and composition of archaeal community associated with the roots of common reed (Phragmites australis) growing in the Beijing Cuihu Wetland, China was investigated using a 16S rDNA library. In total, 235 individual sequences were collected, and a phylogenetic analysis revealed that 69.4 and 11.5 % of clones were affiliated with the Euryarchaeota and the Crenarchaeota, respectively. In Euryarchaeota, the archaeal community was dominated by species in following genera: Methanobacterium in the order Methanobacteriales (60.7 %); Methanoregula and Methanospirillum in the order Methanomicrobiales (20.2 %), and Methanomethylovorans, Methanosarcina and Methanosaeta in the order Methanosarcinales (17.2 %). Of 27 sequences assigned to uncultured Crenarchaeota, 22 were grouped into Group 1.3, and five grouped into Group 1.1b. Hence, the archaeal communities associated with reed roots are largely involved in methane production, and, to a lesser extent, in ammonia oxidization. Quantification of the archaeal amoA gene indicated that ammonia oxidizing archaea were more numerous in the rhizosphere soil than in the root tissue or surrounding water. A total of 19.1 % of the sequences were unclassified, suggesting that many unidentified archaea are probably involved in the reed wetland ecosystem. PMID:25739566

  9. ENERGY-TRANSDUCING PROPERTIES OF PRIMARY PROTON PUMPS RECONSTITUTED INTO ARCHAEAL BIPOLAR LIPID VESICLES

    NARCIS (Netherlands)

    ELFERINK, MGL; DEWIT, JG; DRIESSEN, AJM; KONINGS, WN; Elferink, Marieke G.L.

    1993-01-01

    Archaeal lipids differ considerably from eubacterial and eukaryotic lipids in their structure and physical properties. From the membranes of the extreme thermophilic archaea Sulfolobus acidocaldarius a tetraether lipid fraction was isolated, which can form closed and stable monolayer liposomes in aq

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

    International Nuclear Information System (INIS)

    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.

  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. 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.

  14. 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. PMID:21357612

  15. 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

  16. GRB Orphan Afterglows in Present and Future Radio Transient Surveys

    Science.gov (United States)

    Ghirlanda, G.; Burlon, D.; Ghisellini, G.; Salvaterra, R.; Bernardini, M. G.; Campana, S.; Covino, S.; D'Avanzo, P.; D'Elia, V.; Melandri, A.; Murphy, T.; Nava, L.; Vergani, S. D.; Tagliaferri, G.

    2014-05-01

    Orphan Afterglows (OA) are slow transients produced by Gamma Ray Bursts seen off-axis that become visible on timescales of days/years at optical/NIR and radio frequencies, when the prompt emission at high energies (X and γ rays) has already ceased. Given the typically estimated jet opening angle of GRBs θjet ~ 3°, for each burst pointing to the Earth there should be a factor ~ 700 more GRBs pointing in other directions. Despite this, no secure OAs have been detected so far. Through a population synthesis code we study the emission properties of the population of OA at radio frequencies. OAs reach their emission peak on year-timescales and they last for a comparable amount of time. The typical peak fluxes (which depend on the observing frequency) are of few μJy in the radio band with only a few OA reaching the mJy level. These values are consistent with the upper limits on the radio flux of SN Ib/c observed at late times. We find that the OA radio number count distribution has a typical slope - 1.7 at high fluxes and a flatter ( - 0.4) slope at low fluxes with a break at a frequency-dependent flux. Our predictions of the OA rates are consistent with the (upper) limits of recent radio surveys and archive searches for radio transients. Future radio surveys like VAST/ASKAP at 1.4 GHz should detect ~ 3 × 10- 3 OA deg- 2 yr- 1, MeerKAT and EVLA at 8.4 GHz should see ~ 3 × 10- 1 OA deg- 2 yr- 1. The SKA, reaching the μJy flux limit, could see up to ~ 0.2 - 1.5 OA deg- 2 yr- 1. These rates also depend on the duration of the OA above a certain flux limit and we discuss this effect with respect to the survey cadence.

  17. 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

  18. Phylogenetic Diversity of Archaea and the Archaeal Ammonia Monooxygenase Gene in Uranium Mining-Impacted Locations in Bulgaria

    Directory of Open Access Journals (Sweden)

    Galina Radeva

    2014-01-01

    Full Text Available Uranium mining and milling activities adversely affect the microbial populations of impacted sites. The negative effects of uranium on soil bacteria and fungi are well studied, but little is known about the effects of radionuclides and heavy metals on archaea. The composition and diversity of archaeal communities inhabiting the waste pile of the Sliven uranium mine and the soil of the Buhovo uranium mine were investigated using 16S rRNA gene retrieval. A total of 355 archaeal clones were selected, and their 16S rDNA inserts were analysed by restriction fragment length polymorphism (RFLP discriminating 14 different RFLP types. All evaluated archaeal 16S rRNA gene sequences belong to the 1.1b/Nitrososphaera cluster of Crenarchaeota. The composition of the archaeal community is distinct for each site of interest and dependent on environmental characteristics, including pollution levels. Since the members of 1.1b/Nitrososphaera cluster have been implicated in the nitrogen cycle, the archaeal communities from these sites were probed for the presence of the ammonia monooxygenase gene (amoA. Our data indicate that amoA gene sequences are distributed in a similar manner as in Crenarchaeota, suggesting that archaeal nitrification processes in uranium mining-impacted locations are under the control of the same key factors controlling archaeal diversity.

  19. Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards.

    Science.gov (United States)

    Wang, Hua; Yang, Shao-hui; Yang, Jing-ping; Lv, Ya-min; Zhao, Xing; Pang, Ji-liang

    2014-11-01

    It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profiling. The abundances of total bacteria, total archaea, and selected functional genes (bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ) were determined by quantitative polymerase chain reaction (qPCR). The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was significantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of microbial communities and the abundance of genes involved in the nitrogen cycle.

  20. Functional interaction of yeast and human TATA-binding proteins with an archaeal RNA polymerase and promoter.

    OpenAIRE

    Wettach, J; Gohl, H P; Tschochner, H; Thomm, M

    1995-01-01

    TATA boxes are common structural features of eucaryal class II and archaeal promoters. In addition, a gene encoding a polypeptide with sequence similarity to eucaryal TATA-binding protein (TBP) has recently been detected in Archaea, but its relationship to the archaeal transcription factors A (aTFA) and B (aTFB) was unclear. Here, we demonstrate that yeast and human TBP can substitute for aTFB in a Methanococcus-derived archaeal cell-free transcription system. Template-commitment studies show...

  1. Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning.

    Science.gov (United States)

    Kraková, Lucia; Šoltys, Katarína; Budiš, Jaroslav; Grivalský, Tomáš; Ďuriš, František; Pangallo, Domenico; Szemes, Tomáš

    2016-09-01

    Different protocols based on Illumina high-throughput DNA sequencing and denaturing gradient gel electrophoresis (DGGE)-cloning were developed and applied for investigating hot spring related samples. The study was focused on three target genes: archaeal and bacterial 16S rRNA and mcrA of methanogenic microflora. Shorter read lengths of the currently most popular technology of sequencing by Illumina do not allow analysis of the complete 16S rRNA region, or of longer gene fragments, as was the case of Sanger sequencing. Here, we demonstrate that there is no need for special indexed or tailed primer sets dedicated to short variable regions of 16S rRNA since the presented approach allows the analysis of complete bacterial 16S rRNA amplicons (V1-V9) and longer archaeal 16S rRNA and mcrA sequences. Sample augmented with transposon is represented by a set of approximately 300 bp long fragments that can be easily sequenced by Illumina MiSeq. Furthermore, a low proportion of chimeric sequences was observed. DGGE-cloning based strategies were performed combining semi-nested PCR, DGGE and clone library construction. Comparing both investigation methods, a certain degree of complementarity was observed confirming that the DGGE-cloning approach is not obsolete. Novel protocols were created for several types of laboratories, utilizing the traditional DGGE technique or using the most modern Illumina sequencing. PMID:27338271

  2. Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors?

    Science.gov (United States)

    Siles, José A; Margesin, Rosa

    2016-07-01

    Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site. PMID:26961712

  3. Hadronic-Origin orphan TeV flare from the 1ES 1959+650

    CERN Document Server

    Sahu, Sarira; Sanabria, Juan Carlos

    2013-01-01

    The 1ES 1959+650 is a high-peaked BL Lacertae object. On 4th of June, 2002, it exhibited a strong TeV flare without any low energy counterpart, providing for the first time an example of an orphan flare from a blazar. Observation of this orphan flare is in striking disagreement with the predictions of the leptonic models thus challenging the conventional synchrotron self-Compton (SSC) interpretation of the TeV emission. Here we propose that, the low energy tail of the SSC photons in the blazar jet serve as the target for the Fermi-accelerated high energy protons of energy . 100 TeV, within the jet to produce the TeV photons through the decay of neutral pions from the delta resonance. Our model explains very nicely the observed TeV flux from this orphan flare and we also estimate the high energy neutrino flux from this flaring event.

  4. 77 FR 52744 - Food and Drug Administration/European Medicines Agency Orphan Product Designation and Grant Workshop

    Science.gov (United States)

    2012-08-30

    ... registration process with FDA, and are expected to bring information for at least one candidate orphan drug or... processes for putting together an application. In addition, participants of the HUD or orphan drug... conducted in partnership with the European Organisation for Rare Disease (EURODIS), Genetic Alliance,...

  5. Provision of Vocational Skills Education to Orphans: Lessons from Orphanage Centres in Dar es Salaam City, Tanzania

    Science.gov (United States)

    Meli, Benjamin Mbeba

    2015-01-01

    This paper utilises data from a study that investigated the efficacy of vocational skills training provided to orphans from three orphanages in Temeke District, Dar es Salaam. The three orphanage centres that were studied are Kurasini National Children Home, Saudia and Don Bosco Vocational Centre. The sample comprised of 45 orphans, an official…

  6. 78 FR 51732 - The Food and Drug Administration/European Medicines Agency Orphan Product Designation and Grant...

    Science.gov (United States)

    2013-08-21

    ... 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 Drug Administration's (FDA) Office of Orphan Products...

  7. 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.

  8. 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.

  9. 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. PMID:26508894

  10. Evolution and Dynamics of Orphan Penumbrae in the Solar Photosphere: Analysis from Multi-instrument Observations

    Science.gov (United States)

    Zuccarello, Francesca; Guglielmino, Salvo L.; Romano, Paolo

    2014-05-01

    We investigate the dynamics and magnetic properties of orphan penumbrae observed in the solar photosphere to understand the formation process of such structures. We observed two orphan penumbrae in active region NOAA 11089 during a coordinated observing campaign carried out in 2010 July, involving the Hinode/Solar Optical Telescope (SOT) and Dutch Open Telescope (DOT), benefiting also from continuous observations acquired by the SDO satellite. We follow their evolution during about three days. The two structures form in different ways: one seems to break off the penumbra of a nearby sunspot, the other is formed through the emergence of new flux. Then they fragment while evolving. The SDO Helioseismic and Magnetic Imager measurements indicate the presence of strong line-of-sight motions in the regions occupied by these orphan penumbrae, lasting for several hours and decreasing with time. This is confirmed by SOT spectro-polarimetric measurements of the Fe I 630.2 nm pair. The latter also show that Stokes parameters exhibit significant asymmetries in the orphan penumbral regions, typical of an uncombed filamentary structure. The orphan penumbrae lie above polarity inversion lines, where peculiar plasma motions take place with velocities larger than ±3 km s-1. The vector magnetic field in these regions is highly inclined, with the average magnetic field strength decreasing with time. The DOT observations in the Hα line and SDO Atmospheric Imaging Assembly measurements in the He II 30.4 nm line indicate that there is no counterpart for the orphan penumbrae at midchromospheric heights or above. Our findings suggest that in at least one of the features investigated the emerging flux may be trapped in the low atmospheric layers by the overlying pre-existing fields, forming these filamentary structures.

  11. 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.

  12. Evolution and dynamics of orphan penumbrae in the solar photosphere: Analysis from multi-instrument observations

    Energy Technology Data Exchange (ETDEWEB)

    Zuccarello, Francesca [Dipartimento di Fisica e Astronomia, Università di Catania, Via S. Sofia 78, I-95123 Catania (Italy); Guglielmino, Salvo L.; Romano, Paolo, E-mail: fzu@oact.inaf.it [INAF-Osservatorio Astrofisico di Catania, Via S. Sofia 78, I-95123 Catania (Italy)

    2014-05-20

    We investigate the dynamics and magnetic properties of orphan penumbrae observed in the solar photosphere to understand the formation process of such structures. We observed two orphan penumbrae in active region NOAA 11089 during a coordinated observing campaign carried out in 2010 July, involving the Hinode/Solar Optical Telescope (SOT) and Dutch Open Telescope (DOT), benefiting also from continuous observations acquired by the SDO satellite. We follow their evolution during about three days. The two structures form in different ways: one seems to break off the penumbra of a nearby sunspot, the other is formed through the emergence of new flux. Then they fragment while evolving. The SDO Helioseismic and Magnetic Imager measurements indicate the presence of strong line-of-sight motions in the regions occupied by these orphan penumbrae, lasting for several hours and decreasing with time. This is confirmed by SOT spectro-polarimetric measurements of the Fe I 630.2 nm pair. The latter also show that Stokes parameters exhibit significant asymmetries in the orphan penumbral regions, typical of an uncombed filamentary structure. The orphan penumbrae lie above polarity inversion lines, where peculiar plasma motions take place with velocities larger than ±3 km s{sup –1}. The vector magnetic field in these regions is highly inclined, with the average magnetic field strength decreasing with time. The DOT observations in the Hα line and SDO Atmospheric Imaging Assembly measurements in the He II 30.4 nm line indicate that there is no counterpart for the orphan penumbrae at midchromospheric heights or above. Our findings suggest that in at least one of the features investigated the emerging flux may be trapped in the low atmospheric layers by the overlying pre-existing fields, forming these filamentary structures.

  13. Petrology and tectonic significance of seamounts within transitional crust east of Orphan Knoll, offshore eastern Canada

    Science.gov (United States)

    Pe-Piper, Georgia; Meredyk, Shawn; Zhang, Yuanyuan; Piper, David J. W.; Edinger, Evan

    2013-12-01

    The Early Cretaceous separation of Newfoundland from Iberia-Ireland is a classic example of a magma-poor continental margin with hyperextension and with widespread minor magmatism resulting in seamounts. This study defines the distribution of seamounts east of Orphan Knoll, and documents and interprets the geochemical character of the one recovered lava sample. Video imagery of lava outcrops, and the sample, were obtained by ROV from Orphan seamount, one of a linear series of small seamounts overlying transitional thinned continental crust on the seaward side of Orphan Knoll. New multibeam bathymetry and legacy seismic data show several seamounts that extend irregularly along the fault-bound NE margin of Orphan Knoll. Whole rock geochemistry shows the sample to be highly alkaline basanite or possibly tephrite. Diopside-hedenbergite, kaersutite and K-feldspar phenocrysts were analyzed by electron microprobe and scanning electron microscope, and alteration minerals including kaolinite were identified by X-ray diffraction. The highly alkaline character of the basanite is similar only to Early Cretaceous volcanic and sub-volcanic rocks erupted through thick continental crust of the Mesoproterozoic Grenville Orogeny. The location of the linear set of seamounts is related to margin-parallel faults on the seaward side of Orphan Knoll that provided a pathway for magma, although ENE-trending lineaments in individual seamounts or seamount groups suggest the influence of oceanic fracture zones. A lower gradient crest to Orphan seamount above 2,200 m suggests subaerial erosion, consistent with the presence of kaolinite as an alteration product and the absence of lava pillows at and above this depth.

  14. Challenges faced by grandparents caring for AIDS orphans in Koster, North West Province of South Africa

    OpenAIRE

    Phetlhu, Deliwe; Watson, Mada

    2014-01-01

    Caring for orphans who have lost their parents due to AIDS, and some of whom are infected, is an enormous challenge. This immense responsibility often resides with the grandparents, who are in most cases sickly and not financially capable to undertake the task. The objectives of this study were to explore and describe challenges faced by such grandparents and their needs while caring for AIDS orphans in Koster, North West province, South Africa. Maslow’s theory of human needs was used as a th...

  15. 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. PMID:26613693

  16. Diagnostic Orphans for Alcohol Use Disorders in a Treatment-Seeking Psychiatric Sample

    OpenAIRE

    Ray, Lara A.; Miranda, Robert; Chelminski, Iwona; Young, Diane; ZIMMERMAN, MARK

    2008-01-01

    Individuals who endorse one or two of the DSM-IV criterion items for alcohol dependence but do not meet criteria for either alcohol abuse or dependence have been referred to in the literature as “diagnostic orphans.” The goal of the present study is to compare diagnostic orphans for alcohol use disorders (AUD) to patients with lifetime DSM-IV alcohol abuse, alcohol dependence, and those with no-AUD symptoms on a series of demographic, diagnostic, and clinical measures. Participants were treat...

  17. 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.

  18. 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.

  19. Barriers and Incentives to Orphan Care in a Time of AIDS and Economic Crisis: A Cross-Sectional Survey of Caregivers in Rural Zimbabwe

    Science.gov (United States)

    Howard, Brian H.; Phillips, Carl V.; Matinhure, Nelia; Goodman, Karen J.; McCurdy, Sheryl A; Johnson, Cary A.

    2007-01-01

    Background: Africa is in an orphan-care crisis. In Zimbabwe, where one-fourth of adults are HIV-positive and one-fifth of children are orphans, AIDS and economic decline are straining society's ability to care for orphans within their extended families. Lack of stable care is putting thousands of children at heightened risk of malnourishment,…

  20. The Vertical Distribution of Sediment Archaeal Community in the “Black Bloom” Disturbing Zhushan Bay of Lake Taihu

    Science.gov (United States)

    Fan, Xianfang; Xing, Peng

    2016-01-01

    Using the Illumina sequencing technology, we investigated the vertical distribution of archaeal community in the sediment of Zhushan Bay of Lake Taihu, where the black bloom frequently occurred in summer. Overall, the Miscellaneous Crenarchaeotal Group (MCG), Deep Sea Hydrothermal Vent Group 6 (DHVEG-6), and Methanobacterium dominated the archaeal community. However, we observed significant difference in composition of archaeal community among different depths of the sediment. DHVEG-6 dominated in the surface layer (0–3 cm) sediment. Methanobacterium was the dominating archaeal taxa in the L2 (3–6 cm) and L3 (6–10) sediment. MCG was most abundant in the L4 (10–15 cm) and L5 (15–20 cm) sediment. Besides, DHVEG-6 was significantly affected by the concentration of total phosphorus (TP). And loss on ignition (LOI) was an important environmental factor for Methanobacterium. As the typical archaeal taxa in the surface layer sediment, DHVEG-6 and Methanobacterium might be more adapted to abundant substrate supply from cyanobacterial blooms and take active part in the biomass transformation. We propose that DHVEG-6 and Methanobacterium could be the key archaeal taxa correlated with the “black bloom” formation in Zhushan Bay. PMID:26884723

  1. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.

    Science.gov (United States)

    Evans, Paul N; Parks, Donovan H; Chadwick, Grayson L; Robbins, Steven J; Orphan, Victoria J; Golding, Suzanne D; Tyson, Gene W

    2015-10-23

    Methanogenic and methanotrophic archaea play important roles in the global flux of methane. Culture-independent approaches are providing deeper insight into the diversity and evolution of methane-metabolizing microorganisms, but, until now, no compelling evidence has existed for methane metabolism in archaea outside the phylum Euryarchaeota. We performed metagenomic sequencing of a deep aquifer, recovering two near-complete genomes belonging to the archaeal phylum Bathyarchaeota (formerly known as the Miscellaneous Crenarchaeotal Group). These genomes contain divergent homologs of the genes necessary for methane metabolism, including those that encode the methyl-coenzyme M reductase (MCR) complex. Additional non-euryarchaeotal MCR-encoding genes identified in a range of environments suggest that unrecognized archaeal lineages may also contribute to global methane cycling. These findings indicate that methane metabolism arose before the last common ancestor of the Euryarchaeota and Bathyarchaeota. PMID:26494757

  2. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.

    Science.gov (United States)

    Evans, Paul N; Parks, Donovan H; Chadwick, Grayson L; Robbins, Steven J; Orphan, Victoria J; Golding, Suzanne D; Tyson, Gene W

    2015-10-23

    Methanogenic and methanotrophic archaea play important roles in the global flux of methane. Culture-independent approaches are providing deeper insight into the diversity and evolution of methane-metabolizing microorganisms, but, until now, no compelling evidence has existed for methane metabolism in archaea outside the phylum Euryarchaeota. We performed metagenomic sequencing of a deep aquifer, recovering two near-complete genomes belonging to the archaeal phylum Bathyarchaeota (formerly known as the Miscellaneous Crenarchaeotal Group). These genomes contain divergent homologs of the genes necessary for methane metabolism, including those that encode the methyl-coenzyme M reductase (MCR) complex. Additional non-euryarchaeotal MCR-encoding genes identified in a range of environments suggest that unrecognized archaeal lineages may also contribute to global methane cycling. These findings indicate that methane metabolism arose before the last common ancestor of the Euryarchaeota and Bathyarchaeota.

  3. A human CCT5 gene mutation causing distal neuropathy impairs hexadecamer assembly in an archaeal model.

    Science.gov (United States)

    Min, Wonki; Angileri, Francesca; Luo, Haibin; Lauria, Antonino; Shanmugasundaram, Maruda; Almerico, Anna Maria; Cappello, Francesco; de Macario, Everly Conway; Lednev, Igor K; Macario, Alberto J L; Robb, Frank T

    2014-10-27

    Chaperonins mediate protein folding in a cavity formed by multisubunit rings. The human CCT has eight non-identical subunits and the His147Arg mutation in one subunit, CCT5, causes neuropathy. Knowledge is scarce on the impact of this and other mutations upon the chaperone's structure and functions. To make progress, experimental models must be developed. We used an archaeal mutant homolog and demonstrated that the His147Arg mutant has impaired oligomeric assembly, ATPase activity, and defective protein homeostasis functions. These results establish for the first time that a human chaperonin gene defect can be reproduced and studied at the molecular level with an archaeal homolog. The major advantage of the system, consisting of rings with eight identical subunits, is that it amplifies the effects of a mutation as compared with the human counterpart, in which just one subunit per ring is defective. Therefore, the slight deficit of a non-lethal mutation can be detected and characterized.

  4. An archaeal tRNA-synthetase complex that enhances aminoacylation under extreme conditions

    DEFF Research Database (Denmark)

    Godinic-Mikulcic, Vlatka; Jaric, Jelena; Hausmann, Corinne D;

    2011-01-01

    Aminoacyl-tRNA synthetases (aaRSs) play an integral role in protein synthesis, functioning to attach the correct amino acid with its cognate tRNA molecule. AaRSs are known to associate into higher-order multi-aminoacyl-tRNA synthetase complexes (MSC) involved in archaeal and eukaryotic translation...... the catalytic efficiency of serine attachment to tRNA, but had no effect on the activity of MtArgRS. Further, the most pronounced improvements in the aminoacylation activity of MtSerRS induced by MtArgRS were observed under conditions of elevated temperature and osmolarity. These data indicate that......, although the precise biological role remains largely unknown. To gain further insights into archaeal MSCs, possible protein-protein interactions with the atypical Methanothermobacter thermautotrophicus seryl-tRNA synthetase (MtSerRS) were investigated. Yeast two-hybrid analysis revealed arginyl-tRNA...

  5. Expression, purification and crystallization of an archaeal-type phosphoenolpyruvate carboxylase

    International Nuclear Information System (INIS)

    The expression, purification, crystallization and preliminary diffraction analysis of an archaeal-type phosphoenolpyruvate carboxylase are described. Complete highly redundant X-ray data have been measured from a crystal diffracting to 3.13 Å resolution. An archaeal-type phosphoenolpyruvate carboxylase (PepcA) from Clostridium perfringens has been expressed in Escherichia coli in a soluble form with an amino-terminal His tag. The recombinant protein is enzymatically active and two crystal forms have been obtained. Complete diffraction data extending to 3.13 Å resolution have been measured from a crystal soaked in KAu(CN)2, using radiation at a wavelength just above the Au LIII edge. The asymmetric unit contains two tetramers of PepcA

  6. Quantification of bacterial and archaeal symbionts in high and low microbial abundance sponges using real-time PCR

    KAUST Repository

    Bayer, Kristina

    2014-07-09

    In spite of considerable insights into the microbial diversity of marine sponges, quantitative information on microbial abundances and community composition remains scarce. Here, we established qPCR assays for the specific quantification of four bacterial phyla of representative sponge symbionts as well as the kingdoms Eubacteria and Archaea. We could show that the 16S rRNA gene numbers of Archaea, Chloroflexi, and the candidate phylum Poribacteria were 4-6 orders of magnitude higher in high microbial abundance (HMA) than in low microbial abundance (LMA) sponges and that actinobacterial 16S rRNA gene numbers were 1-2 orders higher in HMA over LMA sponges, while those for Cyanobacteria were stable between HMA and LMA sponges. Fluorescence in situ hybridization of Aplysina aerophoba tissue sections confirmed the numerical dominance of Chloroflexi, which was followed by Poribacteria. Archaeal and actinobacterial cells were detected in much lower numbers. By use of fluorescence-activated cell sorting as a primer- and probe-independent approach, the dominance of Chloroflexi, Proteobacteria, and Poribacteria in A. aerophoba was confirmed. Our study provides new quantitative insights into the microbiology of sponges and contributes to a better understanding of the HMA/LMA dichotomy. The authors quantified sponge symbionts in eight sponge species from three different locations by real time PCR targetting 16S rRNA genes. Additionally, FISH was performed and diversity and abundance of singularized microbial symbionts from Aplysina aerophoba was determined for a comprehensive quantification work. © 2014 Federation of European Microbiological Societies.

