WorldWideScience

Sample records for eukaryotes special focus

  1. Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi.

    Science.gov (United States)

    Cornell, Michael J; Alam, Intikhab; Soanes, Darren M; Wong, Han Min; Hedeler, Cornelia; Paton, Norman W; Rattray, Magnus; Hubbard, Simon J; Talbot, Nicholas J; Oliver, Stephen G

    2007-12-01

    The recent proliferation of genome sequencing in diverse fungal species has provided the first opportunity for comparative genome analysis across a eukaryotic kingdom. Here, we report a comparative study of 34 complete fungal genome sequences, representing a broad diversity of Ascomycete, Basidiomycete, and Zygomycete species. We have clustered all predicted protein-encoding gene sequences from these species to provide a means of investigating gene innovations, gene family expansions, protein family diversification, and the conservation of essential gene functions-empirically determined in Saccharomyces cerevisiae-among the fungi. The results are presented with reference to a phylogeny of the 34 fungal species, based on 29 universally conserved protein-encoding gene sequences. We contrast this phylogeny with one based on gene presence and absence and show that, while the two phylogenies are largely in agreement, there are differences in the positioning of some species. We have investigated levels of gene duplication and demonstrate that this varies greatly between fungal species, although there are instances of coduplication in distantly related fungi. We have also investigated the extent of orthology for protein families and demonstrate unexpectedly high levels of diversity among genes involved in lipid metabolism. These analyses have been collated in the e-Fungi data warehouse, providing an online resource for comparative genomic analysis of the fungi.

  2. An Examination of Special Focus Facility Nursing Homes

    Science.gov (United States)

    Castle, Nicholas G.; Engberg, John

    2010-01-01

    Purpose: Nursing facilities that are determined to have a greater number of quality problems, more serious problems than average, and a demonstrated pattern of quality problems are included in the Special Focus Facility (SFF) initiative. The purpose of this research was to provide descriptive information on these SFFs and to examine the quality…

  3. Foreword to the Special Focus on Mathematics, Data and Knowledge

    KAUST Repository

    Chen, Xiaoyu

    2013-12-01

    There is a growing interest in applying mathematical theories and methods from topology, computational geometry, differential equations, fluid dynamics, quantum statistics, etc. to describe and to analyze scientific regularities of diverse, massive, complex, nonlinear, and fast changing data accumulated continuously around the world and in discovering and revealing valid, insightful, and valuable knowledge that data imply. With increasingly solid mathematical foundations, various methods and techniques have been studied and developed for data mining, modeling, and processing, and knowledge representation, organization, and verification; different systems and mechanisms have been designed to perform data-intensive tasks in many application fields for classification, predication, recommendation, ranking, filtering, etc. This special focus of Mathematics in Computer Science is organized to stimulate original research on the interaction of mathematics with data and knowledge, in particular the exploration of new mathematical theories and methodologies for data modeling and analysis and knowledge discovery and management, the study of mathematical models of big data and complex knowledge, and the development of novel solutions and strategies to enhance the performance of existing systems and mechanisms for data and knowledge processing. The present foreword provides a short review of some key ideas and techniques on how mathematics interacts with data and knowledge, together with a few selected research directions and problems and a brief introduction to the four papers published in the focus. © 2013 Springer Basel.

  4. Eukaryotic origins

    OpenAIRE

    Lake, James A.

    2015-01-01

    The origin of the eukaryotes is a fundamental scientific question that for over 30 years has generated a spirited debate between the competing Archaea (or three domains) tree and the eocyte tree. As eukaryotes ourselves, humans have a personal interest in our origins. Eukaryotes contain their defining organelle, the nucleus, after which they are named. They have a complex evolutionary history, over time acquiring multiple organelles, including mitochondria, chloroplasts, smooth and rough endo...

  5. Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life

    NARCIS (Netherlands)

    Speijer, Dave; Lukeš, Julius; Eliáš, Marek

    2015-01-01

    Sexual reproduction and clonality in eukaryotes are mostly seen as exclusive, the latter being rather exceptional. This view might be biased by focusing almost exclusively on metazoans. We analyze and discuss reproduction in the context of extant eukaryotic diversity, paying special attention to

  6. FEMP Focus - Special Issue 2006 - EPACT 2005 and Presidential Memo

    Energy Technology Data Exchange (ETDEWEB)

    None

    2006-03-01

    Features information about Presidential Memorandum on Energy Conservation, Energy Policy Act 2005 Special Section, ESET FEMP Deploys Teams in Response to Natural Gas Concerns, Natural Gas Tips for Facility Managers, and more for federal agencies.

  7. Cancer vaccines: an update with special focus on ganglioside antigens.

    Science.gov (United States)

    Bitton, Roberto J; Guthmann, Marcel D; Gabri, Mariano R; Carnero, Ariel J L; Alonso, Daniel F; Fainboim, Leonardo; Gomez, Daniel E

    2002-01-01

    Vaccine development is one of the most promising and exciting fields in cancer research; numerous approaches are being studied to developed effective cancer vaccines. The aim of this form of therapy is to teach the patient's immune system to recognize the antigens expressed in tumor cells, but not in normal tissue, to be able to destroy these abnormal cells leaving the normal cells intact. In other words, is an attempt to teach the immune system to recognize antigens that escaped the immunologic surveillance and are by it, therefore able to survive and, in time, disseminate. However each research group developing a cancer vaccine, uses a different technology, targeting different antigens, combining different carriers and adjuvants, and using different immunization schedules. Most of the vaccines are still experimental and not approved by the US or European Regulatory Agencies. In this work, we will offer an update in the knowledge in cancer immunology and all the anticancer vaccine approaches, with special emphasis in ganglioside based vaccines. It has been demonstrated that quantitative and qualitative changes occur in ganglioside expression during the oncogenic transformation. Malignant transformation appears to activate enzymes associated with ganglioside glycosylation, resulting in altered patterns of ganglioside expression in tumors. Direct evidence of the importance of gangliosides as potential targets for active immunotherapy has been suggested by the observation that human monoclonal antibodies against these glycolipids induce shrinkage of human cutaneous melanoma metastasis. Thus, the cellular over-expression and shedding of gangliosides into the interstitial space may play a central role in cell growth regulation, immune tolerance and tumor-angiogenesis, therefore representing a new target for anticancer therapy. Since 1993 researchers at the University of Buenos Aires and the University of Quilmes (Argentina), have taken part in a project carried out by

  8. [Consequences of collective violence with special focus on gender perspective].

    Science.gov (United States)

    Helweg-Larsen, Karin; Kastrup, Marianne C

    2006-09-04

    There is increasing focus on the gender perspective related to the consequences of collective violence. Women run a greater risk of being victims of sexual violence, but few studies have focused on gender differences with respect to physical violence, sexual violations and the impact on health. Further research is needed on these issues as well as research on the identification of evidence based interventions.

  9. New Research Findings on Emotionally Focused Therapy: Introduction to Special Section

    Science.gov (United States)

    Johnson, Susan M.; Wittenborn, Andrea K.

    2012-01-01

    This article introduces the special section "New Research Findings on Emotionally Focused Therapy." Emotionally focused couple therapy researchers have a strong tradition of outcome and process research and this special section presents new findings from three recent studies. The first study furthers the goal of determining the kinds of clients…

  10. Endosymbiotic theories for eukaryote origin

    Science.gov (United States)

    Martin, William F.; Garg, Sriram; Zimorski, Verena

    2015-01-01

    For over 100 years, endosymbiotic theories have figured in thoughts about the differences between prokaryotic and eukaryotic cells. More than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. Very few of those models account for eukaryotic anaerobes. The role of energy and the energetic constraints that prokaryotic cell organization placed on evolutionary innovation in cell history has recently come to bear on endosymbiotic theory. Only cells that possessed mitochondria had the bioenergetic means to attain eukaryotic cell complexity, which is why there are no true intermediates in the prokaryote-to-eukaryote transition. Current versions of endosymbiotic theory have it that the host was an archaeon (an archaebacterium), not a eukaryote. Hence the evolutionary history and biology of archaea increasingly comes to bear on eukaryotic origins, more than ever before. Here, we have compiled a survey of endosymbiotic theories for the origin of eukaryotes and mitochondria, and for the origin of the eukaryotic nucleus, summarizing the essentials of each and contrasting some of their predictions to the observations. A new aspect of endosymbiosis in eukaryote evolution comes into focus from these considerations: the host for the origin of plastids was a facultative anaerobe. PMID:26323761

  11. Endosymbiotic theories for eukaryote origin.

    Science.gov (United States)

    Martin, William F; Garg, Sriram; Zimorski, Verena

    2015-09-26

    For over 100 years, endosymbiotic theories have figured in thoughts about the differences between prokaryotic and eukaryotic cells. More than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. Very few of those models account for eukaryotic anaerobes. The role of energy and the energetic constraints that prokaryotic cell organization placed on evolutionary innovation in cell history has recently come to bear on endosymbiotic theory. Only cells that possessed mitochondria had the bioenergetic means to attain eukaryotic cell complexity, which is why there are no true intermediates in the prokaryote-to-eukaryote transition. Current versions of endosymbiotic theory have it that the host was an archaeon (an archaebacterium), not a eukaryote. Hence the evolutionary history and biology of archaea increasingly comes to bear on eukaryotic origins, more than ever before. Here, we have compiled a survey of endosymbiotic theories for the origin of eukaryotes and mitochondria, and for the origin of the eukaryotic nucleus, summarizing the essentials of each and contrasting some of their predictions to the observations. A new aspect of endosymbiosis in eukaryote evolution comes into focus from these considerations: the host for the origin of plastids was a facultative anaerobe. © 2015 The Authors.

  12. Sustainable Drainage Practices in Spain, Specially Focused on Pervious Pavements

    Directory of Open Access Journals (Sweden)

    Jorge Rodriguez-Hernandez

    2013-01-01

    Full Text Available The Spanish climate is full of contrasts, with torrential rains and long droughts; under these conditions, appropriate water management is essential. In Spain, until the end of the twentieth century, water management and legislative development lagged behind other more developed countries. Nowadays, great efforts are being made to reverse this situation and improve both water management and legislation in order to control the two main problems related to stormwater management in cities: floods and diffuse pollution. In this context, Sustainable Urban Drainage Systems (SUDS were developed as the main solution to these problems. The study of these techniques started in the 1970s in the USA, but they were not studied in Spain until 1993 when the University of Cantabria and CLABSA started to look into solutions for stormwater management. After 20 years of research and application, sustainable drainage in Spain is still behind other countries in spite of the efforts to change this situation, notably by the University of Cantabria with 10 years of experience in these techniques, mainly regarding pervious pavements, where more than 13 related research projects have been carried out. The future challenges focus on the application of pervious pavements for Urban Hydrological Rehabilitation.

  13. Energy management technologies: special focus on textile industry

    International Nuclear Information System (INIS)

    Dayo, F.B.O.

    2000-08-01

    requirement in international competitiveness. The focus of this paper is the review of energy management technologies that can be used to achieve energy efficiency improvement objectives in textile manufacturing. The paper is arranged as follows: in section 2, the characteristics of energy consumption in textile manufacturing are presented; energy efficiency improvement technology options for the textile industry are discussed in section 3, section 4 covers a discussion of process specific technologies for improving energy use efficiency in textile manufacturing; the paper is concluded in section 5 with salient recommendation for promoting rational use of energy in the Nigerian Textile Industrial Sector

  14. Extracellular matrix in canine mammary tumors with special focus on versican, a versatile extracellular proteoglycan

    NARCIS (Netherlands)

    Erdélyi, Ildikó

    2006-01-01

    The extracellular matrix (ECM) research has become fundamental to understand cancer. This thesis focuses on the exploration of ECM composition and organization in canine mammary tumors, with a special interest in the large chondroitin-sulfate proteoglycan (PG), versican. Chapter 1 gives an

  15. Relationship-focused therapy for bulimia and binge eating: Introduction to the special section.

    Science.gov (United States)

    Thompson-Brenner, Heather

    2016-06-01

    Individuals with bulimia nervosa and binge eating disorder commonly report co-occurring interpersonal problems, and treatment that focuses on relationships and relational functioning has shown benefit relative to other forms of treatment. Relational psychotherapy for eating disorders can vary on several important dimensions, such as how structured and symptom-focused versus exploratory and patient-directed it is, whether it focuses on past relationships and patterns in relationships over time versus focusing on current relationships, and whether it includes the relationship with the therapist as an explicit topic of conversation and mechanism for relational change. The cases in this special section provide the opportunity to closely compare 3 therapeutic approaches on each of these dimensions. Psychoanalytic Psychotherapy for Bulimia Nervosa, Integrative Dynamic Therapy for Bulimia Nervosa, and Interpersonal Psychotherapy for the Prevention of Weight Gain and Eating Disorders are each highly distinct approaches. The authors of each case explain the intended mechanisms of treatment response, the measures that assess changes in eating disorder symptoms as well as the mechanisms of change, and provide extensive excerpts from case material to demonstrate and illustrate the particular evidence-based treatment. Therapists and researchers may usefully consider the process and outcome variables described in these interpersonal approaches. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  16. Comparison of technologies for nano device prototyping with a special focus on ion beams: A review

    Science.gov (United States)

    Bruchhaus, L.; Mazarov, P.; Bischoff, L.; Gierak, J.; Wieck, A. D.; Hövel, H.

    2017-03-01

    Nano device prototyping (NDP) is essential for realizing and assessing ideas as well as theories in the form of nano devices, before they can be made available in or as commercial products. In this review, application results patterned similarly to those in the semiconductor industry (for cell phone, computer processors, or memory) will be presented. For NDP, some requirements are different: thus, other technologies are employed. Currently, in NDP, for many applications direct write Gaussian vector scan electron beam lithography (EBL) is used to define the required features in organic resists on this scale. We will take a look at many application results carried out by EBL, self-organized 3D epitaxy, atomic probe microscopy (scanning tunneling microscope/atomic force microscope), and in more detail ion beam techniques. For ion beam techniques, there is a special focus on those based upon liquid metal (alloy) ion sources, as recent developments have significantly increased their applicability for NDP.

  17. Myrmica Ants and Their Butterfly Parasites with Special Focus on the Acoustic Communication

    Directory of Open Access Journals (Sweden)

    F. Barbero

    2012-01-01

    Full Text Available About 10,000 arthropod species live as ants' social parasites and have evolved a number of mechanisms allowing them to penetrate and survive inside the ant nests. Myrmica colonies, in particular, are exploited by numerous social parasites, and the presence of their overwintering brood, as well as of their polygyny, contributes to make them more vulnerable to infestation. Butterflies of the genus Maculinea are among the most investigated Myrmica inquilines. These lycaenids are known for their very complex biological cycles. Maculinea species are obligated parasites that depend on a particular food plant and on a specific Myrmica species for their survival. Maculinea larvae are adopted by Myrmica ants, which are induced to take them into their nests by chemical mimicry. Then the parasite spends the following 11–23 months inside the ants' nest. Mimicking the acoustic emission of the queen ants, Maculinea parasites not only manage to become integrated, but attain highest rank within the colony. Here we review the biology of Maculinea/Myrmica system with a special focus on some recent breakthrough concerning their acoustical patterns.

  18. Introduction to the Special Issue: Water Grabbing? Focus on the (Reappropriation of Finite Water Resources

    Directory of Open Access Journals (Sweden)

    Lyla Mehta

    2012-06-01

    Full Text Available Recent large-scale land acquisitions for agricultural production (including biofuels, popularly known as 'land grabbing', have attracted headline attention. Water as both a target and driver of this phenomenon has been largely ignored despite the interconnectedness of water and land. This special issue aims to fill this gap and to widen and deepen the lens beyond the confines of the literature’s still limited focus on agriculture-driven resource grabbing. The articles in this collection demonstrate that the fluid nature of water and its hydrologic complexity often obscure how water grabbing takes place and what the associated impacts on the environment and diverse social groups are. The fluid properties of water interact with the 'slippery' nature of the grabbing processes: unequal power relations; fuzziness between legality and illegality and formal and informal rights; unclear administrative boundaries and jurisdictions, and fragmented negotiation processes. All these factors combined with the powerful material, discursive and symbolic characteristics of water make 'water grabbing' a site for conflict with potential drastic impacts on the current and future uses and benefits of water, rights as well as changes in tenure relations.

  19. Autophagy in unicellular eukaryotes

    NARCIS (Netherlands)

    Kiel, J.A.K.W.

    2010-01-01

    Cells need a constant supply of precursors to enable the production of macromolecules to sustain growth and survival. Unlike metazoans, unicellular eukaryotes depend exclusively on the extracellular medium for this supply. When environmental nutrients become depleted, existing cytoplasmic components

  20. Innovations and Improvisations: A study in specialized product development focused on business clothing for women with physical disabilities

    OpenAIRE

    Carroll, Katherine Emma

    2001-01-01

    Clothing manufacturers and distributors in the current business climate need to become more flexible and willing to adapt to consumersâ changing needs and preferences in order to satisfy the market (Kincade, 1995). Clothing consumers who have special needs, such as working women with physical disabilities, comprise a group who would benefit from research into specialized products focused on a small target market (Reich & Otten, 1991). However, research shows that consumers with physical d...

  1. Jurisdiction of courts with a focus on the Special Chamber of the Supreme Court of Kosovo

    Directory of Open Access Journals (Sweden)

    Mr.Sc. Sabri Halili

    2013-06-01

    Full Text Available The legal solution offered by the Law establishing the Special Chamber of the Supreme Court of Kosovo is rather challenging for practical implementation. Due to this fact, the decisions of the Special Chamber contain various dilemmas of judges on the jurisdiction of the Chamber on the matters related to natural persons sued by the PAK, which are related to various liabilities of these persons to socially-owned enterprises, namely to the PAK. Since the PAK administers and represents socially owned property in general, it is naturally bound to seek for legal resolutions for all legal contests before a competent court. Naturally, the PAK would seek for such a solution before the Special Chamber of the Supreme Court of Kosovo on PAK-related matters, which is already bound by the title itself, “on PAK-related matters”. Comparisons of remedies by various laws related to subject competence are based on legal literature used in higher education in Kosovo. Analysis of subject competences of regular and special courts is two-fold: the Commercial Court and the Military Court, while the competence of the Special Chamber is only analysed in relation with the Law on Courts, and the Law on the Special Chamber of the Supreme Court, comparing it with the Law on Contested Procedure and the Law on the PAK. The Special Chamber has before and still continues to avoid jurisdiction of this Court, which is sanctioned by Articles 4 and 5 of the Law on the Special Chamber, due to the fact that in cases in which the PAK has sued a natural or legal person, due to debts, occupation of socially owned property, or any other disputed matter, which is directly related to socially owned properties, the Special Chamber proclaims itself incompetent, and transfers the case to regular courts, although the Special Chamber adjudicates “on PAK-related matters”, but in this case only when the PAK is respondent, not when it is claimant.

  2. Defensins: antifungal lessons from eukaryotes

    Directory of Open Access Journals (Sweden)

    Patrícia M. Silva

    2014-03-01

    Full Text Available Over the last years, antimicrobial peptides (AMPs have been the focus of intense research towards the finding of a viable alternative to current antifungal drugs. Defensins are one of the major families of AMPs and the most represented among all eukaryotic groups, providing an important first line of host defense against pathogenic microorganisms. Several of these cysteine-stabilized peptides present a relevant effect against fungi. Defensins are the AMPs with the broader distribution across all eukaryotic kingdoms, namely, Fungi, Plantæ and Animalia, and were recently shown to have an ancestor in a bacterial organism. As a part of the host defense, defensins act as an important vehicle of information between innate and adaptive immune system and have a role in immunomodulation. This multidimensionality represents a powerful host shield, hard for microorganisms to overcome using single approach resistance strategies. Pathogenic fungi resistance to conventional antimycotic drugs is becoming a major problem. Defensins, as other AMPs, have shown to be an effective alternative to the current antimycotic therapies, demonstrating potential as novel therapeutic agents or drug leads. In this review, we summarize the current knowledge on some eukaryotic defensins with antifungal action. An overview of the main targets in the fungal cell and the mechanism of action of these AMPs (namely, the selectivity for some fungal membrane components are presented. Additionally, recent works on antifungal defensins structure, activity and citotoxicity are also reviewed.

  3. Physical activity in patients with heart failure: barriers and motivations with special focus on sex differences

    Directory of Open Access Journals (Sweden)

    Klompstra L

    2015-11-01

    Full Text Available Leonie Klompstra,1 Tiny Jaarsma,1 Anna Strömberg2,31Department of Social and Welfare Studies, Faculty of Health Sciences, 2Department of Medical and Health Sciences, Division of Nursing, 3Department of Cardiology, Linköping University, Linköping, SwedenBackground: Adherence to recommendations for physical activity is low in both male and female patients with heart failure (HF. Men are more physically active than women. In order to successfully promote physical activity, it is therefore essential to explore how much and why HF patients are physically active and if this is related to sex. The aim of this study was therefore to evaluate physical activity in HF patients, to describe the factors related to physical activity, and to examine potential barriers and motivations to physical activity with special focus on sex differences.Methods: The study had a cross-sectional survey design. HF patients living at home received a questionnaire during May–July 2014, with questions on physical activity (from the Short Form-International Physical Activity Questionnaire, and potential barriers and motivations to physical activity.Results: A total of 154 HF patients, 27% women, with a mean age of 70±10 were included. In total, 23% of the patients reported a high level of physical activity, 46% a moderate level, and 34% a low level. Higher education, self-efficacy, and motivation were significantly associated with a higher amount of physical activity. Symptoms or severity of the disease were not related to physical activity. All the potential barriers to exercise were reported to be of importance. Psychological motivations were most frequently rated as being the most important motivation (41% to be physically active. Physical motivations (33% and social motivations were rated as the least important ones (22%. Women had significantly higher total motivation to be physically active. These differences were found in social, physical, and psychological

  4. Reproduction, symbiosis, and the eukaryotic cell

    Science.gov (United States)

    Godfrey-Smith, Peter

    2015-01-01

    This paper develops a conceptual framework for addressing questions about reproduction, individuality, and the units of selection in symbiotic associations, with special attention to the origin of the eukaryotic cell. Three kinds of reproduction are distinguished, and a possible evolutionary sequence giving rise to a mitochondrion-containing eukaryotic cell from an endosymbiotic partnership is analyzed as a series of transitions between each of the three forms of reproduction. The sequence of changes seen in this “egalitarian” evolutionary transition is compared with those that apply in “fraternal” transitions, such as the evolution of multicellularity in animals. PMID:26286983

  5. Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea.

    NARCIS (Netherlands)

    Blombach, F.; Makarova, K.S.; Marrero, J.; Siebers, B.G.; Koonin, E.V.; Oost, J. van der

    2009-01-01

    One of the hallmarks of eukaryotic information processing is the co-existence of 3 distinct, multi-subunit RNA polymerase complexes that are dedicated to the transcription of specific classes of coding or non-coding RNAs. Archaea encode only one RNA polymerase that resembles the eukaryotic RNA

  6. Eukaryotic Cell Panorama

    Science.gov (United States)

    Goodsell, David S.

    2011-01-01

    Diverse biological data may be used to create illustrations of molecules in their cellular context. This report describes the scientific results that support an illustration of a eukaryotic cell, enlarged by one million times to show the distribution and arrangement of macromolecules. The panoramic cross section includes eight panels that extend…

  7. The Diffusion of Disability Rights Policy: A Focus on Special Education in South Korea

    Science.gov (United States)

    Yoo, Joan P.; Palley, Elizabeth

    2014-01-01

    This article examines the development of South Korean special education policy and suggests that different strategies of policy diffusion influenced the design of the policy at different times. Historically, South Korea relied on external pressures and influences, particularly US law and UN guidelines, to develop much of its human rights law,…

  8. E-learning adoption in hospitality education: An analysis with special focus on Singapore

    OpenAIRE

    Revi Nair; Babu P. George

    2016-01-01

    This paper explores issues and challenges in the adoption of e-learning in hospitality education, with special reference to Singapore. Hospitality being a ‘high-touch’ profession and many hospitality related skills being largely intangible, there has been significant industry resistance in technology adoption. There has been concerns from multiple stakeholder groups as to how effectively can technologies compensate for the loss of social context of traditional hands-on learning. However, in S...

  9. Chemistry and pharmacology of Monimiaceae: a special focus on Siparuna and Mollinedia.

    Science.gov (United States)

    Leitão, G G; Simas, N K; Soares, S S; de Brito, A P; Claros, B M; Brito, T B; Delle Monache, F

    1999-05-01

    The chemistry and pharmacology of species of the family Monimiaceae are reviewed, with special attention given to the genera Mollinedia and Siparuna, the two most important and representative in Brazil. The isolation of benzylisoquinoline alkaloids and kaempferol derivatives from Siparuna apiosyce is reported, as well as the isolation of aporphines from the fruits of Siparuna arianeae. Cinnamic acid derivatives and a gamma-lactone were isolated from Mollinedia gilgiana and Mollinedia marliae.

  10. Lung Focused Resuscitation at a Specialized Donor Care Facility Improves Lung Procurement Rates.

    Science.gov (United States)

    Chang, Stephanie H; Kreisel, Daniel; Marklin, Gary F; Cook, Lindsey; Hachem, Ramsey; Kozower, Benjamin D; Balsara, Keki R; Bell, Jennifer M; Frederiksen, Christine; Meyers, Bryan F; Patterson, G Alexander; Puri, Varun

    2018-01-11

    Lung procurement for transplantation occurs in about 20% of brain dead donors and is a major impediment to wider application of lung transplantation. We investigated the impact of lung protective management at a specialized donor care facility on lung procurement rates from brain dead donors. Our local organ procurement organization instituted a protocol of lung protective management at a freestanding specialized donor care facility in 2008. Brain dead donors from 2001-07 (early period) were compared to those from 2009-16 (current period) for lung procurement rates and other solid organ procurement rates using a prospectively maintained database. There was an overall increase in the number of brain dead donors over the study period (early, 791 vs. late, 1333, pprocurement rate (lung donors/all brain dead donors) improved markedly after introduction of lung protective management (early group 157/791, 19.8% vs. current group 452/1333, 33.9%, pprocurement rate (total number of organs procured/donor) also increased over the study period (early, 3.5 organs per donor vs. current, 3.8 organs per donor, p=0.006). Lung protective management in brain dead donors at a specialized donor care facility is associated with higher lung utilization rates compared to conventional management. This strategy does not adversely impact the utilization of other organs in a multi-organ donor. Copyright © 2018 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

  11. Mental health nursing: Daring to be different, special and leading recovery-focused care?

    Science.gov (United States)

    Santangelo, Peter; Procter, Nicholas; Fassett, Denise

    2018-02-01

    How mental health nursing is differentiated from other disciplines and professions, and what special contribution mental health nurses make to health services, is a question at the heart of contemporary practice. One of the significant challenges for mental health nurses is identifying, developing and advancing those aspects of their practice that they consider differentiate them in the multi-disciplinary mental health care team and to articulate clearly what a mental health nurse is and does. This paper draws on data from interviews with 36 mental health nurses in Australia who identified their practice as autonomous. Participants were asked the question, "What's special about mental health nursing?" Constructivist grounded theory techniques were applied to the research process. Findings were formulated and expressed as the 'Ten P's of the professional profile that is mental health nursing', which are 'present', 'personal', 'participant partnering', 'professional', 'phenomenological', 'pragmatic', 'power-sharing', 'psycho-therapeutic', 'proud' and 'profound'. The combined elements of the findings present a theoretical construct of mental health nursing practice as something distinctive and special. It provides a model and exemplar for contemporary practice in mental health nursing, embracing the role of mental health nurses in the health care workforce as being well placed as providers of productive and effective care. © 2017 Australian College of Mental Health Nurses Inc.

  12. Precambrian Skeletonized Microbial Eukaryotes

    Science.gov (United States)

    Lipps, Jere H.

    2017-04-01

    Skeletal heterotrophic eukaryotes are mostly absent from the Precambrian, although algal eukaryotes appear about 2.2 billion years ago. Tintinnids, radiolaria and foraminifera have molecular origins well back into the Precambrian yet no representatives of these groups are known with certainty in that time. These data infer times of the last common ancestors, not the appearance of true representatives of these groups which may well have diversified or not been preserved since those splits. Previous reports of these groups in the Precambrian are misinterpretations of other objects in the fossil record. Reported tintinnids at 1600 mya from China are metamorphic shards or mineral artifacts, the many specimens from 635-715 mya in Mongolia may be eukaryotes but they are not tintinnids, and the putative tintinnids at 580 mya in the Doushantou formation of China are diagenetic alterations of well-known acritarchs. The oldest supposed foraminiferan is Titanotheca from 550 to 565 mya rocks in South America and Africa is based on the occurrence of rutile in the tests and in a few modern agglutinated foraminifera, as well as the agglutinated tests. Neither of these nor the morphology are characteristic of foraminifera; hence these fossils remain as indeterminate microfossils. Platysolenites, an agglutinated tube identical to the modern foraminiferan Bathysiphon, occurs in the latest Neoproterozoic in Russia, Canada, and the USA (California). Some of the larger fossils occurring in typical Ediacaran (late Neoproterozoic) assemblages may be xenophyophorids (very large foraminifera), but the comparison is disputed and flawed. Radiolaria, on occasion, have been reported in the Precambrian, but the earliest known clearly identifiable ones are in the Cambrian. The only certain Precambrian heterotrophic skeletal eukaryotes (thecamoebians) occur in fresh-water rocks at about 750 mya. Skeletonized radiolaria and foraminifera appear sparsely in the Cambrian and radiate in the Ordovician

  13. Bibliometric mapping: eight decades of analytical chemistry, with special focus on the use of mass spectrometry.

    Science.gov (United States)

    Waaijer, Cathelijn J F; Palmblad, Magnus

    2015-01-01

    In this Feature we use automatic bibliometric mapping tools to visualize the history of analytical chemistry from the 1920s until the present. In particular, we have focused on the application of mass spectrometry in different fields. The analysis shows major shifts in research focus and use of mass spectrometry. We conclude by discussing the application of bibliometric mapping and visualization tools in analytical chemists' research.

  14. Shifting Focus: Assessing the Role of U.S. Army Special Forces in the Counterproliferation of Weapons of Mass Destruction

    Science.gov (United States)

    2014-06-01

    1995 (1994), http://thomas.loc.gov/cgi- bin/bdquery/z?d103:SN02182:; TOM :/bss/d103query.html;. 55 Joint Chiefs of Staff, Combating Weapons of Mass...or instead focus on an overall security goal? As an experienced Army Special Operations planner, Lieutenant Colonel Mike Kenny posits that we should...Michael Kenny (Lieutenant Colonel), e-mail discussion with author, February 28, 2014. 109 Petit, Going Big by Getting Small, 111. 110 Defense Institute

  15. E-learning adoption in hospitality education: An analysis with special focus on Singapore

    Directory of Open Access Journals (Sweden)

    Revi Nair

    2016-06-01

    Full Text Available This paper explores issues and challenges in the adoption of e-learning in hospitality education, with special reference to Singapore. Hospitality being a ‘high-touch’ profession and many hospitality related skills being largely intangible, there has been significant industry resistance in technology adoption. There has been concerns from multiple stakeholder groups as to how effectively can technologies compensate for the loss of social context of traditional hands-on learning. However, in Singapore, some polytechnic based schools have practically demonstrated the ways by which technology could be meaningfully integrated into hospitality education.

  16. Characterisation of patient encounters in community pharmacies (with special focus on self-medication).

    Science.gov (United States)

    De Bolle, Leen; Mehuys, Els; Christiaens, Thierry; Van Tongelen, Inge; Remon, Jean-Paul; Boussery, Koen

    2015-06-01

    To characterise patient encounters during routine drug dispensing in community pharmacies. Cross-sectional survey in community pharmacies (Belgium). Fifty-four per cent of all encounters (N = 1650) concerned patients carrying a prescription, of which 39% were prescriptions for new medication and 61% were repeat prescriptions. In 62% of all encounters, patients asked for non-prescribed medication. Almost one-third of self-medication requests related to special patient populations (mainly children and elderly). CONCLUSIONS : Many encounters related to self-medication, and a substantial number of these self-medication requests concerned vulnerable patient populations. © 2014 Royal Pharmaceutical Society.

  17. Status of Oregon's Children: 1997 County Databook. Special Focus: Youth-at-Risk.

    Science.gov (United States)

    Children First for Oregon, Portland.

    This Kids Count databook examines statewide trends in the well-being of Oregon's children, focusing on youth at risk. The statistical report is based on 12 indicators of well-being: (1) juvenile arrests; (2) teen sexuality; (3) high school dropout rate; (4) teen suicide; (5) reading proficiency; (6) math proficiency; (7) child abuse and neglect;…

  18. Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes

    DEFF Research Database (Denmark)

    Alsmark, Cecilia; Foster, Peter G; Sicheritz-Pontén, Thomas

    2013-01-01

    BACKGROUND: The influence of lateral gene transfer on gene origins and biology in eukaryotes is poorly understood compared with those of prokaryotes. A number of independent investigations focusing on specific genes, individual genomes, or specific functional categories from various eukaryotes have...... indicated that lateral gene transfer does indeed affect eukaryotic genomes. However, the lack of common methodology and criteria in these studies makes it difficult to assess the general importance and influence of lateral gene transfer on eukaryotic genome evolution. RESULTS: We used a phylogenomic...... are conserved among lineages, the genes making up those pathways can have very different origins in different eukaryotes. Thus, from the perspective of the effects of lateral gene transfer on individual gene ancestries in different lineages, eukaryotic metabolism appears to be chimeric....

  19. Enterprise human assets valuation with a special focuse on human assets valuation of a knowledge enterprise

    OpenAIRE

    Filipová, Iveta

    2012-01-01

    The dissertation focuses on the valuation of human assets for the purpose of business valuation. The introduction section contains, among others, search of knowledge about the human capital valuation including an identification of "empty spaces" in the business valuation theory in connection with the valuation of human assets. The main aim of the dissertation is the theoretical and experimental development of selected "empty spaces" which were divided into two levels - direct (separate) valua...

  20. Natural history of eukaryotic DNA methylation systems.

    Science.gov (United States)

    Iyer, Lakshminarayan M; Abhiman, Saraswathi; Aravind, L

    2011-01-01

    Methylation of cytosines and adenines in DNA is a widespread epigenetic mark in both prokaryotes and eukaryotes. In eukaryotes, it has a profound influence on chromatin structure and dynamics. Recent advances in genomics and biochemistry have considerably elucidated the functions and provenance of these DNA modifications. DNA methylases appear to have emerged first in bacterial restriction-modification (R-M) systems from ancient RNA-modifying enzymes, in transitions that involved acquisition of novel catalytic residues and DNA-recognition features. DNA adenine methylases appear to have been acquired by ciliates, heterolobosean amoeboflagellates, and certain chlorophyte algae. Six distinct clades of cytosine methylases, including the DNMT1, DNMT2, and DNMT3 clades, were acquired by eukaryotes through independent lateral transfer of their precursors from bacteria or bacteriophages. In addition to these, multiple adenine and cytosine methylases were acquired by several families of eukaryotic transposons. In eukaryotes, the DNA-methylase module was often combined with distinct modified and unmodified peptide recognition domains and other modules mediating specialized interactions, for example, the RFD module of DNMT1 which contains a permuted Sm domain linked to a helix-turn-helix domain. In eukaryotes, the evolution of DNA methylases appears to have proceeded in parallel to the elaboration of histone-modifying enzymes and the RNAi system, with functions related to counter-viral and counter-transposon defense, and regulation of DNA repair and differential gene expression being their primary ancestral functions. Diverse DNA demethylation systems that utilize base-excision repair via DNA glycosylases and cytosine deaminases appear to have emerged in multiple eukaryotic lineages. Comparative genomics suggests that the link between cytosine methylation and DNA glycosylases probably emerged first in a novel R-M system in bacteria. Recent studies suggest that the 5mC is not

  1. Pathophysiology of primary burning mouth syndrome with special focus on taste dysfunction: a review.

    Science.gov (United States)

    Kolkka-Palomaa, M; Jääskeläinen, S K; Laine, M A; Teerijoki-Oksa, T; Sandell, M; Forssell, H

    2015-11-01

    Primary burning mouth syndrome (BMS) is a chronic oral condition characterized by burning pain often accompanied with taste dysfunction and xerostomia. The most compelling evidence concerning BMS pathophysiology comes from studies on the somatosensory system using neurophysiologic or psychophysical methods such as blink reflex, thermal quantitative sensory testing, as well as functional brain imaging. They have provided convincing evidence for neuropathic involvement at several levels of the somatosensory system in BMS pain pathophysiology. The number of taste function studies trying to substantiate the subjective taste disturbances or studies on salivary factors in BMS is much more limited, and most of them suffer from definitional and methodological problems. This review aims to critically evaluate the existing literature on the pathophysiology of BMS, paying special attention to the correctness of case selection and the methodology used in published studies, and to summarize the current state of knowledge. Based on the recognition of several gaps in the current understanding of the pathophysiology of BMS especially as regards taste and pain system interactions, the review ends with future scenarios for research in this area. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  2. [Tuberculosis control programme for the elderly with special focus on early detection].

    Science.gov (United States)

    Kajiki, Akira; Ishikawa, Nobukatsu

    2004-02-01

    tool. One of them is anti-lipoarabinomannan antibody. 74.3% was positive to this among 148 bacteriologically confirmed TB cases; 77.8% for those aged 65 years and above, and 71.1% for those under 65 years. To anti TBGL antibody, 78% of 170 confirmed TB cases were positive; 75% for those aged 65 years and above, 79.8% for those less than 65 years. Multi-lipo antibody developed by Japan BCG Laboratory showed higher sensitivity of 91.5%. GPL-core antibody may increase the sensitivity. 4. Mode of TB detection in nursing homes: Shinji SHISHIDO (Research Institute of Tuberculosis, JATA). 15 elderly TB patients who had been diagnosed in 23 nursing homes in the last 5 years were analyzed. The average age was 80.7 years. 10 were male and 5 were female. 11 were sputum smear positive. The symptoms were fever (8), cough (7), wheezing (2), hemoptysis (1), chest pain (1), body weight loss (1), appetite loss (1). Number of patients by time durations before consulting a doctor of within 2 weeks, 2 weeks to 1 month, 1 to 2 months, 2 to 3 months, 3 to 6 months, and more than 6 months were 6, 1, 1, 3, 2, 2 respectively. The prognosis: 4 died within 10 days after diagnosis, 4 needed examinations for the symptoms but were delayed in diagnosis as they were not admitted due to dementia or disability. The orientation and training to the staff of the nursing homes are needed for early TB diagnosis. 5. Programme for the early detection of TB among the elderly: Tadayuki AHIKO (Murayama Public Health Center, Yamagata Prefecture). Based on the analysis of 138 confirmed TB cases registered in Yamagata Prefecture in 1998, services for early TB detection among the elderly should be 1) periodical chest X-ray examinations by the patients home doctors when underlying high risk diseases such as diabetes or cancer exist, and 2) -sputum examination for the symptomatic patients. A survey to 31 local governments conducting special TB services showed the special screening programme for the bedridden elderly

  3. Mitochondrial specialization revealed by single muscle fiber proteomics: focus on the Krebs cycle.

    Science.gov (United States)

    Schiaffino, S; Reggiani, C; Kostrominova, T Y; Mann, M; Murgia, M

    2015-12-01

    We have developed a highly sensitive mass spectrometry-based proteomic workflow to examine the proteome of single muscle fibers. This study revealed significant differences in the mitochondrial proteome of the four major fiber types present in mouse skeletal muscle. Here, we focus on Krebs cycle enzymes and in particular on the differential distribution of the two mitochondrial isocitrate dehydrogenases, IDH2 and IDH3. Type 1/slow fibers contain high levels of IDH2 and relatively low levels of IDH3, whereas fast 2X and 2B fibers show an opposite expression pattern. The findings suggest that in skeletal muscle, IDH2 functions in the forward direction of the Krebs cycle and that substrate flux along the cycle occurs predominantly via IDH2 in type 1 fibers and via IDH3 in 2X and 2B fibers. IDH2-mediated conversion of isocitrate to α-ketoglutarate leads to the generation of NADPH, which is critical to buffering the H2O2 produced by the respiratory chain. Nicotinamide nucleotide transhydrogenase (NNT), the other major mitochondrial enzyme involved in NADPH generation, is also more abundant in type 1 fibers. We suggest that the continuously active type 1 fibers are endowed with a more efficient H2O2 scavenging capacity to cope with the higher levels of reactive oxygen species production. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  4. Sentinel surveillance systems with special focus on vector-borne diseases.

    Science.gov (United States)

    Racloz, V; Griot, C; Stärk, K D C

    2006-01-01

    In the past few decades, vector-borne diseases have been spreading into countries previously free of these agents. It is necessary for a surveillance method to be tailored to the biology of these agents in order to detect their incursion. Using a sentinel herd system, it is possible to target high-risk areas where occurrence is most probably due to vector presence. Since the 1970s, diseases such as Akabane, vesicular stomatitis and Bluetongue disease have successfully been monitored using cattle herds as sentinels in many countries such as Saudi Arabia, Australia, China, Indonesia, Sultanate of Oman and most recently in countries in Western Europe. This paper reviews the strengths and weaknesses of sentinel herd surveillance systems in general. In order to determine their efficacy, the following criteria were found to be essential: the choice of sentinel locations, sentinel animal, seasonality of sampling and diagnostic testing methods. We conclude that due to its ability to focus on a specific disease, sentinel herd systems have been successful in the early detection of the spread of a targeted agent. This review is used as a basis for recommendations for the development of future sentinel herd systems.

  5. Innovation policy of European chemical companies with special focus on large companies

    Directory of Open Access Journals (Sweden)

    Supriyo Das

    2015-07-01

    Full Text Available According to Arora et alii (1998, the chemical industry is one of the largest and most R&D-intensive manufacturing sectors in all the advanced economies, and its innovative patterns and productivity growth processes can have profound impacts on economic growth as a whole. The European chemical industry supplies virtually all sectors of the economy and accounts for 17.8% of the total sales of chemicals in the world. This paper gives an overview of the European chemical industry and the changing scenario of the world chemical industry by focusing on the top fifteen chemical companies in Europe. It describes the current problems this industry is facing in Europe especially after the economic crisis and shows that the region and the top companies are investing in R&D to bring about innovation and overcome the current challenges. It shows that R&D spending in absolute terms has hardly changed over the years and that the industry is still globally the largest investor in R&D activities. In terms of R&D, BASF has made the greatest investment followed by Bayer and Syngenta, while R&D intensity is highest for Syngenta and Bayer. BASF and Bayer have made most patent applications and have also had the highest number of patents granted. The quality of research in most chemical companies is very high and most of the large European companies make their first patent application in Europe rather than elsewhere. All the large chemical companies use Merger & Acquisition (M&A to gain access to innovation. Industry-academia collaboration is one way to generate innovation in the chemical industry in Europe. Chemical clusters and the geographical distribution of chemical companies play a significant role in generating innovation.

  6. WMO's activities in gender mainstreaming in geosciences, with a special focus on integrated flood management

    Science.gov (United States)

    Manaenkova, Elena; Caponi, Claudio; Alexieva, Assia; Poissonnier, Maud; Tripathi, Ramesh

    2017-04-01

    Statistics show that women represent a minority in science, technology, engineering and mathematics (STEM). They are significantly underrepresented in governance, management and international negotiations. They further comprise only a third of the global workforce at National Meteorological and Hydrological Services and only one out of five senior managers is a woman. This paper presents historical trends and statistics on the participation of women and men in all structures and activities of the World Meteorological Organization (WMO). It explores the root causes of women's underrepresentation in the meteorological, hydrological and climatological profession as well as analyzes its adverse effects in terms of the scarcity of role models for young female professionals and the lack of gender considerations in the provision of weather, hydrological and climate services. The paper presents WMO's approach to addressing these issues through the adoption of a WMO Gender Equality Policy, a comprehensive Gender Action Plan, targeted leadership training, a series of awareness raising campaigns, and specific recommendations on how to make weather, hydrological and climate services more gender-sensitive. As a specific example, the Associated Programme on Flood Management (APFM) of WMO and the Global Water Partnership (GWP) is in the process of developing a training manual for gender mainstreaming in integrated flood management. This generic, instructive, at the same time informative training manual and facilitator's guide will strive to fill gaps in practical knowledge, decision-making and further provide assistance in gender sensitive approaches for both local policy makers and communities affected by floods. The format and contents of the manual are particularly focused on every phase of the flood management cycle, incorporating gender based needs, strategies and actions/approaches. The facilitator or training instructor is encouraged to adapt the materials with local case

  7. Growth and development of children with a special focus on sleep.

    Science.gov (United States)

    Danker-Hopfe, Heidi

    2011-12-01

    The first two decades of life are characterised complex biological processes involving growth and maturation as well as differentiation. The Central Nervous System (CNS) where among others internal and external stimuli are integrated and responses of the body are prepared starts to evolve quite early during ontogenesis. One of the complex behaviours, which are regulated by the brain, is the sleep-wake cycle. The discussion of age-related changes in sleep comprises changes at the physiological level (e.g. changes in the frequency and amplitude of EEG signal, as well as development and distribution of sleep stages), changes in the corresponding behaviour (e.g. changes in the absolute amount of sleep and its distribution in 24h perspective), and finally the subjective perception of sleep and sleep as a measure of well-being. Studies on the impact of a specific factor on sleep during childhood and adolescence have to consider chronological and biological age as well as sex as relevant biological parameters. Even when these factors are controlled for large interindividual differences persist, that is why prospective instead of cross-sectional approaches should be used whenever possible. Furthermore, it has to be distinguished between sleep assessed at the level of brain functioning (i.e. by polysomnography), which gives information on effects at the physiological level and at the level of self-assessment, which focuses on behaviour. Both, sleep at the subjective as well as at the objective level, can to a considerable degree be affected by life style factors, which hence have to be considered as potential confounders. Copyright © 2011 Elsevier Ltd. All rights reserved.

  8. Biofuels from Microalgae: Review of Products, Processes and Potential, with Special Focus on Dunaliella sp.

    Energy Technology Data Exchange (ETDEWEB)

    Huesemann, Michael H.; Benemann, John R.

    2009-12-31

    is required on increasing solvent yields. Dark fermentation of algal biomass can also produce hydrogen, but, as for other fermentations, only at low yields. Hydrogen can also be generated by algae in the light, however, this process has not yet been demonstrated in any way that could be scaled up and, in any event, Dunaliella, is not known to produce hydrogen. In response to nutrient deficiency (nitrogen or silicon), some microalgae accumulate neutral lipids which, after physical extraction, could be converted, via transesterification with methanol, to biodiesel. Nitrogen-limitation does not appear to increase either cellular lipid content or lipid productivity in Dunaliella. Results from life cycle energy analyses indicate that cultivation of microalgal biomass in open raceway ponds has a positive energy output ratio (EOR), approaching up to 10 (i.e., the caloric energy output from the algae is 10 times greater than the fossil energy inputs), but EOR are less than 1 for biomass grown in engineered photobioreactors. Thus, from both an energetic as well as economic perspective, only open ponds systems can be considered. Significant long-term R&D will be required to make microalgal biofuels processes economically competitive. Specifically, future research should focus on (a) the improvement of biomass productivities (i.e., maximizing solar conversion efficiencies), (b) the selection and isolation of algal strains that can be mass cultured and maintained stably for long periods, (c) the production of algal biomass with a high content of lipids, carbohydrates, and co-products, at high productivity, (d) the low cost harvesting of the biomass, and (e) the extraction and conversion processes to actually derive the biofuels. For Dunaliella specifically, the highest potential is in the co-production of biofuels with high-value animal feeds based on their carotenoid content.

  9. Nuclear Waste Separation and Transmutation Research with Special Focus on Russian Transmutation Projects Sponsored by ISTC

    International Nuclear Information System (INIS)

    Conde, Henri; Blomgren, Jan; Olsson, Nils

    2003-03-01

    High-level nuclear reactor waste is made up of relatively few long-lived radioactive species, among them plutonium, that contribute to difficulties with its storage and disposal. Separation of these species from larger waste volumes mainly constituting of uranium (about 95 %) coupled with nuclear incineration to fission products of plutonium and the so called minor actinides (Neptunium, Americium, and Curium) and transmutation of some of the long lived fission products to short lived or stable isotopes represents a viable nuclear waste management strategy to drastically reduce the time and space requirements for a bed-rock repository of the remaining waste. A remarkable increase in the international research and development on partitioning and transmutation has occurred during the recent years. The road-map report published in April 2001 by The European Technical Working Group on ADS for the development of a European demonstration facility for nuclear waste transmutation has high-lighted the ongoing European research and pointed out the need for further research. The road-map has given the different research activities a position in the ultimate goal of producing an ADS demonstrator and is guiding research planning on the national as well as on the EU level. The Advanced Accelerator Application (3A) program in the US, with the long term goals to enhance long term public safety, provide benefits for the repository, reduce proliferation risks and improve prospects for nuclear power has focused the research on nuclear waste transmutation. The reports on the 3A program indicates a change of the US former abandonment position towards reprocessing and fast reactors due to a strong incentive to eliminate the reactor plutonium and to lower the amount of high level reactor waste for the Yucca Mountain repository. The SKB's proposed research and development program for the next 3 years (FUD01) was presented by SKB in September 2001. It is proposed that the research program

  10. Expanding the eukaryotic genetic code

    Energy Technology Data Exchange (ETDEWEB)

    Chin, Jason W.; Cropp, T. Ashton; Anderson, J. Christopher; Schultz, Peter G.

    2017-02-28

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  11. Expanding the eukaryotic genetic code

    Science.gov (United States)

    Chin, Jason W.; Cropp, T. Ashton; Anderson, J. Christopher; Schultz, Peter G.

    2013-01-22

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  12. Origins of eukaryotic sexual reproduction.

    Science.gov (United States)

    Goodenough, Ursula; Heitman, Joseph

    2014-03-01

    Sexual reproduction is a nearly universal feature of eukaryotic organisms. Given its ubiquity and shared core features, sex is thought to have arisen once in the last common ancestor to all eukaryotes. Using the perspectives of molecular genetics and cell biology, we consider documented and hypothetical scenarios for the instantiation and evolution of meiosis, fertilization, sex determination, uniparental inheritance of organelle genomes, and speciation.

  13. Eukaryotic DNA Replicases

    KAUST Repository

    Zaher, Manal S.

    2014-11-21

    The current model of the eukaryotic DNA replication fork includes three replicative DNA polymerases, polymerase α/primase complex (Pol α), polymerase δ (Pol δ), and polymerase ε (Pol ε). The primase synthesizes 8–12 nucleotide RNA primers that are extended by the DNA polymerization activity of Pol α into 30–35 nucleotide RNA-DNA primers. Replication factor C (RFC) opens the polymerase clamp-like processivity factor, proliferating cell nuclear antigen (PCNA), and loads it onto the primer-template. Pol δ utilizes PCNA to mediate highly processive DNA synthesis, while Pol ε has intrinsic high processivity that is modestly stimulated by PCNA. Pol ε replicates the leading strand and Pol δ replicates the lagging strand in a division of labor that is not strict. The three polymerases are comprised of multiple subunits and share unifying features in their large catalytic and B subunits. The remaining subunits are evolutionarily not related and perform diverse functions. The catalytic subunits are members of family B, which are distinguished by their larger sizes due to inserts in their N- and C-terminal regions. The sizes of these inserts vary among the three polymerases, and their functions remain largely unknown. Strikingly, the quaternary structures of Pol α, Pol δ, and Pol ε are arranged similarly. The catalytic subunits adopt a globular structure that is linked via its conserved C-terminal region to the B subunit. The remaining subunits are linked to the catalytic and B subunits in a highly flexible manner.

  14. Recent updates on phthalate exposure and human health: a special focus on liver toxicity and stem cell regeneration.

    Science.gov (United States)

    Praveena, Sarva Mangala; Teh, Seoh Wei; Rajendran, Ranjith Kumar; Kannan, Narayanan; Lin, Chu-Ching; Abdullah, Rozaini; Kumar, Suresh

    2018-03-15

    Phthalates have been blended in various compositions as plasticizers worldwide for a variety of purposes. Consequently, humans are exposed to a wide spectrum of phthalates that needs to be researched and understood correctly. The goal of this review is to focus on phthalate's internal exposure pathways and possible role of human digestion on liver toxicity. In addition, special focus was made on stem cell therapy in reverting liver toxicity. The known entry of higher molecular weight phthalates is through ingestion while inhalation and dermal pathways are for lower molecular weight phthalates. In human body, certain phthalates are digested through phase 1 (hydrolysis, oxidation) and phase 2 (conjugation) metabolic processes. The phthalates that are made bioavailable through digestion enter the blood stream and reach the liver for further detoxification, and these are excreted via urine and/or feces. Bis(2-ethylhexyl) phthalate (DEHP) is a compound well studied involving human metabolism. Liver plays a pivotal role in humans for detoxification of pollutants. Thus, continuous exposure to phthalates in humans may lead to inhibition of liver detoxifying enzymes and may result in liver dysfunction. The potential of stem cell therapy addressed herewith will revert liver dysfunction and lead to restoration of liver function properly.

  15. Folded genome as a platform for the functional compartmentalization of the eukaryotic cell nucleus

    Directory of Open Access Journals (Sweden)

    Ioudinkova E. S.

    2014-03-01

    Full Text Available In a number of recent studies a tight interconnection between the spatial organization of the eukaryotic genome and its functioning has been demonstrated. Moreover, it is becoming evident that the folded DNA by itself consti- tutes an important, if not the key, factor supporting the internal nuclear organization. In this review, we will discuss the current state of chromatin research with the special attention focused on chromosome territories, chromatin folding and dynamics, chromatin domains, transcription and replication factories. Based on this analysis we will show how interphase chromosomes define the assembly of different nuclear compartments and underlie the spatial compartmentalization of the cell nucleus.

  16. Modelling and simulation of flight control electromechanical actuators with special focus on model architecting, multidisciplinary effects and power flows

    Directory of Open Access Journals (Sweden)

    Jian Fu

    2017-02-01

    Full Text Available In the aerospace field, electromechanical actuators are increasingly being implemented in place of conventional hydraulic actuators. For safety-critical embedded actuation applications like flight controls, the use of electromechanical actuators introduces specific issues related to thermal balance, reflected inertia, parasitic motion due to compliance and response to failure. Unfortunately, the physical effects governing the actuator behaviour are multidisciplinary, coupled and nonlinear. Although numerous multi-domain and system-level simulation packages are now available on the market, these effects are rarely addressed as a whole because of a lack of scientific approaches for model architecting, multi-purpose incremental modelling and judicious model implementation. In this publication, virtual prototyping of electromechanical actuators is addressed using the Bond-Graph formalism. New approaches are proposed to enable incremental modelling, thermal balance analysis, response to free-run or jamming faults, impact of compliance on parasitic motion, and influence of temperature. A special focus is placed on friction and compliance of the mechanical transmission with fault injection and temperature dependence. Aileron actuation is used to highlight the proposals for control design, energy consumption and thermal analysis, power network pollution analysis and fault response.

  17. Experimental investigation of the ternary system Ni–Pd–Sn with special focus on the B8-type phase

    International Nuclear Information System (INIS)

    Jandl, Isabella; Ipser, Herbert; Richter, Klaus W.

    2015-01-01

    The ternary alloy system Ni–Pd–Sn was investigated experimentally from 700 °C upwards, with special focus on the general NiAs-type compounds. The phase diagram and crystallographic parameters were studied by means of powder X-ray diffraction (XRD), differential thermal analysis (DTA), light optical microscopy (LOM) and scanning electron microscopy (SEM) in combination with energy dispersive X-ray spectroscopy (EDX). An isothermal section at 700 °C was constructed wherein a continuous phase field between the binary NiAs-type compounds γ (PdSn) and Ni 3 Sn 2 (high temperature modification) was detected. A series of samples throughout this phase field was used to investigate lattice parameter variations, occupation of the atomic sites and the melting behaviour. A partial ordering of the transition metals was observed. Moreover, three vertical sections at 30 at.%, 40 at.% and 50 at.% Sn were determined. Altogether, seven ternary invariant phase reactions were discovered: two ternary eutectic reactions, one ternary eutectoid reaction, three ternary transition reactions and one maximum. A complete reaction scheme for the investigated temperature range is given. Furthermore, a partial liquidus surface projection, except for the low-temperature Sn-rich region, was developed. - Highlights: • Detailed study of the ternary alloy system Ni–Pd–Sn. • 1 Isotherm, 3 vertical sections, a partial liquidus projection and a reaction scheme. • A continuous phase field, between γ and Ni 3 Sn 2 , was discovered. • Lattice parameters and structural features in this phase field were analysed. • A partial order of Ni and Pd in this phase field was observed

  18. Issues Regarding the Retention of Special Education Teachers with a Focus on the Principal's Role

    Science.gov (United States)

    Rank, Kim

    2017-01-01

    Recruitment and retention of special education teachers is a growing problem in the education field. According to the National Center for Education Statistics (NCES) from 2014, 50% of special education teachers will leave the education profession during their first five years of teaching. In order to strengthen school teaching teams, knowledgeable…

  19. Intra-plastid protein trafficking: how plant cells adapted prokaryotic mechanisms to the eukaryotic condition.

    Science.gov (United States)

    Celedon, Jose M; Cline, Kenneth

    2013-02-01

    Protein trafficking and localization in plastids involve a complex interplay between ancient (prokaryotic) and novel (eukaryotic) translocases and targeting machineries. During evolution, ancient systems acquired new functions and novel translocation machineries were developed to facilitate the correct localization of nuclear encoded proteins targeted to the chloroplast. Because of its post-translational nature, targeting and integration of membrane proteins posed the biggest challenge to the organelle to avoid aggregation in the aqueous compartments. Soluble proteins faced a different kind of problem since some had to be transported across three membranes to reach their destination. Early studies suggested that chloroplasts addressed these issues by adapting ancient-prokaryotic machineries and integrating them with novel-eukaryotic systems, a process called 'conservative sorting'. In the last decade, detailed biochemical, genetic, and structural studies have unraveled the mechanisms of protein targeting and localization in chloroplasts, suggesting a highly integrated scheme where ancient and novel systems collaborate at different stages of the process. In this review we focus on the differences and similarities between chloroplast ancestral translocases and their prokaryotic relatives to highlight known modifications that adapted them to the eukaryotic situation. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. An overabundance of phase 0 introns immediately after the start codon in eukaryotic genes

    Directory of Open Access Journals (Sweden)

    Wernersson Rasmus

    2006-10-01

    Full Text Available Abstract Background A knowledge of the positions of introns in eukaryotic genes is important for understanding the evolution of introns. Despite this, there has been relatively little focus on the distribution of intron positions in genes. Results In proteins with signal peptides, there is an overabundance of phase 1 introns around the region of the signal peptide cleavage site. This has been described before. But in proteins without signal peptides, a novel phenomenon is observed: There is a sharp peak of phase 0 intron positions immediately following the start codon, i.e. between codons 1 and 2. This effect is seen in a wide range of eukaryotes: Vertebrates, arthropods, fungi, and flowering plants. Proteins carrying this start codon intron are found to comprise a special class of relatively short, lysine-rich and conserved proteins with an overrepresentation of ribosomal proteins. In addition, there is a peak of phase 0 introns at position 5 in Drosophila genes with signal peptides, predominantly representing cuticle proteins. Conclusion There is an overabundance of phase 0 introns immediately after the start codon in eukaryotic genes, which has been described before only for human ribosomal proteins. We give a detailed description of these start codon introns and the proteins that contain them.

  1. An overabundance of phase 0 introns immediately after the start codon in eukaryotic genes.

    Science.gov (United States)

    Nielsen, Henrik; Wernersson, Rasmus

    2006-10-11

    A knowledge of the positions of introns in eukaryotic genes is important for understanding the evolution of introns. Despite this, there has been relatively little focus on the distribution of intron positions in genes. In proteins with signal peptides, there is an overabundance of phase 1 introns around the region of the signal peptide cleavage site. This has been described before. But in proteins without signal peptides, a novel phenomenon is observed: There is a sharp peak of phase 0 intron positions immediately following the start codon, i.e. between codons 1 and 2. This effect is seen in a wide range of eukaryotes: Vertebrates, arthropods, fungi, and flowering plants. Proteins carrying this start codon intron are found to comprise a special class of relatively short, lysine-rich and conserved proteins with an overrepresentation of ribosomal proteins. In addition, there is a peak of phase 0 introns at position 5 in Drosophila genes with signal peptides, predominantly representing cuticle proteins. There is an overabundance of phase 0 introns immediately after the start codon in eukaryotic genes, which has been described before only for human ribosomal proteins. We give a detailed description of these start codon introns and the proteins that contain them.

  2. Non-coding RNA regulation in pathogenic bacteria located inside eukaryotic cells.

    Science.gov (United States)

    Ortega, Alvaro D; Quereda, Juan J; Pucciarelli, M Graciela; García-del Portillo, Francisco

    2014-01-01

    Intracellular bacterial pathogens have evolved distinct lifestyles inside eukaryotic cells. Some pathogens coexist with the infected cell in an obligate intracellular state, whereas others transit between the extracellular and intracellular environment. Adaptation to these intracellular lifestyles is regulated in both space and time. Non-coding small RNAs (sRNAs) are post-transcriptional regulatory molecules that fine-tune important processes in bacterial physiology including cell envelope architecture, intermediate metabolism, bacterial communication, biofilm formation, and virulence. Recent studies have shown production of defined sRNA species by intracellular bacteria located inside eukaryotic cells. The molecules targeted by these sRNAs and their expression dynamics along the intracellular infection cycle remain, however, poorly characterized. Technical difficulties linked to the isolation of "intact" intracellular bacteria from infected host cells might explain why sRNA regulation in these specialized pathogens is still a largely unexplored field. Transition from the extracellular to the intracellular lifestyle provides an ideal scenario in which regulatory sRNAs are intended to participate; so much work must be done in this direction. This review focuses on sRNAs expressed by intracellular bacterial pathogens during the infection of eukaryotic cells, strategies used with these pathogens to identify sRNAs required for virulence, and the experimental technical challenges associated to this type of studies. We also discuss varied techniques for their potential application to study RNA regulation in intracellular bacterial infections.

  3. Gonococcal attachment to eukaryotic cells

    Energy Technology Data Exchange (ETDEWEB)

    James, J.F.; Lammel, C.J.; Draper, D.L.; Brown, D.A.; Sweet, R.L.; Brooks, G.F.

    The attachment of Neisseria gonorrhoeae to eukaryotic cells grown in tissue culture was analyzed by use of light and electron microscopy and by labeling of the bacteria with (/sup 3/H)- and (/sup 14/C)adenine. Isogenic piliated and nonpiliated N. gonorrhoeae from opaque and transparent colonies were studied. The results of light microscopy studies showed that the gonococci attached to cells of human origin, including Flow 2000, HeLa 229, and HEp 2. Studies using radiolabeled gonococci gave comparable results. Piliated N. gonorrhoeae usually attached in larger numbers than nonpiliated organisms, and those from opaque colonies attached more often than isogenic variants from transparent colonies. Day-to-day variation in rate of attachment was observed. Scanning electron microscopy studies showed the gonococcal attachment to be specific for microvilli of the host cells. It is concluded that more N. gonorrhoeae from opaque colonies, as compared with isogenic variants from transparent colonies, attach to eukaryotic cells grown in tissue culture.

  4. Eukaryotic vs. prokaryotic chemosensory systems.

    Science.gov (United States)

    Sbarbati, Andrea; Merigo, Flavia; Osculati, Francesco

    2010-04-01

    In the last decades, microbiologists demonstrated that microorganisms possess chemosensory capabilities and communicate with each other via chemical signals. In parallel, it was demonstrated that solitary eukaryotic chemosensory cells are diffusely located on the mucosae of digestive and respiratory apparatuses. It is now evident that on the mucosal surfaces of vertebrates, two chemoreceptorial systems (i.e. eukaryotic and prokaryotic) coexist in a common microenvironment. To date, it is not known if the two chemosensory systems reciprocally interact and compete for detection of chemical cues. This appears to be a fruitful field of study and future researches must consider that the mucosal epithelia possess more chemosensory capabilities than previously supposed. (c) 2009 Elsevier Masson SAS. All rights reserved.

  5. Annotated bibliography: Marine geologic hazards of the Hawaiian Islands with special focus on submarine slides and turbidity currents

    Energy Technology Data Exchange (ETDEWEB)

    Normark, W.R.; Herring, H.H.

    1993-10-01

    This annotated bibliography was compiled to highlight the submarine geology of the Hawaiian Islands and identify known and potential marine geologic hazards with special emphasis on turbidity currents, submarine slides and tsunamis. Some references are included that are not specific to Hawaii but are needed to understand the geologic processes that can affect the integrity of submarine cables and other man-made structures. Entries specific to the Hawaiian Island area are shown in bold type.

  6. Massachusetts State Police Special Tactical Operations Team User Focus Group Report - Law Enforcement Advanced Protection (LEAP) Duty Uniforms, Integrated Head Protection, Chemical/Biological Protection and Human Systems Integration

    National Research Council Canada - National Science Library

    Creighton, II, Thomas E; Hibbard, Bradley; Doherty, Stephen; McManus, Kelly

    2008-01-01

    ...) from representatives within the law enforcement community. This focus group consisted exclusively of personnel assigned to the Massachusetts State Police Special Tactical Operations (STOP) Team...

  7. Physical characteristics that predict final basal insulin dose in type 2 diabetes mellitus, with a special focus on BMI

    NARCIS (Netherlands)

    Simon, A. C. R.; Bolli, G. B.; Dain, M.-P.; Wang, E.; Holleman, F.

    2014-01-01

    The possibility to predict final insulin dose based on patient's characteristics would allow for efficient titration for patients with higher dose needs. The primary aim of this post-hoc analysis of the L2T3 study was to determine predictors for final dose. Specifically, we focused on the

  8. Bridging Cultures between Home and School: A Guide for Teachers--With a Special Focus on Immigrant Latino Families.

    Science.gov (United States)

    Trumbull, Elise; Rothstein-Fisch, Carrie; Greenfield, Patricia M.; Quiroz, Blanca

    This book focuses on how to meet the challenges of education in a pluralistic society, presenting the Bridging Cultures framework, which is designed for understanding differences and conflicts that arise in situations where school culture is more individualistic than the home value system. Six sections examine: (1) "The Bridging Cultures…

  9. Technical cooperation with Central and Eastern European countries with special focus on engineering aspects of lifetime optimisation

    International Nuclear Information System (INIS)

    Trampus, P.

    2002-01-01

    A regional Technical Cooperation project for Central and Eastern European countries was established and funded by the IAEA as a response to the region's need. Majority of these countries are now in the process of establishing/strengthening their infrastructure for assessment of structural integrity of primary circuit components for an appropriate level of safety and reliability. Moreover, extension of the operational life of the WWER nuclear power plants (NPPs) became part of the generation strategy in most of these countries. The overall objective of the project is to improve long term integrity of primary circuit components as a fundamental technical prerequisite to ensure plant operation until and beyond the design lifetime. In a series of workshops and technical meetings issues relevant to primary circuit component structural integrity with special regard to operational life optimization have been being addressed. The works under the project are coordinated with the European Commission's integrity related assistance projects, and some of the activities are jointly organized with the WANO Moscow Center. Main conclusions of the central topics are summarized in this paper

  10. Haiku and Flamenco. A Paradigmatic Case of Conceptual Abstraction and Formal Minimalism with Special Focus on Notional and Procedural Meaning

    Directory of Open Access Journals (Sweden)

    María Azucena Penas Ibáñez

    2013-12-01

    Full Text Available The present work deals with the formal and semantic similarities between haiku and flamenco in a first study of this phenomenon, which is new. We study the notional and procedural meaning in haiku, and then in flamenco in order to explore the various minimalist mechanisms that govern the progression ofthought in the two languages. The research is based on the four basic semantic categories proposed by Eugene Nida and Charles R. Taber: Object (None,Event (Verb, Abstract (Adjective and Relation (Preposition. These are universal categories which encompass all the semantic subcategories extant in any language. The Object category corresponds to the Entity in a thought chronology and the Event and Abstract categories correspond to behaviour, and allof them correspond to notional or conceptual meaning. On the other hand, theRelation category is associated with procedural or instrumental meaning, becauseit expresses a connection between terms of other kinds, such as discourse markers, the order of elements in the phrase when it is relevant for the communication of inference, verbs like to be or to have, when they only express relationships. The kireji have a special interest because they are Japanese textstructure markers.

  11. African Women and Religious Change: A study of the Western Igbo of Nigeria with a special focus on Asaba town

    OpenAIRE

    Ibewuike, Victoria O.

    2006-01-01

    This study focuses on a small ethnic group in the western part of Igboland called Asaba. It describes how the religious and socio-political role of women has changed, due to colonialism, modernisation, Western education and Christianity, which were brought by the groups of Europeans and Americans, who penetrated Africa in the nineteenth century. One of the major points of the thesis is that the freeborn women in the traditional “dual-sex”society of the Igbo lost their previous power to speak ...

  12. In silico analysis of cytochrome P450 monooxygenases in chronic granulomatous infectious fungus Sporothrix schenckii: Special focus on CYP51.

    Science.gov (United States)

    Matowane, Retshedisitswe Godfrey; Wieteska, Lukasz; Bamal, Hans Denis; Kgosiemang, Ipeleng Kopano Rosinah; Van Wyk, Mari; Manume, Nessie Agnes; Abdalla, Sara Mohamed Hasaan; Mashele, Samson Sitheni; Gront, Dominik; Syed, Khajamohiddin

    2018-01-01

    Sporotrichosis is an emerging chronic, granulomatous, subcutaneous, mycotic infection caused by Sporothrix species. Sporotrichosis is treated with the azole drug itraconazole as ketoconazole is ineffective. It is a well-known fact that azole drugs act by inhibiting cytochrome P450 monooxygenases (P450s), heme-thiolate proteins. To date, nothing is known about P450s in Sporothrix schenckii and the molecular basis of its resistance to ketoconazole. Here we present genome-wide identification, annotation, phylogenetic analysis and comprehensive P450 family-level comparative analysis of S. schenckii P450s with pathogenic fungi P450s, along with a rationale for ketoconazole resistance by S. schenckii based on in silico structural analysis of CYP51. Genome data-mining of S. schenckii revealed 40 P450s in its genome that can be grouped into 32 P450 families and 39 P450 subfamilies. Comprehensive comparative analysis of P450s revealed that S. schenckii shares 11 P450 families with plant pathogenic fungi and has three unique P450 families: CYP5077, CYP5386 and CYP5696 (novel family). Among P450s, CYP51, the main target of azole drugs was also found in S. schenckii. 3D modeling of S. schenckii CYP51 revealed the presence of characteristic P450 motifs with exceptionally large reductase interaction site 2. In silico analysis revealed number of mutations that can be associated with ketoconazole resistance, especially at the channel entrance to the active site. One of possible reason for better stabilization of itraconazole, compared to ketoconazole, is that the more extended molecule of itraconazole may form a hydrogen bond with ASN-230. This in turn may explain its effectiveness against S. schenckii vis-a-vis resistant to ketoconazole. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. On equilibrium real exchange rates in euro area: Special focus on behavioral equilibrium exchange rates in Ireland and Greece

    Directory of Open Access Journals (Sweden)

    Klára Plecitá

    2012-01-01

    Full Text Available This paper focuses on the intra-euro-area imbalances. Therefore the first aim of this paper is to identify euro-area countries exhibiting macroeconomic imbalances. The subsequent aim is to estimate equilibrium real exchange rates for these countries and to compute their degrees of real exchange rate misalignment. The intra-area balance is assessed using the Cluster Analysis and the Principle Component Analysis; on this basis Greece and Ireland are selected as the two euro-area countries with largest imbalances in 2010. Further the medium-run equilibrium exchange rates for Greece and Ireland are estimated applying the Behavioral Equilibrium Exchange Rate (BEER approach popularised by Clark and MacDonald (1998. In addition, the long-run equilibrium exchange rates are estimated using the Permanent Equilibrium Exchange Rate (PEER model. Employing the BEER and PEER approaches on quarterly time series of real effective exchange rates (REER from 1997: Q1 to 2010: Q4 we identify an undervaluation of the Greek and Irish REER around their entrance to the euro area. For the rest of the period analysed their REER is broadly in line with estimated BEER and PEER levels.

  14. Physician-assisted suicide of patients with dementia. A medical ethical analysis with a special focus on patient autonomy.

    Science.gov (United States)

    Gather, Jakov; Vollmann, Jochen

    2013-01-01

    For many years there has been a controversial international debate on physician-assisted suicide (PAS). While proponents of PAS regularly refer to the unbearable suffering and the right of self-determination of incurably ill patients, critics often warn about the diverse risks of abuse. In our article, we aim to present ethical arguments for and against PAS for patients in an early stage of dementia. Our focus shall be on ethical questions of autonomy, conceptual and empirical findings on competence and the assessment of mental capacity to make health care decisions. While the capacity to make health care decisions represents an ethically significant precondition for PAS, it becomes more and more impaired in the course of the dementia process. We present conditions that should be met in order to ethically justify PAS for patients with dementia. From both a psychiatric and an ethical perspective, a thorough differential diagnosis and an adequate medical and psychosocial support for patients with dementia considering PAS and their relatives should be guaranteed. If, after due deliberation, the patient still wishes assistance with suicide, a transparent and documented assessment of competence should be conducted by a professional psychiatrist. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Comparative genome analysis of 24 bovine-associated Staphylococcus isolates with special focus on the putative virulence genes.

    Science.gov (United States)

    Åvall-Jääskeläinen, Silja; Taponen, Suvi; Kant, Ravi; Paulin, Lars; Blom, Jochen; Palva, Airi; Koort, Joanna

    2018-01-01

    Non-aureus staphylococci (NAS) are most commonly isolated from subclinical mastitis. Different NAS species may, however, have diverse effects on the inflammatory response in the udder. We determined the genome sequences of 20 staphylococcal isolates from clinical or subclinical bovine mastitis, belonging to the NAS species Staphylococcus agnetis, S. chromogenes, and S. simulans , and focused on the putative virulence factor genes present in the genomes. For comparison we used our previously published genome sequences of four S. aureus isolates from bovine mastitis. The pan-genome and core genomes of the non-aureus isolates were characterized. After that, putative virulence factor orthologues were searched in silico . We compared the presence of putative virulence factors in the NAS species and S. aureus and evaluated the potential association between bacterial genotype and type of mastitis (clinical vs. subclinical). The NAS isolates had much less virulence gene orthologues than the S. aureus isolates. One third of the virulence genes were detected only in S. aureus . About 100 virulence genes were present in all S. aureus isolates, compared to about 40 to 50 in each NAS isolate. S. simulans differed the most. Several of the virulence genes detected among NAS were harbored only by S. simulans , but it also lacked a number of genes present both in S. agnetis and S. chromogenes . The type of mastitis was not associated with any specific virulence gene profile. It seems that the virulence gene profiles or cumulative number of different virulence genes are not directly associated with the type of mastitis (clinical or subclinical), indicating that host derived factors such as the immune status play a pivotal role in the manifestation of mastitis.

  16. Comparative genome analysis of 24 bovine-associated Staphylococcus isolates with special focus on the putative virulence genes

    Science.gov (United States)

    Åvall-Jääskeläinen, Silja; Paulin, Lars; Blom, Jochen

    2018-01-01

    Non-aureus staphylococci (NAS) are most commonly isolated from subclinical mastitis. Different NAS species may, however, have diverse effects on the inflammatory response in the udder. We determined the genome sequences of 20 staphylococcal isolates from clinical or subclinical bovine mastitis, belonging to the NAS species Staphylococcus agnetis, S. chromogenes, and S. simulans, and focused on the putative virulence factor genes present in the genomes. For comparison we used our previously published genome sequences of four S. aureus isolates from bovine mastitis. The pan-genome and core genomes of the non-aureus isolates were characterized. After that, putative virulence factor orthologues were searched in silico. We compared the presence of putative virulence factors in the NAS species and S. aureus and evaluated the potential association between bacterial genotype and type of mastitis (clinical vs. subclinical). The NAS isolates had much less virulence gene orthologues than the S. aureus isolates. One third of the virulence genes were detected only in S. aureus. About 100 virulence genes were present in all S. aureus isolates, compared to about 40 to 50 in each NAS isolate. S. simulans differed the most. Several of the virulence genes detected among NAS were harbored only by S. simulans, but it also lacked a number of genes present both in S. agnetis and S. chromogenes. The type of mastitis was not associated with any specific virulence gene profile. It seems that the virulence gene profiles or cumulative number of different virulence genes are not directly associated with the type of mastitis (clinical or subclinical), indicating that host derived factors such as the immune status play a pivotal role in the manifestation of mastitis. PMID:29610707

  17. Comparative genome analysis of 24 bovine-associated Staphylococcus isolates with special focus on the putative virulence genes

    Directory of Open Access Journals (Sweden)

    Silja Åvall-Jääskeläinen

    2018-03-01

    Full Text Available Non-aureus staphylococci (NAS are most commonly isolated from subclinical mastitis. Different NAS species may, however, have diverse effects on the inflammatory response in the udder. We determined the genome sequences of 20 staphylococcal isolates from clinical or subclinical bovine mastitis, belonging to the NAS species Staphylococcus agnetis, S. chromogenes, and S. simulans, and focused on the putative virulence factor genes present in the genomes. For comparison we used our previously published genome sequences of four S. aureus isolates from bovine mastitis. The pan-genome and core genomes of the non-aureus isolates were characterized. After that, putative virulence factor orthologues were searched in silico. We compared the presence of putative virulence factors in the NAS species and S. aureus and evaluated the potential association between bacterial genotype and type of mastitis (clinical vs. subclinical. The NAS isolates had much less virulence gene orthologues than the S. aureus isolates. One third of the virulence genes were detected only in S. aureus. About 100 virulence genes were present in all S. aureus isolates, compared to about 40 to 50 in each NAS isolate. S. simulans differed the most. Several of the virulence genes detected among NAS were harbored only by S. simulans, but it also lacked a number of genes present both in S. agnetis and S. chromogenes. The type of mastitis was not associated with any specific virulence gene profile. It seems that the virulence gene profiles or cumulative number of different virulence genes are not directly associated with the type of mastitis (clinical or subclinical, indicating that host derived factors such as the immune status play a pivotal role in the manifestation of mastitis.

  18. The impact of phosphorus on the immune system and the intestinal microbiota with special focus on the pig.

    Science.gov (United States)

    Heyer, Charlotte M E; Weiss, Eva; Schmucker, Sonja; Rodehutscord, Markus; Hoelzle, Ludwig E; Mosenthin, Rainer; Stefanski, Volker

    2015-06-01

    There is increasing interest in dietary ingredients that are appropriate to support digestive and immune functions, but also maintain a stable microbial ecosystem in the gastrointestinal tract (GIT), particularly in weaned pigs. P is an essential nutrient for both microbes and their host, as it is involved, for example, in bone formation, energy metabolism, cellular signalling and stabilisation of cell membranes. Non-ruminant animals have limited access to phytate, the main storage form of P in plant seeds. The release of P bound to phytate requires phytase activity of plant or microbial origin, resulting in the formation of variable phosphorylated inositol phosphates (InsPs). The present review focuses on interactions between variations in dietary P supply, the immune system of the host, and the intestinal microbial ecosystem. Although results on the interaction between P and the immune system are inconsistent, several studies in different species have shown a positive impact of dietary P and phytase addition on the adaptive immune response. Recent studies with pigs suggest that P supply may influence intestinal microbial composition and activity. Individual InsPs or phosphate may also affect properties of pathogenic micro-organisms, such as metabolism or virulence. In conclusion, P may be considered as part of an integrated approach to support immune functions and maintain a stable microbial ecosystem in the GIT, thereby providing a barrier against potential pathogens. Within this regard, differences in phytate-P content and intrinsic phytase activity of plant feedstuffs, as well as the formation of individual InsPs, have to be taken into account.

  19. An overview of Conservation Agriculture in the dry Mediterranean environments with a special focus on Syria and Lebanon

    Directory of Open Access Journals (Sweden)

    B. Hansmann

    2016-02-01

    Full Text Available Conservation Agriculture (CA, comprising minimum or no mechanical soil disturbance through no-till seeding, organic soil mulch cover, and crop diversification is now practiced on some 157 million ha worldwide, corresponding to about 11% of the global cropped land. CA adoption in the Middle-East is low compared to other regions. Lack of knowledge on CA practices and systems discourages farmers from giving up ploughing. The main reason why farmers in the Middle-East have begun to apply the no-till system has been the cost reduction in fuel, labor and machinery required for land preparation. Soil and water conservation concerns do not appear to be the main drivers in the Middle-Eastern farmers’ decision to adopt or not to adopt CA. The adoption and uptake of CA by Middle Eastern farmers has been slow but it is nonetheless occurring gradually. Collection of information and research parameters related to agricultural practices are needed for designing a suitable soil and water conservation program for sustainable production intensification. Governmental policy encouraging the adoption and spread of CA systems in the Middle-East region is certainly a necessary condition for uptake. The objective of this article is to review the current status of adoption and spread of CA in the Middle-East, focusing mainly on Syria and Lebanon, and the potential beneficial consequences that can be harnessed through CA systems under rainfed conditions in both countries. The benefits include: higher factor productivity, yield and income; improved soil properties; climate change adaptation, including reduced vulnerability to the erratic rainfall distribution; and reduction in machinery, fuel and labor costs.

  20. Prevention and Control Strategies to Counter Zika Virus, a Special Focus on Intervention Approaches against Vector Mosquitoes-Current Updates.

    Science.gov (United States)

    Singh, Raj K; Dhama, Kuldeep; Khandia, Rekha; Munjal, Ashok; Karthik, Kumaragurubaran; Tiwari, Ruchi; Chakraborty, Sandip; Malik, Yashpal S; Bueno-Marí, Rubén

    2018-01-01

    Zika virus (ZIKV) is the most recent intruder that acquired the status of global threat creating panic and frightening situation to public owing to its rapid spread, attaining higher virulence and causing complex clinical manifestations including microcephaly in newborns and Guillain Barré Syndrome. Alike other flaviviruses, the principal mode of ZIKV transmission is by mosquitoes. Advances in research have provided reliable diagnostics for detecting ZIKV infection, while several drug/therapeutic targets and vaccine candidates have been identified recently. Despite these progresses, currently there is neither any effective drug nor any vaccine available against ZIKV. Under such circumstances and to tackle the problem at large, control measures of which mosquito population control need to be strengthened following appropriate mechanical, chemical, biological and genetic control measures. Apart from this, several other known modes of ZIKV transmission which have gained importance in recent past such as intrauterine, sexual intercourse, and blood-borne spread need to be checked and kept under control by adopting appropriate precautions and utmost care during sexual intercourse, blood transfusion and organ transplantation. The virus inactivation by pasteurization, detergents, chemicals, and filtration can effectively reduce viral load in plasma-derived medicinal products. Added to this, strengthening of the surveillance and monitoring of ZIKV as well as avoiding travel to Zika infected areas would aid in keeping viral infection under check. Here, we discuss the salient advances in the prevention and control strategies to combat ZIKV with a focus on highlighting various intervention approaches against the vector mosquitoes of this viral pathogen along with presenting an overview regarding human intervention measures to counter other modes of ZIKV transmission and spread. Additionally, owing to the success of vaccines for a number of infections globally, a separate

  1. Emergence of nonmotor symptoms as the focus of research and treatment of Parkinson's disease: introduction to the special section on nonmotor dysfunctions in Parkinson's disease.

    Science.gov (United States)

    Cronin-Golomb, Alice

    2013-04-01

    Parkinson's disease (PD) is traditionally characterized by the cardinal motor symptoms of tremor, rigidity, slowness of movement, and impairments of posture, gait, and balance. A relatively new focus of research and treatment is the nonmotor symptoms of the disease, following from recent understanding of the neuropathological stages. Disruptions of arousal, mood, sleep, and autonomic function before the first motor signs of PD implicate the lower brainstem, which is affected before the substantia nigra and dopaminergic system. In later stages of the disease, the pathology extends to the cortex, accompanied by impairments in cognition and perception. The articles in this special section advance our knowledge of the brain bases of the nonmotor symptoms of PD, including disrupted visual perception, impaired cognition across a range of domains, and psychiatric and artistic manifestations. Subtypes under investigation include those described by side of disease onset (left or right body side), predominant cognitive profile, and gender. Taken together, the articles in this special section reflect the field's growing focus on the nonmotor symptoms of PD, their brain bases, and the corresponding potential for their treatment.

  2. Modelisation of transport in fractured media with a smeared fractures modeling approach: special focus on matrix diffusion process.

    Science.gov (United States)

    Fourno, A.; Grenier, C.; Benabderrahmane, H.

    2003-04-01

    the fractured network. For a long time scale, the diffusion process can't be neglected. It plays an important retention role for the transport of plume. This is why we focus here on the evaluation of the approach for matrix diffusion. In addition, this is, here, a key issue because one of the specificities of the smeared fractures method is that it can deal with the actual rock block volume. Nevertheless we only devote a limited number of meshes to rock matrix blocks so that the limits of the approach in terms of time and space discretization level as well as transport regimes have to be addressed. So, having implemented the developed smeared fracture approach in our code CAST3M, we study the diffusion process for different transport regimes from dominant fracture network transport to dominant matrix diffusion transport and we estimate the validity as well as the precision of the results for different mesh sizes. This is done by comparing the smeared fracture approach results to reference calculations obtained by explicitly meshing the fractured system. Results show that the smeared fracture approach fairly well captures the main features of transport and reduces the simulation costs. For the cases studied, we succeed in having a good precision with different discretization levels. This finally makes this approach an interesting compromise between precision and versatility associated to low computer costs in the perspective of Monte Carlo simulations. A more realistic application is provided based on data from the Äspö underground laboratory (Sweden) and discussed. Future steps include extension of the approach to 3D cases.

  3. Eukaryotic diversity in historical soil samples

    NARCIS (Netherlands)

    Moon-van der Staay, S.Y.; Tzeneva, V.A.; Staay, van der G.W.M.; Vos, de W.M.; Smidt, H.; Hackstein, J.H.P.

    2006-01-01

    The eukaryotic biodiversity in historical air-dried samples of Dutch agricultural soil has been assessed by random sequencing of an 18S rRNA gene library and by denaturing gradient gel electrophoresis. Representatives of nearly all taxa of eukaryotic soil microbes could be identified, demonstrating

  4. Exploring social norms around cohabitation: The life course, individualization, and culture: Introduction to Special Collection: "Focus on Partnerships: Discourses on cohabitation and marriage throughout Europe and Australia"

    Directory of Open Access Journals (Sweden)

    Brienna Perelli-Harris

    2015-10-01

    Full Text Available Background: Explanations of the increase in cohabitation often rely on the concept of ideational change and shifting social norms. While researchers have investigated cohabitation and the role of social norms from a quantitative perspective, few studies have examined how people discuss the normative context of cohabitation, especially in cross-national comparison. Objective: This article introduces a Special Collection that uses focus group research to compare social norms relating to cohabitation and marriage in 8 countries in Europe. The Introduction explicates the concept of social norms, describes the focus group project, reflects on the method's advantages and limitations, and summarizes the theoretical and methodological contributions of the project. Methods: Collaborators conducted 7−8 focus groups in each country using a standardized questionnaire. They coded each discussion, analyzed the results, and produced a country-specific chapter on a particular theme. They also collaborated on an overview paper that synthesized the overall findings of the project. Results: The articles provide insights into the meanings of partnership formation in each country. In addition, their findings contribute to three main theoretical themes: 1 life courses, sequencing, and intersections; 2 individualization, freedom, and commitment; and 3 culture, religion, and the persistence of the past. Conclusions: This Special Collection contributes to and challenges current explanations of family change by pointing out how social norms shape partnership behavior. The project informs quantitative research by emphasizing the need for a culturally informed interpretation of demographic behavior. We urge researchers to recognize the multiple meanings of cohabitation within each context and across countries.

  5. Spatial distribution of benthic macroorganisms on reef flats at Porto de Galinhas Beach (northeastern Brazil, with special focus on corals and calcified hydroids

    Directory of Open Access Journals (Sweden)

    Juliana Imenis Barradas

    2010-06-01

    Full Text Available Despite their ecological and social-economic importance, coral reefs are under constant threat and thus require proper management practices. Data on the spatial structure of these ecosystems are essential for good quality conservation projects in such areas. This study aimed to quantitatively analyze the spatial distribution of benthic macroorganisms from the reef environment of Porto de Galinhas Beach, with special focus on its corals and calcified hydroids. Reef flats of the area were surveyed by scuba diving, using 10m line transects. A high cover of macroalgae was verified, averaging 53% of the observations. Zoanthids were the second most representative group (11%. A total of 173 colonies of corals and calcified hydroids were observed and 40% of these colonies were partially or totally bleached.

  6. Family Planning Practices, Programmes and Policies in India Including Implants and Injectables with a Special Focus on Jharkhand, India: A Brief Review.

    Science.gov (United States)

    Samal, Janmejaya; Dehury, Ranjit Kumar

    2015-11-01

    The National Family Health Survey (NFHS)-3 clearly delineates that the usage of contraceptive practices has increased considerably but is more inclined toward terminal methods of contraception especially the female sterilization. The fact is also evident from various studies carried out from time to time in different Indian states. Given the context we carried out a short review to understand the family planning practices, programs and policies in India including implants and injectable contraceptives with a special focus on the state of Jharkhand. We found that among the reversible methods IUCD (intra uterine contraceptive devices), OC (oral contraceptive) pills and condoms are the most commonly used methods. In this review, in addition to national picture, we specially focused on the state of Jharkhand owing to its very gloomy picture of family planning practices as per NFHS -3 reports. The current usage of any methods of contraception in Jharkhand is only 35.7% out of which terminal methods especially female sterilization accounts to 23.4% and male sterilization being only 0.4%. Similar picture is also reflected in the conventional methods such as; IUCD-0.6%, oral pill -3.8% and condom-2.7%. Compared to the national figure the unmet need for family planning in Jharkhand is also relatively high for the conventional reversible methods than that of terminal methods which is 11.9 and 11.3 respectively. Injectable contraceptives are available only through private or social marketing channels, because of which their use is limited. The studies carried out in different Indian states show improvement in contraceptive prevalence but the same needs further improvement.

  7. The eukaryotic fossil record in deep time

    Science.gov (United States)

    Butterfield, N.

    2011-12-01

    Eukaryotic organisms are defining constituents of the Phanerozoic biosphere, but they also extend well back into the Proterozoic record, primarily in the form of microscopic body fossils. Criteria for identifying pre-Ediacaran eukaryotes include large cell size, morphologically complex cell walls and/or the recognition of diagnostically eukaryotic cell division patterns. The oldest unambiguous eukaryote currently on record is an acanthomorphic acritarch (Tappania) from the Palaeoproterozoic Semri Group of central India. Older candidate eukaryotes are difficult to distinguish from giant bacteria, prokaryotic colonies or diagenetic artefacts. In younger Meso- and Neoproterozoic strata, the challenge is to recognize particular grades and clades of eukaryotes, and to document their macro-evolutionary expression. Distinctive unicellular forms include mid-Neoproterozoic testate amoebae and phosphate biomineralizing 'scale-microfossils' comparable to an extant green alga. There is also a significant record of seaweeds, possible fungi and problematica from this interval, documenting multiple independent experiments in eukaryotic multicellularity. Taxonomically resolved forms include a bangiacean red alga and probable vaucheriacean chromalveolate algae from the late Mesoproterozoic, and populations of hydrodictyacean and siphonocladalean green algae of mid Neoproterozoic age. Despite this phylogenetic breadth, however, or arguments from molecular clocks, there is no convincing evidence for pre-Ediacaran metazoans or metaphytes. The conspicuously incomplete nature of the Proterozoic record makes it difficult to resolve larger-scale ecological and evolutionary patterns. Even so, both body fossils and biomarker data point to a pre-Ediacaran biosphere dominated overwhelming by prokaryotes. Contemporaneous eukaryotes appear to be limited to conspicuously shallow water environments, and exhibit fundamentally lower levels of morphological diversity and evolutionary turnover than

  8. From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell.

    Science.gov (United States)

    Martijn, Joran; Ettema, Thijs J G

    2013-02-01

    The evolutionary origin of the eukaryotic cell represents an enigmatic, yet largely incomplete, puzzle. Several mutually incompatible scenarios have been proposed to explain how the eukaryotic domain of life could have emerged. To date, convincing evidence for these scenarios in the form of intermediate stages of the proposed eukaryogenesis trajectories is lacking, presenting the emergence of the complex features of the eukaryotic cell as an evolutionary deus ex machina. However, recent advances in the field of phylogenomics have started to lend support for a model that places a cellular fusion event at the basis of the origin of eukaryotes (symbiogenesis), involving the merger of an as yet unknown archaeal lineage that most probably belongs to the recently proposed 'TACK superphylum' (comprising Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota) with an alphaproteobacterium (the protomitochondrion). Interestingly, an increasing number of so-called ESPs (eukaryotic signature proteins) is being discovered in recently sequenced archaeal genomes, indicating that the archaeal ancestor of the eukaryotic cell might have been more eukaryotic in nature than presumed previously, and might, for example, have comprised primitive phagocytotic capabilities. In the present paper, we review the evolutionary transition from archaeon to eukaryote, and propose a new model for the emergence of the eukaryotic cell, the 'PhAT (phagocytosing archaeon theory)', which explains the emergence of the cellular and genomic features of eukaryotes in the light of a transiently complex phagocytosing archaeon.