  7. Fossilization and degradation of archaeal intact polar tetraether lipids in deeply buried marine sediments (Peru Margin)

    OpenAIRE

    Lengger, S. K.; Hopmans, E.C.; Sinninghe Damsté, J.S.; Schouten, S.

    2014-01-01

    Glycerol dibiphytanyl glycerol tetraether (GDGT) lipids are part of the cellular membranes of Thaumarchaeota, an archaeal phylum composed of aerobic ammonia oxidizers, and are used in the paleotemperature proxy TEX86. GDGTs in live cells possess polar head groups and are called intact polar lipids (IPL-GDGTs). Their transformation to core lipids (CL) by cleavage of the head group was assumed to proceed rapidly after cell death, but it has been suggested that some of these IPL-GDGTs can, just ...

  8. Eukaryotic and archaeal TBP and TFB/TF(II)B follow different promoter DNA bending pathways

    OpenAIRE

    Gietl, Andreas; Holzmeister, Phil; Blombach, Fabian; Schulz, Sarah; von Voithenberg, Lena Voith; Lamb, Don C; Werner, Finn; Tinnefeld, Philip; Grohmann, Dina

    2014-01-01

    During transcription initiation, the promoter DNA is recognized and bent by the basal transcription factor TATA-binding protein (TBP). Subsequent association of transcription factor B (TFB) with the TBP–DNA complex is followed by the recruitment of the ribonucleic acid polymerase resulting in the formation of the pre-initiation complex. TBP and TFB/TF(II)B are highly conserved in structure and function among the eukaryotic-archaeal domain but intriguingly have to operate under vastly differen...

  9. Events during Initiation of Archaeal Transcription: Open Complex Formation and DNA-Protein Interactions

    OpenAIRE

    Hausner, Winfried; Thomm, Michael

    2001-01-01

    Transcription in Archaea is initiated by association of a TATA box binding protein (TBP) with a TATA box. This interaction is stabilized by the binding of the transcription factor IIB (TFIIB) orthologue TFB. We show here that the RNA polymerase of the archaeon Methanococcus, in contrast to polymerase II, does not require hydrolysis of the β-γ bond of ATP for initiation of transcription and open complex formation on linearized DNA. Permanganate probing revealed that the archaeal open complex s...

  10. Archaeal Transcription: Function of an Alternative Transcription Factor B from Pyrococcus furiosus▿

    OpenAIRE

    Micorescu, Michael; Grünberg, Sebastian; Franke, Andreas; Cramer, Patrick; Thomm, Michael; Bartlett, Michael

    2007-01-01

    The genome of the hyperthermophile archaeon Pyrococcus furiosus encodes two transcription factor B (TFB) paralogs, one of which (TFB1) was previously characterized in transcription initiation. The second TFB (TFB2) is unusual in that it lacks recognizable homology to the archaeal TFB/eukaryotic TFIIB B-finger motif. TFB2 functions poorly in promoter-dependent transcription initiation, but photochemical cross-linking experiments indicated that the orientation and occupancy of transcription com...

  11. The σ enigma: Bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs

    OpenAIRE

    Burton, Samuel P; Burton, Zachary F.

    2014-01-01

    Structural comparisons of initiating RNA polymerase complexes and structure-based amino acid sequence alignments of general transcription initiation factors (eukaryotic TFIIB, archaeal TFB and bacterial σ factors) show that these proteins are homologs. TFIIB and TFB each have two-five-helix cyclin-like repeats (CLRs) that include a C-terminal helix-turn-helix (HTH) motif (CLR/HTH domains). Four homologous HTH motifs are present in bacterial σ factors that are relics of CLR/HTH domains. Sequen...

  12. Stratified active archaeal communities in the sediments of Jiulong River Estuary, China

    Directory of Open Access Journals (Sweden)

    Qianqian eLi

    2012-08-01

    Full Text Available Here the composition of total and active archaeal communities in a sediment core of Jiulong River estuary at Fujian Province, Southern China was reported. Profiles of CH4 and SO42- concentrations from the sediment core indicated the existence of a sulfate-methane transition zone (SMTZ in which sulfate reduction-coupled anaerobic oxidation of methane occurs. Accordingly, three sediment layers (16-18.5 cm, 71-73.5 cm, 161-163.5 cm from the 1.2 m sediment core were sectioned and named top, middle and bottom, respectively. Total DNA and RNA of each layer were extracted and used for clone libraries and sequence analysis of 16S rRNA genes, the reverse transcription (RT-PCR products of 16S rRNA and methyl CoM reductase alpha subunit (mcrA genes. Phylogenetic analysis indicated that archaeal communities of the three layers were dominated by the Miscellaneous Crenarchaeotal Group (MCG whose ecological functions were still unknown. The MCG could be further divided into seven subgroups, named MCG-A, B, C, D, E, F and G. MCG-A and MCG-G were the most active groups in the estuarine sediments. Known anaerobic methanotrophic archaea (ANMEs were only found as minor components in these estuarine archaeal communities. This study, together with the studies of deep subsurface sediments, would be a very good start point to target and compare the specific active archaeal groups and their roles in the dark, deep subsurface sediment environments.

  13. Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest

    OpenAIRE

    Rasche, Frank; Knapp, Daniela; Kaiser, Christina; Koranda, Marianne; Kitzler, Barbara; Zechmeister-Boltenstern, Sophie; Richter, Andreas; Sessitsch, Angela

    2010-01-01

    It was hypothesized that seasonality and resource availability altered through tree girdling were major determinants of the phylogenetic composition of the archaeal and bacterial community in a temperate beech forest soil. During a 2-year field experiment, involving girdling of beech trees to intercept the transfer of easily available carbon (C) from the canopy to roots, members of the dominant phylogenetic microbial phyla residing in top soils under girdled versus untreated control trees wer...

  14. Significance of archaeal nitrification in hypoxic waters of the Baltic Sea

    OpenAIRE

    Berg, Carlo; Vandieken, Verona; Thamdrup, Bo; Jürgens, Klaus

    2014-01-01

    Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread, and their abundance in many terrestrial and aquatic ecosystems suggests a prominent role in nitrification. AOA also occur in high numbers in oxygen-deficient marine environments, such as the pelagic redox gradients of the central Baltic Sea; however, data on archaeal nitrification rates are scarce and little is known about the factors, for example sulfide, that regulate nitrification in this system. In the present wo...

  15. Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards* #

    OpenAIRE

    Wang, Hua; Yang, Shao-hui; Yang, Jing-ping; Lv, Ya-min; Zhao, Xing; Pang, Ji-liang

    2014-01-01

    It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profili...

  16. Temporal Dynamics of Active Prokaryotic Nitrifiers and Archaeal Communities from River to Sea

    OpenAIRE

    Hugoni, Mylène; Agogué, Hélène; Taib, Najwa; Domaizon, Isabelle; Moné, Anne; Pierre E Galand; Bronner, Gisèle; Debroas, Didier; Mary, Isabelle

    2015-01-01

    International audience To test if different niches for potential nitrifiers exist in estuarine systems, we assessed by pyrosequencing the diversity of archaeal gene transcript markers for taxonomy (16S ribosomal RNA (rRNA)) during an entire year along a salinity gradient in surface waters of the Charente estuary (Atlantic coast, France). We further investigated the potential for estuarine prokaryotes to oxidize ammonia and hydrolyze urea by quantifying thaumarchaeal amoA and ureC and bacte...

  17. Abundance and Composition of Epiphytic Bacterial and Archaeal Ammonia Oxidizers of Marine Red and Brown Macroalgae

    OpenAIRE

    Trias, R. (Rosalía); García-Lledó A. (Arantzazu); Sánchez, N.; López-Jurado, J. L.; Hallin, S. (Sara); Bañeras, Ll. (Lluís)

    2012-01-01

    Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are important for nitrogen cycling in marine ecosystems. Little is known about the diversity and abundance of these organisms on the surface of marine macroalgae, despite the algae’s potential importance to create surfaces and local oxygen-rich environments supporting ammonia oxidation at depths with low dissolved oxygen levels. We determined the abundance and composition of the epiphytic bacterial and archaeal ammonia-oxidizing communities o...

  18. Global Occurrence of Archaeal amoA Genes in Terrestrial Hot Springs▿

    OpenAIRE

    Zhang, Chuanlun L.; Ye, Qi; Huang, Zhiyong; Li, Wenjun; Chen, Jinquan; Song, Zhaoqi; Zhao, Weidong; Bagwell, Christopher; Inskeep, William P.; Ross, Christian; Gao, Lei; Wiegel, Juergen; Romanek, Christopher S.; Shock, Everett L.; Hedlund, Brian P.

    2008-01-01

    Despite the ubiquity of ammonium in geothermal environments and the thermodynamic favorability of aerobic ammonia oxidation, thermophilic ammonia-oxidizing microorganisms belonging to the crenarchaeota kingdom have only recently been described. In this study, we analyzed microbial mats and surface sediments from 21 hot spring samples (pH 3.4 to 9.0; temperature, 41 to 86°C) from the United States, China, and Russia and obtained 846 putative archaeal ammonia monooxygenase large-subunit (amoA) ...

  19. Biogas production and methanogenic archaeal community in mesophilic and thermophilic anaerobic co-digestion processes.

    Science.gov (United States)

    Yu, D; Kurola, J M; Lähde, K; Kymäläinen, M; Sinkkonen, A; Romantschuk, M

    2014-10-01

    Over 258 Mt of solid waste are generated annually in Europe, a large fraction of which is biowaste. Sewage sludge is another major waste fraction. In this study, biowaste and sewage sludge were co-digested in an anaerobic digestion reactor (30% and 70% of total wet weight, respectively). The purpose was to investigate the biogas production and methanogenic archaeal community composition in the anaerobic digestion reactor under meso- (35-37 °C) and thermophilic (55-57 °C) processes and an increasing organic loading rate (OLR, 1-10 kg VS m(-3) d(-1)), and also to find a feasible compromise between waste treatment capacity and biogas production without causing process instability. In summary, more biogas was produced with all OLRs by the thermophilic process. Both processes showed a limited diversity of the methanogenic archaeal community which was dominated by Methanobacteriales and Methanosarcinales (e.g. Methanosarcina) in both meso- and thermophilic processes. Methanothermobacter was detected as an additional dominant genus in the thermophilic process. In addition to operating temperatures, the OLRs, the acetate concentration, and the presence of key substrates like propionate also affected the methanogenic archaeal community composition. A bacterial cell count 6.25 times higher than archaeal cell count was observed throughout the thermophilic process, while the cell count ratio varied between 0.2 and 8.5 in the mesophilic process. This suggests that the thermophilic process is more stable, but also that the relative abundance between bacteria and archaea can vary without seriously affecting biogas production.

  20. 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

  1. Making Good on a Promise: The Education of Civil War Orphans in Pennsylvania, 1863-1893

    Science.gov (United States)

    Bair, Sarah D.

    2011-01-01

    During and after the American Civil War, individual state governments, faced with numerous economic demands, struggled to meet the needs of soldiers and their families. Among other pressing questions, they had to decide what to do with the massive number of dependent children orphaned by the war. In order to protect children, it became more…

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

    NARCIS (Netherlands)

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

    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

  3. 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.

  4. 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)

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

    Science.gov (United States)

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

    2010-01-01

    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). PMID:20205893

  6. 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.

  7. 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.

  8. Bmal1 is a direct transcriptional target of the orphan nuclear receptor, NR2F1

    Science.gov (United States)

    Orphan nuclear receptor NR2F1 (also known as COUP-TFI, Chicken Ovalbumin Upstream Promoter Transcription Factor I) is a highly conserved member of the nuclear receptor superfamily. NR2F1 plays a critical role during embryonic development, particularly in the central and peripheral nervous systems a...

  9. Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor

    NARCIS (Netherlands)

    Alam, Mohammad Tauqeer; Takano, Eriko; Breitling, Rainer

    2011-01-01

    Background: Streptomyces coelicolor, a model organism of antibiotic producing bacteria, has one of the largest genomes of the bacterial kingdom, including 7825 predicted protein coding genes. A large number of these genes, nearly 34%, are functionally orphan (hypothetical proteins with unknown funct

  10. 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...

  11. I Am All about the Future World: Cambodian Children's Views on Their Status as Orphans

    Science.gov (United States)

    Emond, Ruth

    2009-01-01

    The dominant representation of children living in majority world orphanages highlights their vulnerability and fragility. However, little is known about their lived experiences of orphanage care and their perspectives on being regarded as "orphans". This article draws on data from a pilot project undertaken in one orphanage in Cambodia to…

  12. Doctoral "Orphans": Nurturing and Supporting the Success of Postgraduates Who Have Lost Their Supervisors

    Science.gov (United States)

    Wisker, Gina; Robinson, Gillian

    2013-01-01

    Much research into doctoral student-supervisor relations focuses on developing positive interactions. For many students, however, the research experience can be troubled by breakdowns in communication and even the loss of the supervisor(s), turning the student into a doctoral "orphan" and impacting on their academic identity and ability and…

  13. Orphan Trains: Teaching about an Early Twentieth-Century Social Experiment

    Science.gov (United States)

    Chiodo, John J.; Meliza, Evette

    2014-01-01

    Between 1854 and 1930, over 200,000 children left New York City, as well as other major east coast cities, bound for families in rural areas. They traveled to towns in New England, the Midwest, the South, and even as far west as Texas, California, Oregon, and Washington. These orphans were the children of immigrant families who were pouring into…

  14. 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…

  15. Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor.

    NARCIS (Netherlands)

    Alam, M.T.; Takano, E.; Breitling, R.

    2011-01-01

    ABSTRACT: BACKGROUND: Streptomyces coelicolor, a model organism of antibiotic producing bacteria, has one of the largest genomes of the bacterial kingdom, including 7825 predicted protein coding genes. A large number of these genes, nearly 34%, are functionally orphan (hypothetical proteins with unk

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

    Science.gov (United States)

    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...

  17. The Lived Experiences of Orphaned Learners in South Africa: Implications for the Provision of Quality Education

    Science.gov (United States)

    Motha, Kholofelo Charlotte; Frempong, George

    2014-01-01

    Learners living in impoverished communities and subjected to the kind of disadvantage in operation in their home environment are at risk of receiving education of an inferior quality. The situation is worse for orphans, especially those residing in poor communities in that they bring to school peculiar attributes which poses challenges for the…

  18. 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…

  19. Instruments of Science and Citizenship: Science Education for Dutch Orphans During the Late Eighteenth Century.

    NARCIS (Netherlands)

    Roberts, L.L.

    2012-01-01

    One of the two most extensive instrument collections in the Netherlands during the second half of the eighteenth century—rivaling the much better known collection at the University of Leiden—belonged to an orphanage in The Hague that was specially established to mold hand-picked orphans into product

  20. Reconsidering the orphan problem: the emergence of male caregivers in Lesotho.

    Science.gov (United States)

    Block, Ellen

    2016-01-01

    Care for AIDS orphans in southern Africa is frequently characterized as a "crisis", where kin-based networks of care are thought to be on the edge of collapse. Yet these care networks, though strained by AIDS, are still the primary mechanisms for orphan care, in large part because of the essential role grandmothers play in responding to the needs of orphans. Ongoing demographic shifts as a result of HIV/AIDS and an increasingly feminized labor market continue to disrupt and alter networks of care for orphans and vulnerable children. This paper examines the emergence of a small but growing number of male caregivers who are responding to the needs of the extended family. While these men are still few in number, the strength of gendered ideologies of female care means that this group of men is socially, if not statistically significant. Men continue to be considered caregivers of last resort, but their care will close a small but growing gap that threatens to undermine kin-based networks of care in Lesotho and across the region. The adaptation of gender roles reinforces the strength and resilience of kinship networks even when working against deeply entrenched ideas about gendered division of domestic labor. PMID:27297796

  1. An Initial Exploration of the Therapeutic Impact of Music on Genocide Orphans in Rwanda

    Science.gov (United States)

    d'Ardenne, Patricia; Kiyendeye, Moses

    2015-01-01

    The 1994 Rwandan Genocide murdered over a million and brought on incalculable distress to survivors. An non-governmental organisation, "Network for Africa," has a music programme to rehabilitate orphans in Kigali, now entering adulthood. This naturalistic study investigated whether music had transformational meaning for participants.…

  2. Instruments of Science and Citizenship: Science Education for Dutch Orphans during the Late Eighteenth Century

    Science.gov (United States)

    Roberts, Lissa L.

    2012-01-01

    One of the two most extensive instrument collections in the Netherlands during the second half of the eighteenth century--rivaling the much better known collection at the University of Leiden--belonged to an orphanage in The Hague that was specially established to mold hand-picked orphans into productive citizens. (The other was housed at the…

  3. South African AIDS Orphans: Examining Assumptions around Vulnerability from the Perspective of Rural Children and Youth

    Science.gov (United States)

    Henderson, Patricia C.

    2006-01-01

    The article examines assumptions circulating in development or interventionist discourse concerning the vulnerabilities of AIDS orphans in South Africa. Ongoing ethnographic research, begun in March 2003, with 31 rural children and youth between the ages of 14 and 22, in Magangangozi, KwaZulu-Natal, points to the ways in which global terms may…

  4. A generalizable pre-clinical research approach for orphan disease therapy

    Directory of Open Access Journals (Sweden)

    Beaulieu Chandree L

    2012-06-01

    Full Text Available Abstract With the advent of next-generation DNA sequencing, the pace of inherited orphan disease gene identification has increased dramatically, a situation that will continue for at least the next several years. At present, the numbers of such identified disease genes significantly outstrips the number of laboratories available to investigate a given disorder, an asymmetry that will only increase over time. The hope for any genetic disorder is, where possible and in addition to accurate diagnostic test formulation, the development of therapeutic approaches. To this end, we propose here the development of a strategic toolbox and preclinical research pathway for inherited orphan disease. Taking much of what has been learned from rare genetic disease research over the past two decades, we propose generalizable methods utilizing transcriptomic, system-wide chemical biology datasets combined with chemical informatics and, where possible, repurposing of FDA approved drugs for pre-clinical orphan disease therapies. It is hoped that this approach may be of utility for the broader orphan disease research community and provide funding organizations and patient advocacy groups with suggestions for the optimal path forward. In addition to enabling academic pre-clinical research, strategies such as this may also aid in seeding startup companies, as well as further engaging the pharmaceutical industry in the treatment of rare genetic disease.

  5. 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.

  6. Teaching Medication Compliance to Psychiatric Residents: Placing an Orphan Topic into a Training Curriculum

    Science.gov (United States)

    Weiden, Peter J.; Rao, Nyapati

    2005-01-01

    OBJECTIVE: Medication compliance is an orphan topic. Training in the understanding and management of noncompliance does not neatly fall within the domain of psychopharmacology, nor does it clearly fit into other core curricula areas, such as clinical interviewing or psychotherapy training. The objective of this article is to increase awareness…

  7. 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…

  8. Psychological Distress amongst AIDS-Orphaned Children in Urban South Africa

    Science.gov (United States)

    Cluver, Lucie; Gardner, Frances; Operario, Don

    2007-01-01

    Background: South Africa is predicted to have 2.3 million children orphaned by Acquired Immune Deficiency Syndrome (AIDS) by 2020 (Actuarial Society of South Africa, 2005). There is little knowledge about impacts of AIDS-related bereavement on children, to aid planning of services. This study aimed to investigate psychological consequences of AIDS…

  9. Bacterial and archaeal diversities in Yunnan and Tibetan hot springs, China.

    Science.gov (United States)

    Song, Zhao-Qi; Wang, Feng-Ping; Zhi, Xiao-Yang; Chen, Jin-Quan; Zhou, En-Min; Liang, Feng; Xiao, Xiang; Tang, Shu-Kun; Jiang, Hong-Chen; Zhang, Chuanlun L; Dong, Hailiang; Li, Wen-Jun

    2013-04-01

    Thousands of hot springs are located in the north-eastern part of the Yunnan-Tibet geothermal zone, which is one of the most active geothermal areas in the world. However, a comprehensive and detailed understanding of microbial diversity in these hot springs is still lacking. In this study, bacterial and archaeal diversities were investigated in 16 hot springs (pH 3.2-8.6; temperature 47-96°C) in Yunnan Province and Tibet, China by using a barcoded 16S rRNA gene-pyrosequencing approach. Aquificae, Proteobacteria, Firmicutes, Deinococcus-Thermus and Bacteroidetes comprised the large portion of the bacterial communities in acidic hot springs. Non-acidic hot springs harboured more and variable bacterial phyla than acidic springs. Desulfurococcales and unclassified Crenarchaeota were the dominated groups in archaeal populations from most of the non-acidic hot springs; whereas, the archaeal community structure in acidic hot springs was simpler and characterized by Sulfolobales and Thermoplasmata. The phylogenetic analyses showed that Aquificae and Crenarchaeota were predominant in the investigated springs and possessed many phylogenetic lineages that have never been detected in other hot springs in the world. Thus findings from this study significantly improve our understanding of microbial diversity in terrestrial hot springs.

  10. Archaeal community structures in the solfataric acidic hot springs with different temperatures and elemental compositions.

    Science.gov (United States)

    Satoh, Tomoko; Watanabe, Keiko; Yamamoto, Hideo; Yamamoto, Shuichi; Kurosawa, Norio

    2013-01-01

    Archaeal 16S rRNA gene compositions and environmental factors of four distinct solfataric acidic hot springs in Kirishima, Japan were compared. The four ponds were selected by differences of temperature and total dissolved elemental concentration as follows: (1) Pond-A: 93°C and 1679 mg L(-1), (2) Pond-B: 66°C and 2248 mg L(-1), (3) Pond-C: 88°C and 198 mg L(-1), and (4) Pond-D: 67°C and 340 mg L(-1). In total, 431 clones of 16S rRNA gene were classified into 26 phylotypes. In Pond-B, the archaeal diversity was the highest among the four, and the members of the order Sulfolobales were dominant. The Pond-D also showed relatively high diversity, and the most frequent group was uncultured thermoacidic spring clone group. In contrast to Pond-B and Pond-D, much less diverse archaeal clones were detected in Pond-A and Pond-C showing higher temperatures. However, dominant groups in these ponds were also different from each other. The members of the order Sulfolobales shared 89% of total clones in Pond-A, and the uncultured crenarchaeal groups shared 99% of total Pond-C clones. Therefore, species compositions and biodiversity were clearly different among the ponds showing different temperatures and dissolved elemental concentrations.

  11. Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm.

    Science.gov (United States)

    Tupinambá, Daiva Domenech; Cantão, Maurício Egídio; Costa, Ohana Yonara Assis; Bergmann, Jessica Carvalho; Kruger, Ricardo Henrique; Kyaw, Cynthia Maria; Barreto, Cristine Chaves; Quirino, Betania Ferraz

    2016-01-01

    This study compared soil archaeal communities of the Amazon forest with that of an adjacent area under oil palm cultivation by 16S ribosomal RNA gene pyrosequencing. Species richness and diversity were greater in native forest soil than in the oil palm-cultivated area, and 130 OTUs (13.7%) were shared between these areas. Among the classified sequences, Thaumarchaeota were predominant in the native forest, whereas Euryarchaeota were predominant in the oil palm-cultivated area. Archaeal species diversity was 1.7 times higher in the native forest soil, according to the Simpson diversity index, and the Chao1 index showed that richness was five times higher in the native forest soil. A phylogenetic tree of unclassified Thaumarchaeota sequences showed that most of the OTUs belong to Miscellaneous Crenarchaeotic Group. Several archaeal genera involved in nutrient cycling (e.g., methanogens and ammonia oxidizers) were identified in both areas, but significant differences were found in the relative abundances of Candidatus Nitrososphaera and unclassified Soil Crenarchaeotic Group (prevalent in the native forest) and Candidatus Nitrosotalea and unclassified Terrestrial Group (prevalent in the oil palm-cultivated area). More studies are needed to culture some of these Archaea in the laboratory so that their metabolism and physiology can be studied.