  9. A systematic review of pedagogical approaches that can effectively include children with special educational needs in mainstream classrooms with a particular focus on peer group interactive approaches

    OpenAIRE

    Nind, Melanie; Wearmouth, Janice

    2005-01-01

    Background The broad background to this review is a long history of concepts of special pupils and special education and a faith in special pedagogical approaches. The rise of inclusive schools and some important critiques of special pedagogy (e.g. Hart, 1996; Norwich and Lewis, 2001; Thomas and Loxley, 2001) have raised the profile of teaching approaches that ordinary teachers can and do use to include children with special educational needs in mainstream classrooms. Inclusive education i...

  10. [Advance of heterologous expression study of eukaryote-origin laccases].

    Science.gov (United States)

    Ning, Na; Tan, Huijun; Sun, Xinxin; Ni, Jinfeng

    2017-04-25

    Laccases are enzymes belonging to the group of multi-copper oxidases. These enzymes are widely distributed in insects, plants, fungi and bacteria. In general, laccases can oxidize an exceptionally high number of substrates, so they have broad applications in textile, pulp, food and the degradation of lignin. However, low yield, low activity and thermo-instability of laccase in nature limit the application of laccase. High efficient heterologous expression of the protein is an effective way for solving this problem. Here, we summarize the research advances of heterologous expression of eukaryote-origin laccases. We focus on the overexpression of eukaryote-origin laccases using different expression system and the method for improving the production yield and enzyme activity in yeast cells. Information provided in this review would be helpful for researchers in the field.

  11. Transfer of DNA from Bacteria to Eukaryotes

    Directory of Open Access Journals (Sweden)

    Benoît Lacroix

    2016-07-01

    Full Text Available Historically, the members of the Agrobacterium genus have been considered the only bacterial species naturally able to transfer and integrate DNA into the genomes of their eukaryotic hosts. Yet, increasing evidence suggests that this ability to genetically transform eukaryotic host cells might be more widespread in the bacterial world. Indeed, analyses of accumulating genomic data reveal cases of horizontal gene transfer from bacteria to eukaryotes and suggest that it represents a significant force in adaptive evolution of eukaryotic species. Specifically, recent reports indicate that bacteria other than Agrobacterium, such as Bartonella henselae (a zoonotic pathogen, Rhizobium etli (a plant-symbiotic bacterium related to Agrobacterium, or even Escherichia coli, have the ability to genetically transform their host cells under laboratory conditions. This DNA transfer relies on type IV secretion systems (T4SSs, the molecular machines that transport macromolecules during conjugative plasmid transfer and also during transport of proteins and/or DNA to the eukaryotic recipient cells. In this review article, we explore the extent of possible transfer of genetic information from bacteria to eukaryotic cells as well as the evolutionary implications and potential applications of this transfer.

  12. Broadly sampled multigene trees of eukaryotes

    Directory of Open Access Journals (Sweden)

    Logsdon John M

    2008-01-01

    Full Text Available Abstract Background Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, there is an increasing trend to classify eukaryotic diversity into six major supergroups: the 'Amoebozoa', 'Chromalveolata', 'Excavata', 'Opisthokonta', 'Plantae', and 'Rhizaria'. Previous molecular analyses have often suffered from either a broad taxon sampling using only single-gene data or have used multigene data with a limited sample of taxa. This study has two major aims: (1 to place taxa represented by 72 sequences, 61 of which have not been characterized previously, onto a well-sampled multigene genealogy, and (2 to evaluate the support for the six putative supergroups using two taxon-rich data sets and a variety of phylogenetic approaches. Results The inferred trees reveal strong support for many clades that also have defining ultrastructural or molecular characters. In contrast, we find limited to no support for most of the putative supergroups as only the 'Opisthokonta' receive strong support in our analyses. The supergroup 'Amoebozoa' has only moderate support, whereas the 'Chromalveolata', 'Excavata', 'Plantae', and 'Rhizaria' receive very limited or no support. Conclusion Our analytical approach substantiates the power of increased taxon sampling in placing diverse eukaryotic lineages within well-supported clades. At the same time, this study indicates that the six supergroup hypothesis of higher-level eukaryotic classification is likely premature. The use of a taxon-rich data set with 105 lineages, which still includes only a small fraction of the diversity of microbial eukaryotes, fails to resolve deeper phylogenetic relationships and reveals no support for four of the six proposed supergroups. Our analyses provide a point of departure for future taxon- and gene-rich analyses of the

  13. Nucleoporin Nup98: a gatekeeper in the eukaryotic kingdoms.

    Science.gov (United States)

    Iwamoto, Masaaki; Asakawa, Haruhiko; Hiraoka, Yasushi; Haraguchi, Tokuko

    2010-06-01

    The nucleoporin Nup98 is an essential component of the nuclear pore complex. This peripheral nucleoporin with its Gly-Leu-Phe-Gly (GLFG) repeat domain contributes to nuclear-cytoplasmic trafficking, including mRNA export. In addition, accumulating studies indicate that Nup98 plays roles in several important biological events such as gene expression, mitotic checkpoint, and pathogenesis. Nup98 is well conserved among organisms belonging to the fungi and animal kingdoms. These kingdoms belong to the eukaryotic supergroup Opisthokonta. However, there is considerable diversity in the Nup98 orthologs expressed in organisms belonging to other eukaryotic supergroups. Intriguingly, in ciliates, a unicellular organism having two functionally distinct nuclei, GLFG-Nup98 is present in one of the nuclei and a distinct Nup98 ortholog is present in the other nucleus, and these different Nup98s participate in a nucleus-selective transport mechanism. In this review, we focus on Nup98 function and discuss how this nucleoporin has evolved in eukaryotic kingdoms.

  14. diArk – a resource for eukaryotic genome research

    Directory of Open Access Journals (Sweden)

    Kollmar Martin

    2007-04-01

    Full Text Available Abstract Background The number of completed eukaryotic genome sequences and cDNA projects has increased exponentially in the past few years although most of them have not been published yet. In addition, many microarray analyses yielded thousands of sequenced EST and cDNA clones. For the researcher interested in single gene analyses (from a phylogenetic, a structural biology or other perspective it is therefore important to have up-to-date knowledge about the various resources providing primary data. Description The database is built around 3 central tables: species, sequencing projects and publications. The species table contains commonly and alternatively used scientific names, common names and the complete taxonomic information. For projects the sequence type and links to species project web-sites and species homepages are stored. All publications are linked to projects. The web-interface provides comprehensive search modules with detailed options and three different views of the selected data. We have especially focused on developing an elaborate taxonomic tree search tool that allows the user to instantaneously identify e.g. the closest relative to the organism of interest. Conclusion We have developed a database, called diArk, to store, organize, and present the most relevant information about completed genome projects and EST/cDNA data from eukaryotes. Currently, diArk provides information about 415 eukaryotes, 823 sequencing projects, and 248 publications.

  15. A literature update elucidating production of Panax ginsenosides with a special focus on strategies enriching the anti-neoplastic minor ginsenosides in ginseng preparations.

    Science.gov (United States)

    Biswas, Tanya; Mathur, A K; Mathur, Archana

    2017-05-01

    Ginseng, an oriental gift to the world of healthcare and preventive medicine, is among the top ten medicinal herbs globally. The constitutive triterpene saponins, ginsenosides, or panaxosides are attributed to ginseng's miraculous efficacy towards anti-aging, rejuvenating, and immune-potentiating benefits. The major ginsenosides such as Rb1, Rb2, Rc, Rd., Re, and Rg1, formed after extensive glycosylations of the aglycone "dammaranediol," dominate the chemical profile of this genus in vivo and in vitro. Elicitations have successfully led to appreciable enhancements in the production of these major ginsenosides. However, current research on ginseng biotechnology has been focusing on the enrichment or production of the minor ginsenosides (the less glycosylated precursors of the major ginsenosides) in ginseng preparations, which are either absent or are produced in very low amounts in nature or via cell cultures. The minor ginsenosides under current scientific scrutiny include diol ginsenosides such as Rg3, Rh2, compound K, and triol ginsenosides Rg2 and Rh1, which are being touted as the next "anti-neoplastic pharmacophores," with better bioavailability and potency as compared to the major ginsenosides. This review aims at describing the strategies for ginsenoside production with special attention towards production of the minor ginsenosides from the major ginsenosides via microbial biotransformation, elicitations, and from heterologous expression systems.

  16. Professional Opinions And Attitudes On Tax Policy In Bosnia And Herzegovina With A Special Focus On The Federation Of Bosnia And Herzegovina1

    Directory of Open Access Journals (Sweden)

    Lazović-Pita Lejla

    2015-12-01

    Full Text Available This research is based on tax policy opinion survey data collected in Bosnia and Herzegovina (B&H among tax experts. A special focus of the survey was to investigate the consequences of the different institutional environments that exist between the two entities of the country. After having reviewed all previous tax reforms in B&H, the most interesting results suggest that respondents agree on the introduction of a progressive personal income tax (PIT and excise duty on luxury products, the maintenance of personal and family allowances and the maintenance of the current value added tax (VAT and corporate income tax (CIT rates. However, differences exist in the respondents’ perceptions about the introduction of reduced VAT rates, the regressivity of the VAT, and giving priority to the equity principle over the efficiency principle in taxation. Probability modelling highlighted these differences and indicated inconsistencies in the definition of the PIT tax base, namely the comprehensiveness of the PIT base under the S-H-S definition of income.

  17. Comparative genomics and evolution of eukaryotic phospholipidbiosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Lykidis, Athanasios

    2006-12-01

    Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymes and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.

  18. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

    Energy Technology Data Exchange (ETDEWEB)

    Parfrey, Laura Wegener; Walters, William A.; Lauber, Christian L.; Clemente, Jose C.; Berg-Lyons, Donna; Teiling, Clotilde; Kodira, Chinnappa; Mohiuddin, Mohammed; Brunelle, Julie; Driscoll, Mark; Fierer, Noah; Gilbert, Jack A.; Knight, Rob

    2014-06-19

    Eukaryotic microbes (protists) residing in the vertebrate gut influence host health and disease, but their diversity and distribution in healthy hosts is poorly understood. Protists found in the gut are typically considered parasites, but many are commensal and some are beneficial. Further, the hygiene hypothesis predicts that association with our co-evolved microbial symbionts may be important to overall health. It is therefore imperative that we understand the normal diversity of our eukaryotic gut microbiota to test for such effects and avoid eliminating commensal organisms. We assembled a dataset of healthy individuals from two populations, one with traditional, agrarian lifestyles and a second with modern, westernized lifestyles, and characterized the human eukaryotic microbiota via high-throughput sequencing. To place the human gut microbiota within a broader context our dataset also includes gut samples from diverse mammals and samples from other aquatic and terrestrial environments. We curated the SILVA ribosomal database to reflect current knowledge of eukaryotic taxonomy and employ it as a phylogenetic framework to compare eukaryotic diversity across environment. We show that adults from the non-western population harbor a diverse community of protists, and diversity in the human gut is comparable to that in other mammals. However, the eukaryotic microbiota of the western population appears depauperate. The distribution of symbionts found in mammals reflects both host phylogeny and diet. Eukaryotic microbiota in the gut are less diverse and more patchily distributed than bacteria. More broadly, we show that eukaryotic communities in the gut are less diverse than in aquatic and terrestrial habitats, and few taxa are shared across habitat types, and diversity patterns of eukaryotes are correlated with those observed for bacteria. These results outline the distribution and diversity of microbial eukaryotic communities in the mammalian gut and across

  19. Discussion of the Curriculum of the Special Needs School for the Visually Impaired and Teacher Education : Focusing on Absorptive Function and Bouncy Function

    OpenAIRE

    高橋, 眞琴; 佐藤, 貴宣

    2016-01-01

    We discussed of the curriculum of the special needs school for the visually impaired based on ethnographic research from a socio perspective. We analyzed educational practice and teacher’s role taking and performance at the special needs school for the visually impaired. It is namely the elucidation of the process through which the reality peculiar to the special needs school for the visually impaired is accomplished as a reflexivity of definitions of situations and the categorization of the ...

  20. Localization of checkpoint and repair proteins in eukaryotes

    DEFF Research Database (Denmark)

    Lisby, Michael; Rothstein, Rodney

    2005-01-01

    In eukaryotes, the cellular response to DNA damage depends on the type of DNA structure being recognized by the checkpoint and repair machinery. DNA ends and single-stranded DNA are hallmarks of double-strand breaks and replication stress. These two structures are recognized by distinct sets...... of proteins, which are reorganized into a focal assembly at the lesion. Moreover, the composition of these foci is coordinated with cell cycle progression, reflecting the favoring of end-joining in the G1 phase and homologous recombination in S and G2. The assembly of proteins at sites of DNA damage...... focusing on budding yeast and mammalian cells....

  1. Case-control study of low-back pain referred for magnetic resonance imaging, with special focus on whole-body vibration.

    Science.gov (United States)

    Palmer, Keith T; Harris, Clare E; Harris, E Claire; Griffin, Michael J; Bennett, James; Reading, Isabel; Sampson, Madelaine; Coggon, David

    2008-10-01

    This study investigated risk factors for low-back pain among patients referred for magnetic resonance imaging (MRI), with special focus on whole-body vibration. A case-control approach was used. The study population comprised working-aged persons from a catchment area for radiology services. The cases were those in a consecutive series referred for a lumbar MRI because of low-back pain. The controls were age- and gender-matched persons X-rayed for other reasons. Altogether, 252 cases and 820 controls were studied, including 185 professional drivers. The participants were questioned about physical factors loading the spine, psychosocial factors, driving, personal characteristics, mental health, and certain beliefs about low-back pain. Exposure to whole-body vibration was assessed by six measures, including weekly duration of professional driving, hours driven in one period, and current root mean square A(8). Associations with whole-body vibration were examined with adjustment for age, gender, and other potential confounders. Strong associations were found with poor mental health and belief in work as a causal factor for low-back pain, and with occupational sitting for > or =3 hours while not driving. Associations were also found for taller stature, consulting propensity, body mass index, smoking history, fear-avoidance beliefs, frequent twisting, low decision latitude, and low support at work. However, the associations with the six metrics of whole-body vibration were weak and not statistically significant, and no exposure-response relationships were found. Little evidence of a risk from professional driving or whole-body vibration was found. Drivers were substantially less heavily exposed to whole-body vibration than in some earlier surveys. Nonetheless, it seems that, at the population level, whole-body vibration is not an important cause of low-back pain among those referred for MRI.

  2. Wnt Signaling Alteration in the Spinal Cord of Amyotrophic Lateral Sclerosis Transgenic Mice: Special Focus on Frizzled-5 Cellular Expression Pattern.

    Directory of Open Access Journals (Sweden)

    Carlos González-Fernández

    Full Text Available Amyotrophic lateral sclerosis is a chronic neurodegenerative disease characterized by progressive paralysis due to degeneration of motor neurons by unknown causes. Recent evidence shows that Wnt signaling is involved in neurodegenerative processes, including Amyotrophic Lateral Sclerosis. However, to date, little is known regarding the expression of Wnt signaling components in this fatal condition. In the present study we used transgenic SOD1G93A mice to evaluate the expression of several Wnt signaling components, with special focus on Frizzled-5 cellular expression alteration along disease progression.Based on previous studies demonstrating the expression of Wnts and their transcriptional regulation during Amyotrophic lateral sclerosis development, we have analyzed the mRNA expression of several Wnt signaling components in the spinal cord of SOD1G93A transgenic mice at different stages of the disease by using real time quantitative PCR analysis. Strikingly, one of the molecules that seemed not to be altered at mRNA level, Frizzled-5, showed a clear up-regulation at late stages in neurons, as evidenced by immunofluorescence assays. Moreover, increased Frizzled-5 appears to correlate with a decrease in NeuN signal in these cells, suggesting a correlation between neuronal affectation and the increased expression of this receptor.Our data suggest the involvement of Wnt signaling pathways in the pathophysiology of Amyotrophic Lateral Sclerosis and, more specifically, the implication of Frizzled-5 receptor in the response of neuronal cells against neurodegeneration. Nevertheless, further experimental studies are needed to shed light on the specific role of Frizzled-5 and the emerging but increasing Wnt family of proteins research field as a potential target for this neuropathology.

  3. Approach to cardio-oncologic patients with special focus on patients with cardiac implantable electronic devices planned for radiotherapy: results of the European Heart Rhythm Association survey.

    Science.gov (United States)

    Lenarczyk, Radoslaw; Potpara, Tatjana S; Haugaa, Kristina H; Deharo, Jean-Claude; Hernandez-Madrid, Antonio; Del Carmen Exposito Pineda, Maria; Kiliszek, Marek; Dagres, Nikolaos

    2017-09-01

    The aim of this European Heart Rhythm Association (EHRA) survey was to evaluate clinical practice regarding cardio-oncologic patients, with special focus on patients with cardiac implantable electronic devices (CIEDs) planned for anticancer radiotherapy (RT), among members of the EHRA electrophysiology research network. Of the 36 responding centres, 89% managed patients who were diagnosed or treated oncologically, and this diagnosis affected 1-5% of cardiovascular patients in majority of centres (57%). The main side effects of anticancer therapy in patients treated by cardiologists were thromboembolic complications and left ventricular dysfunction (both reported as 'frequent' by 43% of the centres). The main agents associated with complications were anthracyclines, RT, and monoclonal antibodies. Echocardiography was the most common method of screening for cardiovascular complications (93%), and 10% of the centres did not routinely screen for treatment-induced cardiotoxicity. Opinions on the safe radiation dose, methods of device shielding, and risk calculation prior to RT in CIED patients differed among centres. Precaution measures in high-risk CIED patients were very heterogeneous among centres. Our survey has shown that the awareness of cardiac consequences of anticancer therapy is high, despite relatively low proportion of patients treated oncologically among all cardiovascular patients. There is a consensus of which screening methods should be used for cardiotoxicity of anticancer treatment, but the apprehension of screening necessity is low. Methods of risk assessment and safety measures in CIED patients undergoing RT are very heterogeneous among the European centres, underscoring the need for standardization of the approach to cardio-oncologic patients. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2017. For Permissions, please email: journals.permissions@oup.com.

  4. Eukaryotic acquisition of a bacterial operon

    Science.gov (United States)

    The yeast Saccharomyces cerevisiae is one of the champions of basic biomedical research due to its compact eukaryotic genome and ease of experimental manipulation. Despite these immense strengths, its impact on understanding the genetic basis of natural phenotypic variation has been limited by strai...

  5. The origin of the eukaryotic cell

    Science.gov (United States)

    Hartman, H.

    1984-01-01

    The endosymbiotic hypothesis for the origin of the eukaryotic cell has been applied to the origin of the mitochondria and chloroplasts. However as has been pointed out by Mereschowsky in 1905, it should also be applied to the nucleus as well. If the nucleus, mitochondria and chloroplasts are endosymbionts, then it is likely that the organism that did the engulfing was not a DNA-based organism. In fact, it is useful to postulate that this organism was a primitive RNA-based organism. This hypothesis would explain the preponderance of RNA viruses found in eukaryotic cells. The centriole and basal body do not have a double membrane or DNA. Like all MTOCs (microtubule organising centres), they have a structural or morphic RNA implicated in their formation. This would argue for their origin in the early RNA-based organism rather than in an endosymbiotic event involving bacteria. Finally, the eukaryotic cell uses RNA in ways quite unlike bacteria, thus pointing to a greater emphasis of RNA in both control and structure in the cell. The origin of the eukaryotic cell may tell us why it rather than its prokaryotic relative evolved into the metazoans who are reading this paper.

  6. Evidence for a Minimal Eukaryotic Phosphoproteome?

    NARCIS (Netherlands)

    Diks, Sander H.; Parikh, Kaushal; van der Sijde, Marijke; Joore, Jos; Ritsema, Tita; Peppelenbosch, Maikel P.

    2007-01-01

    Background. Reversible phosphorylation catalysed by kinases is probably the most important regulatory mechanism in eukaryotes. Methodology/Principal Findings. We studied the in vitro phosphorylation of peptide arrays exhibiting the majority of PhosphoBase-deposited protein sequences, by factors in

  7. Eukaryotic membrane protein overproduction in Lactococcus lactis

    NARCIS (Netherlands)

    Kunji, Edmund R.S.; Chan, Ka Wai; Slotboom, Dirk Jan; Floyd, Suzanne; O’Connor, Rosemary; Monné, Magnus

    2005-01-01

    Eukaryotic membrane proteins play many vital roles in the cell and are important drug targets. Approximately 25% of all genes identified in the genome are known to encode membrane proteins, but the vast majority have no assigned function. Although the generation of structures of soluble proteins has

  8. Association between diet-related inflammation, all-cause, all-cancer, and cardiovascular disease mortality, with special focus on prediabetics: findings from NHANES III.

    Science.gov (United States)

    Deng, Fang Emily; Shivappa, Nitin; Tang, YiFan; Mann, Joshua R; Hebert, James R

    2017-04-01

    Chronic inflammation is associated with increased risk of cancer, cardiovascular disease (CVD), and diabetes. The role of pro-inflammatory diet in the risk of cancer mortality and CVD mortality in prediabetics is unclear. We examined the relationship between diet-associated inflammation, as measured by dietary inflammatory index (DII) score, and mortality, with special focus on prediabetics. This prospective cohort study used data from the Third National Health and Nutrition Examination Survey (NHANES III). We categorized 13,280 eligible participants, ages 20-90 years, according to glycosylated hemoglobin (HgbA1c) level and identified 2681 with prediabetes, defined as a glycosylated hemoglobin percentage of 5.7-6.4. Computation of DII scores and all statistical analyses were conducted in 2015. The DII was computed based on baseline dietary intake assessed using 24-h dietary recalls (1988-1994). Mortality was determined from the National Death Index records through 2006. Over follow-up ranging between 135 and 168 person-months, a total of 3016 deaths were identified, including 676 cancer, 192 lung cancer, 176 digestive-tract cancer, and 1328 CVD deaths. Cox proportional hazard regression was used to estimate hazard ratios. The prevalence of prediabetes was 20.19 %. After controlling for age, sex, race, HgbA1c, current smoking, physical activity, BMI, and systolic blood pressure, DII scores in tertile III (vs tertile I) was significantly associated with mortality from all causes (HR 1.39, 95 % CI 1.13, 1.72), CVD (HR 1.44, 95 % CI 1.02, 2.04), all cancers (HR 2.02, 95 % CI 1.27, 3.21), and digestive-tract cancer (HR 2.89, 95 % CI 1.08, 7.71). Findings for lung cancer (HR 2.01, 95 % CI 0.93, 4.34) suggested a likely effect. These results were moderately enhanced after additional adjustment for serum low-density lipoprotein and triglyceride and following eliminating deaths during the first year. A pro-inflammatory diet, as indicated by higher DII scores, is

  9. Interaction of Low Temperature Plasmas with Prokaryotic and Eukaryotic Cells

    Science.gov (United States)

    Laroussi, Mounir

    2008-10-01

    Due to promising possibilities for their use in medical applications such as wound healing, surface modification of biocompatible materials, and the sterilization of reusable heat-sensitive medical instruments, low temperature plasmas and plasma jets are making big strides as a technology that can potentially be used in medicine^1-2. At this stage of research, fundamental questions about the effects of plasma on prokaryotic and eukaryotic cells are still not completely answered. An in-depth understanding of the pathway whereby cold plasma interact with biological cells is necessary before real applications can emerge. In this paper, first an overview of non-equilibrium plasma sources (both low and high pressures) will be presented. Secondly, the effects of plasma on bacterial cells will be discussed. Here, the roles of the various plasma agents in the inactivation process will be outlined. In particular, the effects of UV and that of various reactive species (O3, O, OH) are highlighted. Thirdly, preliminary findings on the effects of plasma on few types of eukaryotic cells will be presented. How plasma affects eukaryotic cells, such as mammalian cells, is very important in applications where the viability/preservation of the cells could be an issue (such as in wound treatment). Another interesting aspect is the triggering of apoptosis (programmed cell death). Some investigators have claimed that plasma is able to induce apoptosis in some types of cancer cells. If successfully replicated, this can open up a novel method of cancer treatment. In this talk however, I will briefly focus more on the wound healing potential of cold plasmas. ^1E. A. Blakely, K. A. Bjornstad, J. E. Galvin, O. R. Monteiro, and I. G. Brown, ``Selective Neuron Growth on Ion Implanted and Plasma Deposited Surfaces'', In Proc. IEEE Int. Conf. Plasma Sci., (2002), p. 253. ^2M. Laroussi, ``Non-thermal Decontamination of Biological Media by Atmospheric Pressure Plasmas: Review, Analysis, and

  10. Towards New Antifolates Targeting Eukaryotic Opportunistic Infections

    Energy Technology Data Exchange (ETDEWEB)

    Liu, J.; Bolstad, D; Bolstad, E; Wright, D; Anderson, A

    2009-01-01

    Trimethoprim, an antifolate commonly prescribed in combination with sulfamethoxazole, potently inhibits several prokaryotic species of dihydrofolate reductase (DHFR). However, several eukaryotic pathogenic organisms are resistant to trimethoprim, preventing its effective use as a therapeutic for those infections. We have been building a program to reengineer trimethoprim to more potently and selectively inhibit eukaryotic species of DHFR as a viable strategy for new drug discovery targeting several opportunistic pathogens. We have developed a series of compounds that exhibit potent and selective inhibition of DHFR from the parasitic protozoa Cryptosporidium and Toxoplasma as well as the fungus Candida glabrata. A comparison of the structures of DHFR from the fungal species Candida glabrata and Pneumocystis suggests that the compounds may also potently inhibit Pneumocystis DHFR.

  11. Rolling-circle transposons in eukaryotes.

    Science.gov (United States)

    Kapitonov, V V; Jurka, J

    2001-07-17

    All eukaryotic DNA transposons reported so far belong to a single category of elements transposed by the so-called "cut-and-paste" mechanism. Here, we report a previously unknown category of eukaryotic DNA transposons, Helitron, which transpose by rolling-circle replication. Autonomous Helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons. Helitron-like transposons have conservative 5'-TC and CTRR-3' termini and do not have terminal inverted repeats. They contain 16- to 20-bp hairpins separated by 10--12 nucleotides from the 3'-end and transpose precisely between the 5'-A and T-3', with no modifications of the AT target sites. Together with their multiple diverged nonautonomous descendants, Helitrons constitute approximately 2% of both the Arabidopsis thaliana and Caenorhabditis elegans genomes and also colonize the Oriza sativa genome. Sequence conservation suggests that Helitrons continue to be transposed.

  12. Eukaryotic algal phytochromes span the visible spectrum

    OpenAIRE

    Rockwell, Nathan C.; Duanmu, Deqiang; Martin, Shelley S.; Bachy, Charles; Price, Dana C.; Bhattacharya, Debashish; Worden, Alexandra Z.; Lagarias, J. Clark

    2014-01-01

    Photosynthetic organisms exploit photosensory proteins to respond to changing light conditions. In land plants, phytochromes use the ratio of red to far-red light to detect shading by neighboring plants, leading to changes in growth and development. Light conditions can be more variable for algae because of the wavelength-dependent attenuation of light by water and because of ocean mixing. We studied phytochromes from taxonomically diverse eukaryotic algae from groups considered important for...

  13. An Evolutionary Network of Genes Present in the Eukaryote Common Ancestor Polls Genomes on Eukaryotic and Mitochondrial Origin

    OpenAIRE

    Thiergart, Thorsten; Landan, Giddy; Schenk, Marc; Dagan, Tal; Martin, William F.

    2012-01-01

    To test the predictions of competing and mutually exclusive hypotheses for the origin of eukaryotes, we identified from a sample of 27 sequenced eukaryotic and 994 sequenced prokaryotic genomes 571 genes that were present in the eukaryote common ancestor and that have homologues among eubacterial and archaebacterial genomes. Maximum-likelihood trees identified the prokaryotic genomes that most frequently contained genes branching as the sister to the eukaryotic nuclear homologues. Among the a...

  14. Eukaryotic snoRNAs: a paradigm for gene expression flexibility.

    Science.gov (United States)

    Dieci, Giorgio; Preti, Milena; Montanini, Barbara

    2009-08-01

    Small nucleolar RNAs (snoRNAs) are one of the most ancient and numerous families of non-protein-coding RNAs (ncRNAs). The main function of snoRNAs - to guide site-specific rRNA modification - is the same in Archaea and all eukaryotic lineages. In contrast, as revealed by recent genomic and RNomic studies, their genomic organization and expression strategies are the most varied. Seemingly snoRNA coding units have adopted, in the course of evolution, all the possible ways of being transcribed, thus providing a unique paradigm of gene expression flexibility. By focusing on representative fungal, plant and animal genomes, we review here all the documented types of snoRNA gene organization and expression, and we provide a comprehensive account of snoRNA expressional freedom by precisely estimating the frequency, in each genome, of each type of genomic organization. We finally discuss the relevance of snoRNA genomic studies for our general understanding of ncRNA family evolution and expression in eukaryotes.

  15. Phylogenetic analysis of the core histone doublet and DNA topo II genes of Marseilleviridae: evidence of proto-eukaryotic provenance.

    Science.gov (United States)

    Erives, Albert J

    2017-11-28

    While the genomes of eukaryotes and Archaea both encode the histone-fold domain, only eukaryotes encode the core histone paralogs H2A, H2B, H3, and H4. With DNA, these core histones assemble into the nucleosomal octamer underlying eukaryotic chromatin. Importantly, core histones for H2A and H3 are maintained as neofunctionalized paralogs adapted for general bulk chromatin (canonical H2 and H3) or specialized chromatin (H2A.Z enriched at gene promoters and cenH3s enriched at centromeres). In this context, the identification of core histone-like "doublets" in the cytoplasmic replication factories of the Marseilleviridae (MV) is a novel finding with possible relevance to understanding the origin of eukaryotic chromatin. Here, we analyze and compare the core histone doublet genes from all known MV genomes as well as other MV genes relevant to the origin of the eukaryotic replisome. Using different phylogenetic approaches, we show that MV histone domains encode obligate H2B-H2A and H4-H3 dimers of possible proto-eukaryotic origin. MV core histone moieties form sister clades to each of the four eukaryotic clades of canonical and variant core histones. This suggests that MV core histone moieties diverged prior to eukaryotic neofunctionalizations associated with paired linear chromosomes and variant histone octamer assembly. We also show that MV genomes encode a proto-eukaryotic DNA topoisomerase II enzyme that forms a sister clade to eukaryotes. This is a relevant finding given that DNA topo II influences histone deposition and chromatin compaction and is the second most abundant nuclear protein after histones. The combined domain architecture and phylogenomic analyses presented here suggest that a primitive origin for MV histone genes is a more parsimonious explanation than horizontal gene transfers + gene fusions + sufficient divergence to eliminate relatedness to eukaryotic neofunctionalizations within the H2A and H3 clades without loss of relatedness to each of

  16. Prokaryotes versus Eukaryotes: Who is hosting whom?

    Directory of Open Access Journals (Sweden)

    Guillermo eTellez

    2014-10-01

    Full Text Available Microorganisms represent the largest component of biodiversity in our world. For millions of years, prokaryotic microorganisms have functioned as a major selective force shaping eukaryotic evolution. Microbes that live inside and on animals outnumber the animals’ actual somatic and germ cells by an estimated 10-fold. Collectively, the intestinal microbiome represents a ‘forgotten organ’, functioning as an organ inside another that can execute many physiological responsibilities. The nature of primitive eukaryotes was drastically changed due to the association with symbiotic prokaryotes facilitating mutual coevolution of host and microbe. Phytophagous insects have long been used to test theories of evolutionary diversification; moreover, the diversification of a number of phytophagous insect lineages has been linked to mutualisms with microbes. From termites and honey bees to ruminants and mammals, depending on novel biochemistries provided by the prokaryotic microbiome, the association helps to metabolize several nutrients that the host cannot digest and converting these into useful end products (such as short chain fatty acids, a process which has huge impact on the biology and homeostasis of metazoans. More importantly, in a direct and/or indirect way, the intestinal microbiota influences the assembly of gut-associated lymphoid tissue, helps to educate immune system, affects the integrity of the intestinal mucosal barrier, modulates proliferation and differentiation of its epithelial lineages, regulates angiogenesis, and modifies the activity of enteric as well as the central nervous system,. Despite these important effects, the mechanisms by which the gut microbial community influences the host’s biology remains almost entirely unknown. Our aim here is to encourage empirical inquiry into the relationship between mutualism and evolutionary diversification between prokaryotes and eukaryotes which encourage us to postulate: Who is

  17. Probing eukaryotic cell mechanics via mesoscopic simulations

    Science.gov (United States)

    Pivkin, Igor V.; Lykov, Kirill; Nematbakhsh, Yasaman; Shang, Menglin; Lim, Chwee Teck

    2017-11-01

    We developed a new mesoscopic particle based eukaryotic cell model which takes into account cell membrane, cytoskeleton and nucleus. The breast epithelial cells were used in our studies. To estimate the viscoelastic properties of cells and to calibrate the computational model, we performed micropipette aspiration experiments. The model was then validated using data from microfluidic experiments. Using the validated model, we probed contributions of sub-cellular components to whole cell mechanics in micropipette aspiration and microfluidics experiments. We believe that the new model will allow to study in silico numerous problems in the context of cell biomechanics in flows in complex domains, such as capillary networks and microfluidic devices.

  18. Expression of eukaryotic polypeptides in chloroplasts

    Energy Technology Data Exchange (ETDEWEB)

    Mayfield, Stephen P

    2013-06-04

    The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

  19. Eukaryotic Mismatch Repair in Relation to DNA Replication

    Science.gov (United States)

    Erie, Dorothy A.

    2017-01-01

    Three processes act in series to accurately replicate the eukaryotic nuclear genome. The major replicative DNA polymerases strongly prevent mismatch formation, occasional mismatches that do form are proofread during replication, and rare mismatches that escape proofreading are corrected by mismatch repair (MMR). This review focuses on MMR in light of increasing knowledge about nuclear DNA replication enzymology and the rate and specificity with which mismatches are generated during leading- and lagging-strand replication. We consider differences in MMR efficiency in relation to mismatch recognition, signaling to direct MMR to the nascent strand, mismatch removal, and the timing of MMR. These studies are refining our understanding of relationships between generating and repairing replication errors to achieve accurate replication of both DNA strands of the nuclear genome. PMID:26436461

  20. Eukaryotic promoter prediction based on relative entropy and positional information.

    Science.gov (United States)

    Wu, Shuanhu; Xie, Xudong; Liew, Alan Wee-Chung; Yan, Hong

    2007-04-01

    The eukaryotic promoter prediction is one of the most important problems in DNA sequence analysis, but also a very difficult one. Although a number of algorithms have been proposed, their performances are still limited by low sensitivities and high false positives. We present a method for improving the performance of promoter regions prediction. We focus on the selection of most effective features for different functional regions in DNA sequences. Our feature selection algorithm is based on relative entropy or Kullback-Leibler divergence, and a system combined with position-specific information for promoter regions prediction is developed. The results of testing on large genomic sequences and comparisons with the PromoterInspector and Dragon Promoter Finder show that our algorithm is efficient with higher sensitivity and specificity in predicting promoter regions.

  1. Substrate protein recognition mechanism of archaeal and eukaryotic chaperonins.

    Science.gov (United States)

    Shrestha, Pooja; Jayasinghe, Manori; Stan, George

    2009-03-01

    Chaperonins are double ring-shaped biological nanomachines that assist protein folding. Spectacular conformational changes take place within each chaperonin ring using energy derived from ATP hydrolysis. These changes result in transitions from the open to the closed ring. Substrate proteins bind to the open ring and are encapsulated within the closed ring cavity. We focus on the substrate protein recognition mechanism of archaeal and eukaryotic chaperonins. We predict substrate protein binding sites using structural and bioinformatic analyses of functional states during the chaperonin cycle. Based on large changes in solvent accessible surface area and contact maps we glean the functional role of chaperonin amino acids. During the transition between open to closed chaperonin ring, the largest change in accessible surface area of amino acids is found in helical protrusion and two helices located at the cavity opening. Our calculations suggest that the helical protrusion and two helices constitute the substrate protein binding site.

  2. Mechanisms of heat-shock gene activation in higher eukaryotes

    International Nuclear Information System (INIS)

    Bienz, M.; Pelham, H.R.B.

    1987-01-01

    Heat-shock genes are activated under conditions of heat shock or other environmental stresses. This gene activation is rapid and reversible, resulting in a transition from hardly detectable levels of transcription to extremely high transcription rates causing heat-shock proteins (HSP) to accumulate to high levels. In this review, the components of the heat-shock gene activation systems, including the cis-acting elements and the trans-acting factors, are considered. Data on how these components act together to result in transcription activation and how multiple controls are achieved are summarized. Finally, the questions of how the cell detects the environmental stimulus and translates it into gene activation and how the functions of the gene products relate to this process are addressed. The article focuses on heat-shock gene activation in higher eukaryotes. Only those aspects of heat-shock genes and proteins which are relevant to the question of gene activation are included

  3. Facilitating Transition from High School and Special Education to Adult Life: Focus on Youth with Learning Disorders, Attention-Deficit/Hyperactivity Disorder, and Speech/Language Impairments.

    Science.gov (United States)

    Ascherman, Lee I; Shaftel, Julia

    2017-04-01

    Youth with learning disorders, speech/language disorders, and/or attention-deficit/hyperactivity disorder may experience significant struggles during the transition from high school to postsecondary education and employment. These disorders often occur in combination or concurrently with behavioral and emotional difficulties. Incomplete evaluation may not fully identify the factors underlying academic and personal challenges. This article reviews these disorders, the role of special education law for transitional age youth in public schools, and the Americans with Disabilities Act in postsecondary educational and employment settings. The role of the child and adolescent psychiatrist and the importance of advocacy for these youth are presented. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Algorithmically specialized parallel computers

    CERN Document Server

    Snyder, Lawrence; Gannon, Dennis B

    1985-01-01

    Algorithmically Specialized Parallel Computers focuses on the concept and characteristics of an algorithmically specialized computer.This book discusses the algorithmically specialized computers, algorithmic specialization using VLSI, and innovative architectures. The architectures and algorithms for digital signal, speech, and image processing and specialized architectures for numerical computations are also elaborated. Other topics include the model for analyzing generalized inter-processor, pipelined architecture for search tree maintenance, and specialized computer organization for raster

  5. The impact of customer focus on program participation rates in the Virginia WIC Program (Special Supplemental Nutrition Program for Women, Infants, and Children).

    Science.gov (United States)

    Chance, K G; Green, C G

    2001-01-01

    It has been shown in the for-profit sector (business, service, and manufacturing) that the success of an organization depends on its ability to satisfy customer requirements while eliminating waste and reducing costs. The purpose of this article was to examine the impact of current practices in customer focus on program participation rates in the Virginia WIC Program. The results of this study showed that the use of customer-focused strategies was correlated to program participation rates in the WIC Program. The mean data showed that teamwork and accessibility were at unsatisfactory levels in Virginia.

  6. Asgard archaea illuminate the origin of eukaryotic cellular complexity.

    Science.gov (United States)

    Zaremba-Niedzwiedzka, Katarzyna; Caceres, Eva F; Saw, Jimmy H; Bäckström, Disa; Juzokaite, Lina; Vancaester, Emmelien; Seitz, Kiley W; Anantharaman, Karthik; Starnawski, Piotr; Kjeldsen, Kasper U; Stott, Matthew B; Nunoura, Takuro; Banfield, Jillian F; Schramm, Andreas; Baker, Brett J; Spang, Anja; Ettema, Thijs J G

    2017-01-19

    The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of 'eukaryote-specific' proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.

  7. Are maternal mitochondria the selfish entities that are masters of the cells of eukaryotic multicellular organisms?

    Science.gov (United States)

    Barlow, Peter W; Baldelli, E; Baluška, Frantisek

    2009-01-01

    The Energide concept, as well as the endosymbiotic theory of eukaryotic cell organization and evolution, proposes that present-day cells of eukaryotic organisms are mosaics of specialized and cooperating units, or organelles. Some of these units were originally free-living prokaryotes, which were engulfed during evolutionary time. Mitochondria represent one of these types of previously independent organisms, the Energide, is another type. This new perspective on the organization of the cell has been further expanded to reveal the concept of a public milieu, the cytosol, in which Energides and mitochondria live, each with their own private internal milieu. The present paper discusses how the endosymbiotic theory implicates a new hypothesis about the hierarchical and communicational organization of the integrated prokaryotic components of the eukaryotic cell and provides a new angle from which to consider the theory of evolution and its bearing upon cellular complexity. Thus, it is proposed that the “selfish gene” hypothesis of Dawkins1 is not the only possible perspective for comprehending genomic and cellular evolution. Our proposal is that maternal mitochondria are the selfish “master” entities of the eukaryotic cell with respect not only to their propagation from cell-to-cell and from generation-to-generation but also to their regulation of all other cellular functions. However, it should be recognized that the concept of “master” and “servant” cell components is a metaphor; in present-day living organisms their organellar components are considered to be interdependent and inseparable. PMID:19513277

  8. Phosphorylation Stoichiometries of Human Eukaryotic Initiation Factors

    Directory of Open Access Journals (Sweden)

    Armann Andaya

    2014-06-01

    Full Text Available Eukaryotic translation initiation factors are the principal molecular effectors regulating the process converting nucleic acid to functional protein. Commonly referred to as eIFs (eukaryotic initiation factors, this suite of proteins is comprised of at least 25 individual subunits that function in a coordinated, regulated, manner during mRNA translation. Multiple facets of eIF regulation have yet to be elucidated; however, many of the necessary protein factors are phosphorylated. Herein, we have isolated, identified and quantified phosphosites from eIF2, eIF3, and eIF4G generated from log phase grown HeLa cell lysates. Our investigation is the first study to globally quantify eIF phosphosites and illustrates differences in abundance of phosphorylation between the residues of each factor. Thus, identification of those phosphosites that exhibit either high or low levels of phosphorylation under log phase growing conditions may aid researchers to concentrate their investigative efforts to specific phosphosites that potentially harbor important regulatory mechanisms germane to mRNA translation.

  9. Consistent mutational paths predict eukaryotic thermostability

    Directory of Open Access Journals (Sweden)

    van Noort Vera

    2013-01-01

    Full Text Available Abstract Background Proteomes of thermophilic prokaryotes have been instrumental in structural biology and successfully exploited in biotechnology, however many proteins required for eukaryotic cell function are absent from bacteria or archaea. With Chaetomium thermophilum, Thielavia terrestris and Thielavia heterothallica three genome sequences of thermophilic eukaryotes have been published. Results Studying the genomes and proteomes of these thermophilic fungi, we found common strategies of thermal adaptation across the different kingdoms of Life, including amino acid biases and a reduced genome size. A phylogenetics-guided comparison of thermophilic proteomes with those of other, mesophilic Sordariomycetes revealed consistent amino acid substitutions associated to thermophily that were also present in an independent lineage of thermophilic fungi. The most consistent pattern is the substitution of lysine by arginine, which we could find in almost all lineages but has not been extensively used in protein stability engineering. By exploiting mutational paths towards the thermophiles, we could predict particular amino acid residues in individual proteins that contribute to thermostability and validated some of them experimentally. By determining the three-dimensional structure of an exemplar protein from C. thermophilum (Arx1, we could also characterise the molecular consequences of some of these mutations. Conclusions The comparative analysis of these three genomes not only enhances our understanding of the evolution of thermophily, but also provides new ways to engineer protein stability.

  10. Eukaryotic and Prokaryotic Cytoskeletons: Structure and Mechanics

    Science.gov (United States)

    Gopinathan, Ajay

    2013-03-01

    The eukaryotic cytoskeleton is an assembly of filamentous proteins and a host of associated proteins that collectively serve functional needs ranging from spatial organization and transport to the production and transmission of forces. These systems can exhibit a wide variety of non-equilibrium, self-assembled phases depending on context and function. While much recent progress has been made in understanding the self-organization, rheology and nonlinear mechanical properties of such active systems, in this talk, we will concentrate on some emerging aspects of cytoskeletal physics that are promising. One such aspect is the influence of cytoskeletal network topology and its dynamics on both active and passive intracellular transport. Another aspect we will highlight is the interplay between chirality of filaments, their elasticity and their interactions with the membrane that can lead to novel conformational states with functional implications. Finally we will consider homologs of cytoskeletal proteins in bacteria, which are involved in templating cell growth, segregating genetic material and force production, which we will discuss with particular reference to contractile forces during cell division. These prokaryotic structures function in remarkably similar yet fascinatingly different ways from their eukaryotic counterparts and can enrich our understanding of cytoskeletal functioning as a whole.

  11. Cell cycle control across the eukaryotic kingdom.

    Science.gov (United States)

    Harashima, Hirofumi; Dissmeyer, Nico; Schnittger, Arp

    2013-07-01

    Almost two billion years of evolution have generated a vast and amazing variety of eukaryotic life with approximately 8.7 million extant species. Growth and reproduction of all of these organisms depend on faithful duplication and distribution of their chromosomes to the newly forming daughter cells in a process called the cell cycle. However, most of what is known today about cell cycle control comes from a few model species that belong to the unikonts; that is, to only one of five 'supergroups' that comprise the eukaryotic kingdom. Recently, analyzing species from distantly related clades is providing insights into general principles of cell cycle regulation and shedding light on its evolution. Here, referring to animal and fungal as opposed to non-unikont systems, especially flowering plants from the archaeplastid supergroup, we compare the conservation of central cell cycle regulator functions, the structure of network topologies, and the evolutionary dynamics of substrates of core cell cycle kinases. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. RNA Export through the NPC in Eukaryotes.

    Science.gov (United States)

    Okamura, Masumi; Inose, Haruko; Masuda, Seiji

    2015-03-20

    In eukaryotic cells, RNAs are transcribed in the nucleus and exported to the cytoplasm through the nuclear pore complex. The RNA molecules that are exported from the nucleus into the cytoplasm include messenger RNAs (mRNAs), ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), micro RNAs (miRNAs), and viral mRNAs. Each RNA is transported by a specific nuclear export receptor. It is believed that most of the mRNAs are exported by Nxf1 (Mex67 in yeast), whereas rRNAs, snRNAs, and a certain subset of mRNAs are exported in a Crm1/Xpo1-dependent manner. tRNAs and miRNAs are exported by Xpot and Xpo5. However, multiple export receptors are involved in the export of some RNAs, such as 60S ribosomal subunit. In addition to these export receptors, some adapter proteins are required to export RNAs. The RNA export system of eukaryotic cells is also used by several types of RNA virus that depend on the machineries of the host cell in the nucleus for replication of their genome, therefore this review describes the RNA export system of two representative viruses. We also discuss the NPC anchoring-dependent mRNA export factors that directly recruit specific genes to the NPC.

  13. Regulation of family law at the international and European level, with a special focus on the right to health of the child

    Directory of Open Access Journals (Sweden)

    Samardžić Sandra O.

    2015-01-01

    Full Text Available Family law represents a specific branch of law, given the sensitivity of the relationships which it mainly regulates. It is the reflection of the various influences acting on a given area and often, the differences between countries in the regulation of certain issues can be extremely large. Consequently, attempts to harmonize the rules of family law, especially to unify them, so far have largely been unsuccessful. However, progress can be observed on both, the international and European level. This paper will try to show the most important international and European bodies and within them, instruments issued with the aim of regulating matters falling within the area of family law. In addition, the paper will be made special reference to the part of family law relating to children's rights, namely on the right to health of the child as a basic right, without which other children's rights are meaningless.

  14. The effectiveness of an interconnected use of recovery and stimulating efficiency in microcycle with large loads of special focus (after the example of rowing.

    Directory of Open Access Journals (Sweden)

    Vinogradov V.E.

    2011-06-01

    Full Text Available Efficiency of recovery and stimulations means using is shown by working capacity increase and optimization of organism reactive possibilities. Optimization of physiological properties displayed by sensitivity ventilatory response to СО2-Н+ stimulus, speed of deployment of the reaction of О2 consumption and limits the reaction of pulmonary ventilation and taking into account the phases of recovery. There is evidence that the direction of increase of reactive properties of the body (autonomic neurodynamics by subsidiary means (massage effect, special exercises and other means enhances the ability to more fully mobilize the functionality of athletes, that is, the ability to rapidly, adequately, fully and consistently respond to the training loads.

  15. The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility

    Energy Technology Data Exchange (ETDEWEB)

    Fritz-Laylin, Lillian K.; Prochnik, Simon E.; Ginger, Michael L.; Dacks, Joel; Carpenter, Meredith L.; Field, Mark C.; Kuo, Alan; Paredez, Alex; Chapman, Jarrod; Pham, Jonathan; Shu, Shengqiang; Neupane, Rochak; Cipriano, Michael; Mancuso, Joel; Tu, Hank; Salamov, Asaf; Lindquist, Erika; Shapiro, Harris; Lucas, Susan; Grigoriev, Igor V.; Cande, W. Zacheus; Fulton, Chandler; Rokhsar, Daniel S.; Dawson, Scott C.

    2010-03-01

    Genome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likely present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules.

  16. A 3D Hydrodynamic Model for Cytokinesis of Eukaryotic Cells

    Science.gov (United States)

    2014-08-01

    called cytokinesis. For eukaryotic cells , cell division is a much more complicated process than the division of prokaryotic cells . Despite of extensive...2014 2. REPORT TYPE 3. DATES COVERED 00-00-2014 to 00-00-2014 4. TITLE AND SUBTITLE A 3D Hydrodynamic Model for Cytokinesis of Eukaryotic Cells ...stage of the mitotic cycle of eukaryotic cells , cytokinesis ensues where a parent cell replicates its nucleus with the necessary genetical substances

  17. Synthesis of eukaryotic lipid biomarkers in the bacterial domain

    Science.gov (United States)

    Welander, P. V.; Banta, A. B.; Lee, A. K.; Wei, J. H.

    2017-12-01

    Lipid biomarkers are organic molecules preserved in sediments and sedimentary rocks that can function as geological proxies for certain microbial taxa or for specific environmental conditions. These molecular fossils provide a link between organisms and their environments in both modern and ancient settings and have afforded significant insight into ancient climatic events, mass extinctions, and various evolutionary transitions throughout Earth's history. However, the proper interpretation of lipid biomarkers is dependent on a broad understanding of their diagenetic precursors in modern systems. This includes understanding the taphonomic transformations that these molecules undergo, their biosynthetic pathways, and the ecological conditions that affect their cellular production. In this study, we focus on one group of lipid biomarkers - the sterols. These are polycyclic isoprenoidal lipids that have a high preservation potential and play a critical role in the physiology of most eukaryotes. However, the synthesis and function of these lipids in the bacterial domain has not been fully explored. Here we utilize a combination of bioinformatics, microbial genetics, and biochemistry to demonstrate that bacterial sterol producers are more prevalent in environmental metagenomic samples than in the genomic databases of cultured organisms and to identify novel proteins required to synthesize and modify sterols in bacteria. These proteins represent a distinct pathway for sterol synthesis exclusive to bacteria and indicate that sterol synthesis in bacteria may have evolved independently of eukaryotic sterol biosynthesis. Taken together, these results demonstrate how studies in extant bacteria can provide insight into the biological sources and the biosynthetic pathways of specific lipid biomarkers and in turn may allow for more robust interpretation of biomarker signatures.

  18. Arabinogalactan proteins have deep roots in eukaryotes

    DEFF Research Database (Denmark)

    Hervé, Cécile; Siméon, Amandine; Jam, Murielle

    2016-01-01

    Arabinogalactan proteins (AGPs) are highly glycosylated, hydroxyproline-rich proteins found at the cell surface of plants, where they play key roles in developmental processes. Brown algae are marine, multicellular, photosynthetic eukaryotes. They belong to the phylum Stramenopiles, which...... is unrelated to land plants and green algae (Chloroplastida). Brown algae share common evolutionary features with other multicellular organisms, including a carbohydrate-rich cell wall. They differ markedly from plants in their cell wall composition, and AGPs have not been reported in brown algae. Here we...... investigated the presence of chimeric AGP-like core proteins in this lineage. We report that the genome sequence of the brown algal model Ectocarpus siliculosus encodes AGP protein backbone motifs, in a gene context that differs considerably from what is known in land plants. We showed the occurrence of AGP...

  19. DNA Mismatch Repair in Eukaryotes and Bacteria

    Directory of Open Access Journals (Sweden)

    Kenji Fukui

    2010-01-01

    Full Text Available DNA mismatch repair (MMR corrects mismatched base pairs mainly caused by DNA replication errors. The fundamental mechanisms and proteins involved in the early reactions of MMR are highly conserved in almost all organisms ranging from bacteria to human. The significance of this repair system is also indicated by the fact that defects in MMR cause human hereditary nonpolyposis colon cancers as well as sporadic tumors. To date, 2 types of MMRs are known: the human type and Escherichia coli type. The basic features of the former system are expected to be universal among the vast majority of organisms including most bacteria. Here, I review the molecular mechanisms of eukaryotic and bacterial MMR, emphasizing on the similarities between them.

  20. Protein splicing and its evolution in eukaryotes

    Directory of Open Access Journals (Sweden)

    Starokadomskyy P. L.

    2010-02-01

    Full Text Available Inteins, or protein introns, are parts of protein sequences that are post-translationally excised, their flanking regions (exteins being spliced together. This process was called protein splicing. Originally inteins were found in prokaryotic or unicellular eukaryotic organisms. But the general principles of post-translation protein rearrangement are evolving yielding different post-translation modification of proteins in multicellular organisms. For clarity, these non-intein mediated events call either protein rearrangements or protein editing. The most intriguing example of protein editing is proteasome-mediated splicing of antigens in vertebrates that may play important role in antigen presentation. Other examples of protein rearrangements are maturation of Hg-proteins (critical receptors in embryogenesis as well as maturation of several metabolic enzymes. Despite a lack of experimental data we try to analyze some intriguing examples of protein splicing evolution.

  1. Bacterial proteins pinpoint a single eukaryotic root

    Czech Academy of Sciences Publication Activity Database

    Derelle, R.; Torruella, G.; Klimeš, V.; Brinkmann, H.; Kim, E.; Vlček, Čestmír; Lang, B.F.; Eliáš, M.

    2015-01-01

    Roč. 112, č. 7 (2015), E693-E699 ISSN 0027-8424 R&D Projects: GA ČR GA13-24983S Grant - others:GA MŠk(CZ) ED2.1.00/03.0100; Howard Hughes Medical Institute International Early Career Scientist Program(US) 55007424; Spanish Ministry of Economy and Competitiveness, European Molecular Biology Organization Young Investigator Program(ES) BFU2012-31329; Spanish Ministry of Economy and Competitiveness, "Centro de Excelencia Severo Ochoa" - European Regional Development Fund(ES) Sev-2012-0208, BES-2013-064004 Institutional support: RVO:68378050 Keywords : eukaryote phylogeny * phylogenomics * Opimoda * Diphoda * LECA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.423, year: 2015

  2. Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency

    Science.gov (United States)

    Qian, Wenfeng; Yang, Jian-Rong; Pearson, Nathaniel M.; Maclean, Calum; Zhang, Jianzhi

    2012-01-01

    Cellular efficiency in protein translation is an important fitness determinant in rapidly growing organisms. It is widely believed that synonymous codons are translated with unequal speeds and that translational efficiency is maximized by the exclusive use of rapidly translated codons. Here we estimate the in vivo translational speeds of all sense codons from the budding yeast Saccharomyces cerevisiae. Surprisingly, preferentially used codons are not translated faster than unpreferred ones. We hypothesize that this phenomenon is a result of codon usage in proportion to cognate tRNA concentrations, the optimal strategy in enhancing translational efficiency under tRNA shortage. Our predicted codon–tRNA balance is indeed observed from all model eukaryotes examined, and its impact on translational efficiency is further validated experimentally. Our study reveals a previously unsuspected mechanism by which unequal codon usage increases translational efficiency, demonstrates widespread natural selection for translational efficiency, and offers new strategies to improve synthetic biology. PMID:22479199

  3. Soil eukaryotic functional diversity, a metatranscriptomic approach.

    Science.gov (United States)

    Bailly, Julie; Fraissinet-Tachet, Laurence; Verner, Marie-Christine; Debaud, Jean-Claude; Lemaire, Marc; Wésolowski-Louvel, Micheline; Marmeisse, Roland

    2007-11-01

    To appreciate the functional diversity of communities of soil eukaryotic micro-organisms we evaluated an experimental approach based on the construction and screening of a cDNA library using polyadenylated mRNA extracted from a forest soil. Such a library contains genes that are expressed by each of the different organisms forming the community and represents its metatranscriptome. The diversity of the organisms that contributed to this library was evaluated by sequencing a portion of the 18S rDNA gene amplified from either soil DNA or reverse-transcribed RNA. More than 70% of the sequences were from fungi and unicellular eukaryotes (protists) while the other most represented group was the metazoa. Calculation of richness estimators suggested that more than 180 species could be present in the soil samples studied. Sequencing of 119 cDNA identified genes with no homologues in databases (32%) and genes coding proteins involved in different biochemical and cellular processes. Surprisingly, the taxonomic distribution of the cDNA and of the 18S rDNA genes did not coincide, with a marked under-representation of the protists among the cDNA. Specific genes from such an environmental cDNA library could be isolated by expression in a heterologous microbial host, Saccharomyces cerevisiae. This is illustrated by the functional complementation of a histidine auxotrophic yeast mutant by two cDNA originating possibly from an ascomycete and a basidiomycete fungal species. Study of the metatranscriptome has the potential to uncover adaptations of whole microbial communities to local environmental conditions. It also gives access to an abundant source of genes of biotechnological interest.

  4. An Evolutionary Network of Genes Present in the Eukaryote Common Ancestor Polls Genomes on Eukaryotic and Mitochondrial Origin

    Science.gov (United States)

    Thiergart, Thorsten; Landan, Giddy; Schenk, Marc; Dagan, Tal; Martin, William F.

    2012-01-01

    To test the predictions of competing and mutually exclusive hypotheses for the origin of eukaryotes, we identified from a sample of 27 sequenced eukaryotic and 994 sequenced prokaryotic genomes 571 genes that were present in the eukaryote common ancestor and that have homologues among eubacterial and archaebacterial genomes. Maximum-likelihood trees identified the prokaryotic genomes that most frequently contained genes branching as the sister to the eukaryotic nuclear homologues. Among the archaebacteria, euryarchaeote genomes most frequently harbored the sister to the eukaryotic nuclear gene, whereas among eubacteria, the α-proteobacteria were most frequently represented within the sister group. Only 3 genes out of 571 gave a 3-domain tree. Homologues from α-proteobacterial genomes that branched as the sister to nuclear genes were found more frequently in genomes of facultatively anaerobic members of the rhiozobiales and rhodospirilliales than in obligate intracellular ricketttsial parasites. Following α-proteobacteria, the most frequent eubacterial sister lineages were γ-proteobacteria, δ-proteobacteria, and firmicutes, which were also the prokaryote genomes least frequently found as monophyletic groups in our trees. Although all 22 higher prokaryotic taxa sampled (crenarchaeotes, γ-proteobacteria, spirochaetes, chlamydias, etc.) harbor genes that branch as the sister to homologues present in the eukaryotic common ancestor, that is not evidence of 22 different prokaryotic cells participating at eukaryote origins because prokaryotic “lineages” have laterally acquired genes for more than 1.5 billion years since eukaryote origins. The data underscore the archaebacterial (host) nature of the eukaryotic informational genes and the eubacterial (mitochondrial) nature of eukaryotic energy metabolism. The network linking genes of the eukaryote ancestor to contemporary homologues distributed across prokaryotic genomes elucidates eukaryote gene origins in a

  5. The COG database: an updated version includes eukaryotes

    Directory of Open Access Journals (Sweden)

    Sverdlov Alexander V

    2003-09-01

    Full Text Available Abstract Background The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Results We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens, one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe, and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the

  6. Break induced replication in eukaryotes: mechanisms, functions, and consequences.

    Science.gov (United States)

    Sakofsky, Cynthia J; Malkova, Anna

    2017-08-01

    Break-induced replication (BIR) is an important pathway specializing in repair of one-ended double-strand DNA breaks (DSBs). This type of DSB break typically arises at collapsed replication forks or at eroded telomeres. BIR initiates by invasion of a broken DNA end into a homologous template followed by initiation of DNA synthesis that can proceed for hundreds of kilobases. This synthesis is drastically different from S-phase replication in that instead of a replication fork, BIR proceeds via a migrating bubble and is associated with conservative inheritance of newly synthesized DNA. This unusual mode of DNA replication is responsible for frequent genetic instabilities associated with BIR, including hyper-mutagenesis, which can lead to the formation of mutation clusters, extensive loss of heterozygosity, chromosomal translocations, copy-number variations and complex genomic rearrangements. In addition to budding yeast experimental systems that were initially employed to investigate eukaryotic BIR, recent studies in different organisms including humans, have provided multiple examples of BIR initiated within different cellular contexts, including collapsed replication fork and telomere maintenance in the absence of telomerase. In addition, significant progress has been made towards understanding microhomology-mediated BIR (MMBIR) that can promote complex chromosomal rearrangements, including those associated with cancer and those leading to a number of neurological disorders in humans.

  7. Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor.

    Science.gov (United States)

    Scheckenbach, Frank; Hausmann, Klaus; Wylezich, Claudia; Weitere, Markus; Arndt, Hartmut

    2010-01-05

    Eukaryotic microbial life at abyssal depths remains "uncharted territory" in eukaryotic microbiology. No phylogenetic surveys have focused on the largest benthic environment on this planet, the abyssal plains. Moreover, knowledge of the spatial patterns of deep-sea community structure is scanty, and what little is known originates primarily from morphology-based studies of foraminiferans. Here we report on the great phylogenetic diversity of microbial eukaryotic communities of all 3 abyssal plains of the southeastern Atlantic Ocean--the Angola, Cape, and Guinea Abyssal Plains--from depths of 5,000 m. A high percentage of retrieved clones had no close representatives in genetic databases. Many clones were affiliated with parasitic species. Furthermore, differences between the communities of the Cape Abyssal Plain and the other 2 abyssal plains point to environmental gradients apparently shaping community structure at the landscape level. On a regional scale, local species diversity showed much less variation. Our study provides insight into the community composition of microbial eukaryotes on larger scales from the wide abyssal sea floor realm and marks a direction for more detailed future studies aimed at improving our understanding of deep-sea microbes at the community and ecosystem levels, as well as the ecological principles at play.

  8. Heterogeneous Family of Cyclomodulins: Smart Weapons That Allow Bacteria to Hijack the Eukaryotic Cell Cycle and Promote Infections.

    Science.gov (United States)

    El-Aouar Filho, Rachid A; Nicolas, Aurélie; De Paula Castro, Thiago L; Deplanche, Martine; De Carvalho Azevedo, Vasco A; Goossens, Pierre L; Taieb, Frédéric; Lina, Gerard; Le Loir, Yves; Berkova, Nadia

    2017-01-01

    Some bacterial pathogens modulate signaling pathways of eukaryotic cells in order to subvert the host response for their own benefit, leading to successful colonization and invasion. Pathogenic bacteria produce multiple compounds that generate favorable conditions to their survival and growth during infection in eukaryotic hosts. Many bacterial toxins can alter the cell cycle progression of host cells, impairing essential cellular functions and impeding host cell division. This review summarizes current knowledge regarding cyclomodulins, a heterogeneous family of bacterial effectors that induce eukaryotic cell cycle alterations. We discuss the mechanisms of actions of cyclomodulins according to their biochemical properties, providing examples of various cyclomodulins such as cycle inhibiting factor, γ-glutamyltranspeptidase, cytolethal distending toxins, shiga toxin, subtilase toxin, anthrax toxin, cholera toxin, adenylate cyclase toxins, vacuolating cytotoxin, cytotoxic necrotizing factor, Panton-Valentine leukocidin, phenol soluble modulins, and mycolactone. Special attention is paid to the benefit provided by cyclomodulins to bacteria during colonization of the host.

  9. Heterogeneous Family of Cyclomodulins: Smart Weapons That Allow Bacteria to Hijack the Eukaryotic Cell Cycle and Promote Infections

    Directory of Open Access Journals (Sweden)

    Rachid A. El-Aouar Filho

    2017-05-01

    Full Text Available Some bacterial pathogens modulate signaling pathways of eukaryotic cells in order to subvert the host response for their own benefit, leading to successful colonization and invasion. Pathogenic bacteria produce multiple compounds that generate favorable conditions to their survival and growth during infection in eukaryotic hosts. Many bacterial toxins can alter the cell cycle progression of host cells, impairing essential cellular functions and impeding host cell division. This review summarizes current knowledge regarding cyclomodulins, a heterogeneous family of bacterial effectors that induce eukaryotic cell cycle alterations. We discuss the mechanisms of actions of cyclomodulins according to their biochemical properties, providing examples of various cyclomodulins such as cycle inhibiting factor, γ-glutamyltranspeptidase, cytolethal distending toxins, shiga toxin, subtilase toxin, anthrax toxin, cholera toxin, adenylate cyclase toxins, vacuolating cytotoxin, cytotoxic necrotizing factor, Panton-Valentine leukocidin, phenol soluble modulins, and mycolactone. Special attention is paid to the benefit provided by cyclomodulins to bacteria during colonization of the host.

  10. Eukaryotic checkpoints are absent in the cell division cycle of ...

    Indian Academy of Sciences (India)

    Unknown

    checkpoints' which are known to regulate the eukaryotic cell cycle may be absent or altered in. E. histolytica. [Banerjee S, Das S and Lohia A 2002 Eukaryotic checkpoints are absent in the cell division cycle of Entamoeba histolytica; J. Biosci. (Suppl.

  11. Heavy metal detoxification in eukaryotic microalgae.

    Science.gov (United States)

    Perales-Vela, Hugo Virgilio; Peña-Castro, Julián Mario; Cañizares-Villanueva, Rosa Olivia

    2006-06-01

    Microalgae are aquatic organisms possessing molecular mechanisms that allow them to discriminate non-essential heavy metals from those essential ones for their growth. The different detoxification processes executed by algae are reviewed with special emphasis on those involving the peptides metallothioneins, mainly the post transcriptionally synthesized class III metallothioneins or phytochelatins. Also, the features that make microalgae suitable organisms technologies specially to treat water that is heavily polluted with metals is discussed.

  12. Expression profile of genes coding for DNA repair in human oocytes using pangenomic microarrays, with a special focus on ROS linked decays.

    Science.gov (United States)

    Menezo, Yves; Russo, GianLuigi; Tosti, Elisabetta; El Mouatassim, Said; Benkhalifa, Moncef

    2007-11-01

    To determine the level of expression for mRNAs that regulate DNA repair activity in oocytes at the germinal vesicle (GV) stage. Reactive oxygen species (ROS) have been shown to play a major role in the appearance of deleterious DNA decays, and this study focuses on the repair of damage linked to decay caused by the action of ROS. The oocyte needs a mechanism for repairing DNA decays in the early preimplantation embryo before the onset of genomic activation, since in the absence of repair, residual DNA damage would lead to either apoptosis or tolerance. Tolerance of DNA damage is a source of potential mutations. GV oocytes were selected for this study, both for the ethical reason that they are unsuitable for patient treatment, and because no transcription takes place during the period from GV to MII and then prior to genomic activation. The GV oocyte is therefore a good model for looking at DNA during the first cleavages of early preimplantation development. Six cohorts of GV oocytes were pooled for extraction of mRNA; the DNA was analysed using Affimetrix HG-UG133 Plus 2, containing 54,675 probe sets; spike and housekeeping genes were also added as internal controls. In GV oocytes, DNA repair pathways for oxidized bases are redundant. One step repair procedure (OSR), BER (base excision repair), MMR (mismatch repair) and NER (Nucleotide excision repair) are present. All the recognition proteins are also present. The chromatin assembly factors necessary for the maintenance of genomic stability are highly expressed. Gene expression analysis shows that the oocyte does not allow a high level of tolerance for DNA decays. This regulatory mechanism should avoid transmitting mutations into the next generation.

  13. Nitrogen fixation in eukaryotes – New models for symbiosis

    Directory of Open Access Journals (Sweden)

    Lockhart Peter

    2007-04-01

    Full Text Available Abstract Background Nitrogen, a component of many bio-molecules, is essential for growth and development of all organisms. Most nitrogen exists in the atmosphere, and utilisation of this source is important as a means of avoiding nitrogen starvation. However, the ability to fix atmospheric nitrogen via the nitrogenase enzyme complex is restricted to some bacteria. Eukaryotic organisms are only able to obtain fixed nitrogen through their symbiotic interactions with nitrogen-fixing prokaryotes. These symbioses involve a variety of host organisms, including animals, plants, fungi and protists. Results We have compared the morphological, physiological and molecular characteristics of nitrogen fixing symbiotic associations of bacteria and their diverse hosts. Special features of the interaction, e.g. vertical transmission of symbionts, grade of dependency of partners and physiological modifications have been considered in terms of extent of co-evolution and adaptation. Our findings are that, despite many adaptations enabling a beneficial partnership, most symbioses for molecular nitrogen fixation involve facultative interactions. However, some interactions, among them endosymbioses between cyanobacteria and diatoms, show characteristics that reveal a more obligate status of co-evolution. Conclusion Our review emphasises that molecular nitrogen fixation, a driving force for interactions and co-evolution of different species, is a widespread phenomenon involving many different organisms and ecosystems. The diverse grades of symbioses, ranging from loose associations to highly specific intracellular interactions, might themselves reflect the range of potential evolutionary fates for symbiotic partnerships. These include the extreme evolutionary modifications and adaptations that have accompanied the formation of organelles in eukaryotic cells: plastids and mitochondria. However, age and extensive adaptation of plastids and mitochondria complicate the

  14. Energetics and genetics across the prokaryote-eukaryote divide

    Science.gov (United States)

    2011-01-01

    Background All complex life on Earth is eukaryotic. All eukaryotic cells share a common ancestor that arose just once in four billion years of evolution. Prokaryotes show no tendency to evolve greater morphological complexity, despite their metabolic virtuosity. Here I argue that the eukaryotic cell originated in a unique prokaryotic endosymbiosis, a singular event that transformed the selection pressures acting on both host and endosymbiont. Results The reductive evolution and specialisation of endosymbionts to mitochondria resulted in an extreme genomic asymmetry, in which the residual mitochondrial genomes enabled the expansion of bioenergetic membranes over several orders of magnitude, overcoming the energetic constraints on prokaryotic genome size, and permitting the host cell genome to expand (in principle) over 200,000-fold. This energetic transformation was permissive, not prescriptive; I suggest that the actual increase in early eukaryotic genome size was driven by a heavy early bombardment of genes and introns from the endosymbiont to the host cell, producing a high mutation rate. Unlike prokaryotes, with lower mutation rates and heavy selection pressure to lose genes, early eukaryotes without genome-size limitations could mask mutations by cell fusion and genome duplication, as in allopolyploidy, giving rise to a proto-sexual cell cycle. The side effect was that a large number of shared eukaryotic basal traits accumulated in the same population, a sexual eukaryotic common ancestor, radically different to any known prokaryote. Conclusions The combination of massive bioenergetic expansion, release from genome-size constraints, and high mutation rate favoured a protosexual cell cycle and the accumulation of eukaryotic traits. These factors explain the unique origin of eukaryotes, the absence of true evolutionary intermediates, and the evolution of sex in eukaryotes but not prokaryotes. Reviewers This article was reviewed by: Eugene Koonin, William Martin

  15. Eukaryotic versus prokaryotic marine picoplankton ecology.

    Science.gov (United States)

    Massana, Ramon; Logares, Ramiro

    2013-05-01

    Marine microorganisms contribute markedly to global biomass and ecosystem function. They include a diverse collection of organisms differing in cell size and in evolutionary history. In particular, microbes within the picoplankton are similar in size but belong to two drastically different cellular plans, the prokaryotes and the eukaryotes. Compared with larger organisms, prokaryotes and picoeukaryotes share ecological features, such as high specific activity, large and constant abundances, and high dispersal potential. Still, there are some aspects where their different cell organization influences their ecological performance. First, prokaryotes have a huge metabolic versatility and are involved in all biogeochemical cycles, whereas picoeukaryotes are metabolically less flexible but can exploit diverse predatory life strategies due to their phagocytic capacity. Second, sexual reproduction is absent in prokaryotes but may be present in picoeukaryotes, thus determining different evolutionary diversification dynamics and making species limits clearer in picoeukaryotes. Finally, it is plausible that picoeukaryotes are less flexible to enter a reversible state of low metabolic activity, thus picoeukaryote assemblages may have fewer rare species and may be less resilient to environmental change. In summary, lumping together pico-sized microbes may be convenient for some ecological studies, but it is also important to keep in mind their differences. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  16. Do lipids shape the eukaryotic cell cycle?

    Science.gov (United States)

    Furse, Samuel; Shearman, Gemma C

    2018-01-01

    Successful passage through the cell cycle presents a number of structural challenges to the cell. Inceptive studies carried out in the last five years have produced clear evidence of modulations in the lipid profile (sometimes referred to as the lipidome) of eukaryotes as a function of the cell cycle. This mounting body of evidence indicates that lipids play key roles in the structural transformations seen across the cycle. The accumulation of this evidence coincides with a revolution in our understanding of how lipid composition regulates a plethora of biological processes ranging from protein activity through to cellular signalling and membrane compartmentalisation. In this review, we discuss evidence from biological, chemical and physical studies of the lipid fraction across the cell cycle that demonstrate that lipids are well-developed cellular components at the heart of the biological machinery responsible for managing progress through the cell cycle. Furthermore, we discuss the mechanisms by which this careful control is exercised. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  17. Origins and evolution of viruses of eukaryotes: The ultimate modularity

    International Nuclear Information System (INIS)

    Koonin, Eugene V.; Dolja, Valerian V.; Krupovic, Mart

    2015-01-01

    Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order “Megavirales” that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources

  18. Origins and evolution of viruses of eukaryotes: The ultimate modularity

    Energy Technology Data Exchange (ETDEWEB)

    Koonin, Eugene V., E-mail: koonin@ncbi.nlm.nih.gov [National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 (United States); Dolja, Valerian V., E-mail: doljav@science.oregonstate.edu [Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331 (United States); Krupovic, Mart, E-mail: krupovic@pasteur.fr [Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Paris 75015 (France)

    2015-05-15

    Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order “Megavirales” that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources

  19. Potential of industrial biotechnology with cyanobacteria and eukaryotic microalgae.

    Science.gov (United States)

    Wijffels, René H; Kruse, Olaf; Hellingwerf, Klaas J

    2013-06-01

    Both cyanobacteria and eukaryotic microalgae are promising organisms for sustainable production of bulk products such as food, feed, materials, chemicals and fuels. In this review we will summarize the potential and current biotechnological developments. Cyanobacteria are promising host organisms for the production of small molecules that can be secreted such as ethanol, butanol, fatty acids and other organic acids. Eukaryotic microalgae are interesting for products for which cellular storage is important such as proteins, lipids, starch and alkanes. For the development of new and promising lines of production, strains of both cyanobacteria and eukaryotic microalgae have to be improved. Transformation systems have been much better developed in cyanobacteria. However, several products would be preferably produced with eukaryotic microalgae. In the case of cyanobacteria a synthetic-systems biology approach has a great potential to exploit cyanobacteria as cell factories. For eukaryotic microalgae transformation systems need to be further developed. A promising strategy is transformation of heterologous (prokaryotic and eukaryotic) genes in established eukaryotic hosts such as Chlamydomonas reinhardtii. Experimental outdoor pilots under containment for the production of genetically modified cyanobacteria and microalgae are in progress. For full scale production risks of release of genetically modified organisms need to be assessed. Copyright © 2013. Published by Elsevier Ltd.

  20. Origins and evolution of viruses of eukaryotes: The ultimate modularity.

    Science.gov (United States)

    Koonin, Eugene V; Dolja, Valerian V; Krupovic, Mart

    2015-05-01

    Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order "Megavirales" that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along

  1. Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes.

    Science.gov (United States)

    Nillegoda, Nadinath B; Stank, Antonia; Malinverni, Duccio; Alberts, Niels; Szlachcic, Anna; Barducci, Alessandro; De Los Rios, Paolo; Wade, Rebecca C; Bukau, Bernd

    2017-05-15

    Hsp70 participates in a broad spectrum of protein folding processes extending from nascent chain folding to protein disaggregation. This versatility in function is achieved through a diverse family of J-protein cochaperones that select substrates for Hsp70. Substrate selection is further tuned by transient complexation between different classes of J-proteins, which expands the range of protein aggregates targeted by metazoan Hsp70 for disaggregation. We assessed the prevalence and evolutionary conservation of J-protein complexation and cooperation in disaggregation. We find the emergence of a eukaryote-specific signature for interclass complexation of canonical J-proteins. Consistently, complexes exist in yeast and human cells, but not in bacteria, and correlate with cooperative action in disaggregation in vitro. Signature alterations exclude some J-proteins from networking, which ensures correct J-protein pairing, functional network integrity and J-protein specialization. This fundamental change in J-protein biology during the prokaryote-to-eukaryote transition allows for increased fine-tuning and broadening of Hsp70 function in eukaryotes.

  2. Special Effects Activity Guide.

    Science.gov (United States)

    Boxer, Jennifer; Valenta, Carol

    This guide accompanies "Special Effects," a 40-minute IMAX film and "Special Effects II", a multimedia, interactive traveling exhibit designed by the California Museum of Science and Industry. The exhibit focuses on the underlying scientific and technical processes of special effects from the earliest motion picture to state-of-the-art digital…

  3. Evolution of the Kinetochore Network in Eukaryotes

    NARCIS (Netherlands)

    Tromer, E.C.

    2017-01-01

    Kinetochores are highly specialized macromolecular machines built on top of centromeric chromatin to orchestrate the synchronous and equal distribution of chromosomes during mitosis and meiosis. Each kinetochore consists of up to hundreds of copies of a core complex of ~75 proteins that together

  4. HIV-1 Replication and the Cellular Eukaryotic Translation Apparatus

    Directory of Open Access Journals (Sweden)

    Santiago Guerrero

    2015-01-01

    Full Text Available Eukaryotic translation is a complex process composed of three main steps: initiation, elongation, and termination. During infections by RNA- and DNA-viruses, the eukaryotic translation machinery is used to assure optimal viral protein synthesis. Human immunodeficiency virus type I (HIV-1 uses several non-canonical pathways to translate its own proteins, such as leaky scanning, frameshifting, shunt, and cap-independent mechanisms. Moreover, HIV-1 modulates the host translation machinery by targeting key translation factors and overcomes different cellular obstacles that affect protein translation. In this review, we describe how HIV-1 proteins target several components of the eukaryotic translation machinery, which consequently improves viral translation and replication.

  5. The current state of eukaryotic DNA base damage and repair.

    Science.gov (United States)

    Bauer, Nicholas C; Corbett, Anita H; Doetsch, Paul W

    2015-12-02

    DNA damage is a natural hazard of life. The most common DNA lesions are base, sugar, and single-strand break damage resulting from oxidation, alkylation, deamination, and spontaneous hydrolysis. If left unrepaired, such lesions can become fixed in the genome as permanent mutations. Thus, evolution has led to the creation of several highly conserved, partially redundant pathways to repair or mitigate the effects of DNA base damage. The biochemical mechanisms of these pathways have been well characterized and the impact of this work was recently highlighted by the selection of Tomas Lindahl, Aziz Sancar and Paul Modrich as the recipients of the 2015 Nobel Prize in Chemistry for their seminal work in defining DNA repair pathways. However, how these repair pathways are regulated and interconnected is still being elucidated. This review focuses on the classical base excision repair and strand incision pathways in eukaryotes, considering both Saccharomyces cerevisiae and humans, and extends to some important questions and challenges facing the field of DNA base damage repair. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. MCM Paradox: Abundance of Eukaryotic Replicative Helicases and Genomic Integrity

    Directory of Open Access Journals (Sweden)

    Mitali Das

    2014-01-01

    Full Text Available As a crucial component of DNA replication licensing system, minichromosome maintenance (MCM 2–7 complex acts as the eukaryotic DNA replicative helicase. The six related MCM proteins form a heterohexamer and bind with ORC, CDC6, and Cdt1 to form the prereplication complex. Although the MCMs are well known as replicative helicases, their overabundance and distribution patterns on chromatin present a paradox called the “MCM paradox.” Several approaches had been taken to solve the MCM paradox and describe the purpose of excess MCMs distributed beyond the replication origins. Alternative functions of these MCMs rather than a helicase had also been proposed. This review focuses on several models and concepts generated to solve the MCM paradox coinciding with their helicase function and provides insight into the concept that excess MCMs are meant for licensing dormant origins as a backup during replication stress. Finally, we extend our view towards the effect of alteration of MCM level. Though an excess MCM constituent is needed for normal cells to withstand stress, there must be a delineation of the threshold level in normal and malignant cells. This review also outlooks the future prospects to better understand the MCM biology.

  7. Close Up Special Focus: The Economy.

    Science.gov (United States)

    Mayer, Frederick; LaMotte, Sally

    Designed to parallel five student seminars televised over the Cable-Satellite Public Affairs Network (C-SPAN), this handbook provides an overview of current economic issues for high school students. Selections cover inflation, the crisis in American productivity, unemployment in the United States, global economic interdependence, and the role of…

  8. Potential of industrial biotechnology with cyanobacteria and eukaryotic microalgae.

    NARCIS (Netherlands)

    Wijffels, R.H.; Kruse, O.; Hellingwerf, K.J.

    2013-01-01

    Both cyanobacteria and eukaryotic microalgae are promising organisms for sustainable production of bulk products such as food, feed, materials, chemicals and fuels. In this review we will summarize the potential and current biotechnological developments. Cyanobacteria are promising host organisms

  9. Repair of DNA DSB in higher eukaryotes

    International Nuclear Information System (INIS)

    Wang, H.; Perrault, A.R.; Takeda, Y.; Iliakis, G.

    2003-01-01

    Cells of higher eukaryotes process within minutes double strand breaks (DSBs) in their genome using a NHEJ apparatus that engages DNA-PKcs, Ku, DNA ligase IV, XRCC4, and other as of yet unidentified factors. Although chemical inhibition, or mutation, in any of these factors delays processing, cells ultimately remove the majority of DNA DSBs using an alternative pathway operating with slower kinetics. This alternative pathway is active in mutants deficient in genes of the RAD52 epistasis group. We proposed, therefore, that it reflects an alternative form of NHEJ that operates as a backup (B-NHEJ) to the DNA-PK- dependent (D-NHEJ) pathway, rather than homology directed repair of DSBs. We studied the role of Ku and DNA-PKcs in the coordination of these pathways using as a model end joining of restriction endonuclease linearized plasmid DNA in whole cell extracts. Efficient error-free endjoining observed in such in-vitro reactions is strongly inhibited by anti-Ku antibodies. The inhibition requires DNA-PKcs, despite that fact that Ku efficiently binds DNA ends in the presence of antibodies, or in the absence of DNA-PKcs. Strong inhibition of DNA endjoining is also mediated by wortmannin, an inhibitor of DNA-PKcs, in the presence but not in the absence of Ku, and this inhibition can be rescued by pre-incubating the reaction with double stranded oligonucleotides. The results are compatible with a role of Ku in directing endjoining to a DNA-PK dependent pathway, mediated by efficient end binding and productive interactions with DNA-PKcs. On the other hand, efficient end joining is observed in extracts of cells lacking DNA-PKcs, as well as in Ku-depleted extracts sugggesting the operation of alternative pathways. Extracts depleted of Ku and DNA-PKcs rejoin blunt ends, as well as homologous ends with 3' or 5' protruding single strands with similar efficiency, but addition of Ku suppresses joining of blunt ends and homologous ends with 3' overhangs. We propose that the

  10. Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes

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    Melkonian Michael

    2008-07-01

    Full Text Available Abstract Background Chlamydiae are obligate intracellular bacteria of protists, invertebrates and vertebrates, but have not been found to date in photosynthetic eukaryotes (algae and embryophytes. Genes of putative chlamydial origin, however, are present in significant numbers in sequenced genomes of photosynthetic eukaryotes. It has been suggested that such genes were acquired by an ancient horizontal gene transfer from Chlamydiae to the ancestor of photosynthetic eukaryotes. To further test this hypothesis, an extensive search for proteins of chlamydial origin was performed using several recently sequenced algal genomes and EST databases, and the proteins subjected to phylogenetic analyses. Results A total of 39 proteins of chlamydial origin were retrieved from the photosynthetic eukaryotes analyzed and their identity verified through phylogenetic analyses. The distribution of the chlamydial proteins among four groups of photosynthetic eukaryotes (Viridiplantae, Rhodoplantae, Glaucoplantae, Bacillariophyta was complex suggesting multiple acquisitions and losses. Evidence is presented that all except one of the chlamydial genes originated from an ancient endosymbiosis of a chlamydial bacterium into the ancestor of the Plantae before their divergence into Viridiplantae, Rhodoplantae and Glaucoplantae, i.e. more than 1.1 BYA. The chlamydial proteins subsequently spread through secondary plastid endosymbioses to other eukaryotes. Of 20 chlamydial proteins recovered from the genomes of two Bacillariophyta, 10 were of rhodoplant, and 10 of viridiplant origin suggesting that they were acquired by two different secondary endosymbioses. Phylogenetic analyses of concatenated sequences demonstrated that the viridiplant secondary endosymbiosis likely occurred before the divergence of Chlorophyta and Streptophyta. Conclusion We identified 39 proteins of chlamydial origin in photosynthetic eukaryotes signaling an ancient invasion of the ancestor of the

  11. Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes.

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    Ku, Chuan; Nelson-Sathi, Shijulal; Roettger, Mayo; Garg, Sriram; Hazkani-Covo, Einat; Martin, William F

    2015-08-18

    Endosymbiotic theory in eukaryotic-cell evolution rests upon a foundation of three cornerstone partners--the plastid (a cyanobacterium), the mitochondrion (a proteobacterium), and its host (an archaeon)--and carries a corollary that, over time, the majority of genes once present in the organelle genomes were relinquished to the chromosomes of the host (endosymbiotic gene transfer). However, notwithstanding eukaryote-specific gene inventions, single-gene phylogenies have never traced eukaryotic genes to three single prokaryotic sources, an issue that hinges crucially upon factors influencing phylogenetic inference. In the age of genomes, single-gene trees, once used to test the predictions of endosymbiotic theory, now spawn new theories that stand to eventually replace endosymbiotic theory with descriptive, gene tree-based variants featuring supernumerary symbionts: prokaryotic partners distinct from the cornerstone trio and whose existence is inferred solely from single-gene trees. We reason that the endosymbiotic ancestors of mitochondria and chloroplasts brought into the eukaryotic--and plant and algal--lineage a genome-sized sample of genes from the proteobacterial and cyanobacterial pangenomes of their respective day and that, even if molecular phylogeny were artifact-free, sampling prokaryotic pangenomes through endosymbiotic gene transfer would lead to inherited chimerism. Recombination in prokaryotes (transduction, conjugation, transformation) differs from recombination in eukaryotes (sex). Prokaryotic recombination leads to pangenomes, and eukaryotic recombination leads to vertical inheritance. Viewed from the perspective of endosymbiotic theory, the critical transition at the eukaryote origin that allowed escape from Muller's ratchet--the origin of eukaryotic recombination, or sex--might have required surprisingly little evolutionary innovation.

  12. DNA mismatch repair and its many roles in eukaryotic cells.

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    Liu, Dekang; Keijzers, Guido; Rasmussen, Lene Juel

    2017-07-01

    DNA mismatch repair (MMR) is an important DNA repair pathway that plays critical roles in DNA replication fidelity, mutation avoidance and genome stability, all of which contribute significantly to the viability of cells and organisms. MMR is widely-used as a diagnostic biomarker for human cancers in the clinic, and as a biomarker of cancer susceptibility in animal model systems. Prokaryotic MMR is well-characterized at the molecular and mechanistic level; however, MMR is considerably more complex in eukaryotic cells than in prokaryotic cells, and in recent years, it has become evident that MMR plays novel roles in eukaryotic cells, several of which are not yet well-defined or understood. Many MMR-deficient human cancer cells lack mutations in known human MMR genes, which strongly suggests that essential eukaryotic MMR components/cofactors remain unidentified and uncharacterized. Furthermore, the mechanism by which the eukaryotic MMR machinery discriminates between the parental (template) and the daughter (nascent) DNA strand is incompletely understood and how cells choose between the EXO1-dependent and the EXO1-independent subpathways of MMR is not known. This review summarizes recent literature on eukaryotic MMR, with emphasis on the diverse cellular roles of eukaryotic MMR proteins, the mechanism of strand discrimination and cross-talk/interactions between and co-regulation of MMR and other DNA repair pathways in eukaryotic cells. The main conclusion of the review is that MMR proteins contribute to genome stability through their ability to recognize and promote an appropriate cellular response to aberrant DNA structures, especially when they arise during DNA replication. Although the molecular mechanism of MMR in the eukaryotic cell is still not completely understood, increased used of single-molecule analyses in the future may yield new insight into these unsolved questions. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. On the Diversification of the Translation Apparatus across Eukaryotes

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    Greco Hernández

    2012-01-01

    Full Text Available Diversity is one of the most remarkable features of living organisms. Current assessments of eukaryote biodiversity reaches 1.5 million species, but the true figure could be several times that number. Diversity is ingrained in all stages and echelons of life, namely, the occupancy of ecological niches, behavioral patterns, body plans and organismal complexity, as well as metabolic needs and genetics. In this review, we will discuss that diversity also exists in a key biochemical process, translation, across eukaryotes. Translation is a fundamental process for all forms of life, and the basic components and mechanisms of translation in eukaryotes have been largely established upon the study of traditional, so-called model organisms. By using modern genome-wide, high-throughput technologies, recent studies of many nonmodel eukaryotes have unveiled a surprising diversity in the configuration of the translation apparatus across eukaryotes, showing that this apparatus is far from being evolutionarily static. For some of the components of this machinery, functional differences between different species have also been found. The recent research reviewed in this article highlights the molecular and functional diversification the translational machinery has undergone during eukaryotic evolution. A better understanding of all aspects of organismal diversity is key to a more profound knowledge of life.

  14. Single Cell Genomics and Transcriptomics for Unicellular Eukaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Ciobanu, Doina; Clum, Alicia; Singh, Vasanth; Salamov, Asaf; Han, James; Copeland, Alex; Grigoriev, Igor; James, Timothy; Singer, Steven; Woyke, Tanja; Malmstrom, Rex; Cheng, Jan-Fang

    2014-03-14

    Despite their small size, unicellular eukaryotes have complex genomes with a high degree of plasticity that allow them to adapt quickly to environmental changes. Unicellular eukaryotes live with prokaryotes and higher eukaryotes, frequently in symbiotic or parasitic niches. To this day their contribution to the dynamics of the environmental communities remains to be understood. Unfortunately, the vast majority of eukaryotic microorganisms are either uncultured or unculturable, making genome sequencing impossible using traditional approaches. We have developed an approach to isolate unicellular eukaryotes of interest from environmental samples, and to sequence and analyze their genomes and transcriptomes. We have tested our methods with six species: an uncharacterized protist from cellulose-enriched compost identified as Platyophrya, a close relative of P. vorax; the fungus Metschnikowia bicuspidate, a parasite of water flea Daphnia; the mycoparasitic fungi Piptocephalis cylindrospora, a parasite of Cokeromyces and Mucor; Caulochytrium protosteloides, a parasite of Sordaria; Rozella allomycis, a parasite of the water mold Allomyces; and the microalgae Chlamydomonas reinhardtii. Here, we present the four components of our approach: pre-sequencing methods, sequence analysis for single cell genome assembly, sequence analysis of single cell transcriptomes, and genome annotation. This technology has the potential to uncover the complexity of single cell eukaryotes and their role in the environmental samples.