  12. Assessment of bacterial and archaeal community structure in Swine wastewater treatment processes.

    Science.gov (United States)

    Da Silva, Marcio Luis Busi; Cantão, Mauricio Egídio; Mezzari, Melissa Paola; Ma, Jie; Nossa, Carlos Wolfgang

    2015-07-01

    Microbial communities from two field-scale swine wastewater treatment plants (WWTPs) were assessed by pyrosequencing analyses of bacterial and archaeal 16S ribosomal DNA (rDNA) fragments. Effluent samples from secondary (anaerobic covered lagoons and upflow anaerobic sludge blanket [UASB]) and tertiary treatment systems (open-pond natural attenuation lagoon and air-sparged nitrification-denitrification tank followed by alkaline phosphorus precipitation process) were analyzed. A total of 56,807 and 48,859 high-quality reads were obtained from bacterial and archaeal libraries, respectively. Dominant bacterial communities were associated with the phylum Firmicutes, Bacteroidetes, Proteobacteria, or Actinobacteria. Bacteria and archaea diversity were highest in UASB effluent sample. Escherichia, Lactobacillus, Bacteroides, and/or Prevotella were used as indicators of putative pathogen reduction throughout the WWTPs. Satisfactory pathogen reduction was observed after the open-pond natural attenuation lagoon but not after the air-sparged nitrification/denitrification followed by alkaline phosphorus precipitation treatment processes. Among the archaeal communities, 80% of the reads was related to hydrogeno-trophic methanogens Methanospirillum. Enrichment of hydrogenotrophic methanogens detected in effluent samples from the anaerobic covered lagoons and UASB suggested that CO2 reduction with H2 was the dominant methanogenic pathway in these systems. Overall, the results served to improve our current understanding of major microbial communities' changes downgradient from the pen and throughout swine WWTP as a result of different treatment processes. PMID:25432577

  13. Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm

    Science.gov (United States)

    Tupinambá, Daiva Domenech; Cantão, Maurício Egídio; Costa, Ohana Yonara Assis; Bergmann, Jessica Carvalho; Kruger, Ricardo Henrique; Kyaw, Cynthia Maria; Barreto, Cristine Chaves; Quirino, Betania Ferraz

    2016-01-01

    This study compared soil archaeal communities of the Amazon forest with that of an adjacent area under oil palm cultivation by 16S ribosomal RNA gene pyrosequencing. Species richness and diversity were greater in native forest soil than in the oil palm-cultivated area, and 130 OTUs (13.7%) were shared between these areas. Among the classified sequences, Thaumarchaeota were predominant in the native forest, whereas Euryarchaeota were predominant in the oil palm-cultivated area. Archaeal species diversity was 1.7 times higher in the native forest soil, according to the Simpson diversity index, and the Chao1 index showed that richness was five times higher in the native forest soil. A phylogenetic tree of unclassified Thaumarchaeota sequences showed that most of the OTUs belong to Miscellaneous Crenarchaeotic Group. Several archaeal genera involved in nutrient cycling (e.g., methanogens and ammonia oxidizers) were identified in both areas, but significant differences were found in the relative abundances of Candidatus Nitrososphaera and unclassified Soil Crenarchaeotic Group (prevalent in the native forest) and Candidatus Nitrosotalea and unclassified Terrestrial Group (prevalent in the oil palm-cultivated area). More studies are needed to culture some of these Archaea in the laboratory so that their metabolism and physiology can be studied. PMID:27006640

  14. Temporal Dynamics of Active Prokaryotic Nitrifiers and Archaeal Communities from River to Sea.

    Science.gov (United States)

    Hugoni, Mylène; Agogué, Hélène; Taib, Najwa; Domaizon, Isabelle; Moné, Anne; Galand, Pierre E; Bronner, Gisèle; Debroas, Didier; Mary, Isabelle

    2015-08-01

    To test if different niches for potential nitrifiers exist in estuarine systems, we assessed by pyrosequencing the diversity of archaeal gene transcript markers for taxonomy (16S ribosomal RNA (rRNA)) during an entire year along a salinity gradient in surface waters of the Charente estuary (Atlantic coast, France). We further investigated the potential for estuarine prokaryotes to oxidize ammonia and hydrolyze urea by quantifying thaumarchaeal amoA and ureC and bacterial amoA transcripts. Our results showed a succession of different nitrifiers from river to sea with bacterial amoA transcripts dominating in the freshwater station while archaeal transcripts were predominant in the marine station. The 16S rRNA sequence analysis revealed that Thaumarchaeota marine group I (MGI) were the most abundant overall but other archaeal groups like Methanosaeta were also potentially active in winter (December-March) and Euryarchaeota marine group II (MGII) were dominant in seawater in summer (April-August). Each station also contained different Thaumarchaeota MGI phylogenetic clusters, and the clusters' microdiversity was associated to specific environmental conditions suggesting the presence of ecotypes adapted to distinct ecological niches. The amoA and ureC transcript dynamics further indicated that some of the Thaumarchaeota MGI subclusters were involved in ammonia oxidation through the hydrolysis of urea. Our findings show that ammonia-oxidizing Archaea and Bacteria were adapted to contrasted conditions and that the Thaumarchaeota MGI diversity probably corresponds to distinct metabolisms or life strategies. PMID:25851445

  15. Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm

    Directory of Open Access Journals (Sweden)

    Daiva Domenech Tupinambá

    2016-01-01

    Full Text Available This study compared soil archaeal communities of the Amazon forest with that of an adjacent area under oil palm cultivation by 16S ribosomal RNA gene pyrosequencing. Species richness and diversity were greater in native forest soil than in the oil palm-cultivated area, and 130 OTUs (13.7% were shared between these areas. Among the classified sequences, Thaumarchaeota were predominant in the native forest, whereas Euryarchaeota were predominant in the oil palm-cultivated area. Archaeal species diversity was 1.7 times higher in the native forest soil, according to the Simpson diversity index, and the Chao1 index showed that richness was five times higher in the native forest soil. A phylogenetic tree of unclassified Thaumarchaeota sequences showed that most of the OTUs belong to Miscellaneous Crenarchaeotic Group. Several archaeal genera involved in nutrient cycling (e.g., methanogens and ammonia oxidizers were identified in both areas, but significant differences were found in the relative abundances of Candidatus Nitrososphaera and unclassified Soil Crenarchaeotic Group (prevalent in the native forest and Candidatus Nitrosotalea and unclassified Terrestrial Group (prevalent in the oil palm-cultivated area. More studies are needed to culture some of these Archaea in the laboratory so that their metabolism and physiology can be studied.

  16. 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

  17. 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.

  18. Archaeal communities of Arctic methane-containing permafrost.

    Science.gov (United States)

    Shcherbakova, Victoria; Yoshimura, Yoshitaka; Ryzhmanova, Yana; Taguchi, Yukihiro; Segawa, Takahiro; Oshurkova, Victoria; Rivkina, Elizaveta

    2016-10-01

    In the present study, we used culture-independent methods to investigate the diversity of methanogenic archaea and their distribution in five permafrost samples collected from a borehole in the Kolyma River Lowland (north-east of Russia). Total DNA was extracted from methane-containing permafrost samples of different age and amplified by PCR. The resulting DNA fragments were cloned. Phylogenetic analysis of the sequences showed the presence of archaea in all studied samples; 60%-95% of sequences belonged to the Euryarchaeota. Methanogenic archaea were novel representatives of Methanosarcinales, Methanomicrobiales, Methanobacteriales and Methanocellales orders. Bathyarchaeota (Miscellaneous Crenarchaeota Group) representatives were found among nonmethanogenic archaea in all the samples studied. The Thaumarchaeota representatives were not found in the upper sample, whereas Woesearchaeota (formerly DHVEG-6) were found in the three deepest samples. Unexpectedly, the greatest diversity of archaea was observed at a depth of 22.3 m, probably due to the availability of the labile organic carbon and/or due to the migration of the microbial cells during the freezing front towards the bottom. PMID:27312964

  19. Stigma, marginalization and psychosocial well-being of orphans in Rwanda: exploring the mediation role of social support.

    Science.gov (United States)

    Caserta, Tehetna Alemu; Pirttilä-Backman, Anna-Maija; Punamäki, Raija-Leena

    2016-01-01

    Stigma and marginalization are one of the major challenges orphans face in their daily lives, particularly in developing countries, but little is known about their impacts on mental health. This study examines how orphan-related characteristics, stigma and marginalization are associated with psychosocial well-being. It further analyses the role of social support in mediating between stigma and marginalization and mental health, indicated by emotional well-being and mental distress. The participants in this study were 430 Rwandan orphans who were 10-25 years of age, and of whom 179 were females and 251 were males. Results showed that high levels of stigma and marginalization were associated with a lower level of emotional well-being and higher levels of mental distress. A mediation analysis indicated that low level of social support due to stigma and marginalization contributed significantly to low level of emotional well-being. Once stigma, marginalization and social support were fully accounted for, AIDS orphans exhibited higher levels of mental distress than those who were orphaned by genocide or other causes. Future interventions designed to reduce stigma and marginalization for orphans and actions that facilitate social support can significantly improve emotional well-being and reduce mental distress among orphans. PMID:26883484

  20. Constitutive Activity among Orphan Class-A G Protein Coupled Receptors.

    Directory of Open Access Journals (Sweden)

    Adam L Martin

    Full Text Available The purpose of this study was to evaluate the extent of constitutive activity among orphan class-A G protein coupled receptors within the cAMP signaling pathway. Constitutive signaling was revealed by changes in gene expression under control of the cAMP response element. Gene expression was measured in Chinese hamster ovary cells transiently co-transfected with plasmids containing a luciferase reporter and orphan receptor. Criteria adopted for defining constitutive activation were: 1 200% elevation over baseline reporter gene expression; 2 40% inhibition of baseline expression; and 3 40% inhibition of expression stimulated by 3 μM forskolin. Five patterns of activity were noted: 1 inhibition under both baseline and forskolin stimulated expression (GPR15, GPR17, GPR18, GPR20, GPR25, GPR27, GPR31, GPR32, GPR45, GPR57, GPR68, GPR83, GPR84, GPR132, GPR150, GPR176; 2 no effect on baseline expression, but inhibition of forskolin stimulated expression (GPR4, GPR26, GPR61, GPR62, GPR78, GPR101, GPR119; 3 elevation of baseline signaling coupled with inhibition of forskolin stimulated expression (GPR6, GPR12; 4 elevation of baseline signaling without inhibition of forskolin stimulated expression (GPR3, GPR21, GPR52, GPR65; and 5 no effect on expression (GPR1, GPR19, GPR22, GPR34, GPR35, GPR39, GPR63, GPR82, GPR85, GPR87. Constitutive activity was observed in 75% of the orphan class-A receptors examined (30 of 40. This constitutive signaling cannot be explained by simple overexpression of the receptor. Inhibition of cAMP mediated expression was far more common (65% than stimulation of expression (15%. Orphan receptors that were closely related based on amino acid homology tended to have similar effects on gene expression. These results suggest that identification of inverse agonists may be a fruitful approach for categorizing these orphan receptors and targeting them for pharmacological intervention.

  1. Constitutive Activity among Orphan Class-A G Protein Coupled Receptors.

    Science.gov (United States)

    Martin, Adam L; Steurer, Michael A; Aronstam, Robert S

    2015-01-01

    The purpose of this study was to evaluate the extent of constitutive activity among orphan class-A G protein coupled receptors within the cAMP signaling pathway. Constitutive signaling was revealed by changes in gene expression under control of the cAMP response element. Gene expression was measured in Chinese hamster ovary cells transiently co-transfected with plasmids containing a luciferase reporter and orphan receptor. Criteria adopted for defining constitutive activation were: 1) 200% elevation over baseline reporter gene expression; 2) 40% inhibition of baseline expression; and 3) 40% inhibition of expression stimulated by 3 μM forskolin. Five patterns of activity were noted: 1) inhibition under both baseline and forskolin stimulated expression (GPR15, GPR17, GPR18, GPR20, GPR25, GPR27, GPR31, GPR32, GPR45, GPR57, GPR68, GPR83, GPR84, GPR132, GPR150, GPR176); 2) no effect on baseline expression, but inhibition of forskolin stimulated expression (GPR4, GPR26, GPR61, GPR62, GPR78, GPR101, GPR119); 3) elevation of baseline signaling coupled with inhibition of forskolin stimulated expression (GPR6, GPR12); 4) elevation of baseline signaling without inhibition of forskolin stimulated expression (GPR3, GPR21, GPR52, GPR65); and 5) no effect on expression (GPR1, GPR19, GPR22, GPR34, GPR35, GPR39, GPR63, GPR82, GPR85, GPR87). Constitutive activity was observed in 75% of the orphan class-A receptors examined (30 of 40). This constitutive signaling cannot be explained by simple overexpression of the receptor. Inhibition of cAMP mediated expression was far more common (65%) than stimulation of expression (15%). Orphan receptors that were closely related based on amino acid homology tended to have similar effects on gene expression. These results suggest that identification of inverse agonists may be a fruitful approach for categorizing these orphan receptors and targeting them for pharmacological intervention. PMID:26384023

  2. The disposal of orphan wastes using the greater confinement disposal concept

    International Nuclear Information System (INIS)

    In the United States, radioactive wastes are conventionally classified as high-level wastes, transuranic wastes, or low-level wastes. Each of these types of wastes, by law, has a ''home'' for their final disposal; i.e., high-level wastes are destined for disposal at the proposed repository at Yucca Mountain, transuranic waste for the proposed Waste Isolation Pilot Plant, and low-level waste for shallow-land disposal sites. However, there are some radioactive wastes within the United States Department of Energy (DOE) complex that do not meet the criteria established for disposal of either high-level waste, transuranic waste, or low-level waste. The former are called ''special-case'' or ''orphan'' wastes. This paper describes an ongoing project sponsored by the DOE's Nevada Operations Office for the disposal of orphan wastes at the Radioactive Waste Management Site at Area 5 of the Nevada Test Site using the greater confinement disposal (GCD) concept. The objectives of the GCD project are to evaluate the safety of the site for disposal of orphan wastes by assessing compliance with pertinent regulations through performance assessment, and to examine the feasibility of this disposal concept as a cost-effective, safe alternative for management of orphan wastes within the DOE complex. Decisions on the use of GCD or other alternate disposal concepts for orphan wastes be expected to be addressed in a Programmatic Environmental Impact Statement being prepared by DOE. The ultimate decision to use GCD will require a Record of Decision through the National Environmental Policy Act (NEPA) process. 20 refs., 3 figs., 2 tabs

  3. Hunting the Parent of the Orphan Stream. II. The First High-resolution Spectroscopic Study

    Science.gov (United States)

    Casey, Andrew R.; Keller, Stefan C.; Da Costa, Gary; Frebel, Anna; Maunder, Elizabeth

    2014-03-01

    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. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.

  4. Characterization of an archaeal two-component system that regulates methanogenesis in Methanosaeta harundinacea.

    Directory of Open Access Journals (Sweden)

    Jie Li

    Full Text Available Two-component signal transduction systems (TCSs are a major mechanism used by bacteria in response to environmental changes. Although many sequenced archaeal genomes encode TCSs, they remain poorly understood. Previously, we reported that a methanogenic archaeon, Methanosaeta harundinacea, encodes FilI, which synthesizes carboxyl-acyl homoserine lactones, to regulate transitions of cellular morphology and carbon metabolic fluxes. Here, we report that filI, the cotranscribed filR2, and the adjacent filR1 constitute an archaeal TCS. FilI possesses a cytoplasmic kinase domain (histidine kinase A and histidine kinase-like ATPase and its cognate response regulator. FilR1 carries a receiver (REC domain coupled with an ArsR-related domain with potential DNA-binding ability, while FilR2 carries only a REC domain. In a phosphorelay assay, FilI was autophosphorylated and specifically transferred the phosphoryl group to FilR1 and FilR2, confirming that the three formed a cognate TCS. Through chromatin immunoprecipitation-quantitative polymerase chain reaction (ChIP-qPCR using an anti-FilR1 antibody, FilR1 was shown to form in vivo associations with its own promoter and the promoter of the filI-filR2 operon, demonstrating a regulatory pattern common among TCSs. ChIP-qPCR also detected FilR1 associations with key genes involved in acetoclastic methanogenesis, acs4 and acs1. Electrophoretic mobility shift assays confirmed the in vitro tight binding of FilR1 to its own promoter and those of filI-filR2, acs4, and mtrABC. This also proves the DNA-binding ability of the ArsR-related domain, which is found primarily in Archaea. The archaeal promoters of acs4, filI, acs1, and mtrABC also initiated FilR1-modulated expression in an Escherichia coli lux reporter system, suggesting that FilR1 can up-regulate both archaeal and bacterial transcription. In conclusion, this work identifies an archaeal FilI/FilRs TCS that regulates the methanogenesis of M. harundinacea.

  5. Safety and Security of Radioactive Sealed and Disused/Orphan Sources in Ukraine - German Contribution - 13359

    International Nuclear Information System (INIS)

    Within the scope of 'Nuclear Security of Radioactive Sources', the German government implemented the modernization of Ukrainian State Production Company's transport and storage facility for radioactive sources (TSF) in Kiev. The overall management of optimizing the physical protection of the storage facility (including the construction of a hot cell for handling the radioactive sources) is currently carried out by the German Federal Foreign Office (AA). AA jointly have assigned Gesellschaft fuer Anlagen- und Reaktorsicherheit (GRS) mbH, Germany's leading expert institution in the area of nuclear safety and waste management, to implement the project and to ensure transparency by financial and technical monitoring. Sealed radioactive sources are widely used in industry, medicine and research. Their life cycle starts with the production and finally ends with the interim/long-term storage of the disused sources. In Ukraine, IZOTOP is responsible for all radioactive sources throughout their life cycle. IZOTOP's transport and storage facility (TSF) is the only Ukrainian storage facility for factory-fresh radioactive sources up to an activity of about 1 million Ci (3.7 1016 Bq). The TSF is specially designed for the storage and handling of radioactive sources. Storage began in 1968, and is licensed by the Ukrainian state authorities. Beside the outdated state of TSF's physical protection and the vulnerability of the facility linked with it, the lack of a hot cell for handling and repacking radioactive sources on the site itself represents an additional potential hazard. The project, financed by the German Federal Foreign Office, aims to significantly improve the security of radioactive sources during their storage and handling at the TSF site. Main tasks of the project are a) the modernization of the physical protection of the TSF itself in order to prevent any unauthorized access to radioactive sources as well as b) the construction of a hot cell to reduce the number of

  6. Orphan drugs for sickle vaso-occlusion: dawn of a new era of targeted treatment

    Directory of Open Access Journals (Sweden)

    Dampier C

    2015-11-01

    Full Text Available Carlton Dampier1,2 1Emory University School of Medicine, Emory University, 2AFLAC Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA Abstract: While an orphan disease in the USA, sickle cell disease (SCD, a group of genetic disorders of hemoglobin structure and function, is a major public health problem in much of the rest of the world, particularly sub-Saharan Africa. The pathophysiology of SCD stems from the formation of sickle hemoglobin polymers that deform the erythrocyte into a characteristic sickle shape, the rapidity of which is regulated by its intracellular hemoglobin concentration. Subsequent vaso-occlusion is dependent on adhesion of sickled erythrocytes, and perhaps other cellular elements, including leucocytes and platelets, to abnormal vascular endothelium using a number of receptor–ligand pairs. This propensity for vaso-occlusion may be enhanced by altered vascular tone from excessive amounts of vaso-constrictive factors or diminished amounts of vasodilatory factors. Acute pain is the hallmark symptom caused by sickle polymer formation and subsequent vaso-occlusion, and is represented in the endpoints of most previous and current clinical trial designs. Numerous failures of prior investigational agents have frustrated clinicians and patients alike. Hydroxyurea is currently the only US Food and Drug Administration-approved drug for SCD and reduces the frequency of vaso-occlusive complications in many individuals. A considerable therapeutic need remains as hydroxyurea usage is currently not approved for all types of SCD, is not always clinically effective, and requires frequent monitoring. Recent improvements in our understanding of SCD pathophysiology have generated many new therapeutic targets and associated investigational agents. For example, a number of more specific fetal hemoglobin inducers and several therapies to reduce sickle polymer formation are being tested in preclinical and early

  7. Inventory of orphan oil and natural gas wells in the Dover and Gautreau Village areas of Westmorland County, New Brunswick

    International Nuclear Information System (INIS)

    In 1997, the Government of New Brunswick conducted an inventory of orphan wells in the vicinity of Dover and Gautreau Village in Westmorland County. The term orphan wells refers to those oil and natural gas wells which have been abandoned and have no owner. An abandoned well refers to those wells that are no longer active and have been properly plugged. A total of 19 orphan wells were discovered with the help of landowners and historical maps. These wells are believed to have dated from 1860 to 1906. The locations of the wells were determined digitally using the Global Positioning System. The environmental conditions around the orphan wells were evaluated and classified according to a proposed system used by the State of Michigan. The wells were separated into three categories based on the amount of petroleum contamination of soil and water. Water contamination was further divided into contamination of groundwater and surface water. 7 refs., 34 figs

  8. Spatiotemporal dynamics of bacterial and archaeal communities in household biogas digesters from tropical and subtropical regions of Yunnan Province, China.

    Science.gov (United States)

    Tian, Guangliang; Li, Qiumin; Dong, Minghua; Wu, Yan; Yang, Bin; Zhang, Lijuan; Li, Yingjuan; Yin, Fang; Zhao, Xingling; Wang, Yongxia; Xiao, Wei; Cui, Xiaolong; Zhang, Wudi

    2016-06-01

    A combination of 16S rRNA gene PCR-based techniques and the determination of abiotic factors were used to study community composition, richness, and evenness and the correlation between biotic and abiotic factors in 19 household biogas digesters in tropical and subtropical regions of Yunnan Province, China. The results revealed that both bacterial and archaeal community composition differed between regions and archaeal community composition was more affected by season than bacterial; regardless of sampling location, the dominant bacterial phyla included Chloroflexi, Bacteroidetes, Firmicutes, and Proteobacteria, and the most dominant archaeal phylum was Euryarchaeota; in digesters from both regions, Chloroflexi as the first or second most dominant bacteria accounted for 21.50-26.10 % of bacterial library sequences, and the phylum Crenarchaeota as the second most dominant archaea accounted for 17.65-19.77 % of archaeal library sequences; the species Methanosaeta concilii as the most dominant archaeal species accounted for 67.80-72.80 % of the sequences. This study found that most of the abundant microbial communities in 19 biogas digesters are similar, and this result will provide enlightenment for finding the universal nature in rural biogas digesters at tropical and subtropical regions in China. PMID:26916266

  9. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge.

    Science.gov (United States)

    Zhang, Likui; Kang, Manyu; Xu, Jiajun; Xu, Jian; Shuai, Yinjie; Zhou, Xiaojian; Yang, Zhihui; Ma, Kesen

    2016-01-01

    Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected from inactive hydrothermal vents in the Southwest India Ridge using the high-throughput sequencing technology of Illumina MiSeq2500 platform. Based on the V4 region of 16S rRNA gene, sequence analysis showed that bacterial communities in the two samples were dominated by Proteobacteria, followed by Bacteroidetes, Actinobacteria and Firmicutes. Furthermore, archaeal communities in the two samples were dominated by Thaumarchaeota and Euryarchaeota. Comparative analysis showed that (i) TVG4 displayed the higher bacterial richness and lower archaeal richness than TVG11; (ii) the two samples had more divergence in archaeal communities than bacterial communities. Bacteria and archaea that are potentially associated with nitrogen, sulfur metal and methane cycling were detected in the two samples. Overall, we first provided a comparative picture of bacterial and archaeal communities and revealed their potentially ecological roles in the deep-sea environments of inactive hydrothermal vents in the Southwest Indian Ridge, augmenting microbial communities in inactive hydrothermal vents.

  10. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge

    Science.gov (United States)

    Zhang, Likui; Kang, Manyu; Xu, Jiajun; Xu, Jian; Shuai, Yinjie; Zhou, Xiaojian; Yang, Zhihui; Ma, Kesen

    2016-05-01

    Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected from inactive hydrothermal vents in the Southwest India Ridge using the high-throughput sequencing technology of Illumina MiSeq2500 platform. Based on the V4 region of 16S rRNA gene, sequence analysis showed that bacterial communities in the two samples were dominated by Proteobacteria, followed by Bacteroidetes, Actinobacteria and Firmicutes. Furthermore, archaeal communities in the two samples were dominated by Thaumarchaeota and Euryarchaeota. Comparative analysis showed that (i) TVG4 displayed the higher bacterial richness and lower archaeal richness than TVG11; (ii) the two samples had more divergence in archaeal communities than bacterial communities. Bacteria and archaea that are potentially associated with nitrogen, sulfur metal and methane cycling were detected in the two samples. Overall, we first provided a comparative picture of bacterial and archaeal communities and revealed their potentially ecological roles in the deep-sea environments of inactive hydrothermal vents in the Southwest Indian Ridge, augmenting microbial communities in inactive hydrothermal vents.

  11. Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples.

    Science.gov (United States)

    Pires, Ana C C; Cleary, Daniel F R; Almeida, Adelaide; Cunha, Angela; Dealtry, Simone; Mendonça-Hagler, Leda C S; Smalla, Kornelia; Gomes, Newton C M

    2012-08-01

    Mangroves are complex ecosystems that regulate nutrient and sediment fluxes to the open sea. The importance of bacteria and fungi in regulating nutrient cycles has led to an interest in their diversity and composition in mangroves. However, very few studies have assessed Archaea in mangroves, and virtually nothing is known about whether mangrove rhizospheres affect archaeal diversity and composition. Here, we studied the diversity and composition of Archaea in mangrove bulk sediment and the rhizospheres of two mangrove trees, Rhizophora mangle and Laguncularia racemosa, using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing of archaeal 16S rRNA genes with a nested-amplification approach. DGGE profiles revealed significant structural differences between bulk sediment and rhizosphere samples, suggesting that roots of both mangrove species influence the sediment archaeal community. Nearly all of the detected sequences obtained with pyrosequencing were identified as Archaea, but most were unclassified at the level of phylum or below. Archaeal richness was, furthermore, the highest in the L. racemosa rhizosphere, intermediate in bulk sediment, and the lowest in the R. mangle rhizosphere. This study shows that rhizosphere microhabitats of R. mangle and L. racemosa, common plants in subtropical mangroves located in Rio de Janeiro, Brazil, hosted distinct archaeal assemblages. PMID:22660713

  12. Barriers and incentives to orphan care in a time of AIDS and economic crisis: a cross-sectional survey of caregivers in rural Zimbabwe

    Directory of Open Access Journals (Sweden)

    Goodman Karen J

    2006-02-01

    Full Text Available Abstract Background Africa is in an orphan-care crisis. In Zimbabwe, where one-fourth of adults are HIV-positive and one-fifth of children are orphans, AIDS and economic decline are straining society's ability to care for orphans within their extended families. Lack of stable care is putting thousands of children at heightened risk of malnourishment, emotional underdevelopment, illiteracy, poverty, sexual exploitation, and HIV infection, endangering the future health of the society they are expected to sustain. Methods To explore barriers and possible incentives to orphan care, a quantitative cross-sectional survey in rural eastern Zimbabwe asked 371 adults caring for children, including 212 caring for double orphans, about their well-being, needs, resources, and perceptions and experiences of orphan care. Results Survey responses indicate that: 1 foster caregivers are disproportionately female, older, poor, and without a spouse; 2 98% of non-foster caregivers are willing to foster orphans, many from outside their kinship network; 3 poverty is the primary barrier to fostering; 4 financial, physical, and emotional stress levels are high among current and potential fosterers; 5 financial need may be greatest in single-orphan AIDS-impoverished households; and 6 struggling families lack external support. Conclusion Incentives for sustainable orphan care should focus on financial assistance, starting with free schooling, and development of community mechanisms to identify and support children in need, to evaluate and strengthen families' capacity to provide orphan care, and to initiate and support placement outside the family when necessary.

  13. Review and comparison of clinical evidence submitted to support European Medicines Agency market authorization of orphan-designated oncological treatments

    OpenAIRE

    Winstone, Julie; Chadda, Shkun; Ralston, Stephen; Sajosi, Peter

    2015-01-01

    Background Clinical trials for treatments indicated for orphan diseases may be limited due to the low prevalence of such diseases; this can result in implications for both regulatory and health economic perspectives. This study assessed the pivotal clinical evidence packages submitted to support applications for European Medicines Agency (EMA) marketing authorizations for treatments for orphan conditions, in relation to the size of the eligible patient population. Methods Approved treatments ...

  14. The Prevalence of Posttraumatic Stress Disorder and Associated Mental Health Problems Among Institutionalized Orphans in Dar es salaam, Tanzania

    OpenAIRE

    Myovela, Benjamin

    2012-01-01

    Orphanhood is becoming a more common experience for children in Tanzania, in part as a consequence of the AIDS pandemic, trauma and poverty. The number of orphans and risk of psychopathology has been steadily increasing even in regions where the AIDS epidemic has stabilized. Institutional care for orphaned children is uncommon in sub-Sahara Africa and seen as a last resort primarily as orphanages are often seen as a source of unhealthy psychological development and orphans’ ability to survive...

  15. A Roof Overhead: Creating a Conceptual Long Term Day Facility for Street Children and Orphans in Tehran, Iran

    OpenAIRE

    Safdari, Marjan

    2016-01-01

    With approximately 1.5 million orphans, over 200,000 street children, and 2,500 cases of child violence each year, Iran is not an ideal place for children. Although government groups and non-governmental organizations (NGO) have tried to provide facilities and institutional care centers, there are still many shortages that need to be addressed. Facilities that provide something more than the basic needs of these children are necessary. Orphans and street children face many difficulties during...

  16. Effectiveness of a Motivation and Practical Skills Development Methods on the Oral Hygiene of Orphans Children in Kaunas, Lithuania

    OpenAIRE

    Greta Markeviciute; Julija Narbutaite

    2015-01-01

    ABSTRACT Objectives The aim of this study was to evaluate the effect of a motivation and practical skills development methods on the oral hygiene of orphans. Material and Methods Sixty eight orphans aged between 7 and 17 years from two orphanages in Kaunas were divided into two groups: practical application group and motivation group. Children were clinically examined by determining their oral hygiene status using Silness-Löe plaque index. Questionnaire was used to estimate the oral hygiene k...

  17. Through the Ring of Fire: A Study of the Origin of Orphan Gamma-ray Flares in Blazars

    Science.gov (United States)

    MacDonald, Nicholas R.; Marscher, Alan P.; Jorstad, Svetlana G.; Joshi, Manasvita

    2014-06-01

    Blazars exhibit flares across the electromagnetic spectrum. Many gamma-ray flares are highly correlated with flares detected at optical wavelengths; however, a small subset appear to occur in isolation, with no counterpart in the other wave bands. These "orphan" gamma-ray flares challenge current models of blazar variability, most of which are unable to reproduce this type of behavior. We present numerical calculations of the time variable emission of a blazar based on a proposal by Marscher et al. (2010) to explain such events. In this model, a plasmoid ("blob") consisting of a power-law distribution of electrons propagates relativistically along the spine of a blazar jet and passes through a synchrotron emitting ring of electrons representing a shocked portion of the jet sheath. This ring supplies a source of seed photons that are inverse-Compton scattered by the electrons in the moving blob. As the blob approaches the ring, the photon density in the co-moving frame of the plasma increases, resulting in an orphan gamma-ray flare that then dissipates as the blob passes through and then moves away from the ring. The model includes the effects of radiative cooling and a spatially varying magnetic field. Support for the plausibility of this model is provided by observations by Marscher et al.(2010) of an isolated gamma-ray flare that was correlated with the passage of a superluminal knot through the inner jet of quasar PKS 1510-089. Synthetic light-curves produced by this new model are compared to the observed light-curves from this event. In addition, we present polarimetric observations that point to the existence of a jet sheath in the quasar 3C 273. A rough estimate of the bolometric luminosity of the sheath results in a value of ~10^45 erg s^-1 10% of the jet luminosity). This inferred sheath luminosity indicates that the jet sheath in 3C 273 can provide a significant source of seed photons that need to be taken into account when modeling the non

  18. Nuclear receptor function in skin health and disease: therapeutic opportunities in the orphan and adopted receptor classes.

    Science.gov (United States)

    Yin, Kelvin; Smith, Aaron G

    2016-10-01

    The skin forms a vital barrier between an organism's external environment, providing protection from pathogens and numerous physical and chemical threats. Moreover, the intact barrier is essential to prevent water and electrolyte loss without which terrestrial life could not be maintained. Accordingly, acute disruption of the skin through physical or chemical trauma needs to be repaired timely and efficiently as sustained skin pathologies ranging from mild irritations and inflammation through to malignancy impact considerably on morbidity and mortality. The Nuclear Hormone Receptor Family of transcriptional regulators has proven to be highly valuable targets for addressing a range of pathologies, including metabolic syndrome and cancer. Indeed members of the classic endocrine sub-group, such as the glucocorticoid, retinoid, and Vitamin D receptors, represent mainstay treatment strategies for numerous inflammatory skin disorders, though side effects from prolonged use are common. Emerging evidence has now highlighted important functional roles for nuclear receptors belonging to the adopted and orphan subgroups in skin physiology and patho-physiology. This review will focus on these subgroups and explore the current evidence that suggests these nuclear receptor hold great promise as future stand-alone or complementary drug targets in treating common skin diseases and maintaining skin homeostasis. PMID:27544210

  19. 'Older women', customary obligations and orphan foster caregiving: the case of queen mothers in Manya Klo, Ghana.

    Science.gov (United States)

    Drah, Bright B

    2014-06-01

    Female orphan caregivers in countries heavily affected by HIV in sub-Saharan Africa are often presented as a homogenous group of vulnerable 'older women' that struggles to support orphans. There is a dearth of data on the different kinds of women and how their social characteristics impact their survival strategies and caregiving responsibilities. This study examines the link between the social characteristics of queen mothers in Manya Klo in Ghana and their roles as caregivers. The research findings suggest that queen mothers have become the primary caregivers of orphans, even though they do not have the wherewithal to provide for these orphans. The lack of kin support to queen mothers exacerbates their physical and economic vulnerabilities. They engage in less dignifying economic activities and pay less attention to their own needs in order to meet their customary obligations as orphan caregivers. The growing influence of queen mothers as caregivers for orphans, however, is a reflection of some of the changes that are occurring in customary foster care arrangements. Policy makers and interventionists require in depth understanding of queen mothers and their peculiar circumstances in order to strengthen their roles as leaders and caregivers. PMID:24737050

  20. 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.

  1. Drug discovery and development for Huntington's disease - an orphan indication with high medical need.

    Science.gov (United States)

    Heitz, Freddy; La Rosa, Salvatore; Gonzalez-Couto, Eduardo; Gaviraghi, Giovanni; Terstappen, Georg C

    2008-09-01

    Huntington's disease (HD) is a rare neurodegenerative disorder that progressively destroys the mental capacity and motor control of patients. This loss of motor control results in abnormal body movements (chorea) - the hallmark of HD. Given that no disease-modifying therapy for HD exists and that available symptomatic treatments are not highly efficacious, the medical need for this 'orphan' disease remains high. The number of compounds that are undergoing discovery and development for the treatment of HD has increased significantly in recent years, spurred by legislative incentives for orphan drug development and by support from non-profit foundations. Thus, hope exists for patients with HD that efficacious medicines will become available. PMID:18763216

  2. 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.

  3. Orphan G protein-coupled receptors (GPCRs):biological functions and potential drug targets

    Institute of Scientific and Technical Information of China (English)

    Xiao-long TANG; Ying WANG; Da-li LI; Jian LUO; Ming-yao LIU

    2012-01-01

    The superfamily of G protein-coupled receptors (GPCRs) includes at least 800 seven-transmembrane receptors that participate in diverse physiological and pathological functions.GPCRs are the most successful targets of modern medicine,and approximately 36%of marketed pharmaceuticals target human GPCRs.However,the endogenous ligands of more than 140 GPCRs remain unidentified,leaving the natural functions of those GPCRs in doubt.These are the so-called orphan GPCRs,a great source of drug targets.This review focuses on the signaling transduction pathways of the Adhesion GPCR family,the LGR subfamily,and the PSGR subfamily,and their potential functions in immunology,development,and cancers.In this review,we present the current approaches and difficulties of orphan GPCR deorphanization and characterization.

  4. Orphan {\\gamma}-ray flares from relativistic blobs encountering luminous stars

    CERN Document Server

    Banasiński, P; Sitarek, J

    2016-01-01

    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.

  5. Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis)

    Science.gov (United States)

    Gruninger, Robert J.; McAllister, Tim A.; Forster, Robert J.

    2016-01-01

    The North American Beaver (Castor canadensis) is the second largest living rodent and an iconic symbol of Canada. The beaver is a semi-aquatic browser whose diet consists of lignocellulose from a variety of plants. The beaver is a hindgut fermenter and has an enlarged ceacum that houses a complex microbiome. There have been few studies examining the microbial diversity in gastrointestinal tract of hindgut fermenting herbivores. To examine the bacterial and archaeal communities inhabiting the gastrointestinal tract of the beaver, the microbiome of the ceacum and feaces was examined using culture-independent methods. DNA from the microbial community of the ceacum and feaces of 4 adult beavers was extracted, and the16S rRNA gene was sequenced using either bacterial or archaeal specific primers. A total of 1447 and 1435 unique bacterial OTUs were sequenced from the ceacum and feaces, respectively. On average, the majority of OTUs within the ceacum were classified as Bacteroidetes (49.2%) and Firmicutes (47.6%). The feaces was also dominated by OTUs from Bacteroidetes (36.8%) and Firmicutes (58.9%). The composition of bacterial community was not significantly different among animals. The composition of the ceacal and feacal microbiome differed, but this difference is due to changes in the abundance of closely related OTUs, not because of major differences in the taxonomic composition of the communities. Within these communities, known degraders of lignocellulose were identified. In contrast, to the bacterial microbiome, the archaeal community was dominated by a single species of methanogen, Methanosphaera stadtmanae. The data presented here provide the first insight into the microbial community within the hindgut of the beaver. PMID:27227334

  6. Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees

    Directory of Open Access Journals (Sweden)

    Henry eMueller

    2015-03-01

    Full Text Available Endophytes have an intimate and often symbiotic interaction with their hosts. Less is known about the composition and function of endophytes in trees. In order to evaluate our hypothesis that plant genotype and origin have a strong impact on both, endophytes of leaves from 10 Olea europaea L. cultivars from the Mediterranean basin growing at a single agricultural site in Spain and from nine wild olive trees located in natural habitats in Greece, Cyprus and on Madeira Island were studied. The composition of the bacterial endophytic communities as revealed by 16S rRNA gene amplicon sequencing and the subsequent PCoA analysis showed a strong correlation to the plant genotypes. The bacterial distribution patterns were congruent with the plant origins in Eastern and Western areas of the Mediterranean basin. Subsequently, the endophytic microbiome of wild olives was shown to be closely related to those of cultivated olives of the corresponding geographic origins. The olive leaf endosphere harbored mostly Proteobacteria, followed by Firmicutes, Actinobacteria and Bacteroidetes. The detection of a high portion of archaeal taxa belonging to the phyla Thaumarchaeota, Crenarchaeota and Euryarchaeota in the amplicon libraries was an unexpected discovery, which was confirmed by quantitative real-time PCR revealing an archaeal portion of up to 35.8%. Although the function of these Archaea for their host plant remains speculative, this finding suggests a significant relevance of archaeal endophytes for plant-microbe interactions. In addition, the antagonistic potential of culturable endophytes was determined; all isolates with antagonistic activity against the olive-pathogenic fungus Verticillium dahliae Kleb. belong to Bacillus amyloliquefaciens. In contrast to the specific global structural diversity, BOX-fingerprints of the antagonistic Bacillus isolates were highly similar and independent of the olive genotype from which they were isolated.

  7. Land-use systems affect Archaeal community structure and functional diversity in western Amazon soils

    Directory of Open Access Journals (Sweden)

    Acácio Aparecido Navarrete

    2011-10-01

    Full Text Available The study of the ecology of soil microbial communities at relevant spatial scales is primordial in the wide Amazon region due to the current land use changes. In this study, the diversity of the Archaea domain (community structure and ammonia-oxidizing Archaea (richness and community composition were investigated using molecular biology-based techniques in different land-use systems in western Amazonia, Brazil. Soil samples were collected in two periods with high precipitation (March 2008 and January 2009 from Inceptisols under primary tropical rainforest, secondary forest (5-20 year old, agricultural systems of indigenous people and cattle pasture. Denaturing gradient gel electrophoresis of polymerase chain reaction-amplified DNA (PCR-DGGE using the 16S rRNA gene as a biomarker showed that archaeal community structures in crops and pasture soils are different from those in primary forest soil, which is more similar to the community structure in secondary forest soil. Sequence analysis of excised DGGE bands indicated the presence of crenarchaeal and euryarchaeal organisms. Based on clone library analysis of the gene coding the subunit of the enzyme ammonia monooxygenase (amoA of Archaea (306 sequences, the Shannon-Wiener function and Simpson's index showed a greater ammonia-oxidizing archaeal diversity in primary forest soils (H' = 2.1486; D = 0.1366, followed by a lower diversity in soils under pasture (H' = 1.9629; D = 0.1715, crops (H' = 1.4613; D = 0.3309 and secondary forest (H' = 0.8633; D = 0.5405. All cloned inserts were similar to the Crenarchaeota amoA gene clones (identity > 95 % previously found in soils and sediments and distributed primarily in three major phylogenetic clusters. The findings indicate that agricultural systems of indigenous people and cattle pasture affect the archaeal community structure and diversity of ammonia-oxidizing Archaea in western Amazon soils.

  8. Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage

    Directory of Open Access Journals (Sweden)

    Björn eBreidenbach

    2015-01-01

    Full Text Available We studied the resident (16S rDNA and the active (16S rRNA members of soil archaeal and bacterial communities during rice plant development by sampling three growth stages (vegetative, reproductive and maturity under field conditions. Additionally, the microbial community was investigated in two non-flooded fields (unplanted, cultivated with upland maize in order to monitor the reaction of the microbial communities to non-flooded, dry conditions. The abundance of Bacteria and Archaea was monitored by quantitative PCR showing an increase in 16S rDNA during reproductive stage and stable 16S rRNA copies throughout the growth season. Community profiling by T-RFLP indicated a relatively stable composition during rice plant growth whereas pyrosequencing revealed minor changes in relative abundance of a few bacterial groups. Comparison of the two non-flooded fields with flooded rice fields showed that the community composition of the Bacteria was slightly different, while that of the Archaea was almost the same. Only the relative abundance of Methanosarcinaceae and Soil Crenarchaeotic Group increased in non-flooded versus flooded soil. The abundance of bacterial and archaeal 16S rDNA copies was highest in flooded rice fields, followed by non-flooded maize and unplanted fields. However, the abundance of ribosomal RNA (active microbes was similar indicating maintenance of a high level of ribosomal RNA under the non-flooded conditions, which were unfavorable for anaerobic bacteria and methanogenic archaea. This maintenance possibly serves as preparedness for activity when conditions improve. In summary, the analyses showed that the bacterial and archaeal communities inhabiting Philippine rice field soil were relatively stable over the season but reacted upon change in field management.

  9. Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering.

    Directory of Open Access Journals (Sweden)

    Alica Chroňáková

    Full Text Available Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI and long-term impact (17 years; LTI, one is regenerating from cattle impact (REG and a control is unaffected by cattle (CON. Cattle manure (CMN, the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning.

  10. Exploring the biotechnologial applications in the archaeal domain Explorando as aplicações biotecnológicas do domínio archaea

    Directory of Open Access Journals (Sweden)

    S.M.C. Alquéres

    2007-09-01

    Full Text Available Archaea represent a considerable fraction of the prokaryotic world in marine and terrestrial ecosystems, indicating that organisms from this domain might have a large impact on global energy cycles. The extremophilic nature of many archaea has stimulated intense efforts to understand the physiological adaptations for living in extreme environments. Their unusual properties make them a potentially valuable resource in the development of novel biotechnological processes and industrial applications as new pharmaceuticals, cosmetics, nutritional supplements, molecular probes, enzymes, and fine chemicals. In the present mini-review, we show and discuss some exclusive characteristics of Archaea domain and the current knowledge about the biotechnological uses of the archaeal enzymes. The topics are: archaeal characteristics, phylogenetic division, biotechnological applications, isolation and cultivation of new microbes, achievements in genomics, and metagenomic.As arqueas representam uma considerável fração dos procariotos nos ecossistemas marinhos e terrestes, indicando que estes organismos devem possuir um grande impacto nos ciclos energéticos. A natureza extremofílica de muitas arqueas tem estimulado intensos esforços para compreender sua adaptação fisiológica a ambientes extremos. Suas propriedades incomus as tornam uma fonte valiosa no desenvolvimento de novos processos biotecnológicos e aplicações industriais como novos fármacos, cosméticos, suplementos nutricionais, sondas moleculares, enzimas e reagentes. Na presente mini-revisão, mostramos e discutimos algumas de suas características exclusivas correlacionando-as com seu potencial biotecnológico e aplicação industrial. Os tópicos são: características das arqueas, divisão filogenética, aplicações biotecnológicas, isolamento e cultivo de novos microrganismos, genoma e metagenoma.

  11. Adipogenesis and insulin sensitivity in obesity are regulated by retinoid-related orphan receptor gamma

    OpenAIRE

    Meissburger, Bettina; Ukropec, Jozef; Roeder, Eva; Beaton, Nigel; Geiger, Matthias; Teupser, Daniel; Civan, Burcak; Langhans, Wolfgang; Nawroth, Peter P.; Gasperikova, Daniela; Rudofsky, Gottfried; Wolfrum, Christian

    2011-01-01

    Obesity is a well-known risk factor for the development of secondary complications such as type 2 diabetes. However, only a part of the obese population develops secondary metabolic disorders. Here, we identify the transcription factor retinoid-related orphan receptor gamma (RORγ) as a negative regulator of adipocyte differentiation through expression of its newly identified target gene matrix metalloproteinase 3. In vivo differentiation of adipocyte progenitor cells from Rorγ-deficient mice ...

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

    OpenAIRE

    Picavet, Eline

    2013-01-01

    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 gi...

  13. 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.

  14. The Oncoprotein BCL11A Binds to Orphan Nuclear Receptor TLX and Potentiates its Transrepressive Function

    OpenAIRE

    Sara B. Estruch; Víctor Buzón; Carbó, Laia R.; Lenka Schorova; Jens Lüders; Eva Estébanez-Perpiñá

    2012-01-01

    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 TL...

  15. Niemann–Pick type C disease proteins: orphan transporters or membrane rheostats?

    OpenAIRE

    Munkacsi, Andrew B.; Porto, Anthony F.; Sturley, Stephen L.

    2007-01-01

    Niemann–Pick type C (NPC) disease is a panethnic lysosomal lipidosis, which results in severe cerebellar impairment and death, and is proposed to be a consequence of defective metabolite transport. Numerous models of this disorder have defined the phenotypic impact of misfunction of the NPC proteins, however, their mechanism of action and definition of substrate(s) remain vague and disputed. The proteins may be lipid chaperones, nonspecific transporters, orphan transporters or membrane-sensin...

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

    OpenAIRE

    Ssebunnya Joshua; Jack Susan; Harms Sheila; Kizza Ruth

    2010-01-01

    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...

  17. Expression and function profiling of orphan nuclear receptors using bacterial artificial chromosome (BAC) transgenesis.

    OpenAIRE

    Nemoz-Gaillard, Eric; Tsai, Ming-Jer; Tsai, Sophia Y.

    2003-01-01

    The long term goal of the Nuclear Receptor Signaling Atlas (NURSA) resides in unraveling the physiological and pathological functions of nuclear receptors (NRs) at the molecular, biochemical and cellular levels. This multi-oriented task requires complementary approaches in order to determine the specific function(s) and precise expression and receptor activity patterns for each individual conventional or orphan receptor. To attain this objective, we have chose to turn to technologies recently...

  18. Home Visit——On the Visit to China by a Japanese Orphans Delegation

    Institute of Scientific and Technical Information of China (English)

    Zhang; Xiaoping

    2014-01-01

    <正>There is a group of people,abandoned in China as small children because of war,who were brought up by the kind-hearted Chinese people.These"war orphans"a r e undoubted Japanese,but they speak col loquial Chinese with a northeastern China accent and continued thinking of their homes in China after they returned to live in their native land.

  19. Insights into Orphan Nuclear Receptors as Prognostic Markers and Novel Therapeutic Targets for Breast Cancer

    OpenAIRE

    Aesoy, Reidun; Clyne, Colin D.; Chand, Ashwini L

    2015-01-01

    There is emerging evidence asserting the importance of orphan nuclear receptors (ONRs) in cancer initiation and progression. In breast cancer, there is a lot unknown about ONRs in terms of their expression profile and their transcriptional targets in the various stages of tumor progression. With the classification of breast tumors into distinct molecular subtypes, we assess ONR expression in the different breast cancer subtypes and with patient outcomes. Complementing this, we review evidence...

  20. Process and Outcome Evaluation of a Community Intervention for Orphan Adolescents in Western Kenya

    OpenAIRE

    Hallfors, Denise D.; Cho, Hyunsan; Mbai, Isabella; Milimo, Benson; Itindi, Janet

    2012-01-01

    We conducted a 2-year pilot randomized controlled trial (N = 105) in a high HIV-prevalence area in rural western Kenya to test whether providing young orphan adolescents with uniforms, school fees, and community visitors improves school retention and reduces HIV risk factors. The trial was a community intervention, limited to one community. In this paper, we examined intervention implementation and its association with outcomes using longitudinal data. We used both quantitative and qualitativ...

  1. National campaign for the search and recovery of Orphan radioactive sources

    International Nuclear Information System (INIS)

    This paper aims to describe the main initial approaches of the campaign for the 'Recovery of Orphan Radioactive Sources' undertaken in Spain, in addition to the steps taken, the experience gained and the partial results obtained. The campaign began on 19th February 2007 and this paper reports the findings until 31st December 2007. The paper aims to share the experience gained with others who are considering or are already involved in similar campaigns and to enable opinions to be exchanged with those responsible for such campaigns in other countries. The campaign was initiated by the Spanish Ministry of Industry, Tourism and Trade with the expert assistance of the Nuclear Security Council. The initiative came about as a result of national legislation currently in force regarding the control of highly active and orphan radioactive source, which implements a European Directive. The campaign was commissioned to ENRESA (the Spanish National Company for Radioactive Waste Management) and the work, which began in 2007, will continue into 2008. The campaign aims to seek and recover the largest possible number of orphan radioactive sources (an Orphan radioactive source is understood to be one which is detected outside the standard control system and which, when detected, has an activity level higher than the exemption levels established in national and European regulations), and involves the collaboration of various different agents and organisations where such sources are or may be found. Finally, the paper provides details regarding the number and radiological characteristics of the sources which have already been recovered in Spain during the 2007 campaign. (author)

  2. Diversity of putative archaeal RNA viruses in metagenomic datasets of a yellowstone acidic hot spring.

    OpenAIRE

    Hongming WANG; Yu, Yongxin; Liu, Taigang; Pan, Yingjie; Yan, Shuling; Wang, Yongjie

    2015-01-01

    Two genomic fragments (5,662 and 1,269 nt in size, GenBank accession no. JQ756122 and JQ756123, respectively) of novel, positive-strand RNA viruses that infect archaea were first discovered in an acidic hot spring in Yellowstone National Park (Bolduc et al., 2012). To investigate the diversity of these newly identified putative archaeal RNA viruses, global metagenomic datasets were searched for sequences that were significantly similar to those of the viruses. A total of 3,757 associated read...

  3. Effect of Tree Species and Mycorrhizal Colonization on the Archaeal Population of Boreal Forest Rhizospheres▿

    OpenAIRE

    Bomberg, Malin; Timonen, Sari

    2008-01-01

    Group 1.1c Crenarchaeota are the predominating archaeal group in acidic boreal forest soils. In this study, we show that the detection frequency of 1.1c crenarchaeotal 16S rRNA genes in the rhizospheres of the boreal forest trees increased following colonization by the ectomycorrhizal fungus Paxillus involutus. This effect was very clear in the fine roots of Pinus sylvestris, Picea abies, and Betula pendula, the most common forest trees in Finland. The nonmycorrhizal fine roots had a clearly ...

  4. Seasonal Effects in a Lake Sediment Archaeal Community of the Brazilian Savanna

    OpenAIRE

    Thiago Rodrigues; Elisa Catão; Mercedes M. C. Bustamante; Quirino, Betania F.; Kruger, Ricardo H; Kyaw, Cynthia M

    2014-01-01

    The Cerrado is a biome that corresponds to 24% of Brazil’s territory. Only recently microbial communities of this biome have been investigated. Here we describe for the first time the diversity of archaeal communities from freshwater lake sediments of the Cerrado in the dry season and in the transition period between the dry and rainy seasons, when the first rains occur. Gene libraries were constructed, using Archaea-specific primers for the 16S rRNA and amoA genes. Analysis revealed marked ...

  5. Teachers’ Pastoral Role in Response to the Needs of Orphaned Learners

    Directory of Open Access Journals (Sweden)

    Teresa Auma Ogina

    2010-12-01

    Full Text Available This article discusses a study that explored the way teachers perceive and describe their roles in responding to the needs of orphaned learners. The participants in the study comprised three secondary and two primary school teachers. The data on the teachers’ experiences were collected through semi-structured interviews, and the findings revealed that, although some of the teachers attempted to fulfill some of the orphaned learners’ needs, most were unable to cope with the combined roles of teaching and learning and care giving. The study identified a lack of material, social, and emotional support for grieving learners. The findings indicate that there is a need for teacher development in terms of preparing teachers to provide pastoral care for orphaned learners. For the teachers’ efforts to be more fruitful, there is also an urgent need for supportive school leadership. In addition, the study highlights the need for counsellors and social workers to be appointed to work in collaboration with the teachers in providing for the needs of the learners.

  6. 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...