  15. An Evolutionary Framework for Understanding the Origin of Eukaryotes.

    Science.gov (United States)

    Blackstone, Neil W

    2016-04-27

    Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real-the endosymbiosis that led to the mitochondrion is often described as "non-Darwinian" because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious-all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

  16. An Evolutionary Framework for Understanding the Origin of Eukaryotes

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    Neil W. Blackstone

    2016-04-01

    Full Text Available Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

  17. International Specialization

    DEFF Research Database (Denmark)

    Kleindienst, Ingo; Geisler Asmussen, Christian; Hutzschenreuter, Thomas

    2012-01-01

    arbitrage strategy is characterized by specialization versus replication and argue that these different strategies may have differential impact on profitability and risk reduction. Developing a sophisticated measure of international specialization and using a unique panel data set of 92 German MNEs to test......Whether and how international diversification and cross-border arbitrage affects firm performance remains one of the major unresolved research questions in the strategy and international business literatures. We propose that knowing how much a firm has internationally diversified tells us very...... little about performance implications, if we do not know, and do not ask, how the firm has diversified. Therefore, building on the two broad arguments of operating flexibility and location-specific commitment, we develop a theoretical framework that focuses on the extent to which a firm's international...

  18. Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids

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    Weber Andreas PM

    2011-04-01

    Full Text Available Abstract Background Euglenophytes are a group of photosynthetic flagellates possessing a plastid derived from a green algal endosymbiont, which was incorporated into an ancestral host cell via secondary endosymbiosis. However, the impact of endosymbiosis on the euglenophyte nuclear genome is not fully understood due to its complex nature as a 'hybrid' of a non-photosynthetic host cell and a secondary endosymbiont. Results We analyzed an EST dataset of the model euglenophyte Euglena gracilis using a gene mining program designed to detect laterally transferred genes. We found E. gracilis genes showing affinity not only with green algae, from which the secondary plastid in euglenophytes evolved, but also red algae and/or secondary algae containing red algal-derived plastids. Phylogenetic analyses of these 'red lineage' genes suggest that E. gracilis acquired at least 14 genes via eukaryote-to-eukaryote lateral gene transfer from algal sources other than the green algal endosymbiont that gave rise to its current plastid. We constructed an EST library of the aplastidic euglenid Peranema trichophorum, which is a eukaryovorous relative of euglenophytes, and also identified 'red lineage' genes in its genome. Conclusions Our data show genome mosaicism in E. gracilis and P. trichophorum. One possible explanation for the presence of these genes in these organisms is that some or all of them were independently acquired by lateral gene transfer and contributed to the successful integration and functioning of the green algal endosymbiont as a secondary plastid. Alternative hypotheses include the presence of a phagocytosed alga as the single source of those genes, or a cryptic tertiary endosymbiont harboring secondary plastid of red algal origin, which the eukaryovorous ancestor of euglenophytes had acquired prior to the secondary endosymbiosis of a green alga.

  19. Translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes.

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    Sandra Jeudy

    Full Text Available Mimivirus and Megavirus are the best characterized representatives of an expanding new family of giant viruses infecting Acanthamoeba. Their most distinctive features, megabase-sized genomes carried in particles of size comparable to that of small bacteria, fill the gap between the viral and cellular worlds. These giant viruses are also uniquely equipped with genes coding for central components of the translation apparatus. The presence of those genes, thought to be hallmarks of cellular organisms, revived fundamental interrogations on the evolutionary origin of these viruses and the link they might have with the emergence of eukaryotes. In this work, we focused on the Mimivirus-encoded translation termination factor gene, the detailed primary structure of which was elucidated using computational and experimental approaches. We demonstrated that the translation of this protein proceeds through two internal stop codons via two distinct recoding events: a frameshift and a readthrough, the combined occurrence of which is unique to these viruses. Unexpectedly, the viral gene carries an autoregulatory mechanism exclusively encountered in bacterial termination factors, though the viral sequence is related to the eukaryotic/archaeal class-I release factors. This finding is a hint that the virally-encoded translation functions may not be strictly redundant with the one provided by the host. Lastly, the perplexing occurrence of a bacterial-like regulatory mechanism in a eukaryotic/archaeal homologous gene is yet another oddity brought about by the study of giant viruses.

  20. A comparison of autogenous theories for the origin of eukaryotic cells.

    Science.gov (United States)

    Baum, David A

    2015-12-01

    Eukaryotic cells have many unique features that all evolved on the stem lineage of living eukaryotes, making it difficult to reconstruct the order in which they accumulated. Nuclear endosymbiotic theories hold that three prokaryotes (nucleus, cytoplasm, and mitochondrion) came together to form a eukaryotic cell, whereas autogenous models hold that the nucleus and cytoplasm formed through evolutionary changes in a single prokaryotic lineage. Given several problems with nuclear endosymbiotic theories, this review focuses on autogenous models. Until recently all autogenous models assumed an outside-in (OI) topology, proposing that the nuclear envelope was formed from membrane-bound vesicles within the original cell body. Buzz Baum and I recently proposed an inside-out (IO) alternative, suggesting that the nucleus corresponds to the original cell body, with the cytoplasmic compartment deriving from extracellular protrusions. In this review, I show that OI and IO models are compatible with both mitochondria early (ME) or mitochondria late (ML) formulations. Whereas ME models allow that the relationship between mitochondria and host was mutualistic from the outset, ML models imply that the association began with predation or parasitism, becoming mutualistic later. In either case, the mutualistic interaction that eventually formed was probably syntrophic. Diverse features of eukaryotic cell biology align well with the IOME model, but it would be premature to rule out the OIME model. ML models require that phagocytosis, a complex and energy expensive process, evolved before mitochondria, which seems unlikely. Nonetheless, further research is needed, especially resolution of the phylogenetic affinities of mitochondria. © 2015 Botanical Society of America.

  1. Crystal structure of eukaryotic ribosome and its complexes with inhibitors

    Science.gov (United States)

    Yusupova, Gulnara; Yusupov, Marat

    2017-01-01

    A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated. In this review, we discuss the crystal structure of the entire 80S ribosome from yeast, which reveals its eukaryotic-specific features, and application of X-ray crystallography of the 80S ribosome for investigation of the binding mode for distinct compounds known to inhibit or modulate the protein-translation function of the ribosome. We also refer to a challenging aspect of the structural study of ribosomes, from higher eukaryotes, where the structures of major distinctive features of higher eukaryote ribosome—the high-eukaryote–specific long ribosomal RNA segments (about 1MDa)—remain unresolved. Presently, the structures of the major part of these high-eukaryotic expansion ribosomal RNA segments still remain unresolved. This article is part of the themed issue ‘Perspectives on the ribosome’. PMID:28138070

  2. Evolution of DNA replication protein complexes in eukaryotes and Archaea.

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    Nicholas Chia

    Full Text Available BACKGROUND: The replication of DNA in Archaea and eukaryotes requires several ancillary complexes, including proliferating cell nuclear antigen (PCNA, replication factor C (RFC, and the minichromosome maintenance (MCM complex. Bacterial DNA replication utilizes comparable proteins, but these are distantly related phylogenetically to their archaeal and eukaryotic counterparts at best. METHODOLOGY/PRINCIPAL FINDINGS: While the structures of each of the complexes do not differ significantly between the archaeal and eukaryotic versions thereof, the evolutionary dynamic in the two cases does. The number of subunits in each complex is constant across all taxa. However, they vary subtly with regard to composition. In some taxa the subunits are all identical in sequence, while in others some are homologous rather than identical. In the case of eukaryotes, there is no phylogenetic variation in the makeup of each complex-all appear to derive from a common eukaryotic ancestor. This is not the case in Archaea, where the relationship between the subunits within each complex varies taxon-to-taxon. We have performed a detailed phylogenetic analysis of these relationships in order to better understand the gene duplications and divergences that gave rise to the homologous subunits in Archaea. CONCLUSION/SIGNIFICANCE: This domain level difference in evolution suggests that different forces have driven the evolution of DNA replication proteins in each of these two domains. In addition, the phylogenies of all three gene families support the distinctiveness of the proposed archaeal phylum Thaumarchaeota.

  3. Energide-cell body as smallest unit of eukaryotic life.

    Science.gov (United States)

    Baluška, František; Lyons, Sherrie

    2018-02-21

    The evolutionary origin of the eukaryotic nucleus is obscure and controversial. Currently preferred are autogenic concepts; ideas of a symbiotic origin are mostly discarded and forgotten. Here we briefly discuss these issues and propose a new version of the symbiotic and archaeal origin of the eukaryotic nucleus. The nucleus of eukaryotic cells forms via its perinuclear microtubules, the primary eukaryotic unit known also as the Energide-cell body. As for all other endosymbiotic organelles, new Energides are generated only from other Energides. While the Energide cannot be generated de novo, it can use its secretory apparatus to generate de novo the cell periphery apparatus. We suggest that Virchow's tenet Omnis cellula e cellula should be updated as Omnis Energide e Energide to reflect the status of the Energide as the primary unit of the eukaryotic cell, and life. In addition, the plasma membrane provides feedback to the Energide and renders it protection via the plasma membrane-derived endosomal network. New discoveries suggest archaeal origins of both the Energide and its host cell.

  4. Burkholderia type VI secretion systems have distinct roles in eukaryotic and bacterial cell interactions.

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    Sandra Schwarz

    2010-08-01

    Full Text Available Bacteria that live in the environment have evolved pathways specialized to defend against eukaryotic organisms or other bacteria. In this manuscript, we systematically examined the role of the five type VI secretion systems (T6SSs of Burkholderia thailandensis (B. thai in eukaryotic and bacterial cell interactions. Consistent with phylogenetic analyses comparing the distribution of the B. thai T6SSs with well-characterized bacterial and eukaryotic cell-targeting T6SSs, we found that T6SS-5 plays a critical role in the virulence of the organism in a murine melioidosis model, while a strain lacking the other four T6SSs remained as virulent as the wild-type. The function of T6SS-5 appeared to be specialized to the host and not related to an in vivo growth defect, as ΔT6SS-5 was fully virulent in mice lacking MyD88. Next we probed the role of the five systems in interbacterial interactions. From a group of 31 diverse bacteria, we identified several organisms that competed less effectively against wild-type B. thai than a strain lacking T6SS-1 function. Inactivation of T6SS-1 renders B. thai greatly more susceptible to cell contact-induced stasis by Pseudomonas putida, Pseudomonas fluorescens and Serratia proteamaculans-leaving it 100- to 1000-fold less fit than the wild-type in competition experiments with these organisms. Flow cell biofilm assays showed that T6S-dependent interbacterial interactions are likely relevant in the environment. B. thai cells lacking T6SS-1 were rapidly displaced in mixed biofilms with P. putida, whereas wild-type cells persisted and overran the competitor. Our data show that T6SSs within a single organism can have distinct functions in eukaryotic versus bacterial cell interactions. These systems are likely to be a decisive factor in the survival of bacterial cells of one species in intimate association with those of another, such as in polymicrobial communities present both in the environment and in many infections.

  5. Interaction of tRNA with Eukaryotic Ribosome

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    Dmitri Graifer

    2015-03-01

    Full Text Available This paper is a review of currently available data concerning interactions of tRNAs with the eukaryotic ribosome at various stages of translation. These data include the results obtained by means of cryo-electron microscopy and X-ray crystallography applied to various model ribosomal complexes, site-directed cross-linking with the use of tRNA derivatives bearing chemically or photochemically reactive groups in the CCA-terminal fragment and chemical probing of 28S rRNA in the region of the peptidyl transferase center. Similarities and differences in the interactions of tRNAs with prokaryotic and eukaryotic ribosomes are discussed with concomitant consideration of the extent of resemblance between molecular mechanisms of translation in eukaryotes and bacteria.

  6. Unraveling adaptation in eukaryotic pathways: lessons from protocells.

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    Giovanna De Palo

    2013-10-01

    Full Text Available Eukaryotic adaptation pathways operate within wide-ranging environmental conditions without stimulus saturation. Despite numerous differences in the adaptation mechanisms employed by bacteria and eukaryotes, all require energy consumption. Here, we present two minimal models showing that expenditure of energy by the cell is not essential for adaptation. Both models share important features with large eukaryotic cells: they employ small diffusible molecules and involve receptor subunits resembling highly conserved G-protein cascades. Analyzing the drawbacks of these models helps us understand the benefits of energy consumption, in terms of adjustability of response and adaptation times as well as separation of cell-external sensing and cell-internal signaling. Our work thus sheds new light on the evolution of adaptation mechanisms in complex systems.

  7. DNA mismatch repair and its many roles in eukaryotic cells

    DEFF Research Database (Denmark)

    Liu, Dekang; Keijzers, Guido; Rasmussen, Lene Juel

    2017-01-01

    in the clinic, and as a biomarker of cancer susceptibility in animal model systems. Prokaryotic MMR is well-characterized at the molecular and mechanistic level; however, MMR is considerably more complex in eukaryotic cells than in prokaryotic cells, and in recent years, it has become evident that MMR plays......DNA mismatch repair (MMR) is an important DNA repair pathway that plays critical roles in DNA replication fidelity, mutation avoidance and genome stability, all of which contribute significantly to the viability of cells and organisms. MMR is widely-used as a diagnostic biomarker for human cancers...... novel roles in eukaryotic cells, several of which are not yet well-defined or understood. Many MMR-deficient human cancer cells lack mutations in known human MMR genes, which strongly suggests that essential eukaryotic MMR components/cofactors remain unidentified and uncharacterized. Furthermore...

  8. Nitrate storage and dissimilatory nitrate reduction by eukaryotic microbes

    DEFF Research Database (Denmark)

    Kamp, Anja; Høgslund, Signe; Risgaard-Petersen, Nils

    2015-01-01

    The microbial nitrogen cycle is one of the most complex and environmentally important element cycles on Earth and has long been thought to be mediated exclusively by prokaryotic microbes. Rather recently, it was discovered that certain eukaryotic microbes are able to store nitrate intracellularly...... and use it for dissimilatory nitrate reduction in the absence of oxygen. The paradigm shift that this entailed is ecologically significant because the eukaryotes in question comprise global players like diatoms, foraminifers, and fungi. This review article provides an unprecedented overview of nitrate...... storage and dissimilatory nitrate reduction by diverse marine eukaryotes placed into an eco-physiological context. The advantage of intracellular nitrate storage for anaerobic energy conservation in oxygen-depleted habitats is explained and the life style enabled by this metabolic trait is described...

  9. Construction of a eukaryotic expression plasmid of Humanin.

    Science.gov (United States)

    Luo, Ben-yan; Chen, Xiang-ming; Tang, Min; Chen, Feng; Chen, Zhi

    2005-01-01

    To construct a eukaryotic expression plasmid pcDNA3.1(-)-Humanin. The recombinant plasmid pGEMEX-1-Humanin was digested with restriction endonucleases BamH I and Hind III and the Humanin gene fragments, about 100 bp length, were obtained. Then the Humanin gene fragments were inserted into eukaryotic expression vector pcDNA3.1(-) and the recombinant plasmids pcDNA3.1(-)-Humanin were identified by sequencing. Recombinant plasmid DNA successfully produced a band which had the same size as that of the Humanin positive control. The sequence of recombinant plasmids accorded with the Humnain gene sequence. A eukaryotic expression plasmid of Humanin was successfully constructed.

  10. Construction of a eukaryotic expression plasmid of Humanin*

    Science.gov (United States)

    Luo, Ben-yan; Chen, Xiang-ming; Tang, Min; Chen, Feng; Chen, Zhi

    2005-01-01

    Objective: To construct a eukaryotic expression plasmid pcDNA3.1(-)-Humanin. Methods: The recombinant plasmid pGEMEX-1-Humanin was digested with restriction endonucleases BamH I and Hind III and the Humanin gene fragments, about 100 bp length, were obtained. Then the Humanin gene fragments were inserted into eukaryotic expression vector pcDNA3.1(-) and the recombinant plasmids pcDNA3.1(-)-Humanin were identified by sequencing. Results: Recombinant plasmid DNA successfully produced a band which had the same size as that of the Humanin positive control. The sequence of recombinant plasmids accorded with the Humnain gene sequence. Conclusions: A eukaryotic expression plasmid of Humanin was successfully constructed. PMID:15593385

  11. Introduction to the special focus issue on the impact of diet on gut microbiota composition and function and future opportunities for nutritional modulation of the gut microbiome to improve human health.

    Science.gov (United States)

    Donovan, Sharon M

    2017-03-04

    Over the past decade, application of culture-independent, next generation DNA sequencing has dramatically enhanced our understanding of the composition of the gut microbiome and its association with human states of health and disease. Host genetics, age, and environmental factors such as where and who you live with, use of pre-, pro- and antibiotics, exercise and diet influence the short- and long-term composition of the microbiome. Dietary intake is a key determinant of microbiome composition and diversity and studies to date have linked long-term dietary patterns as well as short-term dietary interventions to the composition and diversity of the gut microbiome. The goal of this special focus issue was to review the role of diet in regulating the composition and function of the gut microbiota across the lifespan, from pregnancy to old age. Overall dietary patterns, as well as perturbations such as undernutrition and obesity, as well as the effects of dietary fiber/prebiotics and fat composition are explored.

  12. Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes

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    Turk Vito

    2009-11-01

    Full Text Available Abstract Background The cystatin superfamily comprises cysteine protease inhibitors that play key regulatory roles in protein degradation processes. Although they have been the subject of many studies, little is known about their genesis, evolution and functional diversification. Our aim has been to obtain a comprehensive insight into their origin, distribution, diversity, evolution and classification in Eukaryota, Bacteria and Archaea. Results We have identified in silico the full complement of the cystatin superfamily in more than 2100 prokaryotic and eukaryotic genomes. The analysis of numerous eukaryotic genomes has provided strong evidence for the emergence of this superfamily in the ancestor of eukaryotes. The progenitor of this superfamily was most probably intracellular and lacked a signal peptide and disulfide bridges, much like the extant Giardia cystatin. A primordial gene duplication produced two ancestral eukaryotic lineages, cystatins and stefins. While stefins remain encoded by a single or a small number of genes throughout the eukaryotes, the cystatins have undergone a more complex and dynamic evolution through numerous gene and domain duplications. In the cystatin superfamily we discovered twenty vertebrate-specific and three angiosperm-specific orthologous families, indicating that functional diversification has occurred only in multicellular eukaryotes. In vertebrate orthologous families, the prevailing trends were loss of the ancestral inhibitory activity and acquisition of novel functions in innate immunity. Bacterial cystatins and stefins may be emergency inhibitors that enable survival of bacteria in the host, defending them from the host's proteolytic activity. Conclusion This study challenges the current view on the classification, origin and evolution of the cystatin superfamily and provides valuable insights into their functional diversification. The findings of this comprehensive study provide guides for future

  13. Construction of a eukaryotic expression plasmid of Humanin*

    OpenAIRE

    Luo, Ben-yan; Chen, Xiang-ming; Tang, Min; Chen, Feng; Chen, Zhi

    2004-01-01

    Objective: To construct a eukaryotic expression plasmid pcDNA3.1(-)-Humanin. Methods: The recombinant plasmid pGEMEX-1-Humanin was digested with restriction endonucleases BamH I and Hind III and the Humanin gene fragments, about 100 bp length, were obtained. Then the Humanin gene fragments were inserted into eukaryotic expression vector pcDNA3.1(-) and the recombinant plasmids pcDNA3.1(-)-Humanin were identified by sequencing. Results: Recombinant plasmid DNA successfully produced a band whic...

  14. Program specialization

    CERN Document Server

    Marlet, Renaud

    2013-01-01

    This book presents the principles and techniques of program specialization - a general method to make programs faster (and possibly smaller) when some inputs can be known in advance. As an illustration, it describes the architecture of Tempo, an offline program specializer for C that can also specialize code at runtime, and provides figures for concrete applications in various domains. Technical details address issues related to program analysis precision, value reification, incomplete program specialization, strategies to exploit specialized program, incremental specialization, and data speci

  15. Comparative Policy Analysis on the Impact of Inclusive Education in Asia and Africa : Focusing on the Right to Education for Children with Disabilities in Cambodia <Special Issue : Right to Education>

    OpenAIRE

    Hayashi, Makiko

    2014-01-01

    The Framework for Action on Special Needs Education was adopted at the World Conference on Special Needs Education held in Salamanca, Spain in 1994. This paper, fi rst questions the notion of inclusion based on diversity claiming whether all groups with special education needs are identified in developing countries as specified in the Salamanca Statement. And second, it continues to make arguments on the feasibility of implementing inclusive educational settings with due consideration of educ...

  16. The biology of eukaryotic promoter prediction - a review

    DEFF Research Database (Denmark)

    Pedersen, Anders Gorm; Baldi, Pierre; Chauvin, Yves

    1999-01-01

    Computational prediction of eukaryotic promoters from the nucleotide sequence is one of the most attractive problems in sequence analysis today, but it is also a very difficult one. Thus, current methods predict in the order of one promoter per kilobase in human DNA, while the average distance...

  17. An algorithm for detecting eukaryotic sequences in metagenomic ...

    Indian Academy of Sciences (India)

    a BLAST search of all these sequences against a database containing sequences of a host genome (e.g. human genome) will take enormous amount of time and computing resources. In this article, we present a novel alignment-free algorithm, called Eu-Detect, that can detect eukaryotic sequences in metagenomic data ...

  18. An algorithm for detecting eukaryotic sequences in metagenomic ...

    Indian Academy of Sciences (India)

    species but also from accidental contamination from the genome of eukaryotic host cells. The latter scenario generally occurs in the case of host-associated metagenomes, e.g. microbes living in human gut. In such cases, one needs to identify and remove contaminating host DNA sequences, since the latter sequences will ...

  19. Recognition of extremophilic archaeal viruses by eukaryotic cells

    DEFF Research Database (Denmark)

    Uldahl, Kristine Buch; Wu, Linping; Hall, Arnaldur

    2016-01-01

    Viruses from the third domain of life, Archaea, exhibit unusual features including extreme stability that allow their survival in harsh environments. In addition, these species have never been reported to integrate into human or any other eukaryotic genomes, and could thus serve for exploration...

  20. Tracking Eukaryotic Production and Burial Through Time with Zinc Isotopes

    Science.gov (United States)

    Tang, T. Y. S.; Planavsky, N.; Owens, J. D.; Love, G. D.; Lyons, T.; Peterson, L. C.; Knoll, A. H.; Dupont, C. L.; Reinhard, C.; Zumberge, A.

    2015-12-01

    Zinc is an important, often co-limiting nutrient for eukaryotes in the oceans today. Given the importance of Zn in the modern oceans, we developed a Zn isotope approach to track the extent of Zn limitation and eukaryotic production through Earth's history. Specifically, we use the isotopic systematics of the pyrite (δ66Znpyr), rock extracts (bitumen) and kerogen pyrolysate (δ66Znorg) within euxinic black shales. We show that δ66Znpyr of euxinic core-top muds from the Cariaco basin capture the global deep seawater signature, validating its use as a seawater proxy. Additionally, we propose that Δ66Znpyr-org can be used to track surface water zinc bioavailability. Detailed studies of short-lived oceanic anoxic events such as Cretaceous OAE2, which punctuate an otherwise dominantly oxic Phanerozoic world, exhibit dramatic shifts in seawater δ66Zn and organic bound zinc. Such perturbations are consistent with the demise of eukaryotes under a nitrogen stressed regime, in which cyanobacteria carry the competitive advantage. Contradictory to previous models, however, our data suggest that zinc remained largely bioavailable throughout these anoxic intervals despite significant drawdown of the global reservoir. The framework developed from studies of the modern, Cenozoic, and Mesozoic can be used to track the Precambrian evolution of the marine Zn cycle and the rise of eukaryotic algae to ecological dominance.

  1. The emerging roles of inositol pyrophosphates in eukaryotic cell ...

    Indian Academy of Sciences (India)

    These energy-rich small molecules are present in all eukaryotic cells, from yeast to mammals, and are involved in a wide range of cellular functions including apoptosis, vesicle trafficking, DNA repair, osmoregulation, phosphate homeostasis, insulin sensitivity, immune signalling, cell cycle regulation, and ribosome ...

  2. Eu-Detect: An algorithm for detecting eukaryotic sequences in ...

    Indian Academy of Sciences (India)

    Plots depicting the classification accuracy of Eu-Detect with various combinations of. 'cumulative sequence count' (40K, 50K, 60K, 70K, 80K) and 'coverage threshold' (20%, 30%, 40%, 50%, 60%, 70%,. 80%). While blue bars represent Eu-Detect's average classification accuracy with eukaryotic data sets, red bars represent.

  3. Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment.

    Science.gov (United States)

    Edgcomb, Virginia P; Kysela, David T; Teske, Andreas; de Vera Gomez, Alvin; Sogin, Mitchell L

    2002-05-28

    Molecular microbial ecology studies have revealed remarkable prokaryotic diversity in extreme hydrothermal marine environments. There are no comparable reports of culture-independent surveys of eukaryotic life in warm, anoxic marine sediments. By using sequence comparisons of PCR-amplified small subunit ribosomal RNAs, we characterized eukaryotic diversity in hydrothermal vent environments of Guaymas Basin in the Gulf of California. Many sequences from these anoxic sediments and the overlaying seawater represent previously uncharacterized protists, including early branching eukaryotic lineages or extended diversity within described taxa. At least two mechanisms, with overlapping consequences, account for the eukaryotic community structure of this environment. The adaptation to anoxic environments is evidenced by specific affinity of environmental sequences to aerotolerant anaerobic species in molecular trees. This pattern is superimposed against a background of widely distributed aerophilic and aerotolerant protists, some of which may migrate into and survive in the sediment whereas others (e.g., phototrophs) are simply deposited by sedimentary processes. In contrast, bacterial populations in these sediments are primarily characteristic of anoxic, reduced, hydrocarbon-rich sedimentary habitats.

  4. Eukaryotic checkpoints are absent in the cell division cycle of ...

    Indian Academy of Sciences (India)

    It has also been shown that although this organism contains sequence homologs of genes which are known to control the cell cycle of most eukaryotes, these genes may be structurally altered and their equivalent function yet to be demonstrated in amoeba. The available information suggests that surveillance mechanisms ...

  5. Geminin: a major DNA replication safeguard in higher eukaryotes

    DEFF Research Database (Denmark)

    Melixetian, Marina; Helin, Kristian

    2004-01-01

    Eukaryotes have evolved multiple mechanisms to restrict DNA replication to once per cell cycle. These mechanisms prevent relicensing of origins of replication after initiation of DNA replication in S phase until the end of mitosis. Most of our knowledge of mechanisms controlling prereplication...

  6. Potential of industrial biotechnology with cyanobacteria and eukaryotic microalgae

    NARCIS (Netherlands)

    Wijffels, R.H.; Kruse, O.; Hellingwerf, K.J.

    2013-01-01

    Both cyanobacteria and eukaryotic microalgae are promising organisms for sustainable production of bulk products such as food, feed, materials, chemicals and fuels. In this review we will summarize the potential and current biotechnological developments.Cyanobacteria are promising host organisms for

  7. Eukaryotic checkpoints are absent in the cell division cycle of ...

    Indian Academy of Sciences (India)

    Unknown

    are known to control the cell cycle of most eukaryotes, these genes may be structurally altered and their equiva- lent function yet to be ... points controlling the cell division of these organisms? Is the cell division cycle of these organisms ..... mitotic-phase inhibitor and may become a useful tool for studies on the relationship ...

  8. Molecular typing of fecal eukaryotic microbiota of human infants and ...

    Indian Academy of Sciences (India)

    The micro-eukaryotic diversity from the human gut was investigated using universal primers directed towards 18S rRNA gene, fecal samples being the source of DNA. The subjects in this study included two breast-fed and two formula-milk-fed infants and their mothers. The study revealed that the infants did not seem to ...

  9. Monitoring disulfide bond formation in the eukaryotic cytosol

    DEFF Research Database (Denmark)

    Østergaard, Henrik; Tachibana, Christine; Winther, Jakob R.

    2004-01-01

    Glutathione is the most abundant low molecular weight thiol in the eukaryotic cytosol. The compartment-specific ratio and absolute concentrations of reduced and oxidized glutathione (GSH and GSSG, respectively) are, however, not easily determined. Here, we present a glutathione-specific green...

  10. An inside-out origin for the eukaryotic cell.

    Science.gov (United States)

    Baum, David A; Baum, Buzz

    2014-10-28

    Although the origin of the eukaryotic cell has long been recognized as the single most profound change in cellular organization during the evolution of life on earth, this transition remains poorly understood. Models have always assumed that the nucleus and endomembrane system evolved within the cytoplasm of a prokaryotic cell. Drawing on diverse aspects of cell biology and phylogenetic data, we invert the traditional interpretation of eukaryotic cell evolution. We propose that an ancestral prokaryotic cell, homologous to the modern-day nucleus, extruded membrane-bound blebs beyond its cell wall. These blebs functioned to facilitate material exchange with ectosymbiotic proto-mitochondria. The cytoplasm was then formed through the expansion of blebs around proto-mitochondria, with continuous spaces between the blebs giving rise to the endoplasmic reticulum, which later evolved into the eukaryotic secretory system. Further bleb-fusion steps yielded a continuous plasma membrane, which served to isolate the endoplasmic reticulum from the environment. The inside-out theory is consistent with diverse kinds of data and provides an alternative framework by which to explore and understand the dynamic organization of modern eukaryotic cells. It also helps to explain a number of previously enigmatic features of cell biology, including the autonomy of nuclei in syncytia and the subcellular localization of protein N-glycosylation, and makes many predictions, including a novel mechanism of interphase nuclear pore insertion.

  11. Uncoupling of Sister Replisomes during Eukaryotic DNA Replication

    NARCIS (Netherlands)

    Yardimci, Hasan; Loveland, Anna B.; Habuchi, Satoshi; van Oijen, Antoine M.; Walter, Johannes C.

    2010-01-01

    The duplication of eukaryotic genomes involves the replication of DNA from multiple origins of replication. In S phase, two sister replisomes assemble at each active origin, and they replicate DNA in opposite directions. Little is known about the functional relationship between sister replisomes.

  12. Exploring the behavior of small eukaryotic gene networks

    NARCIS (Netherlands)

    Bruggeman, F.J.; Oancea, I.; van Driel, R.

    2008-01-01

    Analysis of the genome organization of higher eukaryotes indicates that it contains many clusters of functionally related genes. In these clusters, the activity of a single gene is regulated hierarchically at a local gene-level and a global cluster-level. Whether a single gene can be activated by a

  13. Eu-Detect: An algorithm for detecting eukaryotic sequences in ...

    Indian Academy of Sciences (India)

    Supplementary figure 1. Plots depicting the classification accuracy of Eu-Detect with various combinations of. 'cumulative sequence count' (40K, 50K, 60K, 70K, 80K) and 'coverage threshold' (20%, 30%, 40%, 50%, 60%, 70%,. 80%). While blue bars represent Eu-Detect's average classification accuracy with eukaryotic ...

  14. Polarised asymmetric inheritance of accumulated protein damage in higher eukaryotes

    NARCIS (Netherlands)

    Rujano, Maria A.; Bosveld, Floris; Salomons, Florian A.; Dijk, Freark; van Waarde, Maria A. W. H.; van der Want, Johannes J. L.; de Vos, Rob A. I.; Brunt, Ewout R.; Sibon, Ody C. M.; Kampinga, Harm H.

    2006-01-01

    Disease-associated misfolded proteins or proteins damaged due to cellular stress are generally disposed via the cellular protein quality-control system. However, under saturating conditions, misfolded proteins will aggregate. In higher eukaryotes, these aggregates can be transported to accumulate in

  15. Patterns of intron gain and conservation in eukaryotic genes

    Directory of Open Access Journals (Sweden)

    Wolf Yuri I

    2007-10-01

    Full Text Available Abstract Background: The presence of introns in protein-coding genes is a universal feature of eukaryotic genome organization, and the genes of multicellular eukaryotes, typically, contain multiple introns, a substantial fraction of which share position in distant taxa, such as plants and animals. Depending on the methods and data sets used, researchers have reached opposite conclusions on the causes of the high fraction of shared introns in orthologous genes from distant eukaryotes. Some studies conclude that shared intron positions reflect, almost entirely, a remarkable evolutionary conservation, whereas others attribute it to parallel gain of introns. To resolve these contradictions, it is crucial to analyze the evolution of introns by using a model that minimally relies on arbitrary assumptions. Results: We developed a probabilistic model of evolution that allows for variability of intron gain and loss rates over branches of the phylogenetic tree, individual genes, and individual sites. Applying this model to an extended set of conserved eukaryotic genes, we find that parallel gain, on average, accounts for only ~8% of the shared intron positions. However, the distribution of parallel gains over the phylogenetic tree of eukaryotes is highly non-uniform. There are, practically, no parallel gains in closely related lineages, whereas for distant lineages, such as animals and plants, parallel gains appear to contribute up to 20% of the shared intron positions. In accord with these findings, we estimated that ancestral introns have a high probability to be retained in extant genomes, and conversely, that a substantial fraction of extant introns have retained their positions since the early stages of eukaryotic evolution. In addition, the density of sites that are available for intron insertion is estimated to be, approximately, one in seven basepairs. Conclusion: We obtained robust estimates of the contribution of parallel gain to the observed

  16. Special relativity

    CERN Document Server

    Faraoni, Valerio

    2013-01-01

    This book offers an essential bridge between college-level introductions and advanced graduate-level books on special relativity. It begins at an elementary level, presenting and discussing the basic concepts normally covered in college-level works, including the Lorentz transformation. Subsequent chapters introduce the four-dimensional worldview implied by the Lorentz transformations, mixing time and space coordinates, before continuing on to the formalism of tensors, a topic usually avoided in lower-level courses. The book’s second half addresses a number of essential points, including the concept of causality; the equivalence between mass and energy, including applications; relativistic optics; and measurements and matter in Minkowski spacetime. The closing chapters focus on the energy-momentum tensor of a continuous distribution of mass-energy and its covariant conservation; angular momentum; a discussion of the scalar field of perfect fluids and the Maxwell field; and general coordinates. Every chapter...

  17. Distribution of MRI signal alterations of the cartilage endplate in pre-operated patients with special focus on recurrent lumbar disc herniation; Verteilungsmuster von (Modic-)Signalveraenderungen an den vertebralen Endplatten voroperierter Patienten und ihr Bezug zu Rezidivvorfaellen

    Energy Technology Data Exchange (ETDEWEB)

    Becker, G.T.; Liphofer, J.; Koester, O. [Inst. fuer Diagnostische und Interventionelle Radiologie und Nuklearmedizin, St. Josef-Hospital, Bochum (Germany); Willburger, R.E. [Abt. fuer Rheumaorthopaedie, St. Elisabeth-Hospital, Bochum (Germany); Schmid, G. [Klinik fuer Diagnostische und Interventionelle Radiologie, Johanna-Etienne-Krankenhaus, Neuss (Germany)

    2006-01-01

    Purpose: To study the location of (Modic) MR signal alterations (SA) of the cartilage endplate (CEP) in pre- and non-operated segments L3-S1 with special focus on the presence of recurrent lumbar disc herniation (RLDH). Materials and Methods: In a retrospective study the MR images of vertebrae L3-S1 of 65 consecutive patients with a history of microdiscectomy were evaluated. Of the 190 segments studied, 67 were pre-operated. These were divided into a group with recurrent lumbar disc herniation (RLDH) (n=19) and a group without evidence of RLDH (n=48). Non-operated segments (n=123) were also considered as a separate group. In these three groups the prevalence of different Modic types was determined using the sag. T1- and T2-weighted images, and, in particular, the distribution of SA at the upper and lower CEP was examined by evaluating the sag. T2-weighted images. In order to achieve this, each CEP was divided into nine regions. Results: Pre-operated segments showed significantly more frequent (p<0.001) and more expansive (p<0.001) SA than non-operated segments. Non-operated segments showed SA less frequently in the central region of both upper and lower CEP (p=0.056 and p=0.015, respectively). In operated segments without RLDH, the upper CEP had significantly more SA on the operation side than in the mid-sagittal and contra-lateral regions (p=0.016, p=0.037) and significantly more on the operation side of the lower CEP than in the contra-lateral region (p=0.027). Operated segments with RLDH did not show an emphasis of SA on the operation side. In this group SA occurred significantly more often in the central and ventral mid-sagittal regions of the upper CEP than in the preoperated segments without RLDH. (orig.)

  18. Aminoglycoside interactions and impacts on the eukaryotic ribosome

    Science.gov (United States)

    Prokhorova, Irina; Altman, Roger B.; Djumagulov, Muminjon; Shrestha, Jaya P.; Urzhumtsev, Alexandre; Ferguson, Angelica; Chang, Cheng-Wei Tom; Yusupov, Marat; Blanchard, Scott C.; Yusupova, Gulnara

    2017-01-01

    Aminoglycosides are chemically diverse, broad-spectrum antibiotics that target functional centers within the bacterial ribosome to impact all four principle stages (initiation, elongation, termination, and recycling) of the translation mechanism. The propensity of aminoglycosides to induce miscoding errors that suppress the termination of protein synthesis supports their potential as therapeutic interventions in human diseases associated with premature termination codons (PTCs). However, the sites of interaction of aminoglycosides with the eukaryotic ribosome and their modes of action in eukaryotic translation remain largely unexplored. Here, we use the combination of X-ray crystallography and single-molecule FRET analysis to reveal the interactions of distinct classes of aminoglycosides with the 80S eukaryotic ribosome. Crystal structures of the 80S ribosome in complex with paromomycin, geneticin (G418), gentamicin, and TC007, solved at 3.3- to 3.7-Å resolution, reveal multiple aminoglycoside-binding sites within the large and small subunits, wherein the 6′-hydroxyl substituent in ring I serves as a key determinant of binding to the canonical eukaryotic ribosomal decoding center. Multivalent binding interactions with the human ribosome are also evidenced through their capacity to affect large-scale conformational dynamics within the pretranslocation complex that contribute to multiple aspects of the translation mechanism. The distinct impacts of the aminoglycosides examined suggest that their chemical composition and distinct modes of interaction with the ribosome influence PTC read-through efficiency. These findings provide structural and functional insights into aminoglycoside-induced impacts on the eukaryotic ribosome and implicate pleiotropic mechanisms of action beyond decoding. PMID:29208708

  19. Eukaryotic microorganisms in cold environments. Examples from Pyrenean glaciers

    Directory of Open Access Journals (Sweden)

    Laura eGarcia-Descalzo

    2013-03-01

    Full Text Available Little is known about the viability of eukaryotic microorganisms preserved in icy regions. Here we report on the diversity of microbial eukaryotes in ice samples derived from four Pyrenean glaciers. The species composition of eukaryotic communities in these glaciers is unknown mostly because of the presence of a multi-year ice cap, and it is not clear whether they harbor the same populations. The recent deglaciation of these areas is allowing an easy access to glacial layers that correspond to the Little Ice Age although some isolated deposits are attributed to previous glacial cycles. In this study, we use molecular 18S rRNA-based approaches to characterize some of the microbial eukaryotic populations associated with Pyrenean glaciers. Firstly, we performed a chemical and microscopical characterization of ice samples. Secondly, molecular analyses revealed interesting protist genetic diversity in glaciers. In order to understand the microbial composition of the ice samples the eukaryotic communities resident in the glacial samples were examined by amplifying community DNA and constructing clone libraries with 18S rRNA primers. After removal of potential chimeric sequences and derreplication of identical sequences, phylogenetic analysis demonstrated that several different protists could be identified. Protist diversity was more phylum rich in Aneto and Monte Perdido glaciers. The dominant taxonomic groups across all samples (> 1 % of all sequences were Viridiplantae and Rhizaria. Significant variations in relative abundances of protist phyla between higher and lower glaciers were observed. At the genus level, significant differences were also recorded for the dominant genera Chloromonas, Raphidonema , Heteromita , Koliella and Bodomorpha. In addition, protist community structure showed significant differences between glaciers. The relative abundances of protist groups at different taxonomic levels correlated with the altitude and area of glaciers

  20. Eukaryotic microorganisms in cold environments: examples from Pyrenean glaciers

    Science.gov (United States)

    García-Descalzo, Laura; García-López, Eva; Postigo, Marina; Baquero, Fernando; Alcazar, Alberto; Cid, Cristina

    2013-01-01

    Little is known about the viability of eukaryotic microorganisms preserved in icy regions. Here we report on the diversity of microbial eukaryotes in ice samples derived from four Pyrenean glaciers. The species composition of eukaryotic communities in these glaciers is unknown mostly because of the presence of a multi-year ice cap, and it is not clear whether they harbor the same populations. The recent deglaciation of these areas is allowing an easy access to glacial layers that correspond to the “Little Ice Age” although some isolated deposits are attributed to previous glacial cycles. In this study, we use molecular 18S rRNA-based approaches to characterize some of the microbial eukaryotic populations associated with Pyrenean glaciers. Firstly, we performed a chemical and microscopical characterization of ice samples. Secondly, molecular analyses revealed interesting protist genetic diversity in glaciers. In order to understand the microbial composition of the ice samples the eukaryotic communities resident in the glacial samples were examined by amplifying community DNA and constructing clone libraries with 18S rRNA primers. After removal of potential chimeric sequences and dereplication of identical sequences, phylogenetic analysis demonstrated that several different protists could be identified. Protist diversity was more phylum rich in Aneto and Monte Perdido glaciers. The dominant taxonomic groups across all samples (>1% of all sequences) were Viridiplantae and Rhizaria. Significant variations in relative abundances of protist phyla between higher and lower glaciers were observed. At the genus level, significant differences were also recorded for the dominant genera Chloromonas, Raphidonema, Heteromita, Koliella, and Bodomorpha. In addition, protist community structure showed significant differences between glaciers. The relative abundances of protist groups at different taxonomic levels correlated with the altitude and area of glaciers and with pH of

  1. Bio-chemo-mechanical models for nuclear deformation in adherent eukaryotic cells.

    Science.gov (United States)

    Nava, Michele M; Raimondi, Manuela T; Pietrabissa, Riccardo

    2014-10-01

    Adherent eukaryotic cells are subjected to a broad variety of extracellular and intracellular stimuli regulating their behaviour. These stimuli can be either purely chemical, for example soluble factors binding to the cell membrane, or mechano-chemical, for example integrin-based adhesion complexes stretching the cell cytoskeleton. Here, we focus on mechano-chemical stimuli such as extracellular forces (interstitial flow, pressurization) and intracellular forces (due to cell adhesion), which may combine generating stress-strain states in the cytoskeleton. These states are transferred to the nucleus to influence the transcription of specific genes, likely by changing the chromatin organization and by altering the permeability of the nuclear membrane. While there exists increasing experimental evidence of the mechanosensing role of the cell nucleus, both the underlying molecular mechanisms involved, and the nuclear structural behaviour in response to forces, are still poorly understood. Here, we review the existing literature on computational models developed to investigate the chemo-mechanical behaviour of adherent eukaryotic cells. We analyse two main classes of models of single-cell mechanics, based either on the discrete or on the continuum approaches. We focus on the bio-chemo-mechanical model and modelling techniques accounting for the nuclear body. The modelling techniques are discussed highlighting their ability in predicting cytoskeletal contractility states and nuclear stress-strain states.

  2. Eukaryotes dominate new production in the Sargasso Sea

    Science.gov (United States)

    Fawcett, S. E.; Lomas, M. W.; Ward, B. B.; Casey, J. R.; Sigman, D. M.

    2010-12-01

    The vast subtropical ocean gyres are considered unproductive “deserts” due to the extremely low concentrations of essential nutrients in their sunlit surface waters. Because of intense upper ocean stratification, phytoplankton growth in the subtropical gyres is limited by the slow supply of nitrate from below, and is assumed to be supported predominantly by “regenerated” nitrogen (N): ammonium and other reduced N sources recycled in surface waters. The phytoplankton assemblage of the subtropical Sargasso Sea is dominated by the prokaryotic cyanobacteria, Prochlorococcus and Synechococcus, which occur in very high cell numbers compared to the rarer, and usually larger, eukaryotic algae. Coupling flow cytometry and a new high-sensitivity method for N isotope analysis, we measure the 15N/14N of major phytoplankton taxa and other biologically distinct particle populations collected from the surface waters of the Sargasso Sea during the stratified summer period. We find that the cyanobacteria and eukaryotic phytoplankton show distinct N isotope signatures, indicating that they utilize different sources of N for growth. Prochlorococcus and Synechococcus have a uniformly low 15N/14N, consistent with the expectation that these phytoplankton rely on regenerated N. However, the 15N/14N of eukaryotic phytoplankton is higher and more variable, with a mean 15N/14N comparable to the new nitrate supply from below, indicating that eukaryotes dominate the consumption of this nitrate and rely on it for more than half of their N requirement. Using our measured 15N/14N values for the various sorted autotrophic populations, we calculate eukaryote-specific summer f-ratios of 0.6-0.67 and total community summer f-ratios of 0.15-0.23. These values are higher than those based on comparison of primary production and sediment-trap derived organic carbon (C) export, and agree well with annual f-ratio estimates implied by geochemical tracers. The high 15N/14N of eukaryotic biomass can

  3. Focusing of electromagnetic waves

    International Nuclear Information System (INIS)

    Dhayalan, V.

    1996-01-01

    The focusing of electromagnetic waves inside a slab has been examined together with two special cases in which the slab is reduced to a single interface or a single medium. To that end the exact solutions for the fields inside a layered medium have been used, given in terms of the outside current source in order to obtain the solutions for the focused electric field inside a slab. Both exact and asymptotic solutions of the problem have been considered, and the validity of the latter has been discussed. The author has developed a numerical algorithm for evaluation of the diffraction integral with special emphasis on reducing the computing time. The numerical techniques in the paper can be readily applied to evaluate similar diffraction integrals occurring e.g. in microstrip antennas. 46 refs

  4. Without 'Focus'

    OpenAIRE

    Aldo Sevi; Nirit Kadmon

    2010-01-01

    It is widely accepted that a notion of 'focus', more or less as conceived of in Jackendoff (1972), must be incorporated into our theory of grammar, as a means of accounting for certain observed correlations between prosodic facts and semantic/pragmatic facts. In this paper, we put forth the somewhat radical idea that the time has come to give up this customary view, and eliminate 'focus' from our theory of grammar. We argue that such a move is both economical and fruitful.Research over the ye...

  5. Without 'Focus'

    Directory of Open Access Journals (Sweden)

    Aldo Sevi

    2010-12-01

    Full Text Available It is widely accepted that a notion of 'focus', more or less as conceived of in Jackendoff (1972, must be incorporated into our theory of grammar, as a means of accounting for certain observed correlations between prosodic facts and semantic/pragmatic facts. In this paper, we put forth the somewhat radical idea that the time has come to give up this customary view, and eliminate 'focus' from our theory of grammar. We argue that such a move is both economical and fruitful.Research over the years has revealed that the correlations between prosody, 'focus', and the alleged semantic/pragmatic effects of focus are much less clear and systematic than we may have initially hoped. First we argue that this state of affairs detracts significantly from the utility of our notion of 'focus', to the point of calling into question the very motivation for including it in the grammar. Then we look at some of the central data, and show how they might be analyzed without recourse to a notion of 'focus'. We concentrate on (i the effect of pitch accent placement on discourse congruence, and (ii the choice of 'associate' for the so-called 'focus sensitive' adverb only. We argue that our focus-free approach to the data improves empirical coverage, and begins to reveal patterns that have previously been obscured by preconceptions about 'focus'.ReferencesBeaver, D. & Clark, B. 2008. Sense and Sensitivity: How Focus Determines Meaning. Blackwell.Beaver, D., Clark, B., Flemming, E., Jaeger, T. F. & Wolters, M. 2007. ‘When semantics meets phonetics: Acoustical studies of second occurrence focus’. Language 83.2: 245–76.http://dx.doi.org/10.1353/lan.2007.0053Beckman, M. & Hirschberg, J. 1994. ‘The ToBI Annotation Conventions’. Ms.,http://www.cs.columbia.edu/~julia/files/conv.pdf.Bolinger, D. 1972. ‘Accent is predictable (if you are a mind-reader’. Language 48.3: 633–44.http://dx.doi.org/10.2307/412039Büring, D. 2006. ‘Focus projection and default

  6. Influence of Vitamin B Auxotrophy on Nitrogen Metabolism in Eukaryotic Phytoplankton

    Directory of Open Access Journals (Sweden)

    Erin M Bertrand

    2012-10-01

    Full Text Available While nitrogen availability is known to limit primary production in large parts of the ocean, vitamin starvation amongst eukaryotic phytoplankton is becoming increasingly recognized as an oceanographically relevant phenomenon. Cobalamin (B12 and thiamine (B1 auxotrophy are widespread throughout eukaryotic phytoplankton, with over 50% of cultured isolates requiring B12 and 20% requiring B1. The frequency of vitamin auxotrophy in harmful algal bloom species is even higher. Instances of colimitation between nitrogen and B vitamins have been observed in marine environments, and interactions between these nutrients have been shown to impact phytoplankton species composition. This review evaluates the potential for interactive effects of nitrogen and vitamin B12 and B1 starvation in eukaryotic phytoplankton. B12 plays essential roles in amino acid and one-carbon metabolism, while B1 is important for primary carbohydrate and amino acid metabolism and likely useful as an anti-oxidant. Here we will focus on three potential metabolic interconnections between vitamin, nitrogen and sulfur metabolism that may have ramifications for the role of vitamin and nitrogen scarcities in driving ocean productivity and species composition. These include: (1 B12, B1, and N starvation impacts on osmolyte and antioxidant production, (2 B12 and B1 starvation impacts on polyamine biosynthesis, and (3 influence of B12 and B1 starvation on the diatom urea cycle and amino acid recycling through impacts on the citric acid cycle. We evaluate evidence for these interconnections and identify oceanographic contexts in which each may impact rates of primary production and phytoplankton community composition. Major implications include that B12 and B1 deprivation may impair the ability of phytoplankton to recover from nitrogen starvation and that changes in vitamin and nitrogen availability may synergistically impact harmful algal bloom formation.

  7. Specialization Patterns

    DEFF Research Database (Denmark)

    Schultz, Ulrik Pagh; Lawall, Julia Laetitia; Consel, Charles

    2000-01-01

    of design patterns. In this paper, we analyze the specialization opportunities provided by specific uses of design patterns. Based on the analysis of each design pattern, we define the associated specialization pattern. These specialization opportunities can be declared using the specialization classes......Design patterns offer many advantages for software development, but can introduce inefficiency into the final program. Program specialization can eliminate such overheads, but is most effective when targeted by the user to specific bottlenecks. Consequently, we propose that these concepts...... are complementary. Program specialization can optimize programs written using design patterns, and design patterns provide information about the program structure that can guide specialization. Concretely, we propose specialization patterns, which describe how to apply program specialization to optimize uses...

  8. Specialization Patterns

    DEFF Research Database (Denmark)

    Schultz, Ulrik Pagh; Lawall, Julia Laetitia; Consel, Charles

    2000-01-01

    Design patterns offer many advantages for software development, but can introduce inefficiency into the final program. Program specialization can eliminate such overheads, but is most effective when targeted by the user to specific bottlenecks. Consequently, we propose that these concepts...... are complementary. Program specialization can optimize programs written using design patterns, and design patterns provide information about the program structure that can guide specialization. Concretely, we propose specialization patterns, which describe how to apply program specialization to optimize uses...... of design patterns. In this paper, we analyze the specialization opportunities provided by specific uses of design patterns. Based on the analysis of each design pattern, we define the associated specialization pattern. These specialization opportunities can be declared using the specialization classes...

  9. Focused ultrasound in ophthalmology

    Directory of Open Access Journals (Sweden)

    Silverman RH

    2016-09-01

    Full Text Available Ronald H Silverman1,2 1Department of Ophthalmology, Columbia University Medical Center, 2F.L. Lizzi Center for Biomedical Engineering, Riverside Research, New York, NY, USA Abstract: The use of focused ultrasound to obtain diagnostically significant information about the eye goes back to the 1950s. This review describes the historical and technological development of ophthalmic ultrasound and its clinical application and impact. Ultrasound, like light, can be focused, which is crucial for formation of high-resolution, diagnostically useful images. Focused, single-element, mechanically scanned transducers are most common in ophthalmology. Specially designed transducers have been used to generate focused, high-intensity ultrasound that through thermal effects has been used to treat glaucoma (via cilio-destruction, tumors, and other pathologies. Linear and annular transducer arrays offer synthetic focusing in which precise timing of the excitation of independently addressable array elements allows formation of a converging wavefront to create a focus at one or more programmable depths. Most recently, linear array-based plane-wave ultrasound, in which the array emits an unfocused wavefront and focusing is performed solely on received data, has been demonstrated for imaging ocular anatomy and blood flow. While the history of ophthalmic ultrasound extends back over half-a-century, new and powerful technologic advances continue to be made, offering the prospect of novel diagnostic capabilities. Keywords: ophthalmic ultrasound, ultrasound biomicroscopy (UBM, high-intensity focused ultrasound (HIFU, ultrafast imaging, Doppler imaging 

  10. Metal ion transport in eukaryotic microorganisms: insights from Saccharomyces cerevisiae.

    Science.gov (United States)

    Eide, D J

    2000-01-01

    Metal ions such as iron, copper, manganese, and zinc are essential nutrients for all eukaryotic microorganisms. Therefore, these organisms possess efficient uptake mechanisms to obtain these nutrients from their extracellular environment. Metal ions must also be transported into intracellular organelles where they function as catalytic and structural cofactors for compartmentalized enzymes. Thus, intracellular transport mechanisms are also present. When present in high levels, metal ions can also be toxic, so their uptake and intracellular transport is tightly regulated at both transcriptional and post-transcriptional levels to limit metal ion overaccumulation and facilitate storage and sequestration. Remarkable molecular insight into these processes has come from recent studies of the yeast Saccharomyces cerevisiae. This organism, which is the primary subject of this chapter, serves as a useful paradigm to understand metal ion metabolism in other eukaryotic microbes.

  11. Anionic lipids and the maintenance of membrane electrostatics in eukaryotes.

    Science.gov (United States)

    Platre, Matthieu Pierre; Jaillais, Yvon

    2017-02-01

    A wide range of signaling processes occurs at the cell surface through the reversible association of proteins from the cytosol to the plasma membrane. Some low abundant lipids are enriched at the membrane of specific compartments and thereby contribute to the identity of cell organelles by acting as biochemical landmarks. Lipids also influence membrane biophysical properties, which emerge as an important feature in specifying cellular territories. Such parameters are crucial for signal transduction and include lipid packing, membrane curvature and electrostatics. In particular, membrane electrostatics specifies the identity of the plasma membrane inner leaflet. Membrane surface charges are carried by anionic phospholipids, however the exact nature of the lipid(s) that powers the plasma membrane electrostatic field varies among eukaryotes and has been hotly debated during the last decade. Herein, we discuss the role of anionic lipids in setting up plasma membrane electrostatics and we compare similarities and differences that were found in different eukaryotic cells.

  12. Starting the protein synthesis machine: eukaryotic translation initiation.

    Science.gov (United States)

    Preiss, Thomas; W Hentze, Matthias

    2003-12-01

    The final assembly of the protein synthesis machinery occurs during translation initiation. This delicate process involves both ends of eukaryotic messenger RNAs as well as multiple sequential protein-RNA and protein-protein interactions. As is expected from its critical position in the gene expression pathway between the transcriptome and the proteome, translation initiation is a selective and highly regulated process. This synopsis summarises the current status of the field and identifies intriguing open questions. Copyright 2003 Wiley Periodicals, Inc.

  13. Extreme Diversity of Diplonemid Eukaryotes in the Ocean

    Czech Academy of Sciences Publication Activity Database

    Flegontova, Olga; Flegontov, Pavel; Malviya, S.; Audic, S.; Wincker, P.; de Vargas, C.; Bowler, C.; Lukeš, Julius; Horák, Aleš

    2016-01-01

    Roč. 26, č. 22 (2016), s. 3060-3065 ISSN 0960-9822 R&D Projects: GA ČR GPP506/12/P931; GA ČR(CZ) GA14-23986S Institutional support: RVO:60077344 Keywords : virus-sized particles * microbial eukaryotes * sea-floor * phytoplankton * communities * euglenozoa * dispersal * ecosystem Subject RIV: EG - Zoology Impact factor: 8.851, year: 2016

  14. Sulfate assimilation in eukaryotes: fusions, relocations and lateral transfers

    Directory of Open Access Journals (Sweden)

    Durnford Dion G

    2008-02-01

    Full Text Available Abstract Background The sulfate assimilation pathway is present in photosynthetic organisms, fungi, and many bacteria, providing reduced sulfur for the synthesis of cysteine and methionine and a range of other metabolites. In photosynthetic eukaryotes sulfate is reduced in the plastids whereas in aplastidic eukaryotes the pathway is cytosolic. The only known exception is Euglena gracilis, where the pathway is localized in mitochondria. To obtain an insight into the evolution of the sulfate assimilation pathway in eukaryotes and relationships of the differently compartmentalized isoforms we determined the locations of the pathway in lineages for which this was unknown and performed detailed phylogenetic analyses of three enzymes involved in sulfate reduction: ATP sulfurylase (ATPS, adenosine 5'-phosphosulfate reductase (APR and sulfite reductase (SiR. Results The inheritance of ATPS, APR and the related 3'-phosphoadenosine 5'-phosphosulfate reductase (PAPR are remarkable, with multiple origins in the lineages that comprise the opisthokonts, different isoforms in chlorophytes and streptophytes, gene fusions with other enzymes of the pathway, evidence a eukaryote to prokaryote lateral gene transfer, changes in substrate specificity and two reversals of cellular location of host- and endosymbiont-originating enzymes. We also found that the ATPS and APR active in the mitochondria of Euglena were inherited from its secondary, green algal plastid. Conclusion Our results reveal a complex history for the enzymes of the sulfate assimilation pathway. Whilst they shed light on the origin of some characterised novelties, such as a recently described novel isoform of APR from Bryophytes and the origin of the pathway active in the mitochondria of Euglenids, the many distinct and novel isoforms identified here represent an excellent resource for detailed biochemical studies of the enzyme structure/function relationships.

  15. Focus: Digital

    DEFF Research Database (Denmark)

    Technology has been an all-important and defining element within the arts throughout the 20th century, and it has fundamentally changed the ways in which we produce and consume music. With this Focus we investigate the latest developments in the digital domain – and their pervasiveness and rapid...... production and reception of contemporary music and sound art. With ‘Digital’ we present four composers' very different answers to how technology impact their work. To Juliana Hodkinson it has become an integral part of her sonic writing. Rudiger Meyer analyses the relationships between art and design and how...... technology affects our habits of consumption. Risto Holopainen presents a notion of autonomous instruments and automated composition that, in the end, cannot escape the human while Jøren Rudi reflects on aesthetic elements and artistic approaches to sound in computer games. This focus is edited by Sanne...

  16. Material focus

    DEFF Research Database (Denmark)

    Sokoler, Tomas; Vallgårda, Anna K. A.

    2009-01-01

    In this paper we build on the notion of computational composites, which hold a material perspective on computational technology. We argue that a focus on the material aspects of the technology could be a fruitful approach to achieve new expressions and to gain a new view on the technology's role...... in design. We study two of the computer's material properties: computed causality and connectability and through developing two computational composites that utilize these properties we begin to explore their potential expressions....

  17. Eukaryotic and prokaryotic promoter prediction using hybrid approach.

    Science.gov (United States)

    Lin, Hao; Li, Qian-Zhong

    2011-06-01

    Promoters are modular DNA structures containing complex regulatory elements required for gene transcription initiation. Hence, the identification of promoters using machine learning approach is very important for improving genome annotation and understanding transcriptional regulation. In recent years, many methods have been proposed for the prediction of eukaryotic and prokaryotic promoters. However, the performances of these methods are still far from being satisfactory. In this article, we develop a hybrid approach (called IPMD) that combines position correlation score function and increment of diversity with modified Mahalanobis Discriminant to predict eukaryotic and prokaryotic promoters. By applying the proposed method to Drosophila melanogaster, Homo sapiens, Caenorhabditis elegans, Escherichia coli, and Bacillus subtilis promoter sequences, we achieve the sensitivities and specificities of 90.6 and 97.4% for D. melanogaster, 88.1 and 94.1% for H. sapiens, 83.3 and 95.2% for C. elegans, 84.9 and 91.4% for E. coli, as well as 80.4 and 91.3% for B. subtilis. The high accuracies indicate that the IPMD is an efficient method for the identification of eukaryotic and prokaryotic promoters. This approach can also be extended to predict other species promoters.

  18. Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency

    Directory of Open Access Journals (Sweden)

    Wüst Christian

    2009-11-01

    Full Text Available Abstract Background Complementary-DNA based amplified fragment length polymorphism (cDNA-AFLP is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expression profiles. In spite of the frequent application of this method, studies on the optimization of the cDNA-AFLP assay design are rare and have typically been taxonomically restricted. Here, we model cDNA-AFLPs on all 92 eukaryotic species for which cDNA pools are currently available, using all combinations of eight restriction enzymes standard in cDNA-AFLP screens. Results In silco simulations reveal that cDNA pool coverage is largely determined by the choice of individual restriction enzymes and that, through the choice of optimal enzyme combinations, coverage can be increased from Conclusion The insights gained from in silico screening of cDNA-AFLPs from a broad sampling of eukaryotes provide a set of guidelines that should help to substantially increase the efficiency of future cDNA-AFLP experiments in eukaryotes. In silico simulations also suggest a novel use of cDNA-AFLP screens to determine the number of transcripts expressed in a target tissue, an application that should be invaluable as next-generation sequencing technologies are adapted for differential display.

  19. Nuclear importation of Mariner transposases among eukaryotes: motif requirements and homo-protein interactions.

    Directory of Open Access Journals (Sweden)

    Marie-Véronique Demattei

    Full Text Available Mariner-like elements (MLEs are widespread transposable elements in animal genomes. They have been divided into at least five sub-families with differing host ranges. We investigated whether the ability of transposases encoded by Mos1, Himar1 and Mcmar1 to be actively imported into nuclei varies between host belonging to different eukaryotic taxa. Our findings demonstrate that nuclear importation could restrict the host range of some MLEs in certain eukaryotic lineages, depending on their expression level. We then focused on the nuclear localization signal (NLS in these proteins, and showed that the first 175 N-terminal residues in the three transposases were required for nuclear importation. We found that two components are involved in the nuclear importation of the Mos1 transposase: an SV40 NLS-like motif (position: aa 168 to 174, and a dimerization sub-domain located within the first 80 residues. Sequence analyses revealed that the dimerization moiety is conserved among MLE transposases, but the Himar1 and Mcmar1 transposases do not contain any conserved NLS motif. This suggests that other NLS-like motifs must intervene in these proteins. Finally, we showed that the over-expression of the Mos1 transposase prevents its nuclear importation in HeLa cells, due to the assembly of transposase aggregates in the cytoplasm.

  20. Plasma Focus

    International Nuclear Information System (INIS)

    Bernard, Alain; Jolas, Alain; Garconnet, J.-P.; Mascureau, J. de; Nazet, Christian; Coudeville, Alain; Bekiarian, Andre.

    1977-01-01

    The present report is the edition of the lectures given in a conference on the Focus experiment held at the Centre d'etudes de Limeil, on Oct. 1975. After a survey of the early laboratories one will find the main results obtained in Limeil concerning interferometry, laser scattering, electric and magnetic-measurements, X-ray and neutron emission and also the possible use of explosive current generators instead of capacitor banks at high energy levels. The principal lines of future research are given in the conclusion [fr

  1. Origin of phagotrophic eukaryotes as social cheaters in microbial biofilms

    Directory of Open Access Journals (Sweden)

    Jékely Gáspár

    2007-01-01

    Full Text Available Abstract Background The origin of eukaryotic cells was one of the most dramatic evolutionary transitions in the history of life. It is generally assumed that eukaryotes evolved later then prokaryotes by the transformation or fusion of prokaryotic lineages. However, as yet there is no consensus regarding the nature of the prokaryotic group(s ancestral to eukaryotes. Regardless of this, a hardly debatable fundamental novel characteristic of the last eukaryotic common ancestor was the ability to exploit prokaryotic biomass by the ingestion of entire cells, i.e. phagocytosis. The recent advances in our understanding of the social life of prokaryotes may help to explain the origin of this form of total exploitation. Presentation of the hypothesis Here I propose that eukaryotic cells originated in a social environment, a differentiated microbial mat or biofilm that was maintained by the cooperative action of its members. Cooperation was costly (e.g. the production of developmental signals or an extracellular matrix but yielded benefits that increased the overall fitness of the social group. I propose that eukaryotes originated as selfish cheaters that enjoyed the benefits of social aggregation but did not contribute to it themselves. The cheaters later evolved into predators that lysed other cells and eventually became professional phagotrophs. During several cycles of social aggregation and dispersal the number of cheaters was contained by a chicken game situation, i.e. reproductive success of cheaters was high when they were in low abundance but was reduced when they were over-represented. Radical changes in cell structure, including the loss of the rigid prokaryotic cell wall and the development of endomembranes, allowed the protoeukaryotes to avoid cheater control and to exploit nutrients more efficiently. Cellular changes were buffered by both the social benefits and the protective physico-chemical milieu of the interior of biofilms. Symbiosis

  2. Sport Specialization, Part I

    OpenAIRE

    Myer, Gregory D.; Jayanthi, Neeru; Difiori, John P.; Faigenbaum, Avery D.; Kiefer, Adam W.; Logerstedt, David; Micheli, Lyle J.

    2015-01-01

    Context: There is increased growth in sports participation across the globe. Sports specialization patterns, which include year-round training, participation on multiple teams of the same sport, and focused participation in a single sport at a young age, are at high levels. The need for this type of early specialized training in young athletes is currently under debate. Evidence Acquisition: Nonsystematic review. Study Design: Clinical review. Level of Evidence: Level 4. Conclusion: Sports sp...

  3. Focusing horn

    CERN Multimedia

    1980-01-01

    This was the first magnetic horn developed by Simon Van der Meer to collect antiprotons in the AD complex. It was used for the AA (antiproton accumulator). Making an antiproton beam took a lot of time and effort. Firstly, protons were accelerated to an energy of 26 GeV/c (protons at 26GeV/c, antiprotons at 3.6GeV/c) in the PS and ejected onto a metal target. From the spray of emerging particles, a magnetic horn picked out 3.6 GeV antiprotons for injection into the AA through a wide-aperture focusing quadrupole magnet. For a million protons hitting the target, just one antiproton was captured, 'cooled' and accumulated. It took 3 days to make a beam of 3 x 10^11 -, three hundred thousand million - antiprotons. The development of this technology was a key step to the functioning of CERN's Super Proton Synchrotron as a proton - antiproton collider.

  4. Origin and evolution of the self-organizing cytoskeleton in the network of eukaryotic organelles.

    Science.gov (United States)

    Jékely, Gáspár

    2014-09-02

    The eukaryotic cytoskeleton evolved from prokaryotic cytomotive filaments. Prokaryotic filament systems show bewildering structural and dynamic complexity and, in many aspects, prefigure the self-organizing properties of the eukaryotic cytoskeleton. Here, the dynamic properties of the prokaryotic and eukaryotic cytoskeleton are compared, and how these relate to function and evolution of organellar networks is discussed. The evolution of new aspects of filament dynamics in eukaryotes, including severing and branching, and the advent of molecular motors converted the eukaryotic cytoskeleton into a self-organizing "active gel," the dynamics of which can only be described with computational models. Advances in modeling and comparative genomics hold promise of a better understanding of the evolution of the self-organizing cytoskeleton in early eukaryotes, and its role in the evolution of novel eukaryotic functions, such as amoeboid motility, mitosis, and ciliary swimming. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

  5. Pay your taxes where you add the value : how to avoid tax avoidance and abuse? An overview of measures taken and proposed with a special focus on developing countries

    NARCIS (Netherlands)

    Burgers, Irene; Bouwman, Jan; Schutte, Nico; van Herwaarden, A.J.

    2015-01-01

    This background paper shows: - why the OECD refers to a global ‘patchwork’ of domestic and anti-avoidance rules; - which measures the OECD in its BEPS Project recommends to address the mismatches and loopholes; and - to what extent the special needs of developing countries are recognized. Moreover

  6. Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens.

    Science.gov (United States)

    Greshake, Bastian; Zehr, Simonida; Dal Grande, Francesco; Meiser, Anjuli; Schmitt, Imke; Ebersberger, Ingo

    2016-03-01

    Whole-genome shotgun sequencing of multispecies communities using only a single library layout is commonly used to assess taxonomic and functional diversity of microbial assemblages. Here, we investigate to what extent such metagenome skimming approaches are applicable for in-depth genomic characterizations of eukaryotic communities, for example lichens. We address how to best assemble a particular eukaryotic metagenome skimming data, what pitfalls can occur, and what genome quality can be expected from these data. To facilitate a project-specific benchmarking, we introduce the concept of twin sets, simulated data resembling the outcome of a particular metagenome sequencing study. We show that the quality of genome reconstructions depends essentially on assembler choice. Individual tools, including the metagenome assemblers Omega and MetaVelvet, are surprisingly sensitive to low and uneven coverages. In combination with the routine of assembly parameter choice to optimize the assembly N50 size, these tools can preclude an entire genome from the assembly. In contrast, MIRA, an all-purpose overlap assembler, and SPAdes, a multisized de Bruijn graph assembler, facilitate a comprehensive view on the individual genomes across a wide range of coverage ratios. Testing assemblers on a real-world metagenome skimming data from the lichen Lasallia pustulata demonstrates the applicability of twin sets for guiding method selection. Furthermore, it reveals that the assembly outcome for the photobiont Trebouxia sp. falls behind the a priori expectation given the simulations. Although the underlying reasons remain still unclear, this highlights that further studies on this organism require special attention during sequence data generation and downstream analysis. © 2015 John Wiley & Sons Ltd.

  7. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  8. Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes

    Directory of Open Access Journals (Sweden)

    Reddy Anireddy SN

    2006-01-01

    Full Text Available Abstract Background Kinesins, a superfamily of molecular motors, use microtubules as tracks and transport diverse cellular cargoes. All kinesins contain a highly conserved ~350 amino acid motor domain. Previous analysis of the completed genome sequence of one flowering plant (Arabidopsis has resulted in identification of 61 kinesins. The recent completion of genome sequencing of several photosynthetic and non-photosynthetic eukaryotes that belong to divergent lineages offers a unique opportunity to conduct a comprehensive comparative analysis of kinesins in plant and non-plant systems and infer their evolutionary relationships. Results We used the kinesin motor domain to identify kinesins in the completed genome sequences of 19 species, including 13 newly sequenced genomes. Among the newly analyzed genomes, six represent photosynthetic eukaryotes. A total of 529 kinesins was used to perform comprehensive analysis of kinesins and to construct gene trees using the Bayesian and parsimony approaches. The previously recognized 14 families of kinesins are resolved as distinct lineages in our inferred gene tree. At least three of the 14 kinesin families are not represented in flowering plants. Chlamydomonas, a green alga that is part of the lineage that includes land plants, has at least nine of the 14 known kinesin families. Seven of ten families present in flowering plants are represented in Chlamydomonas, indicating that these families were retained in both the flowering-plant and green algae lineages. Conclusion The increase in the number of kinesins in flowering plants is due to vast expansion of the Kinesin-14 and Kinesin-7 families. The Kinesin-14 family, which typically contains a C-terminal motor, has many plant kinesins that have the motor domain at the N terminus, in the middle, or the C terminus. Several domains in kinesins are present exclusively either in plant or animal lineages. Addition of novel domains to kinesins in lineage

  9. Automatic generation of gene finders for eukaryotic species

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Krogh, A.

    2006-01-01

    Background The number of sequenced eukaryotic genomes is rapidly increasing. This means that over time it will be hard to keep supplying customised gene finders for each genome. This calls for procedures to automatically generate species-specific gene finders and to re-train them as the quantity...... length distributions. The performance of each individual gene predictor on each individual genome is comparable to the best of the manually optimised species-specific gene finders. It is shown that species-specific gene finders are superior to gene finders trained on other species....

  10. Rationales and Approaches for Studying Metabolism in Eukaryotic Microalgae

    Directory of Open Access Journals (Sweden)

    Daniel Veyel

    2014-04-01

    Full Text Available The generation of efficient production strains is essential for the use of eukaryotic microalgae for biofuel production. Systems biology approaches including metabolite profiling on promising microalgal strains, will provide a better understanding of their metabolic networks, which is crucial for metabolic engineering efforts. Chlamydomonas reinhardtii represents a suited model system for this purpose. We give an overview to genetically amenable microalgal strains with the potential for biofuel production and provide a critical review of currently used protocols for metabolite profiling on Chlamydomonas. We provide our own experimental data to underpin the validity of the conclusions drawn.

  11. Geminin: a major DNA replication safeguard in higher eukaryotes

    DEFF Research Database (Denmark)

    Melixetian, Marina; Helin, Kristian

    2004-01-01

    Eukaryotes have evolved multiple mechanisms to restrict DNA replication to once per cell cycle. These mechanisms prevent relicensing of origins of replication after initiation of DNA replication in S phase until the end of mitosis. Most of our knowledge of mechanisms controlling prereplication...... complex (preRC) formation are based on studies from yeast and Xenopus, while much less is known for mammalian cells. Here we discuss our recent data demonstrating that Geminin is required for preventing rereplication in human normal and cancer cells....

  12. DNA resection in eukaryotes: deciding how to fix the break.

    Science.gov (United States)

    Huertas, Pablo

    2010-01-01

    DNA double-strand breaks are repaired by different mechanisms, including homologous recombination and nonhomologous end-joining. DNA-end resection, the first step in recombination, is a key step that contributes to the choice of DSB repair. Resection, an evolutionarily conserved process that generates single-stranded DNA, is linked to checkpoint activation and is critical for survival. Failure to regulate and execute this process results in defective recombination and can contribute to human disease. Here I review recent findings on the mechanisms of resection in eukaryotes, from yeast to vertebrates, provide insights into the regulatory strategies that control it, and highlight the consequences of both its impairment and its deregulation.

  13. Synthesis, delivery and regulation of eukaryotic heme and Fe-S cluster cofactors.

    Science.gov (United States)

    Barupala, Dulmini P; Dzul, Stephen P; Riggs-Gelasco, Pamela Jo; Stemmler, Timothy L

    2016-02-15

    In humans, the bulk of iron in the body (over 75%) is directed towards heme- or Fe-S cluster cofactor synthesis, and the complex, highly regulated pathways in place to accomplish biosynthesis have evolved to safely assemble and load these cofactors into apoprotein partners. In eukaryotes, heme biosynthesis is both initiated and finalized within the mitochondria, while cellular Fe-S cluster assembly is controlled by correlated pathways both within the mitochondria and within the cytosol. Iron plays a vital role in a wide array of metabolic processes and defects in iron cofactor assembly leads to human diseases. This review describes progress towards our molecular-level understanding of cellular heme and Fe-S cluster biosynthesis, focusing on the regulation and mechanistic details that are essential for understanding human disorders related to the breakdown in these essential pathways. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Special Weapons

    Data.gov (United States)

    Federal Laboratory Consortium — Supporting Navy special weapons, the division provides an array of engineering services, technical publication support services, logistics support services, safety...

  15. Pay your taxes where you add the value: how to avoid tax avoidance and abuse? An overview of measures taken and proposed with a special focus on developing countries

    OpenAIRE

    Burgers, Irene; Bouwman, Jan; Schutte, Nico; van Herwaarden, A.J.

    2015-01-01

    This background paper shows: - why the OECD refers to a global ‘patchwork’ of domestic and anti-avoidance rules; - which measures the OECD in its BEPS Project recommends to address the mismatches and loopholes; and - to what extent the special needs of developing countries are recognized. Moreover some suggestions not included in the BEPS Reports on how developing countries might tackle tax abuse are made.

  16. A possible mechanism for exonuclease 1-independent eukaryotic mismatch repair

    Science.gov (United States)

    Kadyrov, Farid A.; Genschel, Jochen; Fang, Yanan; Penland, Elisabeth; Edelmann, Winfried; Modrich, Paul

    2009-01-01

    Mismatch repair contributes to genetic stability, and inactivation of the mammalian pathway leads to tumor development. Mismatch correction occurs by an excision-repair mechanism and has been shown to depend on the 5′ to 3′ hydrolytic activity exonuclease 1 (Exo1) in eukaryotic cells. However, genetic and biochemical studies have indicated that one or more Exo1-independent modes of mismatch repair also exist. We have analyzed repair of nicked circular heteroduplex DNA in extracts of Exo1-deficient mouse embryo fibroblast cells. Exo1-independent repair under these conditions is MutLα-dependent and requires functional integrity of the MutLα endonuclease metal-binding motif. In contrast to the Exo1-dependent reaction, we have been unable to detect a gapped excision intermediate in Exo1-deficient extracts when repair DNA synthesis is blocked. A possible explanation for this finding has been provided by analysis of a purified system comprised of MutSα, MutLα, replication factor C, proliferating cell nuclear antigen, replication protein A, and DNA polymerase δ that supports Exo1-independent repair in vitro. Repair in this system depends on MutLα incision of the nicked heteroduplex strand and dNTP-dependent synthesis-driven displacement of a DNA segment spanning the mismatch. Such a mechanism may account, at least in part, for the Exo1-independent repair that occurs in eukaryotic cells, and hence the modest cancer predisposition of Exo1-deficient mammalian cells. PMID:19420220

  17. Generic eukaryotic core promoter prediction using structural features of DNA.

    Science.gov (United States)

    Abeel, Thomas; Saeys, Yvan; Bonnet, Eric; Rouzé, Pierre; Van de Peer, Yves

    2008-02-01

    Despite many recent efforts, in silico identification of promoter regions is still in its infancy. However, the accurate identification and delineation of promoter regions is important for several reasons, such as improving genome annotation and devising experiments to study and understand transcriptional regulation. Current methods to identify the core region of promoters require large amounts of high-quality training data and often behave like black box models that output predictions that are difficult to interpret. Here, we present a novel approach for predicting promoters in whole-genome sequences by using large-scale structural properties of DNA. Our technique requires no training, is applicable to many eukaryotic genomes, and performs extremely well in comparison with the best available promoter prediction programs. Moreover, it is fast, simple in design, and has no size constraints, and the results are easily interpretable. We compared our approach with 14 current state-of-the-art implementations using human gene and transcription start site data and analyzed the ENCODE region in more detail. We also validated our method on 12 additional eukaryotic genomes, including vertebrates, invertebrates, plants, fungi, and protists.

  18. Characterization of an eukaryotic peptide deformylase from Plasmodium falciparum.

    Science.gov (United States)

    Bracchi-Ricard, V; Nguyen, K T; Zhou, Y; Rajagopalan, P T; Chakrabarti, D; Pei, D

    2001-12-15

    Ribosomal protein synthesis in eubacteria and eukaryotic organelles initiates with an N-formylmethionyl-tRNA(i), resulting in N-terminal formylation of all nascent polypeptides. Peptide deformylase (PDF) catalyzes the subsequent removal of the N-terminal formyl group from the majority of bacterial proteins. Until recently, PDF has been thought as an enzyme unique to the bacterial kingdom. Searches of the genomic DNA databases identified several genes that encode proteins of high sequence homology to bacterial PDF from eukaryotic organisms. The cDNA encoding Plasmodium falciparum PDF (PfPDF) has been cloned and overexpressed in Escherichia coli. The recombinant protein is catalytically active in deformylating N-formylated peptides, shares many of the properties of bacterial PDF, and is inhibited by specific PDF inhibitors. Western blot analysis indicated expression of mature PfPDF in trophozoite, schizont, and segmenter stages of intraerythrocytic development. These results provide strong evidence that a functional PDF is present in P. falciparum. In addition, PDF inhibitors inhibited the growth of P. falciparum in the intraerythrocytic culture. (c)2001 Elsevier Science.

  19. Eukaryotic Replisome Components Cooperate to Process Histones During Chromosome Replication

    Directory of Open Access Journals (Sweden)

    Magdalena Foltman

    2013-03-01

    Full Text Available DNA unwinding at eukaryotic replication forks displaces parental histones, which must be redeposited onto nascent DNA in order to preserve chromatin structure. By screening systematically for replisome components that pick up histones released from chromatin into a yeast cell extract, we found that the Mcm2 helicase subunit binds histones cooperatively with the FACT (facilitiates chromatin transcription complex, which helps to re-establish chromatin during transcription. FACT does not associate with the Mcm2-7 helicase at replication origins during G1 phase but is subsequently incorporated into the replisome progression complex independently of histone binding and uniquely among histone chaperones. The amino terminal tail of Mcm2 binds histones via a conserved motif that is dispensable for DNA synthesis per se but helps preserve subtelomeric chromatin, retain the 2 micron minichromosome, and support growth in the absence of Ctf18-RFC. Our data indicate that the eukaryotic replication and transcription machineries use analogous assemblies of multiple chaperones to preserve chromatin integrity.

  20. In silico ionomics segregates parasitic from free-living eukaryotes.

    Science.gov (United States)

    Greganova, Eva; Steinmann, Michael; Mäser, Pascal; Fankhauser, Niklaus

    2013-01-01

    Ion transporters are fundamental to life. Due to their ancient origin and conservation in sequence, ion transporters are also particularly well suited for comparative genomics of distantly related species. Here, we perform genome-wide ion transporter profiling as a basis for comparative genomics of eukaryotes. From a given predicted proteome, we identify all bona fide ion channels, ion porters, and ion pumps. Concentrating on unicellular eukaryotes (n = 37), we demonstrate that clustering of species according to their repertoire of ion transporters segregates obligate endoparasites (n = 23) on the one hand, from free-living species and facultative parasites (n = 14) on the other hand. This surprising finding indicates strong convergent evolution of the parasites regarding the acquisition and homeostasis of inorganic ions. Random forest classification identifies transporters of ammonia, plus transporters of iron and other transition metals, as the most informative for distinguishing the obligate parasites. Thus, in silico ionomics further underscores the importance of iron in infection biology and suggests access to host sources of nitrogen and transition metals to be selective forces in the evolution of parasitism. This finding is in agreement with the phenomenon of iron withholding as a primordial antimicrobial strategy of infected mammals.

  1. Marine biofilm bacteria evade eukaryotic predation by targeted chemical defense.

    Directory of Open Access Journals (Sweden)

    Carsten Matz

    Full Text Available Many plants and animals are defended from predation or herbivory by inhibitory secondary metabolites, which in the marine environment are very common among sessile organisms. Among bacteria, where there is the greatest metabolic potential, little is known about chemical defenses against bacterivorous consumers. An emerging hypothesis is that sessile bacterial communities organized as biofilms serve as bacterial refuge from predation. By testing growth and survival of two common bacterivorous nanoflagellates, we find evidence that chemically mediated resistance against protozoan predators is common among biofilm populations in a diverse set of marine bacteria. Using bioassay-guided chemical and genetic analysis, we identified one of the most effective antiprotozoal compounds as violacein, an alkaloid that we demonstrate is produced predominately within biofilm cells. Nanomolar concentrations of violacein inhibit protozoan feeding by inducing a conserved eukaryotic cell death program. Such biofilm-specific chemical defenses could contribute to the successful persistence of biofilm bacteria in various environments and provide the ecological and evolutionary context for a number of eukaryote-targeting bacterial metabolites.

  2. Specialized science.

    Science.gov (United States)

    Casadevall, Arturo; Fang, Ferric C

    2014-04-01

    As the body of scientific knowledge in a discipline increases, there is pressure for specialization. Fields spawn subfields that then become entities in themselves that promote further specialization. The process by which scientists join specialized groups has remarkable similarities to the guild system of the middle ages. The advantages of specialization of science include efficiency, the establishment of normative standards, and the potential for greater rigor in experimental research. However, specialization also carries risks of monopoly, monotony, and isolation. The current tendency to judge scientific work by the impact factor of the journal in which it is published may have roots in overspecialization, as scientists are less able to critically evaluate work outside their field than before. Scientists in particular define themselves through group identity and adopt practices that conform to the expectations and dynamics of such groups. As part of our continuing analysis of issues confronting contemporary science, we analyze the emergence and consequences of specialization in science, with a particular emphasis on microbiology, a field highly vulnerable to balkanization along microbial phylogenetic boundaries, and suggest that specialization carries significant costs. We propose measures to mitigate the detrimental effects of scientific specialism.

  3. Special geometry

    International Nuclear Information System (INIS)

    Strominger, A.

    1990-01-01

    A special manifold is an allowed target manifold for the vector multiplets of D=4, N=2 supergravity. These manifolds are of interest for string theory because the moduli spaces of Calabi-Yau threefolds and c=9, (2,2) conformal field theories are special. Previous work has given a local, coordinate-dependent characterization of special geometry. A global description of special geometries is given herein, and their properties are studied. A special manifold M of complex dimension n is characterized by the existence of a holomorphic Sp(2n+2,R)xGL(1,C) vector bundle over M with a nowhere-vanishing holomorphic section Ω. The Kaehler potential on M is the logarithm of the Sp(2n+2,R) invariant norm of Ω. (orig.)

  4. Sport Specialization, Part I

    Science.gov (United States)

    Myer, Gregory D.; Jayanthi, Neeru; Difiori, John P.; Faigenbaum, Avery D.; Kiefer, Adam W.; Logerstedt, David; Micheli, Lyle J.

    2015-01-01

    Context: There is increased growth in sports participation across the globe. Sports specialization patterns, which include year-round training, participation on multiple teams of the same sport, and focused participation in a single sport at a young age, are at high levels. The need for this type of early specialized training in young athletes is currently under debate. Evidence Acquisition: Nonsystematic review. Study Design: Clinical review. Level of Evidence: Level 4. Conclusion: Sports specialization is defined as year-round training (greater than 8 months per year), choosing a single main sport, and/or quitting all other sports to focus on 1 sport. Specialized training in young athletes has risks of injury and burnout, while the degree of specialization is positively correlated with increased serious overuse injury risk. Risk factors for injury in young athletes who specialize in a single sport include year-round single-sport training, participation in more competition, decreased age-appropriate play, and involvement in individual sports that require the early development of technical skills. Adults involved in instruction of youth sports may also put young athletes at risk for injury by encouraging increased intensity in organized practices and competition rather than self-directed unstructured free play. Strength-of-Recommendation Taxonomy (SORT): C. PMID:26502420

  5. A jurisprudential analysis of the renewable energy law in Spain with a special focus of the European development; Rechtswissenschaftliche Analyse des Rechts der Erneuerbaren Energien in Spanien unter besonderer Beruecksichtigung der europarechtlichen Entwicklung. Zusammenfassung der Ergebnisse des Vorhabens

    Energy Technology Data Exchange (ETDEWEB)

    Pause, Fabian

    2011-07-01

    The contribution under consideration summarizes the results of the project 'Jurisprudential analysis of the renewable energy law in Spain with special reference to European legal history'. This project was promoted by the Federal Ministry for the Environment, Nature Conservation and Nuclear Safety (Berlin, Federal Republic of Germany).This contribution covers the law of power generation and heat production from renewable energies in Spain in detail. A comparative analysis of certain aspects of law shall supply findings for the scientific assessment of the German law. The development of the legal framework at the level of municipalities is considered.

  6. Editorial Special Issue: Neuronus

    NARCIS (Netherlands)

    van der Lubbe, Robert Henricus Johannes; Kuniecki, Michal

    2016-01-01

    This special issue of the 12th volume of Advances in Cognitive Psychology is devoted to the Neuronus conference that took place in Kraków in 2015. In this editorial letter, we will focus on a selection of the materials and some follow-up research that was presented during this conference. We will

  7. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees.

    Science.gov (United States)

    Llorens, Carlos; Muñoz-Pomer, Alfonso; Bernad, Lucia; Botella, Hector; Moya, Andrés

    2009-11-02

    Sequencing projects have allowed diverse retroviruses and LTR retrotransposons from different eukaryotic organisms to be characterized. It is known that retroviruses and other retro-transcribing viruses evolve from LTR retrotransposons and that this whole system clusters into five families: Ty3/Gypsy, Retroviridae, Ty1/Copia, Bel/Pao and Caulimoviridae. Phylogenetic analyses usually show that these split into multiple distinct lineages but what is yet to be understood is how deep evolution occurred in this system. We combined phylogenetic and graph analyses to investigate the history of LTR retroelements both as a tree and as a network. We used 268 non-redundant LTR retroelements, many of them introduced for the first time in this work, to elucidate all possible LTR retroelement phylogenetic patterns. These were superimposed over the tree of eukaryotes to investigate the dynamics of the system, at distinct evolutionary times. Next, we investigated phenotypic features such as duplication and variability of amino acid motifs, and several differences in genomic ORF organization. Using this information we characterized eight reticulate evolution markers to construct phenotypic network models. The evolutionary history of LTR retroelements can be traced as a time-evolving network that depends on phylogenetic patterns, epigenetic host-factors and phenotypic plasticity. The Ty1/Copia and the Ty3/Gypsy families represent the oldest patterns in this network that we found mimics eukaryotic macroevolution. The emergence of the Bel/Pao, Retroviridae and Caulimoviridae families in this network can be related with distinct inflations of the Ty3/Gypsy family, at distinct evolutionary times. This suggests that Ty3/Gypsy ancestors diversified much more than their Ty1/Copia counterparts, at distinct geological eras. Consistent with the principle of preferential attachment, the connectivities among phenotypic markers, taken as network-represented combinations, are power

  8. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

    Directory of Open Access Journals (Sweden)

    Bernad Lucia

    2009-11-01

    Full Text Available Abstract Background Sequencing projects have allowed diverse retroviruses and LTR retrotransposons from different eukaryotic organisms to be characterized. It is known that retroviruses and other retro-transcribing viruses evolve from LTR retrotransposons and that this whole system clusters into five families: Ty3/Gypsy, Retroviridae, Ty1/Copia, Bel/Pao and Caulimoviridae. Phylogenetic analyses usually show that these split into multiple distinct lineages but what is yet to be understood is how deep evolution occurred in this system. Results We combined phylogenetic and graph analyses to investigate the history of LTR retroelements both as a tree and as a network. We used 268 non-redundant LTR retroelements, many of them introduced for the first time in this work, to elucidate all possible LTR retroelement phylogenetic patterns. These were superimposed over the tree of eukaryotes to investigate the dynamics of the system, at distinct evolutionary times. Next, we investigated phenotypic features such as duplication and variability of amino acid motifs, and several differences in genomic ORF organization. Using this information we characterized eight reticulate evolution markers to construct phenotypic network models. Conclusion The evolutionary history of LTR retroelements can be traced as a time-evolving network that depends on phylogenetic patterns, epigenetic host-factors and phenotypic plasticity. The Ty1/Copia and the Ty3/Gypsy families represent the oldest patterns in this network that we found mimics eukaryotic macroevolution. The emergence of the Bel/Pao, Retroviridae and Caulimoviridae families in this network can be related with distinct inflations of the Ty3/Gypsy family, at distinct evolutionary times. This suggests that Ty3/Gypsy ancestors diversified much more than their Ty1/Copia counterparts, at distinct geological eras. Consistent with the principle of preferential attachment, the connectivities among phenotypic markers, taken as

  9. Biological processing of dinuclear ruthenium complexes in eukaryotic cells.

    Science.gov (United States)

    Li, Xin; Heimann, Kirsten; Dinh, Xuyen Thi; Keene, F Richard; Collins, J Grant

    2016-10-20

    The biological processing - mechanism of cellular uptake, effects on the cytoplasmic and mitochondrial membranes, intracellular sites of localisation and induction of reactive oxygen species - of two dinuclear polypyridylruthenium(ii) complexes has been examined in three eukaryotic cells lines. Flow cytometry was used to determine the uptake of [{Ru(phen)2}2{μ-bb12}](4+) (Rubb12) and [Ru(phen)2(μ-bb7)Ru(tpy)Cl](3+) {Rubb7-Cl, where phen = 1,10-phenanthroline, tpy = 2,2':6',2''-terpyridine and bbn = bis[4(4'-methyl-2,2'-bipyridyl)]-1,n-alkane} in baby hamster kidney (BHK), human embryonic kidney (HEK-293) and liver carcinoma (HepG2) cell lines. The results demonstrated that the major uptake mechanism for Rubb12 and Rubb7-Cl was active transport, although with a significant contribution from carrier-assisted diffusion for Rubb12 and passive diffusion for Rubb7-Cl. Flow cytometry coupled with Annexin V/TO-PRO-3 double-staining was used to compare cell death by membrane damage or apoptosis. Rubb12 induced significant direct membrane damage, particularly with HepG2 cells, while Rubb7-Cl caused considerably less membrane damage but induced greater levels of apoptosis. Confocal microscopy, coupled with JC-1 assays, demonstrated that Rubb12 depolarises the mitochondrial membrane, whereas Rubb7-Cl had a much smaller affect. Cellular localisation experiments indicated that Rubb12 did not accumulate in the mitochondria, whereas significant mitochondrial accumulation was observed for Rubb7-Cl. The effect of Rubb12 and Rubb7-Cl on intracellular superoxide dismutase activity showed that the ruthenium complexes could induce cell death via a reactive oxygen species-mediated pathway. The results of this study demonstrate that Rubb12 predominantly kills eukaryotic cells by damaging the cytoplasmic membrane. As this dinuclear ruthenium complex has been previously shown to exhibit greater toxicity towards bacteria than eukaryotic cells, the results of the present study suggest that

  10. Specialized languages

    DEFF Research Database (Denmark)

    Mousten, Birthe; Laursen, Anne Lise

    2016-01-01

    -disciplinarily, because they work with both derivative and contributory approaches. Derivative, because specialized language retrieves its philosophy of science as well as methods from both the natural sciences, social sciences and humanistic sciences. Contributory because language results support the communication...... science fields communicate their findings. With this article, we want to create awareness of the work in this special area of language studies and of the inherent cross-disciplinarity that makes LSP special compared to common-core language. An acknowledgement of the importance of this field both in terms...