  7. Hunting the Parent of the Orphan Stream: Identifying Stream Members from Low-Resolution Spectroscopy

    CERN Document Server

    Casey, Andrew R; Keller, Stefan C; Maunder, Elizabeth

    2013-01-01

    We present candidate K-giant members in the Orphan Stream which have been identified from low-resolution data taken with the AAOmega spectrograph on the Anglo-Australian Telescope. From modest S/N spectra and independent cuts in photometry, kinematics, gravity and metallicity we yield self-consistent, highly probable stream members. We find a revised stream distance of 22.5 +/- 2.0 kpc near the celestial equator, and our kinematic signature peaks at Vgsr = 82.1 +/- 1.4 km/s. The observed velocity dispersion of our most probable members is consistent with arising from the velocity uncertainties alone. This indicates that at least along this line-of-sight, the Orphan Stream is kinematically cold. Our data indicates an overall stream metallicity of [Fe/H] = -1.63 +/- 0.19 dex which is more metal-rich than previously found and unbiased by spectral type. Furthermore, the significant metallicity dispersion displayed by our most probable members (0.56 dex) suggests that the unidentified Orphan Stream parent is a dSp...

  8. The representative animal

    OpenAIRE

    Harrison, J. M.

    1994-01-01

    The anthropocentric approach to the study of animal behavior uses representative nonhuman animals to understand human behavior. This approach raises problems concerning the comparison of the behavior of two different species. The datum of behavior analysis is the behavior of humans and representative animal phenotypes. The behavioral phenotype is the product of the ontogeny and phylogeny of each species, and this requires that contributions of genotype as well as behavioral history to experim...

  9. Changes in archaeal abundance and community structure along a salinity gradient in the lower Pearl River and its estuary

    Science.gov (United States)

    Zhang, C.; Wang, J.; Xie, W.; Wang, P.; Wei, Y.; Chen, S.; Zhou, X.

    2013-12-01

    Archaea occur in a wide range of habitats and across broad environmental gradients. At the global scale, salinity is known to be a major driving force for archaeal species diversity. The goal of this study was to examine changes in abundance and diversity of archaeal community DNA and membrane lipids in the water column along a salinity gradient in the lower Pearl River and estuary in the context of water/gas chemistry (pH, nitrate/nitrite, ammonia, methane, carbon dioxide). The pH increased and nitrate/nitrite and ammonia decreased from the lower Pearl River to the estuary. Methane and carbon dioxide fluxes were high in the lower Pearl River and decreased sharply in the estuary and toward the open ocean. The archaeal lipid profile exhibited abrupt changes from dominance of GDGT-0 (a glycerol diakly glycerol tetraether with zero cyclopentyl ring, which is commonly present in methanogens) to dominance of crenarchaeol (a specific biomarker for Thaumarchaeota) with increasing salinity from zero in the lower Pearl River to >0.5% in the estuary. Quantification of the 16S rRNA gene abundance using qPCR revealed a switch from bacteria-dominance to archaea-dominance and the ratio of archaeal nirK/bacterial-amoA genes had a peak value in the estuary, suggesting enhanced activity of ammonia oxidation by archaea. Pyrosequencing of archaeal 16S rRNA, amoA and nirK genes exhibited systematic variation defined by habitat types. Our current studies employ rate measurements of carbon fixation, ammonia oxidation, and nitrate reduction using isotope labeling approaches, which will allow us to link changes in archaeal community structure and ecological function.

  10. Archaeal Viruses Contribute to the Novel Viral Assemblage Inhabiting Oceanic, Basalt-Hosted Deep Subsurface Crustal Fluids

    Science.gov (United States)

    Nigro, O. D.; Rappe, M. S.; Jungbluth, S.; Lin, H. T.; Steward, G.

    2015-12-01

    Fluids contained in the basalt-hosted deep subsurface of the world's oceans represent one of the most inaccessible and understudied biospheres on earth. Recent improvements in sampling infrastructure have allowed us to collect large volumes of crustal fluids (~104 L) from Circulation Obviation Retrofit Kits (CORKs) placed in boreholes located on the eastern flank of the Juan de Fuca Ridge (JdFR). We detected viruses within these fluids by TEM and epifluorescence microscopy in samples collected from 2010 to 2014. Viral abundance, determined by epifluorescence counts, indicated that concentrations of viruses in subsurface basement fluids (~105 ml-1) are lower than the overlying seawater, but are higher in abundance than microbial cells in the same samples. Analysis of TEM images revealed distinct viral morphologies (rod and spindle-shaped) that resemble the morphologies of viral families infecting archaea. There are very few, if any, direct observations of these viral morphologies in marine samples, although they have been observed in enrichment cultures and their signature genes detected in metagenomic studies from hydrothermal vents and marine sediments. Analysis of metagenomes from the JdFR crustal fluids revealed sequences with homology to archaeal viruses from the rudiviridae, bicaudaviridae and fuselloviridae. Prokaryotic communities in fluids percolating through the basaltic basement rock of the JdFR flank are distinct from those inhabiting the overlying sediments and seawater. Similarly, our data support the idea that the viral assemblage in these fluids is distinct from viral assemblages in other marine and terrestrial aquatic environments. Our data also suggest that viruses contribute to the mortality of deep subsurface prokaryotes through cell lysis, and viruses may alter the genetic potential of their hosts through the processes of lysogenic conversion and horizontal gene transfer.

  11. Archaeal and bacterial diversity in an arsenic-rich shallow-sea hydrothermal system undergoing phase separation

    Directory of Open Access Journals (Sweden)

    Roy Edward Price

    2013-07-01

    Full Text Available Phase separation is a ubiquitous process in seafloor hydrothermal vents, creating a large range of salinities. Toxic elements (e.g., arsenic partition into the vapor phase, and thus can be enriched in both high and low salinity fluids. However, investigations of microbial diversity at sites associated with phase separation are rare. We evaluated prokaryotic diversity in arsenic-rich shallow-sea vents off Milos Island (Greece by comparative analysis of 16S rRNA clone sequences from two vent sites with similar pH and temperature but marked differences in salinity. Clone sequences were also obtained for aioA-like functional genes (AFGs. Bacteria in the surface sediments (0 to 1.5 cm at the high salinity site consisted of mainly Epsilonproteobacteria (Arcobacter sp., which transitioned to almost exclusively Firmicutes (Bacillus sp. at ~10 cm depth. However, the low salinity site consisted of Bacteroidetes (Flavobacteria in the surface and Epsilonproteobacteria (Arcobacter sp. at ~10 cm depth. Archaea in the high salinity surface sediments were dominated by the orders Archaeoglobales and Thermococcales, transitioning to Thermoproteales and Desulfurococcales (Staphylothermus sp. in the deeper sediments. In contrast, the low salinity site was dominated by Thermoplasmatales in the surface and Thermoproteales at depth. Similarities in gas and redox chemistry suggest that salinity and/or arsenic concentrations may select for microbial communities that can tolerate these parameters. Many of the archaeal 16S rRNA sequences contained inserts, possibly introns, including members of the Euryarchaeota. Clones containing AFGs affiliated with either Alpha- or Betaproteobacteria, although most were only distantly related to published representatives. Most clones (89% originated from the deeper layer of the low salinity, highest arsenic site. This is the only sample with overlap in 16S rRNA data, suggesting arsenotrophy as an important metabolism in similar

  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. Representing properties locally.

    Science.gov (United States)

    Solomon, K O; Barsalou, L W

    2001-09-01

    Theories of knowledge such as feature lists, semantic networks, and localist neural nets typically use a single global symbol to represent a property that occurs in multiple concepts. Thus, a global symbol represents mane across HORSE, PONY, and LION. Alternatively, perceptual theories of knowledge, as well as distributed representational systems, assume that properties take different local forms in different concepts. Thus, different local forms of mane exist for HORSE, PONY, and LION, each capturing the specific form that mane takes in its respective concept. Three experiments used the property verification task to assess whether properties are represented globally or locally (e.g., Does a PONY have mane?). If a single global form represents a property, then verifying it in any concept should increase its accessibility and speed its verification later in any other concept. Verifying mane for PONY should benefit as much from having verified mane for LION earlier as from verifying mane for HORSE. If properties are represented locally, however, verifying a property should only benefit from verifying a similar form earlier. Verifying mane for PONY should only benefit from verifying mane for HORSE, not from verifying mane for LION. Findings from three experiments strongly supported local property representation and ruled out the interpretation that object similarity was responsible (e.g., the greater overall similarity between HORSE and PONY than between LION and PONY). The findings further suggest that property representation and verification are complicated phenomena, grounded in sensory-motor simulations.

  15. National Plans of Action for Orphans and Vulnerable Children in Sub-Saharan Africa. Where Are the Youngest Children? Working Papers in Early Childhood Development, No. 50

    Science.gov (United States)

    Engle, Patrice

    2008-01-01

    In 2005, an estimated 48 million children aged 0-18 years--12 percent of all children in sub-Saharan Africa--were orphans, and that number is expected to rise to 53 million by 2010. One quarter of all orphans are orphaned because of AIDS, and about 2.6 million children are currently infected with HIV. Untreated, most children born with HIV will…

  16. Archaeal and bacterial diversity in acidic to circumneutral hot springs in the Philippines.

    Science.gov (United States)

    Huang, Qiuyuan; Jiang, Hongchen; Briggs, Brandon R; Wang, Shang; Hou, Weiguo; Li, Gaoyuan; Wu, Geng; Solis, Ramonito; Arcilla, Carlo A; Abrajano, Teofilo; Dong, Hailiang

    2013-09-01

    The microbial diversity was investigated in sediments of six acidic to circumneutral hot springs (Temperature: 60-92 °C, pH 3.72-6.58) in the Philippines using an integrated approach that included geochemistry and 16S rRNA gene pyrosequencing. Both bacterial and archaeal abundances were lower in high-temperature springs than in moderate-temperature ones. Overall, the archaeal community consisted of sequence reads that exhibited a high similarity (nucleotide identity > 92%) to phyla Crenarchaeota, Euryarchaeota, and unclassified Archaea. The bacterial community was composed of sequence reads moderately related (nucleotide identity > 90%) to 17 phyla, with Aquificae and Firmicutes being dominant. These phylogenetic groups were correlated with environmental conditions such as temperature, dissolved sulfate and calcium concentrations in spring water, and sediment properties including total nitrogen, pyrite, and elemental sulfur. Based on the phylogenetic inference, sulfur metabolisms appear to be key physiological functions in these hot springs. Sulfobacillus (within phylum Firmicutes) along with members within Sulfolobales were abundant in two high-temperature springs (> 76 °C), and they were hypothesized to play an important role in regulating the sulfur cycling under high-temperature conditions. The results of this study improve our understanding of microbial diversity and community composition in acidic to circumneutral terrestrial hot springs and their relationships with geochemical conditions.

  17. Archaeal Populations in Hypersaline Sediments Underlying Orange Microbial Mats in the Napoli Mud Volcano▿†

    Science.gov (United States)

    Lazar, Cassandre Sara; L'Haridon, Stéphane; Pignet, Patricia; Toffin, Laurent

    2011-01-01

    Microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. Sediments associated with a brine pool and microbial orange mats of the Napoli mud volcano were recovered during the Medeco cruise. Based on analysis of RNA-derived sequences, the “active” archaeal community was composed of many uncultured lineages, such as rice cluster V or marine benthic group D. Function methyl coenzyme M reductase (mcrA) genes were affiliated with the anaerobic methanotrophic Archaea (ANME) of the ANME-1, ANME-2a, and ANME-2c groups, suggesting that AOM occurred in these sediment layers. Enrichment cultures showed the presence of viable marine methylotrophic Methanococcoides in shallow sediment layers. Thus, the archaeal community diversity seems to show that active methane cycling took place in the hypersaline microbial mat-associated sediments of the Napoli mud volcano. PMID:21335391

  18. Co-expression and co-purification of archaeal and eukaryal box C/D RNPs.

    Directory of Open Access Journals (Sweden)

    Yu Peng

    Full Text Available Box C/D ribonucleoprotein particles (RNPs are 2'-O-methylation enzymes required for maturation of ribosomal and small nuclear RNA. Previous biochemical and structural studies of the box C/D RNPs were limited by the unavailability of purified intact RNPs. We developed a bacterial co-expression strategy based on the combined use of a multi-gene expression system and a tRNA-scaffold construct that allowed the expression and purification of homogeneous archaeal and human box C/D RNPs. While the co-expressed and co-purified archaeal box C/D RNP was found to be fully active in a 2'-O-methylation assay, the intact human U14 box C/D RNP showed no detectable catalytic activity, consistent with the earlier findings that assembly of eukaryotic box C/D RNPs is nonspontaneous and requires additional protein factors. Our systems provide a means for further biochemical and structural characterization of box C/D RNPs and their assembly factors.

  19. Bacterial and archaeal community structures in the Arctic deep-sea sediment

    Institute of Scientific and Technical Information of China (English)

    LI Yan; LIU Qun; LI Chaolun; DONG Yi; ZHANG Wenyan; ZHANG Wuchang; XIAO Tian

    2015-01-01

    Microbial community structures in the Arctic deep-sea sedimentary ecosystem are determined by organic matter input, energy availability, and other environmental factors. However, global warming and earlier ice-cover melting are affecting the microbial diversity. To characterize the Arctic deep-sea sediment microbial diversity and its rela-tionship with environmental factors, we applied Roche 454 sequencing of 16S rDNA amplicons from Arctic deep-sea sediment sample. Both bacterial and archaeal communities’ richness, compositions and structures as well as tax-onomic and phylogenetic affiliations of identified clades were characterized. Phylotypes relating to sulfur reduction and chemoorganotrophic lifestyle are major groups in the bacterial groups;while the archaeal community is domi-nated by phylotypes most closely related to the ammonia-oxidizing Thaumarchaeota (96.66%) and methanogenic Euryarchaeota (3.21%). This study describes the microbial diversity in the Arctic deep marine sediment (>3 500 m) near the North Pole and would lay foundation for future functional analysis on microbial metabolic processes and pathways predictions in similar environments.

  20. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.

    Directory of Open Access Journals (Sweden)

    Jenna Morgan Lang

    Full Text Available Over 3000 microbial (bacterial and archaeal genomes have been made publically available to date, providing an unprecedented opportunity to examine evolutionary genomic trends and offering valuable reference data for a variety of other studies such as metagenomics. The utility of these genome sequences is greatly enhanced when we have an understanding of how they are phylogenetically related to each other. Therefore, we here describe our efforts to reconstruct the phylogeny of all available bacterial and archaeal genomes. We identified 24, single-copy, ubiquitous genes suitable for this phylogenetic analysis. We used two approaches to combine the data for the 24 genes. First, we concatenated alignments of all genes into a single alignment from which a Maximum Likelihood (ML tree was inferred using RAxML. Second, we used a relatively new approach to combining gene data, Bayesian Concordance Analysis (BCA, as implemented in the BUCKy software, in which the results of 24 single-gene phylogenetic analyses are used to generate a "primary concordance" tree. A comparison of the concatenated ML tree and the primary concordance (BUCKy tree reveals that the two approaches give similar results, relative to a phylogenetic tree inferred from the 16S rRNA gene. After comparing the results and the methods used, we conclude that the current best approach for generating a single phylogenetic tree, suitable for use as a reference phylogeny for comparative analyses, is to perform a maximum likelihood analysis of a concatenated alignment of conserved, single-copy genes.

  1. Archaeal membrane-associated proteases: insights on Haloferax volcanii and other haloarchaea

    Directory of Open Access Journals (Sweden)

    Maria Ines Giménez

    2015-02-01

    Full Text Available The function of membrane proteases range from general house-keeping to regulation of cellular processes. Although the biological role of these enzymes in archaea is poorly understood, some of them are implicated in the biogenesis of the archaeal cell envelope and surface structures. The membrane-bound ATP-dependent Lon protease is essential for cell viability and affects membrane carotenoid content in Haloferax volcanii. At least two different proteases are needed in this archaeon to accomplish the posttranslational modifications of the S-layer glycoprotein. The rhomboid protease RhoII is involved in the N-glycosylation of the S-layer protein with a sulfoquinovose-containing oligosaccharide while archaeosortase ArtA mediates the proteolytic processing coupled-lipid modification of this glycoprotein facilitating its attachment to the archaeal cell surface. Interestingly, two different signal peptidase I homologs exist in H. volcanii, Sec11a and Sec11b, which likely play distinct physiological roles. Type IV prepilin peptidase PibD processes flagellin/pilin precursors, being essential for the biogenesis and function of the archaellum and other cell surface structures in H. volcanii.

  2. Overexpression, purification and crystallization of an archaeal DNA ligase from Pyrococcus furiosus

    International Nuclear Information System (INIS)

    Crystals of the archaeal DNA ligase from Pyrococcus furiosus were obtained using 6.6%(v/v) ethanol as a precipitant and diffracted X-rays to 1.7 Å resolution. DNA ligases seal single-strand breaks in double-stranded DNA and their function is essential to maintain the integrity of the genome during various aspects of DNA metabolism, such as replication, excision repair and recombination. DNA-strand breaks are frequently generated as reaction intermediates in these events and the sealing of these breaks depends solely on the proper function of DNA ligase. Crystals of the archaeal DNA ligase from Pyrococcus furiosus were obtained using 6.6%(v/v) ethanol as a precipitant and diffracted X-rays to 1.7 Å resolution. They belong to the monoclinic space group P21, with unit-cell parameters a = 61.1, b = 88.3, c = 63.4 Å, β = 108.9°. The asymmetric unit contains one ligase molecule

  3. Ecological structuring of bacterial and archaeal taxa in surface ocean waters.

    Science.gov (United States)

    Yilmaz, Pelin; Iversen, Morten H; Hankeln, Wolfgang; Kottmann, Renzo; Quast, Christian; Glöckner, Frank O

    2012-08-01

    The Global Ocean Sampling (GOS) expedition is currently the largest and geographically most comprehensive metagenomic dataset, including samples from the Atlantic, Pacific, and Indian Oceans. This study makes use of the wide range of environmental conditions and habitats encompassed within the GOS sites in order to investigate the ecological structuring of bacterial and archaeal taxon ranks. Community structures based on taxonomically classified 16S ribosomal RNA (rRNA) gene fragments at phylum, class, order, family, and genus rank levels were examined using multivariate statistical analysis, and the results were inspected in the context of oceanographic environmental variables and structured habitat classifications. At all taxon rank levels, community structures of neritic, oceanic, estuarine biomes, as well as other exotic biomes (salt marsh, lake, mangrove), were readily distinguishable from each other. A strong structuring of the communities with chlorophyll a concentration and a weaker yet significant structuring with temperature and salinity were observed. Furthermore, there were significant correlations between community structures and habitat classification. These results were used for further investigation of one-to-one relationships between taxa and environment and provided indications for ecological preferences shaped by primary production for both cultured and uncultured bacterial and archaeal clades. PMID:22416918

  4. Archaeal Genome Guardians Give Insights into Eukaryotic DNA Replication and Damage Response Proteins

    Directory of Open Access Journals (Sweden)

    David S. Shin

    2014-01-01

    Full Text Available As the third domain of life, archaea, like the eukarya and bacteria, must have robust DNA replication and repair complexes to ensure genome fidelity. Archaea moreover display a breadth of unique habitats and characteristics, and structural biologists increasingly appreciate these features. As archaea include extremophiles that can withstand diverse environmental stresses, they provide fundamental systems for understanding enzymes and pathways critical to genome integrity and stress responses. Such archaeal extremophiles provide critical data on the periodic table for life as well as on the biochemical, geochemical, and physical limitations to adaptive strategies allowing organisms to thrive under environmental stress relevant to determining the boundaries for life as we know it. Specifically, archaeal enzyme structures have informed the architecture and mechanisms of key DNA repair proteins and complexes. With added abilities to temperature-trap flexible complexes and reveal core domains of transient and dynamic complexes, these structures provide insights into mechanisms of maintaining genome integrity despite extreme environmental stress. The DNA damage response protein structures noted in this review therefore inform the basis for genome integrity in the face of environmental stress, with implications for all domains of life as well as for biomanufacturing, astrobiology, and medicine.

  5. Geographic distribution of archaeal ammonia oxidizing ecotypes in the Atlantic Ocean

    Directory of Open Access Journals (Sweden)

    Eva eSintes

    2016-02-01

    Full Text Available In marine ecosystems, Thaumarchaeota are most likely the major ammonia oxidizers. While ammonia concentrations vary by about two orders of magnitude in the oceanic water column, archaeal ammonia oxidizers (AOA vary by only one order of magnitude from surface to bathypelagic waters. Thus, the question arises whether the key enzyme responsible for ammonia oxidation, ammonia monooxygenase (amo, exhibits different affinities to ammonia along the oceanic water column and consequently, whether there are different ecotypes of AOA present in the oceanic water column. We determined the abundance and phylogeny of archaeal ammonia oxidizers (AOA based on their amoA gene. Two ecotypes of AOA exhibited a distribution pattern reflecting the reported availability of ammonia and the physico-chemical conditions throughout the Atlantic, and from epi- to bathypelagic waters. The distinction between these two ecotypes was not only detectable at the nucleotide level. Consistent changes were also detected at the amino acid level. These changes include substitutions of polar to hydrophobic amino acid, and glycine substitutions that could have an effect on the configuration of the amo protein and thus, on its activity. Although we cannot identify the specific effect, the ratio of non-synonymous to synonymous substitutions (dN/dS between the two ecotypes indicates a strong positive selection between them. Consequently, our results point to a certain degree of environmental selection on these two ecotypes that have led to their niche specialization.

  6. Bacterial and archaeal dynamics in phylogeny and function in the North Atlantic deep waters

    Science.gov (United States)

    Herndl, G. J.; Brink, M.; Agogue, H.

    2009-04-01

    The diversity and specific functional aspects linked to the N cycle of the bacterio- and archaeoplankton were investigated in the major deep water masses of the North Atlantic following the main driver of the thermohaline circulation, the North Atlantic Deep Water, from 65°N to 5°S. The phylogenetic composition of Bacteria and Archaea is not only depth-dependent but, specific water masses harbor specific prokaryotic communities. The specific composition of these communities in a particular water mass is maintained even over large distances. The distribution of archaeal and bacterial amoA genes were also determined. Archaeal amoA copy numbers decreased drastically with depth especially in the eastern subtropical Atlantic. This coincides with the lower nutrient concentration of the deep waters in the southern parts of the North Atlantic and the older age of the deep-water masses there. These data demonstrate that the diversity and potential nitrification activity are closely linked to the hydrology and chemical characteristics of the major water masses in the North Atlantic.

  7. Archaeal Life on Tangkuban Perahu- Sampling and Culture Growth in Indonesian Laboratories

    Directory of Open Access Journals (Sweden)

    SRI HANDAYANI

    2012-09-01

    Full Text Available The aim of the expedition to Tangkuban Perahu, West Java was to obtain archaeal samples from the solfatara fields located in Domas crater. This was one of the places, where scientists from the University of Regensburg Germany had formerly isolated Indonesian archaea, especially Thermoplasma and Sulfolobus species but not fully characterized. We collected five samples from mud holes with temperatures from 57 to 88 oC and pH of 1.5-2. A portion of each sample was grown at the University of Regensburg in modified Allen’s medium at 80 oC. From four out of five samples enrichment cultures were obtained, autotrophically on elemental sulphur and heterotrophically on sulfur and yeast extract; electron micrographs are presented. In the laboratories of Universitas Indonesia the isolates were cultured at 55-60 oC in order to grow tetraetherlipid synthesizing archaea, both Thermoplasmatales and Sulfolobales. Here, we succeeded to culture the same type of archaeal cells, which had been cultured in Regensburg, probably a Sulfolobus species and in Freundt’s medium, Thermoplasma species. The harvested cells are documented by phase contrast microscope equipped with a digital camera. Our next steps will be to further characterize genetically the cultured cells from Tangkuban Perahu isolates.

  8. 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.

  9. Representing distance, consuming distance

    DEFF Research Database (Denmark)

    Larsen, Gunvor Riber

    Title: Representing Distance, Consuming Distance Abstract: Distance is a condition for corporeal and virtual mobilities, for desired and actual travel, but yet it has received relatively little attention as a theoretical entity in its own right. Understandings of and assumptions about distance...

  10. Birth of Archaeal Cells: Molecular Phylogenetic Analyses of G1P Dehydrogenase, G3P Dehydrogenases, and Glycerol Kinase Suggest Derived Features of Archaeal Membranes Having G1P Polar Lipids

    Science.gov (United States)

    2016-01-01

    Bacteria and Eukarya have cell membranes with sn-glycerol-3-phosphate (G3P), whereas archaeal membranes contain sn-glycerol-1-phosphate (G1P). Determining the time at which cells with either G3P-lipid membranes or G1P-lipid membranes appeared is important for understanding the early evolution of terrestrial life. To clarify this issue, we reconstructed molecular phylogenetic trees of G1PDH (G1P dehydrogenase; EgsA/AraM) which is responsible for G1P synthesis and G3PDHs (G3P dehydrogenase; GpsA and GlpA/GlpD) and glycerol kinase (GlpK) which is responsible for G3P synthesis. Together with the distribution of these protein-encoding genes among archaeal and bacterial groups, our phylogenetic analyses suggested that GlpA/GlpD in the Commonote (the last universal common ancestor of all extant life with a cellular form, Commonote commonote) acquired EgsA (G1PDH) from the archaeal common ancestor (Commonote archaea) and acquired GpsA and GlpK from a bacterial common ancestor (Commonote bacteria). In our scenario based on this study, the Commonote probably possessed a G3P-lipid membrane synthesized enzymatically, after which the archaeal lineage acquired G1PDH followed by the replacement of a G3P-lipid membrane with a G1P-lipid membrane.

  11. Prevalence and predictors of HIV-related stigma among institutional- and community-based caregivers of orphans and vulnerable children living in five less-wealthy countries

    Directory of Open Access Journals (Sweden)

    Messer Lynne C

    2010-08-01

    was positively associated with years of formal education. Conclusions The caregiver-child relationship is central to a child's development. OAC already face stigma as a result of their orphaned or abandoned status; the addition of HIV-related stigma represents a double burden for these children. Further research on the prevalence of HIV-related acceptance and stigma among caregivers and implications of such stigma for child development will be critical as the policy community responds to the global HIV/AIDS orphan crisis.