  11. An Interactive Exercise To Learn Eukaryotic Cell Structure and Organelle Function.

    Science.gov (United States)

    Klionsky, Daniel J.; Tomashek, John J.

    1999-01-01

    Describes a cooperative, interactive problem-solving exercise for studying eukaryotic cell structure and function. Highlights the dynamic aspects of movement through the cell. Contains 15 references. (WRM)

  12. Special Delivery.

    Science.gov (United States)

    Zimmer, Phil

    1986-01-01

    Specialized publications such as "Opera News,""Gourmet," and "Forbes" can bring an institution's story to targeted audiences. The experiences of Chautauqua Institution are described. Some of the benefits of marketing articles to these publications are discussed. (MLW)

  13. Ancient photosynthetic eukaryote biofilms in an Atacama Desert coastal cave

    Science.gov (United States)

    Azua-Bustos, A.; Gonzalez-Silva, C.; Mancilla, R.A.; Salas, L.; Palma, R.E.; Wynne, J.J.; McKay, C.P.; Vicuna, R.

    2009-01-01

    Caves offer a stable and protected environment from harsh and changing outside prevailing conditions. Hence, they represent an interesting habitat for studying life in extreme environments. Here, we report the presence of a member of the ancient eukaryote red algae Cyanidium group in a coastal cave of the hyperarid Atacama Desert. This microorganism was found to form a seemingly monospecific biofilm growing under extremely low photon flux levels. Our work suggests that this species, Cyanidium sp. Atacama, is a new member of a recently proposed novel monophyletic lineage of mesophilic "cave" Cyanidium sp., distinct from the remaining three other lineages which are all thermo-acidophilic. The cave described in this work may represent an evolutionary island for life in the midst of the Atacama Desert. ?? Springer Science + Business Media, LLC 2009.

  14. Eukaryotic and prokaryotic microbial communities during microalgal biomass production.

    Science.gov (United States)

    Lakaniemi, Aino-Maija; Hulatt, Chris J; Wakeman, Kathryn D; Thomas, David N; Puhakka, Jaakko A

    2012-11-01

    Eukaryotic and bacterial communities were characterized and quantified in microalgal photobioreactor cultures of freshwater Chlorella vulgaris and marine Dunaliella tertiolecta. The microalgae exhibited good growth, whilst both cultures contained diverse bacterial communities. Both cultures included Proteobacteria and Bacteroidetes, while C. vulgaris cultures also contained Actinobacteria. The bacterial genera present in the cultures were different due to different growth medium salinities and possibly different extracellular products. Bacterial community profiles were relatively stable in D. tertiolecta cultures but not in C. vulgaris cultures likely due to presence of ciliates (Colpoda sp.) in the latter. The presence of ciliates did not, however, cause decrease in total number of C. vulgaris or bacteria during 14 days of cultivation. Quantitative PCR (qPCR) reliably showed relative microalgal and bacterial cell numbers in the batch cultures with stable microbial communities, but was not effective when bacterial communities varied. Raw culture samples were successfully used as qPCR templates. Copyright © 2012 Elsevier Ltd. All rights reserved.

  15. Pi sensing and signalling: from prokaryotic to eukaryotic cells.

    Science.gov (United States)

    Qi, Wanjun; Baldwin, Stephen A; Muench, Stephen P; Baker, Alison

    2016-06-15

    Phosphorus is one of the most important macronutrients and is indispensable for all organisms as a critical structural component as well as participating in intracellular signalling and energy metabolism. Sensing and signalling of phosphate (Pi) has been extensively studied and is well understood in single-cellular organisms like bacteria (Escherichia coli) and Saccharomyces cerevisiae In comparison, the mechanism of Pi regulation in plants is less well understood despite recent advances in this area. In most soils the available Pi limits crop yield, therefore a clearer understanding of the molecular basis underlying Pi sensing and signalling is of great importance for the development of plants with improved Pi use efficiency. This mini-review compares some of the main Pi regulation pathways in prokaryotic and eukaryotic cells and identifies similarities and differences among different organisms, as well as providing some insight into future research. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  16. A general strategy to construct small molecule biosensors in eukaryotes.

    Science.gov (United States)

    Feng, Justin; Jester, Benjamin W; Tinberg, Christine E; Mandell, Daniel J; Antunes, Mauricio S; Chari, Raj; Morey, Kevin J; Rios, Xavier; Medford, June I; Church, George M; Fields, Stanley; Baker, David

    2015-12-29

    Biosensors for small molecules can be used in applications that range from metabolic engineering to orthogonal control of transcription. Here, we produce biosensors based on a ligand-binding domain (LBD) by using a method that, in principle, can be applied to any target molecule. The LBD is fused to either a fluorescent protein or a transcriptional activator and is destabilized by mutation such that the fusion accumulates only in cells containing the target ligand. We illustrate the power of this method by developing biosensors for digoxin and progesterone. Addition of ligand to yeast, mammalian, or plant cells expressing a biosensor activates transcription with a dynamic range of up to ~100-fold. We use the biosensors to improve the biotransformation of pregnenolone to progesterone in yeast and to regulate CRISPR activity in mammalian cells. This work provides a general methodology to develop biosensors for a broad range of molecules in eukaryotes.

  17. Crystal structures of two eukaryotic nucleases involved in RNA metabolism

    DEFF Research Database (Denmark)

    Jonstrup, Anette Thyssen; Midtgaard, Søren Fuglsang; Van, Lan Bich

    specific transcripts. Here, we present the crystal structure of the S. pombe Pop2p protein to 1.4 Å resolution. The high resolution structure provides a clear picture of the active site architecture. Structural alignment of single nucleotides and poly(A)-oligonucleotides from earlier co-crystal structures...... form the 3'-end of mRNA, is normally the first and also rate-limiting step in cellular mRNA degradation and therefore a key process in the control of eukaryotic mRNA turnover. Since Ccr4p is believed to be the main deadenylase the precise role of Pop2p in the complex is less clear. Nevertheless, Pop2p...

  18. Saccharomyces cerevisiae: a versatile eukaryotic system in virology

    Directory of Open Access Journals (Sweden)

    Breinig Tanja

    2007-10-01

    Full Text Available Abstract The yeast Saccharomyces cerevisiae is a well-established model system for understanding fundamental cellular processes relevant to higher eukaryotic organisms. Less known is its value for virus research, an area in which Saccharomyces cerevisiae has proven to be very fruitful as well. The present review will discuss the main achievements of yeast-based studies in basic and applied virus research. These include the analysis of the function of individual proteins from important pathogenic viruses, the elucidation of key processes in viral replication through the development of systems that allow the replication of higher eukayotic viruses in yeast, and the use of yeast in antiviral drug development and vaccine production.

  19. Polarised asymmetric inheritance of accumulated protein damage in higher eukaryotes.

    Directory of Open Access Journals (Sweden)

    María A Rujano

    2006-12-01

    Full Text Available Disease-associated misfolded proteins or proteins damaged due to cellular stress are generally disposed via the cellular protein quality-control system. However, under saturating conditions, misfolded proteins will aggregate. In higher eukaryotes, these aggregates can be transported to accumulate in aggresomes at the microtubule organizing center. The fate of cells that contain aggresomes is currently unknown. Here we report that cells that have formed aggresomes can undergo normal mitosis. As a result, the aggregated proteins are asymmetrically distributed to one of the daughter cells, leaving the other daughter free of accumulated protein damage. Using both epithelial crypts of the small intestine of patients with a protein folding disease and Drosophila melanogaster neural precursor cells as models, we found that the inheritance of protein aggregates during mitosis occurs with a fixed polarity indicative of a mechanism to preserve the long-lived progeny.

  20. Eukaryotic and prokaryotic contributions to colonic hydrogen sulfide synthesis.

    Science.gov (United States)

    Flannigan, Kyle L; McCoy, Kathy D; Wallace, John L

    2011-07-01

    Hydrogen sulfide (H(2)S) is an important modulator of many aspects of digestive function, both in health and disease. Colonic tissue H(2)S synthesis increases markedly during injury and inflammation and appears to contribute to resolution. Some of the bacteria residing in the colon can also produce H(2)S. The extent to which bacterial H(2)S synthesis contributes to what is measured as colonic H(2)S synthesis is not clear. Using conventional and germ-free mice, we have delineated the eukaryotic vs. prokaryotic contributions to colonic H(2)S synthesis, both in healthy and colitic mice. Colonic tissue H(2)S production is entirely dependent on the presence of the cofactor pyridoxal 5'-phosphate (vitamin B(6)), while bacterial H(2)S synthesis appears to occur independent of this cofactor. As expected, approximately one-half of the H(2)S produced by feces is derived from eukaryotic cells. While colonic H(2)S synthesis is markedly increased when the tissue is inflamed, and, in proportion to the extent of inflammation, fecal H(2)S synthesis does not change and tissue granulocytes do not appear to be the source of the elevated H(2)S production. Rats fed a B vitamin-deficient diet for 6 wk exhibited significantly diminished colonic H(2)S synthesis, but fecal H(2)S synthesis was not different from that of rats on the control diet. Our results demonstrate that H(2)S production by colonic bacteria does not contribute significantly to what is measured as colonic tissue H(2)S production, using the acetate trapping assay system employed in this study.

  1. Eukaryotic Translation Initiation Factor eIFiso4G Is Required to Regulate Violaxanthin De-epoxidase Expression in Arabidopsis*

    Science.gov (United States)

    Chen, Zhong; Jolley, Blair; Caldwell, Christian; Gallie, Daniel R.

    2014-01-01

    The eukaryotic translation initiation factor (eIF) 4G is a scaffold protein that organizes the assembly of those initiation factors needed to recruit the 40 S ribosomal subunit to an mRNA. Plants, like many eukaryotes, express two eIF4G isoforms. eIFiso4G, one of the isoforms specific to plants, is unique among eukaryotic eIF4G proteins in that it is highly divergent and unusually small in size, raising the possibility of functional specialization. In this study, the role of eIFiso4G in plant growth was investigated using null mutants for the eIF4G isoforms in Arabidopsis. eIFiso4G loss of function mutants exhibited smaller cell, leaf, plant size, and biomass accumulation that correlated with its reduced photosynthetic activity, phenotypes not observed with the eIF4G loss of function mutant. Although no change in photorespiration or dark respiration was observed in the eIFiso4G loss of function mutant, a reduction in chlorophyll levels and an increase in the level of nonphotochemical quenching were observed. An increase in xanthophyll cycle activity and the generation of reactive oxygen species contributed to the qE and qI components of nonphotochemical quenching, respectively. An increase in the transcript and protein levels of violaxanthin de-epoxidase in the eIFiso4G loss of function mutant and an increase in its xanthophyll de-epoxidation state correlated with the higher qE associated with loss of eIFiso4G expression. These observations indicate that eIFiso4G expression is required to regulate violaxanthin de-epoxidase expression and to support photosynthetic activity. PMID:24706761

  2. Eukaryotic translation initiation factor eIFiso4G is required to regulate violaxanthin De-epoxidase expression in Arabidopsis.

    Science.gov (United States)

    Chen, Zhong; Jolley, Blair; Caldwell, Christian; Gallie, Daniel R

    2014-05-16

    The eukaryotic translation initiation factor (eIF) 4G is a scaffold protein that organizes the assembly of those initiation factors needed to recruit the 40 S ribosomal subunit to an mRNA. Plants, like many eukaryotes, express two eIF4G isoforms. eIFiso4G, one of the isoforms specific to plants, is unique among eukaryotic eIF4G proteins in that it is highly divergent and unusually small in size, raising the possibility of functional specialization. In this study, the role of eIFiso4G in plant growth was investigated using null mutants for the eIF4G isoforms in Arabidopsis. eIFiso4G loss of function mutants exhibited smaller cell, leaf, plant size, and biomass accumulation that correlated with its reduced photosynthetic activity, phenotypes not observed with the eIF4G loss of function mutant. Although no change in photorespiration or dark respiration was observed in the eIFiso4G loss of function mutant, a reduction in chlorophyll levels and an increase in the level of nonphotochemical quenching were observed. An increase in xanthophyll cycle activity and the generation of reactive oxygen species contributed to the qE and qI components of nonphotochemical quenching, respectively. An increase in the transcript and protein levels of violaxanthin de-epoxidase in the eIFiso4G loss of function mutant and an increase in its xanthophyll de-epoxidation state correlated with the higher qE associated with loss of eIFiso4G expression. These observations indicate that eIFiso4G expression is required to regulate violaxanthin de-epoxidase expression and to support photosynthetic activity. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Special Operations - Myths and facts

    DEFF Research Database (Denmark)

    Jensen, Lars H. Ehrensvärd

    The brief addresses some of the myths, which have induced an institutional resistance at the political and military decision levels against understanding and considering special operations as a valuable strategic tool in contemporary and future conflict prevention, crisis management, and conflict...... management. The brief gives a generic overview over what special operations factually are, thus focusing on developing a broader understanding of the usefulness of special operations in the strategy of a small state....

  4. Music Software for Special Needs.

    Science.gov (United States)

    McCord, Kimberly

    2001-01-01

    Discusses the use of computer software for students with special needs in the music classroom. Focuses on software programs that are appropriate for children with special needs such as: "Musicshop,""Band-in-a-Box,""Rock Rap'n Roll,""Music Mania,""Music Ace" and "Music Ace 2," and "Children's Songbook." (CMK)

  5. Eukaryotic community diversity and spatial variation during drinking water production (by seawater desalination) and distribution in a full-scale network

    KAUST Repository

    Belila, Abdelaziz

    2016-12-01

    results raise questions concerning the source of the major eukaryotic community in the network and the emergence of fungi as a dominant group in the drinking water distribution system suggests that these microorganisms need special attention.

  6. RNase MRP and the RNA processing cascade in the eukaryotic ancestor.

    Science.gov (United States)

    Woodhams, Michael D; Stadler, Peter F; Penny, David; Collins, Lesley J

    2007-02-08

    Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. An example is RNase MRP processing ribosomal RNA (rRNA) in ribosome biogenesis. One hypothesis is that this complexity was present early in eukaryotic evolution; an alternative is that an initial simpler network later gained complexity by gene duplication in lineages that led to animals, fungi and plants. Recently there has been a rapid increase in support for the complexity-early theory because the vast majority of these RNA-processing reactions are found throughout eukaryotes, and thus were likely to be present in the last common ancestor of living eukaryotes, herein called the Eukaryotic Ancestor. We present an overview of the RNA processing cascade in the Eukaryotic Ancestor and investigate in particular, RNase MRP which was previously thought to have evolved later in eukaryotes due to its apparent limited distribution in fungi and animals and plants. Recent publications, as well as our own genomic searches, find previously unknown RNase MRP RNAs, indicating that RNase MRP has a wide distribution in eukaryotes. Combining secondary structure and promoter region analysis of RNAs for RNase MRP, along with analysis of the target substrate (rRNA), allows us to discuss this distribution in the light of eukaryotic evolution. We conclude that RNase MRP can now be placed in the RNA-processing cascade of the Eukaryotic Ancestor, highlighting the complexity of RNA-processing in early eukaryotes. Promoter analyses of MRP-RNA suggest that regulation of the critical processes of rRNA cleavage can vary, showing that even these key cellular processes (for which we expect high conservation) show some species-specific variability. We present our consensus MRP-RNA secondary structure as a useful model for further searches.

  7. The Significance of Experiences of Nature for People with Parkinson’s Disease, with Special Focus on Freezing of Gait—The Necessity for a Biophilic Environment. A Multi-Method Single Subject Study

    Science.gov (United States)

    Ottosson, Johan; Lavesson, Lillian; Pinzke, Stefan; Grahn, Patrik

    2015-01-01

    Freezing of Gait (FOG) is a common condition in people with Parkinson’s disease (PD). FOG entails suddenly experiencing difficulties moving or feeling that one’s feet are as glued to the ground. It is triggered, e.g., when passing through doorways. Earlier studies suggest that being in natural environments affects FOG in a positive way. Five subjects were recruited to serve as five single subject cases. We used interviews, observations, questionnaires and collected gait pattern data with aid of an accelerometer. A special designed outdoor setting was used, where we investigated whether passing through hedge openings with or without built elements triggered FOG. We found that no one experienced a FOG reaction when they passed through hedge openings without built elements. However, FOG was triggered when a doorframe was inserted into a hedge opening, and/or when peripheral vision was blocked. We interpret the results such that the doorframe triggered a phobic reflex, causing a freezing reaction. Passing through hedge openings does not trigger FOG, which we interpret as a biophilic reaction. Our results, if repeated in future studies, may have significance to everyday lives of PD patients, who could get a simpler life by consciously prioritizing stays in natural surroundings. PMID:26132480

  8. Eelgrass Leaf Surface Microbiomes Are Locally Variable and Highly Correlated with Epibiotic Eukaryotes

    Directory of Open Access Journals (Sweden)

    Mia M. Bengtsson

    2017-07-01

    Full Text Available Eelgrass (Zostera marina is a marine foundation species essential for coastal ecosystem services around the northern hemisphere. Like all macroscopic organisms, it possesses a microbiome (here defined as an associated prokaryotic community which may play critical roles in modulating the interaction of eelgrass with its environment. For example, its leaf surface microbiome could inhibit or attract eukaryotic epibionts which may overgrow the eelgrass leading to reduced primary productivity and subsequent eelgrass meadow decline. We used amplicon sequencing of the 16S and 18S rRNA genes of prokaryotes and eukaryotes to assess the leaf surface microbiome (prokaryotes as well as eukaryotic epibionts in- and outside lagoons on the German Baltic Sea coast. Prokaryote microbiomes varied substantially both between sites inside lagoons and between open coastal and lagoon sites. Water depth, leaf area and biofilm chlorophyll a concentration explained a large amount of variation in both prokaryotic and eukaryotic community composition. The prokaryotic microbiome and eukaryotic epibiont communities were highly correlated, and network analysis revealed disproportionate co-occurrence between a limited number of eukaryotic taxa and several bacterial taxa. This suggests that eelgrass leaf surfaces are home to a mosaic of microbiomes of several epibiotic eukaryotes, in addition to the microbiome of the eelgrass itself. Our findings thereby underline that eukaryotic diversity should be taken into account in order to explain prokaryotic microbiome assembly and dynamics in aquatic environments.

  9. Heavy metal whole-cell biosensors using eukaryotic microorganisms: an updated critical review.

    Directory of Open Access Journals (Sweden)

    Juan-Carlos eGutierrez

    2015-02-01

    Full Text Available This review analyzes the advantages and disadvantages of using eukaryotic microorganisms to design whole-cell biosensors (WCBs for monitoring environmental heavy metal pollution in soil or aquatic habitats. Basic considerations for designing an eukaryotic WCB are also shown. A comparative analysis of the promoter genes used to design whole-cell biosensors is carried out, and the sensitivity and reproducibility of the main reporter genes used is also reviewed. Three main eukaryotic taxonomic groups are considered: yeasts, microalgae and ciliated protozoa. Models that have been widely analyzed as potential WCBs are the Saccharomyces cerevisiae model among yeasts, the Tetrahymena thermophila model for ciliates and Chlamydomonas model for microalgae. The advantages and disadvantages of each microbial group are discussed, and a ranking of sensitivity to the same type of metal pollutant from reported eukaryotic WCBs is also shown. General conclusions and possible future developments of eukaryotic WCBs are reported.

  10. On the Archaeal Origins of Eukaryotes and the Challenges of Inferring Phenotype from Genotype.

    Science.gov (United States)

    Dey, Gautam; Thattai, Mukund; Baum, Buzz

    2016-07-01

    If eukaryotes arose through a merger between archaea and bacteria, what did the first true eukaryotic cell look like? A major step toward an answer came with the discovery of Lokiarchaeum, an archaeon whose genome encodes small GTPases related to those used by eukaryotes to regulate membrane traffic. Although 'Loki' cells have yet to be seen, their existence has prompted the suggestion that the archaeal ancestor of eukaryotes engulfed the future mitochondrion by phagocytosis. We propose instead that the archaeal ancestor was a relatively simple cell, and that eukaryotic cellular organization arose as the result of a gradual transfer of bacterial genes and membranes driven by an ever-closer symbiotic partnership between a bacterium and an archaeon. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  11. On the age of eukaryotes: evaluating evidence from fossils and molecular clocks.

    Science.gov (United States)

    Eme, Laura; Sharpe, Susan C; Brown, Matthew W; Roger, Andrew J

    2014-08-01

    Our understanding of the phylogenetic relationships among eukaryotic lineages has improved dramatically over the few past decades thanks to the development of sophisticated phylogenetic methods and models of evolution, in combination with the increasing availability of sequence data for a variety of eukaryotic lineages. Concurrently, efforts have been made to infer the age of major evolutionary events along the tree of eukaryotes using fossil-calibrated molecular clock-based methods. Here, we review the progress and pitfalls in estimating the age of the last eukaryotic common ancestor (LECA) and major lineages. After reviewing previous attempts to date deep eukaryote divergences, we present the results of a Bayesian relaxed-molecular clock analysis of a large dataset (159 proteins, 85 taxa) using 19 fossil calibrations. We show that for major eukaryote groups estimated dates of divergence, as well as their credible intervals, are heavily influenced by the relaxed molecular clock models and methods used, and by the nature and treatment of fossil calibrations. Whereas the estimated age of LECA varied widely, ranging from 1007 (943-1102) Ma to 1898 (1655-2094) Ma, all analyses suggested that the eukaryotic supergroups subsequently diverged rapidly (i.e., within 300 Ma of LECA). The extreme variability of these and previously published analyses preclude definitive conclusions regarding the age of major eukaryote clades at this time. As more reliable fossil data on eukaryotes from the Proterozoic become available and improvements are made in relaxed molecular clock modeling, we may be able to date the age of extant eukaryotes more precisely. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

  12. Special Reports.

    Science.gov (United States)

    Young, Peter R.; And Others

    1994-01-01

    Includes six special reports: "Libraries and the National Information Infrastructure" (Peter R. Young and Jane Williams); "Library Cooperation and Networking" (JoAn Segal); "Mexican Information Resources in Electronic Format" (Shirley Ainsworth); "The International Role of U.S. Librarians" (Hannelore B.…

  13. Biofuels Special

    International Nuclear Information System (INIS)

    Osborne, J.; Adolf, S.; Cragg, C.; Smits, M.; Kanen, J.L.M.; Kemfert, C.; De Jong, R.; Schroeter, S.; Terzic, B.

    2009-01-01

    The EU has decided to push ahead with biofuels, deflecting criticism with stringent environmental safeguards. In a special section correspondents of the magazine take stock of the ups and downs of the biofuels business. As it turns out, national policies differ widely, leading to a very uneven playing field. Nevertheless, it appears that biofuels have reached the point of no return

  14. Principals' and Special Education Teachers' Perceptions of Special Education Teachers' Roles and Responsibilities

    Science.gov (United States)

    Mott, Japhia

    2013-01-01

    This explanatory mixed methods study focuses on the perceptions of principals and special education teachers about special education teachers' roles and responsibilities. An online survey was conducted with 11 principals and 41 special education teachers (Resource Specialists and Special Day Class teachers). Independent semi-structured interviews…

  15. The prokaryote-eukaryote dichotomy: meanings and mythology.

    Science.gov (United States)

    Sapp, Jan

    2005-06-01

    Drawing on documents both published and archival, this paper explains how the prokaryote-eukaryote dichotomy of the 1960s was constructed, the purposes it served, and what it implied in terms of classification and phylogeny. In doing so, I first show how the concept was attributed to Edouard Chatton and the context in which he introduced the terms. Following, I examine the context in which the terms were reintroduced into biology in 1962 by Roger Stanier and C. B. van Niel. I study the discourse over the subsequent decade to understand how the organizational dichotomy took on the form of a natural classification as the kingdom Monera or superkingdom Procaryotae. Stanier and van Niel admitted that, in regard to constructing a natural classification of bacteria, structural characteristics were no more useful than physiological properties. They repeatedly denied that bacterial phylogenetics was possible. I thus examine the great historical irony that the "prokaryote," in both its organizational and phylogenetic senses, was defined (negatively) on the basis of structure. Finally, we see how phylogenetic research based on 16S rRNA led by Carl Woese and his collaborators confronted the prokaryote concept while moving microbiology to the center of evolutionary biology.

  16. Eukaryotic LYR Proteins Interact with Mitochondrial Protein Complexes

    Directory of Open Access Journals (Sweden)

    Heike Angerer

    2015-02-01

    Full Text Available In eukaryotic cells, mitochondria host ancient essential bioenergetic and biosynthetic pathways. LYR (leucine/tyrosine/arginine motif proteins (LYRMs of the Complex1_LYR-like superfamily interact with protein complexes of bacterial origin. Many LYR proteins function as extra subunits (LYRM3 and LYRM6 or novel assembly factors (LYRM7, LYRM8, ACN9 and FMC1 of the oxidative phosphorylation (OXPHOS core complexes. Structural insights into complex I accessory subunits LYRM6 and LYRM3 have been provided by analyses of EM and X-ray structures of complex I from bovine and the yeast Yarrowia lipolytica, respectively. Combined structural and biochemical studies revealed that LYRM6 resides at the matrix arm close to the ubiquinone reduction site. For LYRM3, a position at the distal proton-pumping membrane arm facing the matrix space is suggested. Both LYRMs are supposed to anchor an acyl-carrier protein (ACPM independently to complex I. The function of this duplicated protein interaction of ACPM with respiratory complex I is still unknown. Analysis of protein-protein interaction screens, genetic analyses and predicted multi-domain LYRMs offer further clues on an interaction network and adaptor-like function of LYR proteins in mitochondria.

  17. The Superoxide Reductase from the Early Diverging Eukaryote Giardia Intestinalis

    International Nuclear Information System (INIS)

    Cabelli, D.E.; Testa, F.; Mastronicola, D.; Bordi, E.; Pucillo, L.P.; Sarti, P.; Saraiva, L.M.; Giuffre, A.; Teixeira, M.

    2011-01-01

    Unlike superoxide dismutases (SODs), superoxidereductases (SORs) eliminate superoxide anion (O 2 # sm b ullet# - ) not through its dismutation, but via reduction to hydrogen peroxide (H 2 O 2 ) in the presence of an electron donor. The microaerobic protist Giardia intestinalis, responsible for a common intestinal disease in humans, though lacking SOD and other canonical reactive oxygen species-detoxifying systems, is among the very few eukaryotes encoding a SOR yet identified. In this study, the recombinant SOR from Giardia (SOR Gi ) was purified and characterized by pulse radiolysis and stopped-flow spectrophotometry. The protein, isolated in the reduced state, after oxidation by superoxide or hexachloroiridate(IV), yields a resting species (T final ) with Fe 3+ ligated to glutamate or hydroxide depending on pH (apparent pK a = 8.7). Although showing negligible SOD activity, reduced SOR Gi reacts with O 2 # sm b ullet# - with a pH-independent second-order rate constant k 1 = 1.0 x 10 9 M -1 s -1 and yields the ferric-(hydro)peroxo intermediate T 1 ; this in turn rapidly decays to the T final state with pH-dependent rates, without populating other detectable intermediates. Immunoblotting assays show that SOR Gi is expressed in the disease-causing trophozoite of Giardia. We propose that the superoxide-scavenging activity of SOR in Giardia may promote the survival of this air-sensitive parasite in the fairly aerobic proximal human small intestine during infection.

  18. Searching for the role of protein phosphatases in eukaryotic microorganisms

    Directory of Open Access Journals (Sweden)

    da-Silva A.M.

    1999-01-01

    Full Text Available Preference for specific protein substrates together with differential sensitivity to activators and inhibitors has allowed classification of serine/threonine protein phosphatases (PPs into four major types designated types 1, 2A, 2B and 2C (PP1, PP2A, PP2B and PP2C, respectively. Comparison of sequences within their catalytic domains has indicated that PP1, PP2A and PP2B are members of the same gene family named PPP. On the other hand, the type 2C enzyme does not share sequence homology with the PPP members and thus represents another gene family, known as PPM. In this report we briefly summarize some of our studies about the role of serine/threonine phosphatases in growth and differentiation of three different eukaryotic models: Blastocladiella emersonii, Neurospora crassa and Dictyostelium discoideum. Our observations suggest that PP2C is the major phosphatase responsible for dephosphorylation of amidotransferase, an enzyme that controls cell wall synthesis during Blastocladiella emersonii zoospore germination. We also report the existence of a novel acid- and thermo-stable protein purified from Neurospora crassa mycelia, which specifically inhibits the PP1 activity of this fungus and mammals. Finally, we comment on our recent results demonstrating that Dictyostelium discoideum expresses a gene that codes for PP1, although this activity has never been demonstrated biochemically in this organism.

  19. Economic Analysis and Feasibility of Rainwater Harvesting Systems in Urban and Peri-Urban Environments: A Review of the Global Situation with a Special Focus on Australia and Kenya

    Directory of Open Access Journals (Sweden)

    Caleb Christian Amos

    2016-04-01

    Full Text Available Rainwater harvesting (RWH plays an important role in increasing water security for individuals and governments. The demand for tools to enable technical and economic analysis of RWH systems has led to a substantial body of research in the recent past. This paper focuses on the economic aspects of domestic RWH in urban and peri-urban environments. In this regard, key issues are identified and discussed including quality and quantity of harvested water, the water demand profile, the scale of installation, interest rates, the period of analysis, real estate value, and the water-energy-food nexus. Kenya and Australia are used as reference points having different economies and opposing RWH policies. It has been found that the previous studies on financial aspects of RWH systems often had conflicting results. Most of the economic analyses have ignored the full benefits that a RWH system can offer. In view of the varying and conflicting results, there is a need to standardize the methods of economic analysis of RWH systems.

  20. The elderly, the young and the pregnant traveler -- A retrospective data analysis from a large Swiss Travel Center with a special focus on malaria prophylaxis and yellow fever vaccination.

    Science.gov (United States)

    Jaeger, Veronika K; Tschudi, Nadine; Rüegg, Rolanda; Hatz, Christoph; Bühler, Silja

    2015-01-01

    Vulnerable individuals such as elderly, children/adolescents and pregnant/breastfeeding women increasingly travel overseas. We describe the travel and vaccination patterns of these groups at the largest Travel Clinic in Switzerland especially focusing on travel to yellow fever and malaria-endemic countries, and yellow fever vaccination (YFV) and malaria medications. An analysis of pre-travel visits between 2010 and 2012 at the Travel Clinic of the University of Zurich, was performed assessing differences between the elderly, young and middle-aged travelers as well as between pregnant/breastfeeding and other female travelers. Overall, the vulnerable groups did not differ from other travelers regarding their travel patterns. YFV was the most often administered vaccine to elderly travelers; half of them received it for the first time. More than 30% of children/adolescents received YFV, but no child below six months was vaccinated. 80% of young travelers and a similar percentage of pregnant women went to malaria-endemic regions. Twenty-five pregnant/breastfeeding women traveled to YF endemic areas. Travel patterns of vulnerable travelers are comparable to those of other travelers. In view of the limited data on malaria medications and precautions against YFV during pregnancy and at the extreme ages of life, giving travel advice to these groups is challenging. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Horizontal transfer of bacterial polyphosphate kinases to eukaryotes: implications for the ice age and land colonisation.

    Science.gov (United States)

    Whitehead, Michael P; Hooley, Paul; W Brown, Michael R

    2013-06-05

    Studies of online database(s) showed that convincing examples of eukaryote PPKs derived from bacteria type PPK1 and PPK2 enzymes are rare and currently confined to a few simple eukaryotes. These enzymes probably represent several separate horizontal transfer events. Retention of such sequences may be an advantage for tolerance to stresses such as desiccation or nutrient depletion for simple eukaryotes that lack more sophisticated adaptations available to multicellular organisms. We propose that the acquisition of encoding sequences for these enzymes by horizontal transfer enhanced the ability of early plants to colonise the land. The improved ability to sequester and release inorganic phosphate for carbon fixation by photosynthetic algae in the ocean may have accelerated or even triggered global glaciation events. There is some evidence for DNA sequences encoding PPKs in a wider range of eukaryotes, notably some invertebrates, though it is unclear that these represent functional genes.Polyphosphate (poly P) is found in all cells, carrying out a wide range of essential roles. Studied mainly in prokaryotes, the enzymes responsible for synthesis of poly P in eukaryotes (polyphosphate kinases PPKs) are not well understood. The best characterised enzyme from bacteria known to catalyse the formation of high molecular weight polyphosphate from ATP is PPK1 which shows some structural similarity to phospholipase D. A second bacterial PPK (PPK2) resembles thymidylate kinase. Recent reports have suggested a widespread distribution of these bacteria type enzymes in eukaryotes. On - line databases show evidence for the presence of genes encoding PPK1 in only a limited number of eukaryotes. These include the photosynthetic eukaryotes Ostreococcus tauri, O. lucimarinus, Porphyra yezoensis, Cyanidioschyzon merolae and the moss Physcomitrella patens, as well as the amoeboid symbiont Capsaspora owczarzaki and the non-photosynthetic eukaryotes Dictyostelium (3 species

  2. Editorial Special Issue: Neuronus

    Science.gov (United States)

    Van der Lubbe, Rob H. J.; Kuniecki, Michał

    2016-01-01

    This special issue of the 12th volume of Advances in Cognitive Psychology is devoted to the Neuronus conference that took place in Kraków in 2015. In this editorial letter, we will focus on a selection of the materials and some follow-up research that was presented during this conference. We will also briefly introduce the conference contributions that successfully passed an external reviewing process. PMID:28154611

  3. Specialization, outsourcing and wages

    DEFF Research Database (Denmark)

    Munch, Jakob Roland; Skaksen, Jan Rose

    2009-01-01

    This paper studies the impact of outsourcing on individual wages. In contrast to the standard approach in the literature, we focus on domestic outsourcing as well as foreign outsourcing. We argue that if outsourcing is associated with specialization gains arising from an increase in the division...... of labor, domestic outsourcing tends to increase wages for both unskilled and skilled labor. We use a panel data set of workers in Danish manufacturing industries to show that domestic and foreign outsourcing affect wages as predicted....

  4. The independent prokaryotic origins of eukaryotic fructose-1, 6-bisphosphatase and sedoheptulose-1, 7-bisphosphatase and the implications of their origins for the evolution of eukaryotic Calvin cycle

    Directory of Open Access Journals (Sweden)

    Jiang Yong-Hai

    2012-10-01

    Full Text Available Abstract Background In the Calvin cycle of eubacteria, the dephosphorylations of both fructose-1, 6-bisphosphate (FBP and sedoheptulose-1, 7-bisphosphate (SBP are catalyzed by the same bifunctional enzyme: fructose-1, 6-bisphosphatase/sedoheptulose-1, 7-bisphosphatase (F/SBPase, while in that of eukaryotic chloroplasts by two distinct enzymes: chloroplastic fructose-1, 6-bisphosphatase (FBPase and sedoheptulose-1, 7-bisphosphatase (SBPase, respectively. It was proposed that these two eukaryotic enzymes arose from the divergence of a common ancestral eubacterial bifunctional F/SBPase of mitochondrial origin. However, no specific affinity between SBPase and eubacterial FBPase or F/SBPase can be observed in the previous phylogenetic analyses, and it is hard to explain why SBPase and/or F/SBPase are/is absent from most extant nonphotosynthetic eukaryotes according to this scenario. Results Domain analysis indicated that eubacterial F/SBPase of two different resources contain distinct domains: proteobacterial F/SBPases contain typical FBPase domain, while cyanobacterial F/SBPases possess FBPase_glpX domain. Therefore, like prokaryotic FBPase, eubacterial F/SBPase can also be divided into two evolutionarily distant classes (Class I and II. Phylogenetic analysis based on a much larger taxonomic sampling than previous work revealed that all eukaryotic SBPase cluster together and form a close sister group to the clade of epsilon-proteobacterial Class I FBPase which are gluconeogenesis-specific enzymes, while all eukaryotic chloroplast FBPase group together with eukaryotic cytosolic FBPase and form another distinct clade which then groups with the Class I FBPase of diverse eubacteria. Motif analysis of these enzymes also supports these phylogenetic correlations. Conclusions There are two evolutionarily distant classes of eubacterial bifunctional F/SBPase. Eukaryotic FBPase and SBPase do not diverge from either of them but have two independent origins

  5. Special lecture

    International Nuclear Information System (INIS)

    Yoshikawa, H.

    1998-01-01

    In his special lecture, given at the Artsimovich-Kadomtsev Memorial Session of the 17th IAEA Fusion Energy Conference in Yokohama, October 1998, Prof. H. Yoshikawa stated that the fusion program had come to a crossroads. He was wondering whether the future would lead to cooperation between nations, striving to overcome the difficulties the world is confronted with, or if it would lead to despair

  6. Special offer

    CERN Multimedia

    Staff Association

    2010-01-01

    Special offer for members of the Staff Association and their families 10% reduction on all products in the SEPHORA shop (sells perfume, beauty products etc.) in Val Thoiry ALL YEAR ROUND. Plus 20% reduction during their “vente privée”* three or four times a year. Simply present your Staff Association membership card when you make your purchase. * next “vente privée” from 24th to 29th May 2010  

  7. Special offer

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    Staff Association

    2011-01-01

    SPECIAL OFFER FOR OUR MEMBERS Tarif unique Adulte/Enfant Entrée Zone terrestre 19 euros instead of 23 euros Entrée “Zone terrestre + aquatique” 24 euros instead of 31 euros Free for children under 3, with limited access to the attractions. Walibi Rhône-Alpes is open daily from 22 June to 31 August, and every week end from 3 September until 31 October. Closing of the “zone aquatique” 11 September.

  8. Quantitative prediction of shrimp disease incidence via the profiles of gut eukaryotic microbiota.

    Science.gov (United States)

    Xiong, Jinbo; Yu, Weina; Dai, Wenfang; Zhang, Jinjie; Qiu, Qiongfen; Ou, Changrong

    2018-04-01

    One common notion is emerging that gut eukaryotes are commensal or beneficial, rather than detrimental. To date, however, surprisingly few studies have been taken to discern the factors that govern the assembly of gut eukaryotes, despite growing interest in the dysbiosis of gut microbiota-disease relationship. Herein, we firstly explored how the gut eukaryotic microbiotas were assembled over shrimp postlarval to adult stages and a disease progression. The gut eukaryotic communities changed markedly as healthy shrimp aged, and converged toward an adult-microbiota configuration. However, the adult-like stability was distorted by disease exacerbation. A null model untangled that the deterministic processes that governed the gut eukaryotic assembly tended to be more important over healthy shrimp development, whereas this trend was inverted as the disease progressed. After ruling out the baseline of gut eukaryotes over shrimp ages, we identified disease-discriminatory taxa (species level afforded the highest accuracy of prediction) that characteristic of shrimp health status. The profiles of these taxa contributed an overall 92.4% accuracy in predicting shrimp health status. Notably, this model can accurately diagnose the onset of shrimp disease. Interspecies interaction analysis depicted how the disease-discriminatory taxa interacted with one another in sustaining shrimp health. Taken together, our findings offer novel insights into the underlying ecological processes that govern the assembly of gut eukaryotes over shrimp postlarval to adult stages and a disease progression. Intriguingly, the established model can quantitatively and accurately predict the incidences of shrimp disease.

  9. Repertory of eukaryotes (eukaryome) in the human gastrointestinal tract: taxonomy and detection methods.

    Science.gov (United States)

    Hamad, I; Raoult, D; Bittar, F

    2016-01-01

    Eukaryotes are an important component of the human gut, and their relationship with the human host varies from parasitic to commensal. Understanding the diversity of human intestinal eukaryotes has important significance for human health. In the past few decades, most of the multitudes of techniques that are involved in the diagnosis of the eukaryotic population in the human intestinal tract were confined to pathological and parasitological aspects that mainly rely on traditionally based methods. However, development of culture-independent molecular techniques comprised of direct DNA extraction from faeces followed by sequencing, offer new opportunities to estimate the occurrence of eukaryotes in the human gut by providing data on the entire eukaryotic community, particularly not-yet-cultured or fastidious organisms. Further broad surveys of the eukaryotic communities in the gut based on high throughput tools such as next generation sequencing might lead to uncovering the real diversity of these ubiquitous organisms in the human intestinal tract and discovering the unrecognized roles of these eukaryotes in modulating the host immune system and inducing changes in host gut physiology and ecosystem. © 2015 John Wiley & Sons Ltd.

  10. Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era.

    Science.gov (United States)

    Kollmar, Martin; Mühlhausen, Stefanie

    2017-09-04

    The last eukaryotic common ancestor already had an amazingly complex cell possessing genomic and cellular features such as spliceosomal introns, mitochondria, cilia-dependent motility, and a cytoskeleton together with several intracellular transport systems. In contrast to the microtubule-based dyneins and kinesins, the actin-filament associated myosins are considerably divergent in extant eukaryotes and a unifying picture of their evolution has not yet emerged. Here, we manually assembled and annotated 7852 myosins from 929 eukaryotes providing an unprecedented dense sequence and taxonomic sampling. For classification we complemented phylogenetic analyses with gene structure comparisons resulting in 79 distinct myosin classes. The intron pattern analysis and the taxonomic distribution of the classes suggest two myosins in the last eukaryotic common ancestor, a class-1 prototype and another myosin, which is most likely the ancestor of all other myosin classes. The sparse distribution of class-2 and class-4 myosins outside their major lineages contradicts their presence in the last eukaryotic common ancestor but instead strongly suggests early eukaryote-eukaryote horizontal gene transfer. By correlating the evolution of myosin diversity with the history of Earth we found that myosin innovation occurred in independent major "burst" events in the major eukaryotic lineages. Most myosin inventions happened in the Mesoproterozoic era. In the late Neoproterozoic era, a process of extensive independent myosin loss began simultaneously with further eukaryotic diversification. Since the Cambrian explosion, myosin repertoire expansion is driven by lineage- and species-specific gene and genome duplications leading to subfunctionalization and fine-tuning of myosin functions.

  11. MetWAMer: eukaryotic translation initiation site prediction

    Directory of Open Access Journals (Sweden)

    Brendel Volker

    2008-09-01

    Full Text Available Abstract Background Translation initiation site (TIS identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the MetWAMer package for TIS prediction in eukaryotic open reading frames of non-viral origin. MetWAMer can be used as a stand-alone, third-party tool for post-processing gene structure annotations generated by external computational programs and/or pipelines, or directly integrated into gene structure prediction software implementations. Results MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the k-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5'-complete coverage. Conclusion We demonstrate that improvements in statistically-based models for TIS prediction can be achieved by taking the class of each potential start-methionine into account pending certain testing conditions, and that our perceptron-based model is suitable for the TIS identification task. MetWAMer represents a well-documented, extensible, and freely available software system that can be readily re-trained for differing target applications and/or extended with existing and novel TIS prediction methods, to support further research efforts in this area.

  12. Structural and biomechanical basis of mitochondrial movement in eukaryotic cells

    Directory of Open Access Journals (Sweden)

    Wu M

    2013-10-01

    Full Text Available Min Wu,1 Aruna Kalyanasundaram,2 Jie Zhu1 1Laboratory of Biomechanics and Engineering, Institute of Biophysics, College of Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; 2College of Pharmacology, University of Illinois at Chicago, Chicago, IL, USA Abstract: Mitochondria serve as energy-producing organelles in eukaryotic cells. In addition to providing the energy supply for cells, the mitochondria are also involved in other processes, such as proliferation, differentiation, information transfer, and apoptosis, and play an important role in regulation of cell growth and the cell cycle. In order to achieve these functions, the mitochondria need to move to the corresponding location. Therefore, mitochondrial movement has a crucial role in normal physiologic activity, and any mitochondrial movement disorder will cause irreparable damage to the organism. For example, recent studies have shown that abnormal movement of the mitochondria is likely to be the reason for Charcot–Marie–Tooth disease, amyotrophic lateral sclerosis, Alzheimer's disease, Huntington's disease, Parkinson's disease, and schizophrenia. So, in the cell, especially in the particular polarized cell, the appropriate distribution of mitochondria is crucial to the function and survival of the cell. Mitochondrial movement is mainly associated with the cytoskeleton and related proteins. However, those components play different roles according to cell type. In this paper, we summarize the structural basis of mitochondrial movement, including microtubules, actin filaments, motor proteins, and adaptin, and review studies of the biomechanical mechanisms of mitochondrial movement in different types of cells. Keywords: mitochondrial movement, microtubules, actin filaments, motor proteins, adaptin

  13. The Superoxide Reductase from the Early Diverging Eukaryote Giardia Intestinalis

    Energy Technology Data Exchange (ETDEWEB)

    Cabelli, D.E.; Testa, F.; Mastronicola, D.; Bordi, E.; Pucillo, L.P.; Sarti, P.; Saraiva, L.M.; Giuffre, A.; Teixeira, M.

    2011-10-15

    Unlike superoxide dismutases (SODs), superoxidereductases (SORs) eliminate superoxide anion (O{sub 2}{sup {sm_bullet}-}) not through its dismutation, but via reduction to hydrogen peroxide (H{sub 2}O{sub 2}) in the presence of an electron donor. The microaerobic protist Giardia intestinalis, responsible for a common intestinal disease in humans, though lacking SOD and other canonical reactive oxygen species-detoxifying systems, is among the very few eukaryotes encoding a SOR yet identified. In this study, the recombinant SOR from Giardia (SOR{sub Gi}) was purified and characterized by pulse radiolysis and stopped-flow spectrophotometry. The protein, isolated in the reduced state, after oxidation by superoxide or hexachloroiridate(IV), yields a resting species (T{sub final}) with Fe{sup 3+} ligated to glutamate or hydroxide depending on pH (apparent pK{sub a} = 8.7). Although showing negligible SOD activity, reduced SOR{sub Gi} reacts with O{sub 2}{sup {sm_bullet}-} with a pH-independent second-order rate constant k{sub 1} = 1.0 x 10{sup 9} M{sup -1} s{sup -1} and yields the ferric-(hydro)peroxo intermediate T{sub 1}; this in turn rapidly decays to the T{sub final} state with pH-dependent rates, without populating other detectable intermediates. Immunoblotting assays show that SOR{sub Gi} is expressed in the disease-causing trophozoite of Giardia. We propose that the superoxide-scavenging activity of SOR in Giardia may promote the survival of this air-sensitive parasite in the fairly aerobic proximal human small intestine during infection.