  12. Archaeal tetraether membrane lipid fluxes in the northeastern Pacific and the Arabian Sea: implications for TEX86 paleothermometry

    NARCIS (Netherlands)

    Wuchter, C.; Schouten, S.; Wakeham, S.G.; Sinninghe Damsté, J.S.

    2006-01-01

    The newly introduced temperature proxy, the tetraether index of archaeal lipids with 86 carbon atoms (TEX86), is based on the number of cyclopentane moieties in the glycerol dialkyl glycerol tetraether (GDGT) lipids of marine Crenarchaeota. The composition of sedimentary GDGTs used for TEX86 paleoth

  13. Structure and genome organization of AFV2, a novel archaeal lipothrixvirus with unusual terminal and core structures

    DEFF Research Database (Denmark)

    Häring, Monika; Vestergaard, Gisle Alberg; Brügger, Kim;

    2005-01-01

    A novel filamentous virus, AFV2, from the hyperthermophilic archaeal genus Acidianus shows structural similarity to lipothrixviruses but differs from them in its unusual terminal and core structures. The double-stranded DNA genome contains 31,787 bp and carries eight open reading frames homologous...

  14. Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an extracellular stage of the reproductive cycle

    DEFF Research Database (Denmark)

    Prangishvili, David; Vestergaard, Gisle Alberg; Häring, Monika;

    2006-01-01

    A novel virus, ATV, of the hyperthermophilic archaeal genus Acidianus has the unique property of undergoing a major morphological development outside of, and independently of, the host cell. Virions are extruded from host cells as lemon-shaped tail-less particles, after which they develop long...

  15. Spatial isolation and environmental factors drive distinct bacterial and archaeal communities in different types of petroleum reservoirs in China

    Science.gov (United States)

    Gao, Peike; Tian, Huimei; Wang, Yansen; Li, Yanshu; Li, Yan; Xie, Jinxia; Zeng, Bing; Zhou, Jiefang; Li, Guoqiang; Ma, Ting

    2016-02-01

    To investigate the spatial distribution of microbial communities and their drivers in petroleum reservoir environments, we performed pyrosequencing of microbial partial 16S rRNA, derived from 20 geographically separated water-flooding reservoirs, and two reservoirs that had not been flooded, in China. The results indicated that distinct underground microbial communities inhabited the different reservoirs. Compared with the bacteria, archaeal alpha-diversity was not strongly correlated with the environmental variables. The variation of the bacterial and archaeal community compositions was affected synthetically, by the mining patterns, spatial isolation, reservoir temperature, salinity and pH of the formation brine. The environmental factors explained 64.22% and 78.26% of the total variance for the bacterial and archaeal communities, respectively. Despite the diverse community compositions, shared populations (48 bacterial and 18 archaeal genera) were found and were dominant in most of the oilfields. Potential indigenous microorganisms, including Carboxydibrachium, Thermosinus, and Neptunomonas, were only detected in a reservoir that had not been flooded with water. This study indicates that: 1) the environmental variation drives distinct microbial communities in different reservoirs; 2) compared with the archaea, the bacterial communities were highly heterogeneous within and among the reservoirs; and 3) despite the community variation, some microorganisms are dominant in multiple petroleum reservoirs.

  16. Detection and analysis of elusive members of a novel and diverse archaeal community within a thermal spring streamer consortium.

    Science.gov (United States)

    Colman, Daniel R; Thomas, Raquela; Maas, Kendra R; Takacs-Vesbach, Cristina D

    2015-03-01

    Recent metagenomic analyses of Yellowstone National Park (YNP) thermal spring communities suggested the presence of minor archaeal populations that simultaneous PCR-based assays using traditional 'universal' 16S rRNA gene primers failed to detect. Here we use metagenomics to identify PCR primers effective at detecting elusive members of the Archaea, assess their efficacy, and describe the diverse and novel archaeal community from a circum-neutral thermal spring from the Bechler region of YNP. We determined that a less commonly used PCR primer, Arch349F, captured more diversity in this spring than the widely used A21F primer. A search of the PCR primers against the RDP 16S rRNA gene database indicated that Arch349F also captured the largest percentage of Archaea, including 41 % more than A21F. Pyrosequencing using the Arch349F primer recovered all of the phylotypes present in the clone-based portion of the study and the metagenome of this spring in addition to several other populations of Archaea, some of which are phylogenetically novel. In contrast to the lack of amplification with traditional 16S rRNA gene primers, our comprehensive analyses suggested a diverse archaeal community in the Bechler spring, with implications for recently discovered groups such as the Geoarchaeota and other undescribed archaeal groups.

  17. Archaeal ammonia oxidation in volcanic grassland soils of Iceland. Effects of elevated temperature and N availability on processes and organisms

    NARCIS (Netherlands)

    Daebeler, A.

    2014-01-01

    Thaumarchaea are recognized today as the most abundant and ubiquitously dis­tributed archaeal organisms, especially in the oceans and soil. Their phylogenetic placement as a phylum, the capability of all cultivated Thaumarchaea to oxidize ammonia for energy conservation as well as many further aspec

  18. Archaeal amoA gene diversity points to distinct biogeography of ammonia-oxidizing Crenarchaeota in the ocean

    NARCIS (Netherlands)

    Sintes, Eva; Bergauer, Kristin; De Corte, Daniele; Yokokawa, Taichi; Herndl, Gerhard J.

    2013-01-01

    Mesophilic ammonia-oxidizing Archaea (AOA) are abundant in a diverse range of marine environments, including the deep ocean, as revealed by the quantification of the archaeal amoA gene encoding the alpha-subunit of the ammonia monooxygenase. Using two different amoA primer sets, two distinct ecotype

  19. The Histamine H4 Receptor: From Orphan to the Clinic

    Directory of Open Access Journals (Sweden)

    Robin L. Thurmond

    2015-03-01

    Full Text Available The histamine H4 receptor (H4R was first noted as a sequence in genomic databases that had features of a G-protein coupled receptor. This putative receptor was found to bind histamine consistent with its homology to other histamine receptors and thus became the fourth member of the histamine receptor family. Due to the previous success of drugs that target the H1 and H2 receptors, an effort was made to understand the function of this receptor and determine if it represented a drug target. Taking advantage of the vast literature on histamine, a search for histamine activity that did not appear to be mediated by the other three histamine receptors was undertaken. From this asthma and pruritus emerged as areas of particular interest. Histamine has long been suspected to play a role in the pathogenesis of asthma, but antihistamines that target the H1 and H2 receptors have not been shown to be effective for this condition. The use of selective ligands in animal models of asthma has now potentially filled this gap by showing a role for the H4R in mediating lung function and inflammation. A similar story exists for chronic pruritus associated with conditions such as atopic dermatitis. Antihistamines that target the H1 receptor are effective in reducing acute pruritus, but are ineffective in pruritus experienced by patients with atopic dermatitis. As for asthma, animal models have now suggested a role for the H4R in mediating pruritic responses, with antagonists to the H4R reducing pruritus in a number of different conditions. The anti-pruritic effect of H4R antagonists has recently been shown in human clinical studies, validating the preclinical findings in the animal models. A selective H4R antagonist inhibited histamine-induced pruritus in health volunteers and reduced pruritus in patients with atopic dermatitis. The history to date of the H4R provides an excellent example of the deorphanization of a novel receptor and the translation of this into

  20. Forest strata drive spatial structure of bacterial and archaeal communities and microbial methane cycling in neotropical bromeliad wetlands

    Science.gov (United States)

    Martinson, Guntars; Brandt, Franziska; Conrad, Ralf

    2016-04-01

    Several thousands of tank bromeliads per hectare of neotropical forest create a unique wetland ecosystem that harbors diverse communities of archaea and bacteria and emit substantial amounts of methane. We studied spatial distribution of archaeal and bacterial communities, microbial methane cycling and their environmental drivers in tank bromeliad wetlands. We selected tank bromeliads of different species and functional types (terrestrial and canopy bromeliads) in a neotropical montane forest of Southern Ecuador and sampled the organic tank slurry. Archaeal and bacterial communities were characterized using terminal-restriction fragment length polymorphism (T-RFLP) and Illumina MiSeq sequencing, respectively, and linked with physico-chemical tank-slurry properties. Additionally, we performed tank-slurry incubations to measure methane production potential, stable carbon isotope fractionation and pathway of methane formation. Archaeal and bacterial community composition in bromeliad wetlands was dominated by methanogens and by Alphaproteobacteria, respectively, and did not differ between species but between functional types. Hydrogenotrophic Methanomicrobiales were the dominant methanogens among all bromeliads but the relative abundance of aceticlastic Methanosaetaceae increased in terrestrial bromeliads. Complementary, hydrogenotrophic methanogenesis was the dominant pathway of methane formation but the relative contribution of aceticlastic methanogenesis increased in terrestrial bromeliads and led to a concomitant increase in total methane production. Rhodospirillales were characteristic for canopy bromeliads, Planctomycetales and Actinomycetalis for terrestrial bromeliads. While nitrogen concentration and pH explained 32% of the archaeal community variability, 29% of the bacterial community variability was explained by nitrogen, acetate and propionate concentrations. Our study demonstrates that bromeliad functional types, associated with different forest strata

  1. Archaeal community in a human-disturbed watershed in southeast China: diversity, distribution, and responses to environmental changes.

    Science.gov (United States)

    Hu, Anyi; Wang, Hongjie; Li, Jiangwei; Liu, Jing; Chen, Nengwang; Yu, Chang-Ping

    2016-05-01

    The response of freshwater bacterial community to anthropogenic disturbance has been well documented, yet the studies of freshwater archaeal community are rare, especially in lotic environments. Here, we investigated planktonic and benthic archaeal communities in a human-perturbed watershed (Jiulong River Watershed, JRW) of southeast China by using Illumina 16S ribosomal RNA gene amplicon sequencing. The results of taxonomic assignments indicated that SAGMGC-1, Methanobacteriaceae, Methanospirillaceae, and Methanoregulaceae were the four most abundant families in surface waters, accounting for 12.65, 23.21, 18.58 and 10.97 % of planktonic communities, whereas Nitrososphaeraceae and Miscellaneous Crenarchaeotic Group occupied more than 49 % of benthic communities. The compositions of archaeal communities and populations in waters and sediments were significantly different from each other. Remarkably, the detection frequencies of families Methanobacteriaceae and Methanospirillaceae, and genera Methanobrevibacter and Methanosphaera in planktonic communities correlated strongly with bacterial fecal indicator, suggesting some parts of methanogenic Archaea may come from fecal contamination. Because soluble reactive phosphorus (SRP) and the ratio of dissolved inorganic nitrogen to SRP instead of nitrogen nutrients showed significant correlation with several planktonic Nitrosopumilus- and Nitrosotalea-like OTUs, Thaumarchaeota may play an unexplored role in biogeochemical cycling of river phosphorus. Multivariate statistical analyses revealed that the variation of α-diversity of planktonic archaeal community was best explained by water temperature, whereas nutrient concentrations and stoichiometry were the significant drivers of β-diversity of planktonic and benthic communities. Taken together, these results demonstrate that the structure of archaeal communities in the JRW is sensitive to anthropogenic disturbances caused by riparian human activities. PMID:26810199

  2. A study of archaeal enzymes involved in polar lipid synthesis linking amino acid sequence information, genomic contexts and lipid composition

    Directory of Open Access Journals (Sweden)

    Hiromi Daiyasu

    2005-01-01

    Full Text Available Cellular membrane lipids, of which phospholipids are the major constituents, form one of the characteristic features that distinguish Archaea from other organisms. In this study, we focused on the steps in archaeal phospholipid synthetic pathways that generate polar lipids such as archaetidylserine, archaetidylglycerol, and archaetidylinositol. Only archaetidylserine synthase (ASS, from Methanothermobacter thermautotrophicus, has been experimentally identified. Other enzymes have not been fully examined. Through database searching, we detected many archaeal hypothetical proteins that show sequence similarity to members of the CDP alcohol phosphatidyltransferase family, such as phosphatidylserine synthase (PSS, phosphatidylglycerol synthase (PGS and phosphatidylinositol synthase (PIS derived from Bacteria and Eukarya. The archaeal hypothetical proteins were classified into two groups, based on the sequence similarity. Members of the first group, including ASS from M. thermautotrophicus, were closely related to PSS. The rough agreement between PSS homologue distribution within Archaea and the experimentally identified distribution of archaetidylserine suggested that the hypothetical proteins are ASSs. We found that an open reading frame (ORF tends to be adjacent to that of ASS in the genome, and that the order of the two ORFs is conserved. The sequence similarity of phosphatidylserine decarboxylase to the product of the ORF next to the ASS gene, together with the genomic context conservation, suggests that the ORF encodes archaetidylserine decarboxylase, which may transform archaetidylserine to archaetidylethanolamine. The second group of archaeal hypothetical proteins was related to PGS and PIS. The members of this group were subjected to molecular phylogenetic analysis, together with PGSs and PISs and it was found that they formed two distinct clusters in the molecular phylogenetic tree. The distribution of members of each cluster within Archaea

  3. 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.

  4. Orphan Basin crustal structure from a dense wide-angle seismic profile - Tomographic inversion

    Science.gov (United States)

    Watremez, Louise; Lau, K. W. Helen; Nedimović, Mladen R.; Louden, Keith E.; Karner, Garry D.

    2014-05-01

    Orphan Basin is located on the eastern margin of Canada, offshore of Newfoundland and East of Flemish Cap. It is an aborted continental rift formed by multiple episodes of rifting. The crustal structure across the basin has been determined by an earlier refraction study using 15 instruments on a 550 km long line. It shows that the continental crust was extended over an unusually wide region but did not break apart. The crustal structure of the basin thus documents stages in the formation of a magma-poor rifted margin up to crustal breakup. The OBWAVE (Orphan Basin Wide-Angle Velocity Experiment) survey was carried out to image crustal structures across the basin and better understand the processes of formation of this margin. The spacing of the 89 recording stations varies from 3 to 5 km along this 500-km-long line, which was acquired along a pre-existing reflection line. The highest resolution section corresponds to the part of the profile where the crust was expected to be the thinnest. We present the results from a joint tomography inversion of first and Moho reflected arrival times. The high data density allows us to define crustal structures with greater detail than for typical studies and to improve the understanding of the processes leading to the extreme stretching of continental crust. The final model was computed following a detailed parametric study to determine the optimal parameters controlling the ray-tracing and the inversion processes. The final model shows very good resolution. In particular, Monte Carlo standard deviations of crustal velocities and Moho depths are generally Orphan Basin is the result of rifting of a non-homogeneous Avalon terrane where the lower crust is primarily ductile.

  5. 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

  6. The human orphan nuclear receptor tailless (TLX, NR2E1 is druggable.

    Directory of Open Access Journals (Sweden)

    Cindy Benod

    Full Text Available Nuclear receptors (NRs are an important group of ligand-dependent transcriptional factors. Presently, no natural or synthetic ligand has been identified for a large group of orphan NRs. Small molecules to target these orphan NRs will provide unique resources for uncovering regulatory systems that impact human health and to modulate these pathways with drugs. The orphan NR tailless (TLX, NR2E1, a transcriptional repressor, is a major player in neurogenesis and Neural Stem Cell (NSC derived brain tumors. No chemical probes that modulate TLX activity are available, and it is not clear whether TLX is druggable. To assess TLX ligand binding capacity, we created homology models of the TLX ligand binding domain (LBD. Results suggest that TLX belongs to an emerging class of NRs that lack LBD helices α1 and α2 and that it has potential to form a large open ligand binding pocket (LBP. Using a medium throughput screening strategy, we investigated direct binding of 20,000 compounds to purified human TLX protein and verified interactions with a secondary (orthogonal assay. We then assessed effects of verified binders on TLX activity using luciferase assays. As a result, we report identification of three compounds (ccrp1, ccrp2 and ccrp3 that bind to recombinant TLX protein with affinities in the high nanomolar to low micromolar range and enhance TLX transcriptional repressive activity. We conclude that TLX is druggable and propose that our lead compounds could serve as scaffolds to derive more potent ligands. While our ligands potentiate TLX repressive activity, the question of whether it is possible to develop ligands to de-repress TLX activity remains open.

  7. 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.

  8. OSMOSE experiment representativity studies.

    Energy Technology Data Exchange (ETDEWEB)

    Aliberti, G.; Klann, R.; Nuclear Engineering Division

    2007-10-10

    The OSMOSE program aims at improving the neutronic predictions of advanced nuclear fuels through measurements in the MINERVE facility at the CEA-Cadarache (France) on samples containing the following separated actinides: Th-232, U-233, U-234, U-235, U-236, U-238, Np-237, Pu-238, Pu-239, Pu-240, Pu-241, Pu-242, Am-241, Am-243, Cm-244 and Cm-245. The goal of the experimental measurements is to produce a database of reactivity-worth measurements in different neutron spectra for the separated heavy nuclides. This database can then be used as a benchmark for integral reactivity-worth measurements to verify and validate reactor analysis codes and integral cross-section values for the isotopes tested. In particular, the OSMOSE experimental program will produce very accurate sample reactivity-worth measurements for a series of actinides in various spectra, from very thermalized to very fast. The objective of the analytical program is to make use of the experimental data to establish deficiencies in the basic nuclear data libraries, identify their origins, and provide guidelines for nuclear data improvements in coordination with international programs. To achieve the proposed goals, seven different neutron spectra can be created in the MINERVE facility: UO2 dissolved in water (representative of over-moderated LWR systems), UO2 matrix in water (representative of LWRs), a mixed oxide fuel matrix, two thermal spectra containing large epithermal components (representative of under-moderated reactors), a moderated fast spectrum (representative of fast reactors which have some slowing down in moderators such as lead-bismuth or sodium), and a very hard spectrum (representative of fast reactors with little moderation from reactor coolant). The different spectra are achieved by changing the experimental lattice within the MINERVE reactor. The experimental lattice is the replaceable central part of MINERVE, which establishes the spectrum at the sample location. This configuration

  9. 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.

  10. Retinoic Acid-Related Orphan Receptors (RORs: Regulatory Functions in Immunity, Development, Circadian Rhythm, and Metabolism

    Directory of Open Access Journals (Sweden)

    Donald N. Cook

    2015-12-01

    Full Text Available In this overview, we provide an update on recent progress made in understanding the mechanisms of action, physiological functions, and roles in disease of retinoic acid related orphan receptors (RORs. We are particularly focusing on their roles in the regulation of adaptive and innate immunity, brain function, retinal development, cancer, glucose and lipid metabolism, circadian rhythm, metabolic and inflammatory diseases and neuropsychiatric disorders. We also summarize the current status of ROR agonists and inverse agonists, including their regulation of ROR activity and their therapeutic potential for management of various diseases in which RORs have been implicated.

  11. TFIIB-directed transcriptional activation by the orphan nuclear receptor hepatocyte nuclear factor 4.

    OpenAIRE

    Malik, S; Karathanasis, S K

    1996-01-01

    The orphan nuclear receptor hepatocyte nuclear factor 4 (HNF-4) is required for development and maintenance of the liver phenotype. HNF-4 activates several hepatocyte-specific genes, including the gene encoding apolipoprotein AI (apoAI), the major protein component of plasma high-density lipoprotein. The apoAI gene is activated by HNF-4 through a nuclear receptor binding element (site A) located in its liver-specific enhancer. To decipher the mechanism whereby HNF-4 enhances apoAI gene transc...

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

    OpenAIRE

    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 t...

  13. The orphan COUP-TF nuclear receptors are markers for neurogenesis from cnidarians to vertebrates

    OpenAIRE

    Gauchat-Feiss, Dominique Madeleine; Escriva, Hector; Miljkovic-Licina, Marijana; Chera, Simona; Langlois, Marie-Claire; Begue, Agnès; Laudet, Vincent; Galliot, Brigitte

    2004-01-01

    In bilaterians, COUP-TF nuclear receptors participate in neurogenesis and/or CNS patterning. In hydra, the nervous system is formed of sensory mechanoreceptor cells (nematocytes) and neuronal cells, both lineages deriving from a common stem cell. The hydra COUP-TF gene, hyCOUP-TF, which encodes highly conserved DNA-binding and ligand-binding domains, belongs to the monophyletic COUP-TFs orphan receptor family (NR2F). In adult polyps, hyCOUP-TF is expressed in nematoblasts and a subset of neur...

  14. The orphan receptor Rev-erbα gene is a target of the circadian clock pacemaker

    OpenAIRE

    Triqueneaux, Gérard; Thenot, Sandrine; Kakizawa, Tomoko; Antoch, Marina P.; Safi, Rachid; Takahashi, Joseph S.; Delaunay, Franck; Laudet, Vincent

    2004-01-01

    Rev-erbα is a ubiquitously expressed orphan nuclear receptor which functions as a constitutive transcriptional repressor and is expressed in vertebrates according to a robust circadian rhythm. We report here that two Rev-erbα mRNA isoforms, namely Rev-erbα1 and Rev-erbα2, are generated through alternative promoter usage and that both show a circadian expression pattern in an in vitro system using serum-shocked fibroblasts. Both promoter regions P1 (Rev-erbα1) and P2 (Rev-erbα2) contain severa...

  15. The σ enigma: bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs.

    Science.gov (United States)

    Burton, Samuel P; Burton, Zachary F

    2014-01-01

    Structural comparisons of initiating RNA polymerase complexes and structure-based amino acid sequence alignments of general transcription initiation factors (eukaryotic TFIIB, archaeal TFB and bacterial σ factors) show that these proteins are homologs. TFIIB and TFB each have two-five-helix cyclin-like repeats (CLRs) that include a C-terminal helix-turn-helix (HTH) motif (CLR/HTH domains). Four homologous HTH motifs are present in bacterial σ factors that are relics of CLR/HTH domains. Sequence similarities clarify models for σ factor and TFB/TFIIB evolution and function and suggest models for promoter evolution. Commitment to alternate modes for transcription initiation appears to be a major driver of the divergence of bacteria and archaea. PMID:25483602

  16. Biological Membranes in Extreme Conditions: Simulations of Anionic Archaeal Tetraether Lipid Membranes.

    Directory of Open Access Journals (Sweden)

    Luis Felipe Pineda De Castro

    Full Text Available In contrast to the majority of organisms that have cells bound by di-ester phospholipids, archaeal membranes consist of di- and tetraether phospholipids. Originating from organisms that withstand harsh conditions (e.g., low pH and a wide range of temperatures such membranes have physical properties that make them attractive materials for biological research and biotechnological applications. We developed force-field parameters based on the widely used Generalized Amber Force Field (GAFF to enable the study of anionic tetraether membranes of the model archaean Sulfolobus acidocaldarius by computer simulations. The simulations reveal that the physical properties of these unique membranes depend on the number of cyclopentane rings included in each lipid unit, and on the size of cations that are used to ensure charge neutrality. This suggests that the biophysical properties of Sulfolobus acidocaldarius cells depend not only on the compositions of their membranes but also on the media in which they grow.

  17. Archaeal Abundance across a pH Gradient in an Arable Soil and Its Relationship to Bacterial and Fungal Growth Rates

    OpenAIRE

    Bengtson, Per; Sterngren, Anna E.; Rousk, Johannes

    2012-01-01

    Soil pH is one of the most influential factors for the composition of bacterial and fungal communities, but the influence of soil pH on the distribution and composition of soil archaeal communities has yet to be systematically addressed. The primary aim of this study was to determine how total archaeal abundance (quantitative PCR [qPCR]-based estimates of 16S rRNA gene copy numbers) is related to soil pH across a pH gradient (pH 4.0 to 8.3). Secondarily, we wanted to assess how archaeal abund...

  18. MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes

    Directory of Open Access Journals (Sweden)

    Yang Yi-Fan

    2007-03-01

    Full Text Available Abstract Background Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also facilitate comparative studies of prokaryotic genomes. Results This paper describes a new prokaryotic genefinding algorithm based on a comprehensive statistical model of protein coding Open Reading Frames (ORFs and Translation Initiation Sites (TISs. The former is based on a linguistic "Entropy Density Profile" (EDP model of coding DNA sequence and the latter comprises several relevant features related to the translation initiation. They are combined to form a so-called Multivariate Entropy Distance (MED algorithm, MED 2.0, that incorporates several strategies in the iterative program. The iterations enable us to develop a non-supervised learning process and to obtain a set of genome-specific parameters for the gene structure, before making the prediction of genes. Conclusion Results of extensive tests show that MED 2.0 achieves a competitive high performance in the gene prediction for both 5' and 3' end matches, compared to the current best prokaryotic gene finders. The advantage of the MED 2.0 is particularly evident for GC-rich genomes and archaeal genomes. Furthermore, the genome-specific parameters given by MED 2.0 match with the current understanding of prokaryotic genomes and may serve as tools for comparative genomic studies. In particular, MED 2.0 is shown to reveal divergent translation initiation mechanisms in archaeal genomes while making a more accurate prediction of TISs compared to the existing gene finders and the current GenBank annotation.

  19. Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest.

    Science.gov (United States)

    Rasche, Frank; Knapp, Daniela; Kaiser, Christina; Koranda, Marianne; Kitzler, Barbara; Zechmeister-Boltenstern, Sophie; Richter, Andreas; Sessitsch, Angela

    2011-03-01

    It was hypothesized that seasonality and resource availability altered through tree girdling were major determinants of the phylogenetic composition of the archaeal and bacterial community in a temperate beech forest soil. During a 2-year field experiment, involving girdling of beech trees to intercept the transfer of easily available carbon (C) from the canopy to roots, members of the dominant phylogenetic microbial phyla residing in top soils under girdled versus untreated control trees were monitored at bimonthly intervals through 16S rRNA gene-based terminal restriction fragment length polymorphism profiling and quantitative PCR analysis. Effects on nitrifying and denitrifying groups were assessed by measuring the abundances of nirS and nosZ genes as well as bacterial and archaeal amoA genes. Seasonal dynamics displayed by key phylogenetic and nitrogen (N) cycling functional groups were found to be tightly coupled with seasonal alterations in labile C and N pools as well as with variation in soil temperature and soil moisture. In particular, archaea and acidobacteria were highly responsive to soil nutritional and soil climatic changes associated with seasonality, indicating their high metabolic versatility and capability to adapt to environmental changes. For these phyla, significant interrelations with soil chemical and microbial process data were found suggesting their potential, but poorly described contribution to nitrification or denitrification in temperate forest soils. In conclusion, our extensive approach allowed us to get novel insights into effects of seasonality and resource availability on the microbial community, in particular on hitherto poorly studied bacterial phyla and functional groups.

  20. Representing and Performing Businesses

    DEFF Research Database (Denmark)

    Boll, Karen

    2014-01-01

    This article investigates a segmentation model used by the Danish Tax and Customs Administration to classify businesses’ motivational postures. The article uses two different conceptualisations of performativity to analyse what the model’s segmentations do: Hacking’s notion of making up people...... and MacKenzie’s idea of performativity. Based on these two approaches, the article demonstrates that the segmentation model represents and performs the businesses as it makes up certain new ways to be a business and as the businesses can be seen as moving targets. Inspired by MacKenzie the argument...... around it is in motion and can be shaped, however, it sees itself as stable. This assumption turns out to be problematic as the tax administration questions the model’s ability to produce valid comparisons. The article presents a detailed analysis of the model’s performativity, providing an example...

  1. Representative of the municipality

    International Nuclear Information System (INIS)

    Full text of publication follows. The decommissioning of the Vandellos-I nuclear power plant was a big challenge for the host community of Vandellos i l'Hospitalet de l'Infant and the close-by region. Closing down of the facility resulted in a rise of unemployment and a decrease of municipal income. The public was concerned with three issues: safety, transparency and information about the decommissioning, and economic future. Therefore, from the very beginning, municipal governments entered into negotiations with ENRESA on socio-economic benefits, including local employment in dismantling activities, and other types of financial and non-financial compensation. The ADE business association, i.e. a network of business organisations was created that guided the allotment of work to local firms. To satisfy public demand, local municipalities focused on the triad of safety, dialogue and local development, considered the three 'pillars of trust'. A Municipal Monitoring Commission was created, made up of representatives of affected municipalities, the regional government, the ADE business association, trade unions, the local university, the NPP management and ENRESA to monitor the dismantling process and regularly inform the local public. Items that were handled by this Commission included: - Work process monitoring. - Workers. - Materials Control. - Conventional and radioactive or contaminated waste management. - Emanation waste management (liquid and gas) - Safety (training and accidents). - Surveillance (radiological and environmental: dust, noise). - Effects. - Fulfillment of agreed conditions. A number of communication tools and channels were used, e.g., public information meetings, an information centre, the municipal magazine, the municipal radio station, and meetings with representatives of the local press. Particularly innovative was the idea to ask academics from the University of Tarragona to help with 'translating' technical information into language that could

  2. 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.

  3. FTZ-F1-related orphan receptors in Xenopus laevis: transcriptional regulators differentially expressed during early embryogenesis.

    OpenAIRE

    Ellinger-Ziegelbauer, H.; Hihi, A K; Laudet, V; Keller, H.; Wahli, W; Dreyer, C

    1994-01-01

    Orphan receptors of the FTZ-F1-related group of nuclear receptors (xFF1r) were identified in Xenopus laevis by isolation of cDNAs from a neurula stage library. Two cDNAs were found, which encode full length, highly related receptor proteins, xFF1rA and B, whose closet relative known so far is the murine LRH-1 orphan receptor. xFF1rA protein expressed by a recombinant vaccinia virus system specifically binds to FTZ-F1 response elements (FRE; PyCAAGGPyCPu). In cotransfection studies, xFF1rA con...

  4. 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.

  5. 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 ...

  6. Analysis of in planta Expressed Orphan Genes in the Rice Blast Fungus Magnaporthe oryzae

    Directory of Open Access Journals (Sweden)

    Abu Sadat

    2014-12-01

    Full Text Available Genomes contain a large number of unique genes which have not been found in other species. Although the origin of such “orphan” genes remains unclear, they are thought to be involved in species-specific adaptive processes. Here, we analyzed seven orphan genes (MoSPC1 to MoSPC7 prioritized based on in planta expressed sequence tag data in the rice blast fungus, Magnaporthe oryzae. Expression analysis using qRT-PCR confirmed the expression of four genes (MoSPC1, MoSPC2, MoSPC3 and MoSPC7 during plant infection. However, individual deletion mutants of these four genes did not differ from the wild-type strain for all phenotypes examined, including pathogenicity. The length, GC contents, codon adaptation index and expression during mycelial growth of the four genes suggest that these genes formed during the evolutionary history of M. oryzae. Synteny analyses using closely related fungal species corroborated the notion that these genes evolved de novo in the M. oryzae genome. In this report, we discuss our inability to detect phenotypic changes in the four deletion mutants. Based on these results, the four orphan genes may be products of de novo gene birth processes, and their adaptive potential is in the course of being tested for retention or extinction through natural selection.

  7. Oncogenic conversion of a novel orphan nuclear receptor by chromosome translocation.

    Science.gov (United States)

    Labelle, Y; Zucman, J; Stenman, G; Kindblom, L G; Knight, J; Turc-Carel, C; Dockhorn-Dworniczak, B; Mandahl, N; Desmaze, C; Peter, M

    1995-12-01

    A recurrent t(9;22) (q22;q12) chromosome translocation has been described in extraskeletal myxoid chondrosarcoma (EMC). Fluorescent in situ hybridization experiments performed on one EMC tumour indicated that the chromosome 22 breakpoint occurred in the EWS gene. Northern blot analysis revealed an aberrant EWS transcript which is cloned by a modified RT-PCR procedure. This transcript consists of an in-frame fusion of the 5' end of EWS to a previously unidentified gene, which was named TEC. This fusion transcript was detected in six of eight EMC studied, and three different junction types between the two genes were found. In all junction types, the putative translation product contained the amino-terminal transactivation domain of EWS linked to the entire TEC protein. Homology analysis showed that the predicted TEC protein contains a DNA-binding domain characteristic of nuclear receptors. The highest identity scores were observed with the NURR1 family of orphan nuclear receptors. These receptors are involved in the control of cell proliferation and differentiation by modulating the response to growth factors and retinoic acid. This work provides, after the PML/RAR alpha gene fusion, the second example of the oncogenic conversion of a nuclear receptor and the first example involving the orphan subfamily. Analysis of the disturbance induced by the EWS/TEc protein in the nuclear receptor network and their target genes may lead to new approaches for EMC treatment. PMID:8634690

  8. Extremely Soft X-Ray Flash as the Indicator of Off-axis Orphan GRB Afterglow

    Science.gov (United States)

    Urata, Yuji; Huang, Kuiyun; Yamazaki, Ryo; Sakamoto, Takanori

    2015-06-01

    We verified the off-axis jet model of X-ray flashes (XRFs) and examined a discovery of off-axis orphan gamma-ray burst (GRB) 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}{obs}{src}, (2) redshift measurements, and (3) multicolor observations of an earlier (or brightening) phase. XRF 020903 was the only sample selected on the basis of these criteria. A complete optical multicolor afterglow light curve of XRF 020903 obtained from archived data and photometric results in the 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, {θ }{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 (\\gt ∼ 2{θ }{jet}) could be discovered using an 8 m class telescope with wide-field imagers such as the Subaru Hyper-Suprime-Cam and the Large Synoptic Survey Telescope.

  9. 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.

  10. A Qualitative Study of Mental Health Problems Among Orphaned Children and Adolescents in Tanzania.

    Science.gov (United States)

    Dorsey, Shannon; Lucid, Leah; Murray, Laura; Bolton, Paul; Itemba, Dafrosa; Manongi, Rachel; Whetten, Kathryn

    2015-11-01

    Low- and middle-income countries have a high number of orphans, many of whom have unmet mental health needs. Effective mental health interventions are needed; however, it is necessary to understand how mental health symptoms and needs are perceived locally to tailor interventions and refine measurement of intervention effects. We used an existing rapid ethnographic assessment approach to identify mental health problems from the perspective of orphans and guardians to inform a subsequent randomized controlled trial of a Western-developed, evidence-based psychosocial intervention, Trauma-focused Cognitive Behavioral Therapy. Local Kiswahili-speaking interviewers conducted 73 free list interviews and 34 key informant interviews. Results identified both common cross-cultural experiences and symptoms as well as uniquely described symptoms (e.g., lacking peace, being discriminated against) not typically targeted by the intervention or included on standardized measures of intervention effects. We discuss implications for adapting mental health interventions in low- and middle-income countries and assessing effectiveness. PMID:26488916

  11. Identification of a Binding Site for Unsaturated Fatty Acids in the Orphan Nuclear Receptor Nurr1.

    Science.gov (United States)

    de Vera, Ian Mitchelle S; Giri, Pankaj K; Munoz-Tello, Paola; Brust, Richard; Fuhrmann, Jakob; Matta-Camacho, Edna; Shang, Jinsai; Campbell, Sean; Wilson, Henry D; Granados, Juan; Gardner, William J; Creamer, Trevor P; Solt, Laura A; Kojetin, Douglas J

    2016-07-15

    Nurr1/NR4A2 is an orphan nuclear receptor, and currently there are no known natural ligands that bind Nurr1. A recent metabolomics study identified unsaturated fatty acids, including arachidonic acid and docosahexaenoic acid (DHA), that interact with the ligand-binding domain (LBD) of a related orphan receptor, Nur77/NR4A1. However, the binding location and whether these ligands bind other NR4A receptors were not defined. Here, we show that unsaturated fatty acids also interact with the Nurr1 LBD, and solution NMR spectroscopy reveals the binding epitope of DHA at its putative ligand-binding pocket. Biochemical assays reveal that DHA-bound Nurr1 interacts with high affinity with a peptide derived from PIASγ, a protein that interacts with Nurr1 in cellular extracts, and DHA also affects cellular Nurr1 transactivation. This work is the first structural report of a natural ligand binding to a canonical NR4A ligand-binding pocket and indicates a natural ligand can bind and affect Nurr1 function. PMID:27128111

  12. X-RAY OBSERVATIONS OF DISRUPTED RECYCLED PULSARS: NO REFUGE FOR ORPHANED CENTRAL COMPACT OBJECTS

    International Nuclear Information System (INIS)

    We present a Chandra X-ray survey of the disrupted recycled pulsars (DRPs), isolated radio pulsars with P > 20 ms and Bs 10 G. These observations were motivated as a search for the immediate descendants of the ≈10 central compact objects (CCOs) in supernova remnants (SNRs), 3 of which have similar timing and magnetic properties as the DRPs, but are bright, thermal X-ray sources consistent with minimal neutron star (NS) cooling curves. Since none of the DPRs were detected in this survey, there is no evidence that they are ''orphaned'' CCOs, NSs whose SNRs has dissipated. Upper limits on their thermal X-ray luminosities are in the range of log Lx [erg s–1] = 31.8-32.8, which implies cooling ages >104-105 yr, roughly 10 times the ages of the ≈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, Bs ) 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 the fall-back of supernova ejecta, but quickly regrow to join the normal pulsar population

  13. 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.

  14. Trends in individual reimbursement of orphan drugs in Latvia in 2008–2011

    Directory of Open Access Journals (Sweden)

    Logviss K.

    2014-01-01

    Full Text Available Orphan drugs (ODs are medicinal products intended for diagnosis, prevention or treatment of life-threatening or very serious diseases affecting less than 5 in 10 000 people in the European Union (EU. These drugs are called “orphans” because the pharmaceutical industry has little interest, under normal market conditions, in developing and marketing products intended for only a small number of patients suffering from very rare conditions. Because of the small market, ODs are often very expensive. Whereas decisions surrounding orphan designation and marketing authorization of ODs are taken at the EU level, decisions governing pricing and reimbursement of ODs are a member state responsibility. In Latvia drug reimbursement covers drugs which are included in the national reimbursement drug list or, based on the medical council's decision, drugs can also be reimbursed within the framework of individual reimbursement system with limit of 10 000 LVL (€ 14 229 per patient per year. Due to the big costs and the small number of patients ODs are often not included in the reimbursement list and therefore are reimbursed individually.

  15. The influence of orphan care and other household shocks on health status over time: a longitudinal study of children's caregivers in rural Malawi.

    Science.gov (United States)

    Littrell, Megan; Boris, Neil W; Brown, Lisanne; Hill, Michael; Macintyre, Kate

    2011-12-01

    In the context of rising rates of orphanhood in AIDS-affected settings, very little is understood about implications for caregiver well-being given increasing and intensifying responsibilities for the care of orphaned children. Emotional distress and self-reported health status as well as shifts in household orphan care, wealth, food security and recent illness and death among household members were measured among a panel of 1219 caregivers in rural Malawi between 2007 and 2009. Logistic regression was used to identify predictors of improved and diminished caregiver health and emotional distress. Results suggest that becoming an orphan caregiver is associated with a shift from good to poor health status (adjusted odds ratio [AOR]=2.29, 95% confidence interval [CI]=1.16-4.54), and that elevated levels of distress and poor health both persist over time in comparison with care for non-orphans only. Once engaged in orphan care, taking on additional orphans is associated with increased emotional distress in relation to not caring for orphans (AOR=3.16, 95% CI=1.30-7.73) as well as in relation to maintaining the same number of orphans in care over time (AOR=2.84, 95% CI=1.04-7.70). In addition, findings illustrate the strong influence of household wealth and food security on caregiver well-being. Food insecurity and poverty that persist or develop over time are associated with increasing distress. Conversely, maintenance or improvement in food security and household wealth are associated with decreases in distress. Providing all aspects of household maintenance and care for children, primary caregivers are key to the extended family solution for orphaned and vulnerable children. Bolstering the foundation of rural African families to ensure care and protection of these children involves targeting support to orphan caregivers but must also include addressing the issues of poverty and food insecurity that pose a wider threat to caregiving capacity. PMID:21711171

  16. Archaeal and bacterial tetraether lipids in tropical ponds with contrasted salinity (Guadeloupe, French West Indies): Implications for tetraether-based environmental proxies

    OpenAIRE

    Huguet, Arnaud; Grossi, Vincent; Belmahdi, Imène; Fosse, Céline; Derenne, Sylvie

    2015-01-01

    International audience The occurrence and distribution of archaeal and bacterial glycerol dialkyl glycerol tetraether lipids (GDGTs) in continental saline environments have been rarely investigated. Here, the abundance and distribution of archaeal isoprenoid GDGTs (iGDGTs) and archaeol, and of bacterial branched GDGTs (brGDGTs) in four tropical water ponds of contrasting salinity in two islands from the French Western Indies, Grande-Terre and La Désirade, have been determined. The sediment...

  17. Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs

    OpenAIRE

    Frade, Pedro R.; Katharina Roll; Kristin Bergauer; Herndl, Gerhard J.

    2016-01-01

    Comparative studies on the distribution of archaeal versus bacterial communities associated with the surface mucus layer of corals have rarely taken place. It has therefore remained enigmatic whether mucus-associated archaeal and bacterial communities exhibit a similar specificity towards coral hosts and whether they vary in the same fashion over spatial gradients and between reef locations. We used microbial community profiling (terminal-restriction fragment length polymorphism, T-RFLP) and ...

  18. 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).

  19. 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…

  20. 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…

  1. Effectiveness of Group Activity Play Therapy on Internalizing and Externalizing Behavior Problems of Preadolescent Orphans in Uganda

    Science.gov (United States)

    Ojiambo, Deborah

    2011-01-01

    This pilot study investigated the impact of group activity play therapy (GAPT) on displaced orphans aged 10 to 12 years living in a large children's village in Uganda. Teachers and housemothers identified 60 preadolescents exhibiting clinical levels of internalizing and externalizing behavior problems. The participants' ethnicity was…

  2. How Zimbabwean AIDS Orphans Negotiate Their Personal Identities within the Fields of Home and School in a Stigmatising Society

    Science.gov (United States)

    Kwenda, Chiwimbiso M.

    2009-01-01

    This study is based on field data originally collected for a PhD research project in a small district of Zimbabwe. The study attempts to answer the question about how AIDS orphaned children in a selected context in Zimbabwe construct their concept of self as members of their changed and recomposing families, and as members of their school and…

  3. The orphan gene ybjN conveys pleiotropic effects on multicellular behavior and survival of Escherichia coli

    Science.gov (United States)

    YbjN, an enterobacteria-specific protein, is a multicopy suppressor of ts9 temperature sensitivity in Escherichia coli. In this study, we further explored the roles of ybjN, an orphan gene in E. coli. First, we demonstrated that ybjN gene was down-regulated about 10-fold in ts9 strain compared to th...

  4. Length of Institutionalization, Contact with Relatives and Previous Hospitalizations as Predictors of Social and Emotional Behavior in Young Ugandan Orphans

    Science.gov (United States)

    Nielsen, Ashley; Coleman, Priscilla K.; Guinn, Matthew; Robb, Clifford

    2004-01-01

    The objectives of this study were to describe the socially based emotions and behaviors of 33 orphans in Uganda and to examine social history correlates of variability in the outcome measures. The toddlers were generally not very aggressive or prosocially oriented, and they displayed rather limited affect. More time was spent alone than with…

  5. National Strategy for Regaining Control over Orphan Sources and Improving Control over Vulnerable Sources. Specific Safety Guide (French Edition)

    International Nuclear Information System (INIS)

    This Safety Guide is intended to provide recommendations on the establishment of a national strategy for regaining control over orphan radioactive sources and for improving control over vulnerable radioactive sources. It provides guidance on how to assess the national situation, and develop and implement a national strategy to achieve these goals

  6. Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing.

    Science.gov (United States)

    Wang, Lei; Huang, Xu; Zheng, Tian-Ling

    2016-08-15

    This study aimed to investigate microbial responses to nitrate stimulation in oiled mangrove mesocosm. Both supplementary oil and nitrate changed the water and sediment chemical properties contributing to the shift of microbial communities. Denitrifying genes nirS and nirK were increased several times by the interaction of oil spiking and nitrate addition. Bacterial chao1 was reduced by oil spiking and further by nitrate stimulation, whereas archaeal chao1 was only inhibited by oil pollution on early time. Sampling depth explained most of variation and significantly impacted bacterial and archaeal communities, while oil pollution only significantly impacted bacterial communities (pexplaining less variation, nitrate addition coupled with oil spiking enhanced the growth of hydrocarbon degraders in mangrove. The findings demonstrate the impacts of environmental factors and their interactions in shaping microbial communities during nitrate stimulation. Our study suggests introducing genera Desulfotignum and Marinobacter into oiled mangrove for bioaugmentation. PMID:27262497

  7. Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing.

    Science.gov (United States)

    Wang, Lei; Huang, Xu; Zheng, Tian-Ling

    2016-08-15

    This study aimed to investigate microbial responses to nitrate stimulation in oiled mangrove mesocosm. Both supplementary oil and nitrate changed the water and sediment chemical properties contributing to the shift of microbial communities. Denitrifying genes nirS and nirK were increased several times by the interaction of oil spiking and nitrate addition. Bacterial chao1 was reduced by oil spiking and further by nitrate stimulation, whereas archaeal chao1 was only inhibited by oil pollution on early time. Sampling depth explained most of variation and significantly impacted bacterial and archaeal communities, while oil pollution only significantly impacted bacterial communities (poil spiking enhanced the growth of hydrocarbon degraders in mangrove. The findings demonstrate the impacts of environmental factors and their interactions in shaping microbial communities during nitrate stimulation. Our study suggests introducing genera Desulfotignum and Marinobacter into oiled mangrove for bioaugmentation.

  8. Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring.

    Directory of Open Access Journals (Sweden)

    Changrui Lu

    Full Text Available BACKGROUND: The exosome complex is an essential RNA 3'-end processing and degradation machinery. In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry. METHODOLOGY/PRINCIPAL FINDINGS: Here we report an asymmetric 2.9 A Sulfolobus solfataricus archaeal exosome structure in which the three-fold symmetry is broken due to combined rigid body and thermal motions mainly within the RNA-binding ring. Since increased conformational flexibility was also observed in the RNA-binding ring of the related bacterial PNPase, we speculate that this may reflect an evolutionarily conserved mechanism to accommodate diverse RNA substrates for degradation. CONCLUSION/SIGNIFICANCE: This study clearly shows the dynamic structures within the RNA-binding domains, which provides additional insights on mechanism of asymmetric RNA binding and processing.

  9. Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts

    Science.gov (United States)

    Woese, C. R.; Achenbach, L.; Rouviere, P.; Mandelco, L.

    1991-01-01

    A major and too little recognized source of artifact in phylogenetic analysis of molecular sequence data is compositional difference among sequences. The problem becomes particularly acute when alignments contain ribosomal RNAs from both mesophilic and thermophilic species. Among prokaryotes the latter are considerably higher in G + C content than the former, which often results in artificial clustering of thermophilic lineages and their being placed artificially deep in phylogenetic trees. In this communication we review archaeal phylogeny in the light of this consideration, focusing in particular on the phylogenetic position of the sulfate reducing species Archaeoglobus fulgidus, using both 16S rRNA and 23S rRNA sequences. The analysis shows clearly that the previously reported deep branching of the A. fulgidus lineage (very near the base of the euryarchaeal side of the archaeal tree) is incorrect, and that the lineage actually groups with a previously recognized unit that comprises the Methanomicrobiales and extreme halophiles.

  10. Bacterial and Archaeal Communities Variability Associated with Upwelling and Anthropogenic Pressures in the Protection Area of Arraial do Cabo (Cabo Frio region - RJ).

    Science.gov (United States)

    Coelho-Souza, Sergio A; Araújo, Fábio V; Cury, Juliano C; Jesus, Hugo E; Pereira, Gilberto C; Guimarães, Jean R D; Peixoto, Raquel S; Dávila, Alberto M R; Rosado, Alexandre S

    2015-09-01

    Upwelling systems contain a high diversity of pelagic microorganisms and their composition and activity are defined by factors like temperature and nutrient concentration. Denaturing gradient gel electrophoresis (DGGE) technique was used to verify the spatial and temporal genetic variability of Bacteria and Archaea in two stations of the Arraial do Cabo coastal region, one under upwelling pressure and another under anthropogenic pressure. In addition, biotic and abiotic variables were measured in surface and deep waters from three other stations between these stations. Six samplings were done during a year and adequately represented the degrees of upwelling and anthropogenic pressures to the system. Principal Component Analysis (PCA) showed negative correlations between the concentrations of ammonia and phosphorous with prokaryotic secondary production and the total heterotrophic bacteria. PCA also showed negative correlation between temperature and the abundance of prokaryotic cells. Bacterial and archaeal compositions were changeable as were the oceanographic conditions, and upwelling had a regional pressure while anthropogenic pressure was punctual. We suggest that the measurement of prokaryotic secondary production was associated with both Bacteria and Archaea activities, and that substrate availability and temperature determine nutrients cycling. PMID:26375020

  11. Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers

    Directory of Open Access Journals (Sweden)

    Céline Brochier-Armanet

    2006-01-01

    Full Text Available Reverse gyrase, an enzyme of uncertain funtion, is present in all hyperthermophilic archaea and bacteria. Previous phylogenetic studies have suggested that the gene for reverse gyrase has an archaeal origin and was transferred laterally (LGT to the ancestors of the two bacterial hyperthermophilic phyla, Thermotogales and Aquificales. Here, we performed an in-depth analysis of the evolutionary history of reverse gyrase in light of genomic progress. We found genes coding for reverse gyrase in the genomes of several thermophilic bacteria that belong to phyla other than Aquificales and Thermotogales. Several of these bacteria are not, strictly speaking, hyperthermophiles because their reported optimal growth temperatures are below 80 °C. Furthermore, we detected a reverse gyrase gene in the sequence of the large plasmid of Thermus thermophilus strain HB8, suggesting a possible mechanism of transfer to the T. thermophilus strain HB8 involving plasmids and transposases. The archaeal part of the reverse gyrase tree is congruent with recent phylogenies of the archaeal domain based on ribosomal proteins or RNA polymerase subunits. Although poorly resolved, the complete reverse gyrase phylogeny suggests an ancient acquisition of the gene by bacteria via one or two LGT events, followed by its secondary distribution by LGT within bacteria. Finally, several genes of archaeal origin located in proximity to the reverse gyrase gene in bacterial genomes have bacterial homologues mostly in thermophiles or hyperthermophiles, raising the possibility that they were co-transferred with the reverse gyrase gene. Our new analysis of the reverse gyrase history strengthens the hypothesis that the acquisition of reverse gyrase may have been a crucial evolutionary step in the adaptation of bacteria to high-temperature environments. However, it also questions the role of this enzyme in thermophilic bacteria and the selective advantage its presence could provide.

  12. Archaeal tetraether membrane lipid fluxes in the northeastern Pacific and the Arabian Sea: implications for TEX86 paleothermometry

    OpenAIRE

    Wuchter, C.; Schouten, S.; Wakeham, S.G.; Sinninghe Damsté, J.S.

    2006-01-01

    The newly introduced temperature proxy, the tetraether index of archaeal lipids with 86 carbon atoms (TEX86), is based on the number of cyclopentane moieties in the glycerol dialkyl glycerol tetraether (GDGT) lipids of marine Crenarchaeota. The composition of sedimentary GDGTs used for TEX86 paleothermometry is thought to reflect sea surface temperature (SST). However, marine Crenarchaeota occur ubiquitously in the world oceans over the entire depth range and not just in surface waters. We an...

  13. [Effects of long-term fertilization on bacterial and archaeal diversity and community structure within subtropical red paddy soils].

    Science.gov (United States)

    Yuan, Hong-zhao; Wu, Hao; Ge, Ti-da; Li, Ke-lin; Wu, Jin-shui; Wang, Jiu-rong

    2015-06-01

    Paddy soils not only function as an important sink for "missing carbon" but also play an important role in the production of greenhouse gases such as N2O and CH4. Dynamic changes in greenhouse gases in the atmosphere are closely related to microbially mediated carbon and nitrogen transformation processes occurring in soil. Using soil samples collected from a long-term fertilization experimental site in Taojiang County, subtropical China (established in 1986), we determined the effects of long-term (>25 years) non-fertilization (CK), chemical fertilization (NPK), and NPK combined with rice straw residues (NPKS) on soil bacterial and archaeal community structures. The 16S rRNA genotypes from the three differently treated soils were divided into 9 bacterial phylotypes, mainly including Proteobacteria, Acidobacteria, Chloroflexi, and archaea of Crenarchaeota and Euryarchaeota. The relative abundance of Proteobacteria, Acidobacteria and Crenarchaeota increased in the soils under NPK and NPKS treatments, with the increase being greater in the latter treatment. LUBSHUFF statistical analyses also demonstrated that there was significant difference among the microbial community compositions in CK-, NPK- and NPKS-treated soils. The abundance of bacterial and archaeal 16S rRNA genes ranged from 0.58 x 10(10) to 1.06 x 10(10) copies · g(-1) dry soil and from 1.16 x 10(6) to 1.72 x 10(6) copies · g(-1) dry soil, respectively. Application of fertilizers increased the bacterial and archaeal abundance and diversity in the treated soils, with NPKS > NPK. Long-term chemical and organic applications significantly affected the abundance, diversity and composition of bacterial and archaeal communities in paddy ecosystems. PMID:26572036

  14. Archaeal and bacterial community dynamics and bioprocess performance of a bench-scale two-stage anaerobic digester.

    Science.gov (United States)

    Gonzalez-Martinez, Alejandro; Garcia-Ruiz, Maria Jesus; Rodriguez-Sanchez, Alejandro; Osorio, Francisco; Gonzalez-Lopez, Jesus

    2016-07-01

    Two-stage technologies have been developed for anaerobic digestion of waste-activated sludge. In this study, the archaeal and bacterial community structure dynamics and bioprocess performance of a bench-scale two-stage anaerobic digester treating urban sewage sludge have been studied by the means of high-throughput sequencing techniques and physicochemical parameters such as pH, dried sludge, volatile dried sludge, acid concentration, alkalinity, and biogas generation. The coupled analyses of archaeal and bacterial communities and physicochemical parameters showed a direct relationship between archaeal and bacterial populations and bioprocess performance during start-up and working operation of a two-stage anaerobic digester. Moreover, results demonstrated that archaeal and bacterial community structure was affected by changes in the acid/alkalinity ratio in the bioprocess. Thus, a predominance of the acetoclastic methanogen Methanosaeta was observed in the methanogenic bioreactor at high-value acid/alkaline ratio, while a predominance of Methanomassilicoccaeceae archaea and Methanoculleus genus was observed in the methanogenic bioreactor at low-value acid/alkaline ratio. Biodiversity tag-iTag sequencing studies showed that methanogenic archaea can be also detected in the acidogenic bioreactor, although its biological activity was decreased after 4 months of operation as supported by physicochemical analyses. Also, studies of the VFA producers and VFA consumers microbial populations showed as these microbiota were directly affected by the physicochemical parameters generated in the bioreactors. We suggest that the results obtained in our study could be useful for future implementations of two-stage anaerobic digestion processes at both bench- and full-scale. PMID:26940050

  15. Similarities and Contrasts in the Archaeal Community of Two Japanese Mountains: Mt. Norikura Compared to Mt. Fuji.

    Science.gov (United States)

    Singh, Dharmesh; Takahashi, Koichi; Park, Jungok; Adams, Jonathan M

    2016-02-01

    The community ecology, abundance, and diversity patterns of soil archaea are poorly understood-despite the fact that they are a major branch of life that is ubiquitous and important in nitrogen cycling in terrestrial ecosystems. We set out to investigate the elevational patterns of archaeal ecology, and how these compare with other groups of organisms. Many studies of different groups of organisms (plants, birds, etc.) have shown a series of distinct communities with elevation, and often a diversity maximum in mid-elevations. We investigated the soil archaeal communities on Mt. Norikura, Japan, using 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene. There was a strong mid-elevation maximum in diversity, and a mid-elevation maximum in abundance of soil archaea 16S rRNA and amoA genes. These diversity and abundance maximums could not be correlated with any identifiable soil parameter, nor plant diversity. Discrete, predictable communities of archaea occurred at each elevational level, also not explicable in terms of pH or major nutrients. When we compared the archaeal community and diversity patterns with those found in an earlier study of Mt Fuji, both mountains showed mid-elevation maximums in diversity and abundance of archaea, possibly a result of some common environmental factor such as soil disturbance frequency. However, they showed distinct sets of archaeal communities at similar elevational sampling points. Presumably, the difference reflects their distinct geology (Norikura being andesitic, while Fuji is basaltic) and the resulting combinations of soil chemistry and environmental conditions, although no explanatory variable was found. Clearly, many soil archaea have strongly defined niches and will only occur in a narrow subset of the range of possible climate and soil conditions. The findings of a mid-elevation diversity maximum on Norikura provides a further instance of how widespread this unexplained pattern is in nature, in a wide variety of

  16. Seasonal Changes of Freshwater Ammonia-Oxidizing Archaeal Assemblages and Nitrogen Species in Oligotrophic Alpine Lakes▿ †

    OpenAIRE

    Auguet, Jean-Christophe; Nomokonova, Natalya; Camarero, Lluis; Casamayor, Emilio O.

    2011-01-01

    The annual changes in the composition and abundance of ammonia-oxidizing archaea (AOA) were analyzed monthly in surface waters of three high mountain lakes within the Limnological Observatory of the Pyrenees (LOOP; northeast Spain) using both 16S rRNA and functional (ammonia monooxygenase gene, amoA) gene sequencing as well as quantitative PCR amplification. The set of biological data was related to changes in nitrogen species and to other relevant environmental variables. The whole archaeal ...

  17. Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the arctic mid-ocean spreading ridge

    Directory of Open Access Journals (Sweden)

    Steffen Leth eJørgensen

    2013-10-01

    Full Text Available In marine sediments archaea often constitute a considerable part of the microbial community, of which the Deep Sea Archaeal Group (DSAG is one of the most predominant. Despite their high abundance no members from this archaeal group have so far been characterized and thus their metabolism is unknown. Here we show that the relative abundance of DSAG marker genes can be correlated with geochemical parameters, allowing prediction of both the potential electron donors and acceptors of these organisms. We estimated the abundance of 16S rRNA genes from Archaea, Bacteria and DSAG in 52 sediment horizons from two cores collected at the slow-spreading Arctic Mid-Ocean Ridge, using qPCR. The results indicate that members of the DSAG make up the entire archaeal population in certain horizons and constitute up to ~ 50% of the total microbial community. The quantitative data were correlated to 30 different geophysical and geochemical parameters obtained from the same sediment horizons. We observed a significant correlation between the relative abundance of DSAG 16S rRNA genes and the content of organic carbon (p < 0.0001. Further, significant co-variation with iron oxide, and dissolved iron and manganese (all p < 0.0000, indicated a direct or indirect link to iron and manganese cycling. Neither of these parameters correlated with the relative abundance of archaeal or bacterial 16S rRNA genes, nor did any other major electron donor or acceptor measured. Phylogenetic analysis of DSAG 16S rRNA gene sequences reveals three monophyletic lineages with no apparent habitat-specific distribution. In this study we support the hypothesis that members of the DSAG are tightly linked to the content of organic carbon and directly or indirectly involved in the cycling of iron and/or manganese compounds. Further, we provide a molecular tool to assess their abundance in environmental samples and enrichment cultures.

  18. Rates and risks for prolonged grief disorder in a sample of orphaned and widowed genocide survivors

    Directory of Open Access Journals (Sweden)

    Jacob Nadja

    2010-07-01

    Full Text Available Abstract Background The concept of Prolonged Grief Disorder (PGD has been defined in recent years by Prigerson and co-workers, who have developed and empirically tested consensus and diagnostic criteria for PGD. Using these most recent criteria defining PGD, the aim of this study was to determine rates of and risks for PGD in survivors of the 1994 Rwandan genocide who had lost a parent and/or the husband before, during or after the 1994 events. Methods The PG-13 was administered to 206 orphans or half orphans and to 194 widows. A regression analysis was carried out to examine risk factors of PGD. Results 8.0% (n = 32 of the sample met criteria for PGD with an average of 12 years post-loss. All but one person had faced multiple losses and the majority indicated that their grief-related loss was due to violent death (70%. Grief was predicted mainly by time since the loss, by the violent nature of the loss, the severity of symptoms of posttraumatic stress disorder (PTSD and the importance given to religious/spiritual beliefs. By contrast, gender, age at the time of bereavement, bereavement status (widow versus orphan, the number of different types of losses reported and participation in the funeral ceremony did not impact the severity of prolonged grief reactions. Conclusions A significant portion of the interviewed sample continues to experience grief over interpersonal losses and unresolved grief may endure over time if not addressed by clinical intervention. Severity of grief reactions may be associated with a set of distinct risk factors. Subjects who lose someone through violent death seem to be at special risk as they have to deal with the loss experience as such and the traumatic aspects of the loss. Symptoms of PTSD may hinder the completion of the mourning process. Religious beliefs may facilitate the mourning process and help to find meaning in the loss. These aspects need to be considered in the treatment of PGD.

  19. Phylogenetic analysis of the archaeal community in an alkaline-saline soil of the former lake Texcoco (Mexico).

    Science.gov (United States)

    Valenzuela-Encinas, César; Neria-González, Isabel; Alcántara-Hernández, Rocio J; Enríquez-Aragón, J Arturo; Estrada-Alvarado, Isabel; Hernández-Rodríguez, César; Dendooven, Luc; Marsch, Rodolfo

    2008-03-01

    The soil of the former lake Texcoco is an extreme environment localized in the valley of Mexico City, Mexico. It is highly saline and alkaline, where Na+, Cl(-), HCO3(-) and CO3(2-) are the predominant ions, with a pH ranging from 9.8 to 11.7 and electrolytic conductivities in saturation extracts from 22 to 150 dS m(-1). Metagenomic DNA from the archaeal community was extracted directly from soil and used as template to amplify 16S ribosomal gene by PCR. PCR products were used to construct gene libraries. The ribosomal library showed that the archaeal diversity included Natronococcus sp., Natronolimnobius sp., Natronobacterium sp., Natrinema sp., Natronomonas sp., Halovivax sp., "Halalkalicoccus jeotgali" and novel clades within the family of Halobacteriaceae. Four clones could not be classified. It was found that the archaeal diversity in an alkaline-saline soil of the former lake Texcoco, Mexico, was low, but showed yet uncharacterized and unclassified species.

  20. Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities.

    Science.gov (United States)

    Kittelmann, Sandra; Seedorf, Henning; Walters, William A; Clemente, Jose C; Knight, Rob; Gordon, Jeffrey I; Janssen, Peter H

    2013-01-01

    Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats.

  1. Phylogenetic and functional analysis of metagenome sequence from high-temperature archaeal habitats demonstrate linkages between metabolic potential and geochemistry

    Directory of Open Access Journals (Sweden)

    William P. Inskeep

    2013-05-01

    Full Text Available Geothermal habitats in Yellowstone National Park (YNP provide an unparalled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (~40-45 Mbase Sanger sequencing per site was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G+C content and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemical attributes (e.g., sulfide, oxygen, pH. These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high temperature systems of YNP.

  2. Archaeal diversity and abundance within different layers of summer sea-ice and seawater from Prydz Bay, Antarctica

    Institute of Scientific and Technical Information of China (English)

    MA Jifei; DU Zongjun; LUO Wei; YU Yong; ZENG Yixin; CHEN Bo; LI Huirong

    2014-01-01

    Fluorescence in-situ hybridization (FISH) and 16S rRNA gene clone library analyses were used to determine the abundance and diversity of archaea in Prydz Bay, Antarctica. Correlation analysis was also performed to assess links between physicochemical parameters and archaeal abundance and diversity within the sea-ice. Samples of sea-ice and seawater were collected during the 26th Chinese National Antarctic Research Expedition. The results of FISH showed that archaea were relatively abundant within the top layer of the sea-ice, and correlation analysis suggested that the concentration of 4NH+ might be one of the main factors underlying this distribution pattern. However, using 16S rRNA gene libraries, archaea were not detected in the top and middle layers of the sea-ice. All archaeal clones obtained from the bottom layer of the sea-ice were grouped into the Marine Group I Crenarchaeota while the archaeal clones from seawater were assigned to Marine Group I Crenarchaeota, Marine Group II Euryarchaeota, and Marine Group III Euryarchaeota. Overall, the ifndings of this study showed that the diversity of archaea in the sea-ice in Prydz Bay was low.

  3. Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes

    Directory of Open Access Journals (Sweden)

    Tim Soderberg

    2005-01-01

    Full Text Available A phylogenetic analysis of the genes encoding enzymes in the pentose phosphate pathway (PPP, the ribulose monophosphate (RuMP pathway, and the chorismate pathway of aromatic amino acid biosynthesis, employing data from 13 complete archaeal genomes, provides a potential explanation for the enigmatic phylogenetic patterns of the PPP genes in archaea. Genomic and biochemical evidence suggests that three archaeal species (Methanocaldococcus jannaschii, Thermoplasma acidophilum and Thermoplasma volcanium produce ribose-5-phosphate via the nonoxidative PPP (NOPPP, whereas nine species apparently lack an NOPPP but may employ a reverse RuMP pathway for pentose synthesis. One species (Halobacterium sp. NRC-1 lacks both the NOPPP and the RuMP pathway but may possess a modified oxidative PPP (OPPP, the details of which are not yet known. The presence of transketolase in several archaeal species that are missing the other two NOPPP genes can be explained by the existence of differing requirements for erythrose-4-phosphate (E4P among archaea: six species use transketolase to make E4P as a precursor to aromatic amino acids, six species apparently have an alternate biosynthetic pathway and may not require the ability to make E4P, and one species (Pyrococcus horikoshii probably does not synthesize aromatic amino acids at all.

  4. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry.

    Science.gov (United States)

    Inskeep, William P; Jay, Zackary J; Herrgard, Markus J; Kozubal, Mark A; Rusch, Douglas B; Tringe, Susannah G; Macur, Richard E; Jennings, Ryan deM; Boyd, Eric S; Spear, John R; Roberto, Francisco F

    2013-01-01

    Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (∼40-45 Mb Sanger sequencing per site) was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G + C content) and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport, and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemical attributes (e.g., sulfide, oxygen, pH). These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high-temperature systems of YNP.

  5. Divergent responses of methanogenic archaeal communities in two rice cultivars to elevated ground-level O3.

    Science.gov (United States)

    Zhang, Jianwei; Tang, Haoye; Zhu, Jianguo; Lin, Xiangui; Feng, Youzhi

    2016-06-01

    Inhibitive effect of elevated ground-level ozone (O3) on paddy methane (CH4) emission varies with rice cultivars. However, little information is available on its microbial mechanism. For this purpose, the responses of methane-metabolizing microorganisms, methanogenic archaea and methanotrophic bacteria to O3 pollution were investigated in the O3-tolerant (YD6) and the O3-sensitive (IIY084) cultivars at two rice growth stages in Free Air Concentration Elevation of O3 (O3-FACE) system of China. It was found that O3 pollution didn't change the abundances of Type I and Type II methanotrophic bacteria at two rice stages. For methanogenic archaea, their abundances in both cultivars were decreased by O3 pollution at the tillering stage. Furthermore, a greater negative influence on methanogenic archaeal community was observed on IIY084 than on YD6: at tillering stage, the alpha diversity indices of methanogenic archaeal community in IIY084 was decreased to a greater extent than in YD6; IIY084 shifted methanogenic archaeal community composition and decreased the abundances and the diversities of Methanosarcinaceae and Methanosaetaceae as well as the abundance of Methanomicrobiales, while the diversity of Methanocellaceae were increased in YD6. These findings indicate that the variations in the responses of paddy CH4 emission to O3 pollution between cultivars could result from the divergent responses of their methanogenic archaea. PMID:26895536

  6. Cross genome phylogenetic analysis of human and Drosophila G protein-coupled receptors: application to functional annotation of orphan receptors

    Directory of Open Access Journals (Sweden)

    Sowdhamini Ramanathan

    2005-08-01

    Full Text Available Abstract Background The cell-membrane G-protein coupled receptors (GPCRs are one of the largest known superfamilies and are the main focus of intense pharmaceutical research due to their key role in cell physiology and disease. A large number of putative GPCRs are 'orphans' with no identified natural ligands. The first step in understanding the function of orphan GPCRs is to identify their ligands. Phylogenetic clustering methods were used to elucidate the chemical nature of receptor ligands, which led to the identification of natural ligands for many orphan receptors. We have clustered human and Drosophila receptors with known ligands and orphans through cross genome phylogenetic analysis and hypothesized higher relationship of co-clustered members that would ease ligand identification, as related receptors share ligands with similar structure or class. Results Cross-genome phylogenetic analyses were performed to identify eight major groups of GPCRs dividing them into 32 clusters of 371 human and 113 Drosophila proteins (excluding olfactory, taste and gustatory receptors and reveal unexpected levels of evolutionary conservation across human and Drosophila GPCRs. We also observe that members of human chemokine receptors, involved in immune response, and most of nucleotide-lipid receptors (except opsins do not have counterparts in Drosophila. Similarly, a group of Drosophila GPCRs (methuselah receptors, associated in aging, is not present in humans. Conclusion Our analysis suggests ligand class association to 52 unknown Drosophila receptors and 95 unknown human GPCRs. A higher level of phylogenetic organization was revealed in which clusters with common domain architecture or cellular localization or ligand structure or chemistry or a shared function are evident across human and Drosophila genomes. Such analyses will prove valuable for identifying the natural ligands of Drosophila and human orphan receptors that can lead to a better understanding

  7. The first archaeal ATP-dependent glucokinase, from the hyperthermophilic crenarchaeon Aeropyrum pernix, represents a monomeric, extremely thermophilic ROK glucokinase with broad hexose specificity.

    Science.gov (United States)

    Hansen, Thomas; Reichstein, Bianca; Schmid, Roland; Schönheit, Peter

    2002-11-01

    An ATP-dependent glucokinase of the hyperthermophilic aerobic crenarchaeon Aeropyrum pernix was purified 230-fold to homogeneity. The enzyme is a monomeric protein with an apparent molecular mass of about 36 kDa. The apparent K(m) values for ATP and glucose (at 90 degrees C and pH 6.2) were 0.42 and 0.044 mM, respectively; the apparent V(max) was about 35 U/mg. The enzyme was specific for ATP as a phosphoryl donor, but showed a broad spectrum for phosphoryl acceptors: in addition to glucose, which showed the highest catalytic efficiency (k(cat)/K(m)), the enzyme also phosphorylates glucosamin, fructose, mannose, and 2-deoxyglucose. Divalent cations were required for maximal activity: Mg(2+), which was most effective, could partially be replaced with Co(2+), Mn(2+), and Ni(2+). The enzyme had a temperature optimum of at least 100 degrees C and showed significant thermostability up to 100 degrees C. The coding function of open reading frame (ORF) APE2091 (Y. Kawarabayasi, Y. Hino, H. Horikawa, S. Yamazaki, Y. Haikawa, K. Jin-no, M. Takahashi, M. Sekine, S. Baba, A. Ankai, H. Kosugi, A. Hosoyama, S. Fukui, Y. Nagai, K. Nishijima, H. Nakazawa, M. Takamiya, S. Masuda, T. Funahashi, T. Tanaka, Y. Kudoh, J. Yamazaki, N. Kushida, A. Oguchi, and H. Kikuchi, DNA Res. 6:83-101, 145-152, 1999), previously annotated as gene glk, coding for ATP-glucokinase of A. pernix, was proved by functional expression in Escherichia coli. The purified recombinant ATP-dependent glucokinase showed a 5-kDa higher molecular mass on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, but almost identical kinetic and thermostability properties in comparison to the native enzyme purified from A. pernix. N-terminal amino acid sequence of the native enzyme revealed that the translation start codon is a GTG 171 bp downstream of the annotated start codon of ORF APE2091. The amino acid sequence deduced from the truncated ORF APE2091 revealed sequence similarity to members of the ROK family, which comprise bacterial sugar kinases and transcriptional repressors. This is the first report of the characterization of an ATP-dependent glucokinase from the domain of Archaea, which differs from its bacterial counterparts by its monomeric structure and its broad specificity for hexoses.

  8. 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.

  9. A Fieldable-Prototype Large-Area Gamma-ray Imager for Orphan Source Search

    Energy Technology Data Exchange (ETDEWEB)

    Ziock, Klaus-Peter [ORNL; Fabris, Lorenzo [ORNL; Carr, Dennis [Lawrence Livermore National Laboratory (LLNL); Collins, Jeff [Lawrence Livermore National Laboratory (LLNL); Cunningham, Mark F [Lawrence Livermore National Laboratory (LLNL); Habte Ghebretatios, Frezghi [ORNL; Karnowski, Thomas Paul [ORNL; Marchant, William [University of California, Berkeley

    2008-01-01

    We have constructed a unique instrument for use in the search for orphan sources. The system uses gamma-ray imaging to "see through" the natural background variations that effectively limit the search range of normal devices to ~10 m. The imager is mounted in a 4.9- m-long trailer and can be towed by a large personal vehicle. Source locations are determined both in range and along the direction of travel as the vehicle moves. A fully inertial platform coupled to a Global Positioning System receiver is used to map the gamma-ray images onto overhead geospatial imagery. The resulting images provide precise source locations, allowing rapid follow-up work. The instrument simultaneously searches both sides of the street to a distance of 50 m (100-m swath) for milliCurieclass sources with near-perfect performance.

  10. 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). PMID:27504025

  11. 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.

  12. Structural Basis for Hydroxycholesterols as Natural Ligands of Orphan Nuclear Receptor ROR[gamma

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Lihua; Martynowski, Dariusz; Zheng, Songyang; Wada, Taira; Xie, Wen; Li, Yong (Pitt); (Xiamen)

    2010-09-03

    The retinoic acid-related orphan receptor {gamma} (ROR{gamma}) has important roles in development and metabolic homeostasis. Although the biological functions of ROR{gamma} have been studied extensively, no ligands for ROR{gamma} have been identified, and no structure of ROR{gamma} has been reported. In this study, we showed that hydroxycholesterols promote the recruitment of coactivators by ROR{gamma} using biochemical assays. We also report the crystal structures of the ROR{gamma} ligand-binding domain bound with hydroxycholesterols. The structures reveal the binding modes of various hydroxycholesterols in the ROR{gamma} pocket, with the receptors all adopting the canonical active conformation. Mutations that disrupt the binding of hydroxycholesterols abolish the constitutive activity of ROR{gamma}. Our observations suggest an important role for the endogenous hydroxycholesterols in modulating ROR{gamma}-dependent biological processes.

  13. 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.

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

    DEFF Research Database (Denmark)

    Dowdall, M.; Smethurst, M.A.; Andersson, Kasper Grann;

    limit. Fourteen individual organi-sations from seven different countries supplied results. Results from participants indicate that for strong sources of isotopes with simple spectra featuring high energy peaks, location and identification is not a problem. Problems arise for isotopes with low energy...... signals or that present a weak signal even when visible for extended periods. Experienced analysts tended to perform better in identifica-tion of sources even if they were inexperienced in mobile measurements whereas those with experience in such measurements were more confident in providing more precise......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...

  15. 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.

  16. 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).

  17. 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.

    2015-01-01

    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. PMID:26498026

  18. Archaeal diversity in deep-sea hydrothermal sediments from the East Pacific Rise%东太平洋海隆深海热液区沉积物古菌多样性分析

    Institute of Scientific and Technical Information of China (English)

    刘青; 谢运标; 陈逍遥; 周梅先

    2014-01-01

    Archaeal diversity of deep-sea hydrothermal sediments from 3 sites on the East Pacific Rise was investiga-ted and analyzed with polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).Phyloge-netic analyses revealed that a total of 296 random 16S rRNA gene clones were assigned to Thaumarchaeota (47.64%),Euryarchaeota (44.93%),Crenarchaeota (6.77%)and unclassified Archaea (0.68%).Among them,the genus Nitrosopumilus belonging to the phylum Thaumarchaeota and the class Thermoplasmata belonging to the phylum Euryarchaeota were the dominant groups,representing 35.47% and 27.03% of archaeal clones,re-spectively.In addition,some archaeal 16S rRNA gene sequences were affiliated with deep-sea hydrothermal vent Euryarchaeota 3,5 and 6 (DHVE3,DHVE5 and DHVE6),and Marine Benthic Group B and G (MBGB and MB-GE ).Archaeal communities in sediments from 3 sites on East Pacific Rise were clearly distinct from each other.97 archaeal clones from S5-TVG1 site were divided to Thaumarchaeota (49.48%),Euryarchaeota (49.48%)and Crenarchaeota (1.03%).103 archaeal clones from S14-TVG10 site belonged to Thaumarchaeota(84.47%)and Euryarchaeota (15.53%).96 archaeal clones from S16-TVG12 site were assigned to Euryarchaeota(71.88%), Crenarchaeota (19.79%),Thaumarchaeota (6.25%)and unclassified Archaea (2.08%).Our results indicate that Archaea is abundant and there are a lot of novel archaeal groups in deep-sea hydrothermal sediments from 3 sites on the East Pacific Rise,and the distinct community structure and diversity of Archaea in deep-sea hydrother-mal sediments suggested that the sampling area was influenced by hydrothermalism.%采用PCR-RFLP方法对东太平洋海隆深海热液区3个站位沉积物中的古菌多样性进行了初步研究.结果显示,从古菌16S rRNA基因文库中随机挑取的296个阳性克隆分属奇古菌门(Thaumar-chaeota,47.64%)、广古菌门(Euryarchaeota,44.93%)、泉古菌门(Crenarchaeota,6.77

  19. 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. PMID:23334923

  20. 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