  14. The Role of Eukaryotic and Prokaryotic ABC Transporter Family in Failure of Chemotherapy.

    Science.gov (United States)

    El-Awady, Raafat; Saleh, Ekram; Hashim, Amna; Soliman, Nehal; Dallah, Alaa; Elrasheed, Azza; Elakraa, Ghada

    2016-01-01

    Over the years chemotherapy failure has been a vital research topic as researchers have been striving to discover reasons behind it. The extensive studies carried out on chemotherapeutic agents confirm that resistance to chemotherapy is a major reason for treatment failure. "Resistance to chemotherapy," however, is a comprehensive phrase that refers to a variety of different mechanisms in which ATP-binding cassette (ABC) mediated efflux dominates. The ABC is one of the largest gene superfamily of transporters among both eukaryotes and prokaryotes; it represents a variety of genes that code for proteins, which perform countless functions, including drug efflux - a natural process that protects cells from foreign chemicals. Up to date, chemotherapy failure due to ABC drug efflux is an active research topic that continuously provides further evidence on multiple drug resistance (MDR), aiding scientists in tackling and overcoming this issue. This review focuses on drug resistance by ABC efflux transporters in human, viral, parasitic, fungal and bacterial cells and highlights the importance of the MDR permeability glycoprotein being the mutual ABC transporter among all studied organisms. Current developments and future directions to overcome this problem are also discussed.

  15. The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota.

    Science.gov (United States)

    Scanlan, Pauline D; Stensvold, Christen R; Rajilić-Stojanović, Mirjana; Heilig, Hans G H J; De Vos, Willem M; O'Toole, Paul W; Cotter, Paul D

    2014-10-01

    To date, the majority of research into the human gut microbiota has focused on the bacterial fraction of the community. Inevitably, this has resulted in a poor understanding of the diversity and functionality of other intestinal microorganisms in the human gut. One such nonbacterial member is the microbial eukaryote Blastocystis, which has been implicated in the aetiology of a range of different intestinal and extra-intestinal diseases. However, prevalence data from different studies are conflicting, and crucially, there is limited information on its incidence and diversity in healthy individuals. Here, we survey the prevalence, genetic diversity and temporal stability of Blastocystis in a group of healthy adults (n = 105) using a sensitive PCR assay. Blastocystis was present in 56% of our sample set, which is much higher than previously reported from an industrialised county (Ireland). Moreover, a diversity of different subtypes (species) were detected, and Blastocystis was present in a subset of individuals sampled over a period of time between 6 and 10 years, indicating that it is capable of long-term host colonisation. These results show that Blastocystis is a common and diverse member of the healthy gut microbiota, thereby extending our knowledge of the microbial ecology of the healthy human intestine. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  16. Mechanism of Diphtheria Toxin Catalytic Domain Delivery to the Eukaryotic Cell Cytosol and the Cellular Factors that Directly Participate in the Process

    Science.gov (United States)

    Murphy, John R.

    2011-01-01

    Research on diphtheria and anthrax toxins over the past three decades has culminated in a detailed understanding of their structure function relationships (e.g., catalytic (C), transmembrane (T), and receptor binding (R) domains), as well as the identification of their eukaryotic cell surface receptor, an understanding of the molecular events leading to the receptor-mediated internalization of the toxin into an endosomal compartment, and the pH triggered conformational changes required for pore formation in the vesicle membrane. Recently, a major research effort has been focused on the development of a detailed understanding of the molecular interactions between each of these toxins and eukaryotic cell factors that play an essential role in the efficient translocation of their respective catalytic domains through the trans-endosomal vesicle membrane pore and delivery into the cell cytosol. In this review, I shall focus on recent findings that have led to a more detailed understanding of the mechanism by which the diphtheria toxin catalytic domain is delivered to the eukaryotic cell cytosol. While much work remains, it is becoming increasingly clear that the entry process is facilitated by specific interactions with a number of cellular factors in an ordered sequential fashion. In addition, since diphtheria, anthrax lethal factor and anthrax edema factor all carry multiple coatomer I complex binding motifs and COPI complex has been shown to play an essential role in entry process, it is likely that the initial steps in catalytic domain entry of these divergent toxins follow a common mechanism. PMID:22069710

  17. Special offer

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    2011-01-01

    OFFRE SPECIALE POUR NOS MEMBRES Les vendredis 29 juillet, 5 et 12 août, Aquaparc fermera ses portes exceptionnellement à 22h00. Pour ces évènements, des tarifs défiant toute concurrence vous sont proposés. Au programme : Clown spécialiste de la sculpture de ballons de 16h00 à 21h00 Ambiance Salsa avec danseurs professionnel : Démonstration et Cours de Salsa. Les tarifs : Pour une entrée à partir de 15h00 : Enfant : CHF 22.- Adulte : CHF 26.-  

  18. Special offers

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    Are you a member of the Staff Association? Did you know that as a member you can benefit from the following special offers: BCGE (Banque Cantonale de Genève): personalized banking solutions with preferential conditions. TPG: reduced rates on annual transport passes for active and retired staff. Aquaparc: reduced ticket prices for children and adults at this Swiss waterpark in Le Bouveret. FNAC: 5% reduction on FNAC vouchers. For more information about all these offers, please consult our web site: http://association.web.cern.ch/association/en/OtherActivities/Offers.html

  19. Special Offers

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    Are you a member of the Staff Association? Did you know that as a member you can benefit from the following special offers: BCGE (Banque Cantonale de Genève): personalized banking solutions with preferential conditions. TPG: reduced rates on annual transport passes for active and retired staff. Aquaparc: reduced ticket prices for children and adults at this Swiss waterpark in Le Bouveret. Walibi: reduced prices for children and adults at this French attraction park in Les Avenières. FNAC: 5% reduction on FNAC vouchers. For more information about all these offers, please consult our web site: http://association.web.cern.ch/association/en/OtherActivities/Offers.html

  20. Special graphites

    International Nuclear Information System (INIS)

    Leveque, P.

    1964-01-01

    A large fraction of the work undertaken jointly by the Commissariat a l'Energie Atomique (CEA) and the Pechiney Company has been the improvement of the properties of nuclear pile graphite and the opening up of new fields of graphite application. New processes for the manufacture of carbons and special graphites have been developed: forged graphite, pyro-carbons, high density graphite agglomeration of graphite powders by cracking of natural gas, impervious graphites. The physical properties of these products and their reaction with various oxidising gases are described. The first irradiation results are also given. (authors) [fr

  1. Characterization of Greenbeard Genes Involved in Long-Distance Kind Discrimination in a Microbial Eukaryote.

    Science.gov (United States)

    Heller, Jens; Zhao, Jiuhai; Rosenfield, Gabriel; Kowbel, David J; Gladieux, Pierre; Glass, N Louise

    2016-04-01

    Microorganisms are capable of communication and cooperation to perform social activities. Cooperation can be enforced using kind discrimination mechanisms in which individuals preferentially help or punish others, depending on genetic relatedness only at certain loci. In the filamentous fungus Neurospora crassa, genetically identical asexual spores (germlings) communicate and fuse in a highly regulated process, which is associated with fitness benefits during colony establishment. Recognition and chemotropic interactions between isogenic germlings requires oscillation of the mitogen-activated protein kinase (MAPK) signal transduction protein complex (NRC-1, MEK-2, MAK-2, and the scaffold protein HAM-5) to specialized cell fusion structures termed conidial anastomosis tubes. Using a population of 110 wild N. crassa isolates, we investigated germling fusion between genetically unrelated individuals and discovered that chemotropic interactions are regulated by kind discrimination. Distinct communication groups were identified, in which germlings within one communication group interacted at high frequency, while germlings from different communication groups avoided each other. Bulk segregant analysis followed by whole genome resequencing identified three linked genes (doc-1, doc-2, and doc-3), which were associated with communication group phenotype. Alleles at doc-1, doc-2, and doc-3 fell into five haplotypes that showed transspecies polymorphism. Swapping doc-1 and doc-2 alleles from different communication group strains was necessary and sufficient to confer communication group affiliation. During chemotropic interactions, DOC-1 oscillated with MAK-2 to the tips of conidial anastomosis tubes, while DOC-2 was statically localized to the plasma membrane. Our data indicate that doc-1, doc-2, and doc-3 function as "greenbeard" genes, involved in mediating long-distance kind recognition that involves actively searching for one's own type, resulting in cooperation between

  2. A feature analysis of lower solubility proteins in three eukaryotic systems.

    Science.gov (United States)

    Albu, Razvan F; Chan, Gerard T; Zhu, Mang; Wong, Eric T C; Taghizadeh, Farnaz; Hu, Xiaoke; Mehran, Arya E; Johnson, James D; Gsponer, Jörg; Mayor, Thibault

    2015-04-06

    Because misfolded and damaged proteins can form potentially harmful aggregates, all living organisms have evolved a wide variety of quality control mechanisms. However, the timely clearance of aggregation-prone species may not always be achieved, potentially leading to the accumulation of low solubility proteins. At the same time, promiscuity, which can be a driving force for aggregation, is also important to the functionality of certain proteins which have a large number of interaction partners. Considerable efforts have been made towards characterizing why some proteins appear to be more aggregation-prone than others. In this study, we analyze the features of proteins which precipitate following centrifugation in unstressed yeast cells, human SH-SY5Y cells and mouse brain tissue. By normalizing for protein abundance, we devised an approach whereby lower solubility proteins are reliably identified. Our findings indicate that these tend to be longer, low abundance proteins, which contain fewer hydrophobic amino acids. Furthermore, low solubility proteins also contain more low complexity and disordered regions. Overall, we observed an increase in features that link low solubility proteins to functional aggregates. Our results indicate that lower solubility proteins from three biologically distinct model systems share several common traits, shedding light on potentially universal solubility determinants. We set up a novel approach to identify lower solubility proteins in unstressed cells by comparing precipitated proteins with those that remain soluble after centrifugation. By analyzing three eukaryotic model systems in parallel, we were able to identify traits which cross the species barrier, as well as species-specific characteristics. Notably, our analyses revealed a number of primary and secondary structural features that set apart lower solubility proteins, a number of which connected them to a greater potential for promiscuity. This article is part of a Special

  3. Phylogenetic analysis of P5 P-type ATPases, a eukaryotic lineage of secretory pathway pumps

    DEFF Research Database (Denmark)

    Møller, Annette; Asp, Torben; Holm, Preben Bach

    2008-01-01

    Eukaryotes encompass a remarkable variety of organisms and unresolved lineages. Different phylogenetic analyses have lead to conflicting conclusions as to the origin and associations between lineages and species. In this work, we investigated evolutionary relationship of a family of cation pumps...... exclusive for the secretory pathway of eukaryotes by combining the identification of lineage-specific genes with phylogenetic evolution of common genes. Sequences of P5 ATPases, which are regarded to be cation pumps in the endoplasmic reticulum (ER), were identified in all eukaryotic lineages but not in any...... far, while P5B ATPases appear to be lost in three eukaryotic lineages; excavates, entamoebas and land plants. A lineage-specific gene expansion of up to four different P5B ATPases is seen in animals....

  4. Bacterial and eukaryotic systems collide in the three Rs of Methanococcus.

    Science.gov (United States)

    Parker, Richard P; Walters, Alison D; Chong, James P J

    2011-01-01

    Methanococcus maripaludis S2 is a methanogenic archaeon with a well-developed genetic system. Its mesophilic nature offers a simple system in which to perform complementation using bacterial and eukaryotic genes. Although information-processing systems in archaea are generally more similar to those in eukaryotes than those in bacteria, the order Methanococcales has a unique complement of DNA replication proteins, with multiple MCM (minichromosome maintenance) proteins and no obvious originbinding protein. A search for homologues of recombination and repair proteins in M. maripaludis has revealed a mixture of bacterial, eukaryotic and some archaeal-specific homologues. Some repair pathways appear to be completely absent, but it is possible that archaeal-specific proteins could carry out these functions. The replication, recombination and repair systems in M. maripaludis are an interesting mixture of eukaryotic and bacterial homologues and could provide a system for uncovering novel interactions between proteins from different domains of life.

  5. Meeting Report: Minutes from EMBO: Ten Years of Comparative Genomics of Eukaryotic Microorganisms

    Czech Academy of Sciences Publication Activity Database

    Lukeš, Julius; López-García, P.; Louis, E.; Boekhout, T.

    2016-01-01

    Roč. 167, č. 3 (2016), s. 217-221 ISSN 1434-4610 Institutional support: RVO:60077344 Keywords : protist * eukaryotic microorganisms * genomics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.794, year: 2016

  6. Non-coding RNA regulation in pathogenic bacteria located inside eukaryotic cells

    NARCIS (Netherlands)

    Ortega, Alvaro D.; Quereda, Juan J; Pucciarelli, M Graciela; García-del Portillo, Francisco

    2014-01-01

    Intracellular bacterial pathogens have evolved distinct lifestyles inside eukaryotic cells. Some pathogens coexist with the infected cell in an obligate intracellular state, whereas others transit between the extracellular and intracellular environment. Adaptation to these intracellular lifestyles

  7. Internalization of a polysialic acid-binding Escherichia coli bacteriophage into eukaryotic neuroblastoma cells.

    Science.gov (United States)

    Lehti, Timo A; Pajunen, Maria I; Skog, Maria S; Finne, Jukka

    2017-12-04

    Eukaryotic organisms are continuously exposed to bacteriophages, which are efficient gene transfer agents in bacteria. However, bacteriophages are considered not to pass the eukaryotic cell membrane and enter nonphagocytic cells. Here we report the binding and penetration of Escherichia coli PK1A2 bacteriophage into live eukaryotic neuroblastoma cells in vitro. The phage interacts with cell surface polysialic acid, which shares structural similarity with the bacterial phage receptor. Using fluorescence and electron microscopy, we show that phages are internalized via the endolysosomal route and persist inside the human cells up to one day without affecting cell viability. Phage capsid integrity is lost in lysosomes, and the phage DNA is eventually degraded. We did not detect the entry of phage DNA into the nucleus; however, we speculate that this might occur as a rare event, and propose that this potential mechanism could explain prokaryote-eukaryote gene flow.

  8. Alternatives to vitamin B1 uptake revealed with discovery of riboswitches in multiple marine eukaryotic lineages

    OpenAIRE

    McRose, Darcy; Guo, Jian; Monier, Adam; Sudek, Sebastian; Wilken, Susanne; Yan, Shuangchun; Mock, Thomas; Archibald, John M; Begley, Tadhg P; Reyes-Prieto, Adrian; Worden, Alexandra Z

    2014-01-01

    Vitamin B1 (thiamine pyrophosphate, TPP) is essential to all life but scarce in ocean surface waters. In many bacteria and a few eukaryotic groups thiamine biosynthesis genes are controlled by metabolite-sensing mRNA-based gene regulators known as riboswitches. Using available genome sequences and transcriptomes generated from ecologically important marine phytoplankton, we identified 31 new eukaryotic riboswitches. These were found in alveolate, cryptophyte, haptophyte and rhizarian phytopla...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-12-10

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

  10. Eukaryotic beta-alanine synthases are functionally related but have a high degree of structural diversity

    DEFF Research Database (Denmark)

    Gojkovic, Zoran; Sandrini, Michael; Piskur, Jure

    2001-01-01

    activity was used to clone analogous genes from different eukaryotes. Putative PYD3 sequences from the yeast S. kluyveri, the slime mold Dictyostelium discoideum, and the fruit fly Drosophila melanogaster complemented the pyd3 defect. When the S. kluyveri PYD3 gene was expressed in S. cerevisiae, which has......-carbamyl-beta -alanine, but not by uracil. This wrork establishes S. kluyveri as a model organism for studying pyrimidine degradation and beta -alanine production in eukaryotes....

  11. Construction of sized eukaryotic cDNA libraries using low input of total environmental metatranscriptomic RNA.

    Science.gov (United States)

    Yadav, Rajiv Kumar; Barbi, Florian; Ziller, Antoine; Luis, Patricia; Marmeisse, Roland; Reddy, M Sudhakara; Fraissinet-Tachet, Laurence

    2014-09-03

    Construction of high quality cDNA libraries from the usually low amounts of eukaryotic mRNA extracted from environmental samples is essential in functional metatranscriptomics for the selection of functional, full-length genes encoding proteins of interest. Many of the inserts in libraries constructed by standard methods are represented by truncated cDNAs due to premature stoppage of reverse transcriptase activity and preferential cloning of short cDNAs. We report here a simple and cost effective technique for preparation of sized eukaryotic cDNA libraries from as low as three microgram of total soil RNA dominated by ribosomal and bacterial RNA. cDNAs synthesized by a template switching approach were size-fractionated by two dimensional agarose gel electrophoresis prior to PCR amplification and cloning. Effective size selection was demonstrated by PCR amplification of conserved gene families specific of each size class. Libraries of more than one million independent inserts whose sizes ranged between one and four kb were thus produced. Up to 80% of the insert sequences were homologous to eukaryotic gene sequences present in public databases. A simple and cost effective technique has been developed to construct sized eukaryotic cDNA libraries from environmental samples. This technique will facilitate expression cloning of environmental eukaryotic genes and contribute to a better understanding of basic biological and/or ecological processes carried out by eukaryotic microbial communities.

  12. Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes.

    Science.gov (United States)

    Liu, Huiquan; Fu, Yanping; Jiang, Daohong; Li, Guoqing; Xie, Jiatao; Cheng, Jiasen; Peng, Youliang; Ghabrial, Said A; Yi, Xianhong

    2010-11-01

    Horizontal gene transfer commonly occurs from cells to viruses but rarely occurs from viruses to their host cells, with the exception of retroviruses and some DNA viruses. However, extensive sequence similarity searches in public genome databases for various organisms showed that the capsid protein and RNA-dependent RNA polymerase genes from totiviruses and partitiviruses have widespread homologs in the nuclear genomes of eukaryotic organisms, including plants, arthropods, fungi, nematodes, and protozoa. PCR amplification and sequencing as well as comparative evidence of junction coverage between virus and host sequences support the conclusion that these viral homologs are real and occur in eukaryotic genomes. Sequence comparison and phylogenetic analysis suggest that these genes were likely transferred horizontally from viruses to eukaryotic genomes. Furthermore, we present evidence showing that some of the transferred genes are conserved and expressed in eukaryotic organisms and suggesting that these viral genes are also functional in the recipient genomes. Our findings imply that horizontal transfer of double-stranded RNA viral genes is widespread among eukaryotes and may give rise to functionally important new genes, thus entailing that RNA viruses may play significant roles in the evolution of eukaryotes.

  13. Why did eukaryotes evolve only once? Genetic and energetic aspects of conflict and conflict mediation.

    Science.gov (United States)

    Blackstone, Neil W

    2013-07-19

    According to multi-level theory, evolutionary transitions require mediating conflicts between lower-level units in favour of the higher-level unit. By this view, the origin of eukaryotes and the origin of multicellularity would seem largely equivalent. Yet, eukaryotes evolved only once in the history of life, whereas multicellular eukaryotes have evolved many times. Examining conflicts between evolutionary units and mechanisms that mediate these conflicts can illuminate these differences. Energy-converting endosymbionts that allow eukaryotes to transcend surface-to-volume constraints also can allocate energy into their own selfish replication. This principal conflict in the origin of eukaryotes can be mediated by genetic or energetic mechanisms. Genome transfer diminishes the heritable variation of the symbiont, but requires the de novo evolution of the protein-import apparatus and was opposed by selection for selfish symbionts. By contrast, metabolic signalling is a shared primitive feature of all cells. Redox state of the cytosol is an emergent feature that cannot be subverted by an individual symbiont. Hypothetical scenarios illustrate how metabolic regulation may have mediated the conflicts inherent at different stages in the origin of eukaryotes. Aspects of metabolic regulation may have subsequently been coopted from within-cell to between-cell pathways, allowing multicellularity to emerge repeatedly.

  14. Patterns of kinesin evolution reveal a complex ancestral eukaryote with a multifunctional cytoskeleton

    Directory of Open Access Journals (Sweden)

    Richards Thomas A

    2010-04-01

    Full Text Available Abstract Background The genesis of the eukaryotes was a pivotal event in evolution and was accompanied by the acquisition of numerous new cellular features including compartmentalization by cytoplasmic organelles, mitosis and meiosis, and ciliary motility. Essential for the development of these features was the tubulin cytoskeleton and associated motors. It is therefore possible to map ancient cell evolution by reconstructing the evolutionary history of motor proteins. Here, we have used the kinesin motor repertoire of 45 extant eukaryotes to infer the ancestral state of this superfamily in the last common eukaryotic ancestor (LCEA. Results We bioinformatically identified 1624 putative kinesin proteins, determined their protein domain architectures and calculated a comprehensive Bayesian phylogeny for the kinesin superfamily with statistical support. These data enabled us to define 51 anciently-derived kinesin paralogs (including three new kinesin families and 105 domain architectures. We then mapped these characters across eukaryotes, accounting for secondary loss within established eukaryotic groupings, and alternative tree topologies. Conclusions We show that a minimum of 11 kinesin families and 3 protein domain architectures were present in the LCEA. This demonstrates that the microtubule-based cytoskeleton of the LCEA was surprisingly highly developed in terms of kinesin motor types, but that domain architectures have been extensively modified during the diversification of the eukaryotes. Our analysis provides molecular evidence for the existence of several key cellular functions in the LCEA, and shows that a large proportion of motor family diversity and cellular complexity had already arisen in this ancient cell.

  15. Is memory for music special?

    Science.gov (United States)

    Schulkind, Matthew D

    2009-07-01

    Although psychologists since Hermann Ebbinghaus have studied memory, research in this area has focused on visual and verbal stimuli with little attention paid to music. This bias is surprising because of the ubiquity of music in human cultures across history as well as current cultural beliefs that memory for music is "special." This paper examines the question of whether memory for music is special by addressing two related questions: First, do cultural beliefs about the mnemonic power of music stand up to empirical test? Second, can theories designed to explain memory for non-musical stimuli be applied to musical stimuli? A review of the literature suggests that music is special in some circumstances but not others and that some theories designed to explain cognitive processing of linguistic stimuli apply reasonably well to musical stimuli. Thus, although the question of whether memory for music is special remains open, the unique structure of musical stimuli strongly suggests that memory for music is indeed special.

  16. Special Offers

    CERN Multimedia

    Association du personnel

    2011-01-01

    Are you a member of the Staff Association? Did you know that as a member you can benefit from the following special offers: BCGE (Banque Cantonale de Genève): personalized banking solutions with preferential conditions.     TPG: reduced rates on annual transport passes for active and retired staff.     Aquaparc: reduced ticket prices for children and adults at this Swiss waterpark in Le Bouveret.     Walibi: reduced prices for children and adults at this French attraction park in Les Avenières.       FNAC: 5% reduction on FNAC vouchers.       For more information about all these offers, please consult our web site: http://association.web.cern.ch/association/en/OtherActivities/Offers.html

  17. Special Offers

    CERN Multimedia

    Staff Association

    2011-01-01

    Are you a member of the Staff Association? Did you know that as a member you can benefit from the following special offers: BCGE (Banque Cantonale de Genève): personalized banking solutions with preferential conditions.     TPG: reduced rates on annual transport passes for all active and retired staff.     Aquaparc: reduced ticket prices for children and adults at this Swiss waterpark in Le Bouveret.     Walibi: reduced prices for children and adults at this French attraction park in Les Avenières.       FNAC: 5% reduction on FNAC vouchers.       For more information about all these offers, please consult our web site: http://association.web.cern.ch/association/en/OtherActivities/Offers.html

  18. Special convoy

    CERN Multimedia

    TS-IC Group

    2007-01-01

    A special wide-load convoy will affect traffic between Hall 180 (Meyrin site) and Point 1 (ATLAS) on Tuesday 29 May. The following measures will be in place: Partial closure of Route Arago and Route Einstein between 9.00 a.m. and 12 midday, depending on the rate at which the convoy advances. Closure of Route Einstein between 12 and 2.00 p.m. between Building 104 and Route Veksler (see diagram). Closure of Entrance B in both directions between 12 and 2.30 p.m. Please use Entrance A. For safety reasons, cyclists and pedestrians will not be allowed to ride or walk alongside the convoy. Please comply with the instructions given by the convoy officers. TS-IC Group (tel : 160319 - 163012)

  19. Special relativity

    International Nuclear Information System (INIS)

    French, A.P.

    1982-01-01

    This book is an introduction to special relativity theory. After a discussion of the limits of Newton's mechanics and the pecularities in the propagation of light the Lorentz transformation is introduced. Then the measurement of space and time intervals in the framework of relativity theory is considered. Thereafter the addition of velocities and acceleration are considered in this framework. Then relativistic kinematics of particle interactions are described. Then the four-dimensional calculus in space-time coordinates is introduced. Finally an introduction is given to the treatment of the electromagnetic field in the framework of relativity theory. Every chapter contains exercise problems with solutions. This book is suited for all students who want to get some fundamental knowledge about relativity theory. (HSI) [de

  20. Growth Hormone Resistance—Special Focus on Inflammatory Bowel Disease

    Directory of Open Access Journals (Sweden)

    Christoffer Soendergaard

    2017-05-01

    Full Text Available Growth hormone (GH plays major anabolic and catabolic roles in the body and is important for regulating several aspects of growth. During an inflammatory process, cells may develop a state of GH resistance during which their response to GH stimulation is limited. In this review, we will emphasize specific mechanisms governing the formation of GH resistance in the active phase of inflammatory bowel disease. The specific molecular effects mediated through individual inflammatory mediators and processes will be highlighted to provide an overview of the transcriptional, translational and post-translational inflammation-mediated impacts on the GH receptor (GHR along with the impacts on GH-induced intracellular signaling. We also will review GH’s effects on mucosal healing and immune cells in the context of experimental colitis, human inflammatory bowel disease and in patients with short bowel syndrome.

  1. World Energy Outlook 2007 Special Report: Focus on Energy Poverty

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2007-07-01

    Energy poverty affects many Indians and is an important issue for the Indian government. The number of households with access to electricity has risen over the past couple of decades, but access is still far from universal and the availability of modern cooking fuels and technologies is still limited, especially in rural areas. We use an energy development index, based on access to electricity and cleaner cooking fuels and on overall electricity generation per capita, to emphasise the disparity in energy poverty across India and relative to other developing countries. There are still some 412 million people without access to electricity in India. In all three WEO scenarios, the number of people without access declines, but it falls much faster in the High Growth Scenario. In that scenario, all households in India have access to electricity in 2030. In the Reference Scenario, the electrification rate in 2030 in India is 96% but nearly 60 million people in rural areas will still lack access. At an investment cost of $41 per person, it would cost some $17 billion to connect all those without electricity today to the central grid. But gridbased electrification is often not available to remote villages and households, because of the high cost of expanding the network. Diesel generators, mini-hydro, wind turbines, biomass gasifiers and photovoltaics, or a combination of these, could be more economic. The number of people relying on fuelwood and dung for cooking and heating declines from 668 million in 2005 to 395 million in 2030 in the High Growth Scenario, 77 million fewer people than in the Reference Scenario. About 22% of the population would still rely on these fuels in India in 2030, even with higher growth. According to the World Health Organization, the use of fuelwood and dung for cooking and heating causes over 400 000 premature deaths in India annually, mostly women and children. The concentration of particulate matter in the air in Indian households using biomass is over 2 000 microgrammes per cubic metre, compared to the US standard of 150. LPG and kerosene subsidies have been very ineffective in improving the welfare of the poor, particularly in rural areas. The current subsidy scheme benefits most richer households, mainly in urban areas, and has, for the most part, failed to shift fuel consumption patterns away from biomass in poor households. It is estimated that 40% of the subsidies for LPG and kerosene go to the richest 7% of the population.

  2. Special Issue of Policy in Focus features IDRC supported projects ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2016-04-20

    Apr 20, 2016 ... These issues have been at the core of a series of projects supported by IDRC that have also been prioritised by The International Policy Centre for Inclusive Growth's (IPC-IG) research and knowledge-sharing activities. IDRC has supported research to examine how social protection impacts labour markets, ...

  3. Exposure to polycyclic aromatic hydrocarbons with special focus on cancer

    Directory of Open Access Journals (Sweden)

    Thamaraiselvan Rengarajan

    2015-03-01

    Full Text Available Polycyclic aromatic hydrocarbons (PAHs are a group of compounds consisting of two or more fused aromatic rings. Most of them are formed during incomplete combustion of organic materials such as wood and fossil fuels, petroleum products, and coal. The composition of PAH mixtures varies with the source and is also affected by selective weathering effects in the environment. PAHs are ubiquitous pollutants frequently found in a variety of environments such as fresh water and marine sediments, the atmosphere, and ice. Due to their widespread distribution, the environmental pollution due to PAHs has aroused global concern. Many PAHs and their epoxides are highly toxic, mutagenic and/or carcinogenic to microorganisms as well as to higher forms of life including humans. The main aim of this review is to provide contemporary information on PAH sources, route of exposure, worldwide emission rate, and adverse effects on humans, especially with reference to cancer.

  4. A Special Focus on Selexipag - Treatment of Pulmonary Arterial Hypertension

    DEFF Research Database (Denmark)

    Sørensen, Louise Marqvard; Wehland, Markus; Krüger, Marcus

    2017-01-01

    selexipag and PAH. RESULTS: With only few cases per million, PAH is a rare disease, but when untreated it can be life threatening. PAH is linked to elevated levels of endothelin (ET-1) and decreased levels of nitric oxide (NO) and prostacyclin (PGI2). PAH-specific therapeutic approaches concentrate...... receptor antagonists (ERA). The most common adverse effects (AEs), associated with selexipag, are headache, diarrhea, jaw pain, and nausea. Nevertheless, Selexipag was generally well tolerated during the GRIPHON trial. CONCLUSIONS: Selexipag is a valuable addition to PAH therapeutics especially by reducing...

  5. Special journal issue focuses on urban violence, poverty, and ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2015-10-02

    Oct 2, 2015 ... The Democratic Republic of Congo (DRC) is experiencing escalating urban violence and crime in an atmosphere of unstable institutions and security, increasing inequality, and a chronic lack of basic public services. There is an urgent need for critical analysis of the underlying causes of violence and the ...

  6. Focus on `Gender and Language' special issue: introduction ...

    African Journals Online (AJOL)

    The paper by Appalraju and De Kadt (2002) is on gender in relation to bilingualism, and these researches find a relationship between gender, social mobility and ... Reddy (2002) critically examines homophobic media texts in the southern African context and in doing so extends the work on gender, sexuality and insults.

  7. Geomembrane special study

    International Nuclear Information System (INIS)

    1988-07-01

    The objective of the Geomembrane Special Study was to asses the suitability of geomembranes in Uranium Mill Tailings Remedial Action (UMTRA) Project pile designs. Geomembranes, also called flexible membrane liners, are made of polymer resins and are thermoplastic materials. Part of the special study was to evaluate regulatory compliance and acceptability issues. This study was proposed because of the extensive use of geomembranes in hazardous waste site remedial actions and their accepted use in Resource Conservation and Recovery Act (RCRA) cells as both covers and liners to limit infiltration, or as part of leachate collection systems. This study has reviewed the recent geomembrane literature focusing on: (1) longevity; (2) performance; (3) constructibility; and (4) quality control/quality assurance considerations. In addition to these technical considerations, regulatory compliance and acceptability concerns were also evaluated. This report describes the results of the literature review, including correspondence with manufacturers, resin producers, experts in the field, and long-term major users. 12 refs., 2 tabs

  8. Fabrication, characterization and in vitro profile based interaction with eukaryotic and prokaryotic cells of alginate-chitosan-silica biocomposite.

    Science.gov (United States)

    Balaure, Paul Catalin; Andronescu, Ecaterina; Grumezescu, Alexandru Mihai; Ficai, Anton; Huang, Keng-Shiang; Yang, Chih-Hui; Chifiriuc, Carmen Mariana; Lin, Yung-Sheng

    2013-01-30

    This work is focused on the fabrication of a new drug delivery system based on polyanionic matrix (e.g. sodium alginate), polycationic matrix (e.g. chitosan) and silica network. The FT-IR, SEM, DTA-TG, eukaryotic cell cycle and viability, and in vitro assay of the influence of the biocomposite on the efficacy of antibiotic drugs were investigated. The obtained results demonstrated the biocompatibility and the ability of the fabricated biocomposite to maintain or improve the efficacy of the following antibiotics: piperacillin-tazobactam, cefepime, piperacillin, imipenem, gentamicin, ceftazidime against Pseudomonas aeruginosa ATCC 27853 and cefazolin, cefaclor, cefuroxime, ceftriaxone, cefoxitin, trimethoprim/sulfamethoxazole against Escherichia coli ATCC 25922 reference strains. Copyright © 2012 Elsevier B.V. All rights reserved.

  9. Sports Specialization, Part II

    Science.gov (United States)

    Myer, Gregory D.; Jayanthi, Neeru; DiFiori, John P.; Faigenbaum, Avery D.; Kiefer, Adam W.; Logerstedt, David; Micheli, Lyle J.

    2016-01-01

    Context: Many coaches, parents, and children believe that the best way to develop elite athletes is for them to participate in only 1 sport from an early age and to play it year-round. However, emerging evidence to the contrary indicates that efforts to specialize in 1 sport may reduce opportunities for all children to participate in a diverse year-round sports season and can lead to lost development of lifetime sports skills. Early sports specialization may also reduce motor skill development and ongoing participation in games and sports as a lifestyle choice. The purpose of this review is to employ the current literature to provide evidence-based alternative strategies that may help to optimize opportunities for all aspiring young athletes to maximize their health, fitness, and sports performance. Evidence Acquisition: Nonsystematic review with critical appraisal of existing literature. Study Design: Clinical review. Level of Evidence: Level 4. Conclusion: Based on the current evidence, parents and educators should help provide opportunities for free unstructured play to improve motor skill development and youth should be encouraged to participate in a variety of sports during their growing years to influence the development of diverse motor skills. For those children who do choose to specialize in a single sport, periods of intense training and specialized sport activities should be closely monitored for indicators of burnout, overuse injury, or potential decrements in performance due to overtraining. Last, the evidence indicates that all youth should be involved in periodized strength and conditioning (eg, integrative neuromuscular training) to help them prepare for the demands of competitive sport participation, and youth who specialize in a single sport should plan periods of isolated and focused integrative neuromuscular training to enhance diverse motor skill development and reduce injury risk factors. Strength of Recommendation Taxonomy (SORT): B. PMID

  10. Special offers

    CERN Document Server

    Association du personnel

    2012-01-01

    Special discount to the members of the Staff Association Aquaparc Discounted prices on admission of whole day. Children from 5 to 15 years: 26.– CHF instead of 35.– CHF; Adults from 16 years: 32.– CHF instead of 43.– CHF.Tickets on sale to the Staff Association Secretariat. BCGE Account management on salary account and annual subscription to credit cards free of charge. Other benefits on mortgage loan and financial planning. Comédie de Genève 20% off on full price tickets (also available for partner): from 24 to 32 CHF a ticket instead of 30 to 40 CHF depending on the shows. Ezee Suisse 15% off on the range of electric bikes upon presentation of your Staff Association membership card before payment. FNAC 5% discount on gifts card available in four Swiss shops without any restriction. Gifts card on sale to the Staff Association Secretariat. FutureKids 15% off for the Staff Association members who enrol their children of 5 to 16 years old in ...

  11. Specialization, Outsourcing and Wages

    DEFF Research Database (Denmark)

    Munch, Jakob Roland; Rose Skaksen, Jan

    2005-01-01

    arising from an increase in the extent of the market for intermediate goods, domestic outsourcing tends to increase wages for both unskilled and skilled labor. We use a panel data set of workers in Danish manufacturing industries to show that domestic and foreign outsurcing affect wages as predicted......This paper studies the impact of outsourcing on individual wages. In contrast to the standard approach in the literature, we focus on domestic outsourcing as well as foreign outsourcing. By using a simple theoretical model, we argue that, if outsourcing is associated with specialization gains...

  12. Phylogenetic diversity and in situ detection of eukaryotes in anaerobic sludge digesters.

    Directory of Open Access Journals (Sweden)

    Miri Matsubayashi

    Full Text Available Eukaryotic communities in aerobic wastewater treatment processes are well characterized, but little is known about them in anaerobic processes. In this study, abundance, diversity and morphology of eukaryotes in anaerobic sludge digesters were investigated by quantitative real-time PCR (qPCR, 18S rRNA gene clone library construction and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH. Samples were taken from four different anaerobic sludge digesters in Japan. Results of qPCR of rRNA genes revealed that Eukarya accounted from 0.1% to 1.4% of the total number of microbial rRNA gene copy numbers. The phylogenetic affiliations of a total of 251 clones were Fungi, Alveolata, Viridiplantae, Amoebozoa, Rhizaria, Stramenopiles and Metazoa. Eighty-five percent of the clones showed less than 97.0% sequence identity to described eukaryotes, indicating most of the eukaryotes in anaerobic sludge digesters are largely unknown. Clones belonging to the uncultured lineage LKM11 in Cryptomycota of Fungi were most abundant in anaerobic sludge, which accounted for 50% of the total clones. The most dominant OTU in each library belonged to either the LKM11 lineage or the uncultured lineage A31 in Alveolata. Principal coordinate analysis indicated that the eukaryotic and prokaryotic community structures were related. The detection of anaerobic eukaryotes, including the members of the LKM11 and A31 lineages in anaerobic sludge digesters, by CARD-FISH revealed their sizes in the range of 2-8 μm. The diverse and uncultured eukaryotes in the LKM11 and the A31 lineages are common and ecologically relevant members in anaerobic sludge digester.

  13. Mitochondria, the Cell Cycle, and the Origin of Sex via a Syncytial Eukaryote Common Ancestor.

    Science.gov (United States)

    Garg, Sriram G; Martin, William F

    2016-07-02

    Theories for the origin of sex traditionally start with an asexual mitosing cell and add recombination, thereby deriving meiosis from mitosis. Though sex was clearly present in the eukaryote common ancestor, the order of events linking the origin of sex and the origin of mitosis is unknown. Here, we present an evolutionary inference for the origin of sex starting with a bacterial ancestor of mitochondria in the cytosol of its archaeal host. We posit that symbiotic association led to the origin of mitochondria and gene transfer to host's genome, generating a nucleus and a dedicated translational compartment, the eukaryotic cytosol, in which-by virtue of mitochondria-metabolic energy was not limiting. Spontaneous protein aggregation (monomer polymerization) and Adenosine Tri-phosphate (ATP)-dependent macromolecular movement in the cytosol thereby became selectable, giving rise to continuous microtubule-dependent chromosome separation (reduction division). We propose that eukaryotic chromosome division arose in a filamentous, syncytial, multinucleated ancestor, in which nuclei with insufficient chromosome numbers could complement each other through mRNA in the cytosol and generate new chromosome combinations through karyogamy. A syncytial (or coenocytic, a synonym) eukaryote ancestor, or Coeca, would account for the observation that the process of eukaryotic chromosome separation is more conserved than the process of eukaryotic cell division. The first progeny of such a syncytial ancestor were likely equivalent to meiospores, released into the environment by the host's vesicle secretion machinery. The natural ability of archaea (the host) to fuse and recombine brought forth reciprocal recombination among fusing (syngamy and karyogamy) progeny-sex-in an ancestrally meiotic cell cycle, from which the simpler haploid and diploid mitotic cell cycles arose. The origin of eukaryotes was the origin of vertical lineage inheritance, and sex was required to keep vertically

  14. Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients.

    Science.gov (United States)

    Hamad, Ibrahim; Abou Abdallah, Rita; Ravaux, Isabelle; Mokhtari, Saadia; Tissot-Dupont, Hervé; Michelle, Caroline; Stein, Andreas; Lagier, Jean-Christophe; Raoult, Didier; Bittar, Fadi

    2018-01-01

    Research on the relationship between changes in the gut microbiota and human disease, including AIDS, is a growing field. However, studies on the eukaryotic component of the intestinal microbiota have just begun and have not yet been conducted in HIV-infected patients. Moreover, eukaryotic community profiling is influenced by the use of different methodologies at each step of culture-independent techniques. Herein, initially, four DNA extraction protocols were compared to test the efficiency of each method in recovering eukaryotic DNA from fecal samples. Our results revealed that recovering eukaryotic components from fecal samples differs significantly among DNA extraction methods. Subsequently, the composition of the intestinal eukaryotic microbiota was evaluated in HIV-infected patients and healthy volunteers through clone sequencing, high-throughput sequencing of nuclear ribosomal internal transcribed spacers 1 (ITS1) and 2 (ITS2) amplicons and real-time PCRs. Our results revealed that not only richness (Chao-1 index) and alpha diversity (Shannon diversity) differ between HIV-infected patients and healthy volunteers, depending on the molecular strategy used, but also the global eukaryotic community composition, with little overlapping taxa found between techniques. Moreover, our results based on cloning libraries and ITS1/ITS2 metabarcoding sequencing showed significant differences in fungal composition between HIV-infected patients and healthy volunteers, but without distinct clusters separating the two groups. Malassezia restricta was significantly more prevalent in fecal samples of HIV-infected patients, according to cloning libraries, whereas operational taxonomic units (OTUs) belonging to Candida albicans and Candida tropicalis were significantly more abundant in fecal samples of HIV-infected patients compared to healthy subjects in both ITS subregions. Finally, real-time PCR showed the presence of Microsporidia, Giardia lamblia, Blastocystis and

  15. Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients.

    Directory of Open Access Journals (Sweden)

    Ibrahim Hamad

    Full Text Available Research on the relationship between changes in the gut microbiota and human disease, including AIDS, is a growing field. However, studies on the eukaryotic component of the intestinal microbiota have just begun and have not yet been conducted in HIV-infected patients. Moreover, eukaryotic community profiling is influenced by the use of different methodologies at each step of culture-independent techniques. Herein, initially, four DNA extraction protocols were compared to test the efficiency of each method in recovering eukaryotic DNA from fecal samples. Our results revealed that recovering eukaryotic components from fecal samples differs significantly among DNA extraction methods. Subsequently, the composition of the intestinal eukaryotic microbiota was evaluated in HIV-infected patients and healthy volunteers through clone sequencing, high-throughput sequencing of nuclear ribosomal internal transcribed spacers 1 (ITS1 and 2 (ITS2 amplicons and real-time PCRs. Our results revealed that not only richness (Chao-1 index and alpha diversity (Shannon diversity differ between HIV-infected patients and healthy volunteers, depending on the molecular strategy used, but also the global eukaryotic community composition, with little overlapping taxa found between techniques. Moreover, our results based on cloning libraries and ITS1/ITS2 metabarcoding sequencing showed significant differences in fungal composition between HIV-infected patients and healthy volunteers, but without distinct clusters separating the two groups. Malassezia restricta was significantly more prevalent in fecal samples of HIV-infected patients, according to cloning libraries, whereas operational taxonomic units (OTUs belonging to Candida albicans and Candida tropicalis were significantly more abundant in fecal samples of HIV-infected patients compared to healthy subjects in both ITS subregions. Finally, real-time PCR showed the presence of Microsporidia, Giardia lamblia, Blastocystis

  16. Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes

    Directory of Open Access Journals (Sweden)

    Roger Andrew J

    2003-06-01

    Full Text Available Abstract Background Lateral gene transfer can introduce genes with novel functions into genomes or replace genes with functionally similar orthologs or paralogs. Here we present a study of the occurrence of the latter gene replacement phenomenon in the four gene families encoding different classes of glutamate dehydrogenase (GDH, to evaluate and compare the patterns and rates of lateral gene transfer (LGT in prokaryotes and eukaryotes. Results We extend the taxon sampling of gdh genes with nine new eukaryotic sequences and examine the phylogenetic distribution pattern of the various GDH classes in combination with maximum likelihood phylogenetic analyses. The distribution pattern analyses indicate that LGT has played a significant role in the evolution of the four gdh gene families. Indeed, a number of gene transfer events are identified by phylogenetic analyses, including numerous prokaryotic intra-domain transfers, some prokaryotic inter-domain transfers and several inter-domain transfers between prokaryotes and microbial eukaryotes (protists. Conclusion LGT has apparently affected eukaryotes and prokaryotes to a similar extent within the gdh gene families. In the absence of indications that the evolution of the gdh gene families is radically different from other families, these results suggest that gene transfer might be an important evolutionary mechanism in microbial eukaryote genome evolution.

  17. Proton-pumping rhodopsins are abundantly expressed by microbial eukaryotes in a high-Arctic fjord.

    Science.gov (United States)

    Vader, Anna; Laughinghouse, Haywood D; Griffiths, Colin; Jakobsen, Kjetill S; Gabrielsen, Tove M

    2018-02-01

    Proton-pumping rhodopsins provide an alternative pathway to photosynthesis by which solar energy can enter the marine food web. Rhodopsin genes are widely found in marine bacteria, also in the Arctic, and were recently reported from several eukaryotic lineages. So far, little is known about rhodopsin expression in Arctic eukaryotes. In this study, we used metatranscriptomics and 18S rDNA tag sequencing to examine the mid-summer function and composition of marine protists (size 0.45-10 µm) in the high-Arctic Billefjorden (Spitsbergen), especially focussing on the expression of microbial proton-pumping rhodopsins. Rhodopsin transcripts were highly abundant, at a level similar to that of genes involved in photosynthesis. Phylogenetic analyses placed the environmental rhodopsins within disparate eukaryotic lineages, including dinoflagellates, stramenopiles, haptophytes and cryptophytes. Sequence comparison indicated the presence of several functional types, including xanthorhodopsins and a eukaryotic clade of proteorhodopsin. Transcripts belonging to the proteorhodopsin clade were also abundant in published metatranscriptomes from other oceanic regions, suggesting a global distribution. The diversity and abundance of rhodopsins show that these light-driven proton pumps play an important role in Arctic microbial eukaryotes. Understanding this role is imperative to predicting the future of the Arctic marine ecosystem faced by a changing light climate due to diminishing sea-ice. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  18. Functional capacity of Shiga-toxin promoter sequences in eukaryotic cells.

    Science.gov (United States)

    Bentancor, Leticia V; Bilen, Marcos F; Mejías, María P; Fernández-Brando, Romina J; Panek, Cecilia A; Ramos, Maria V; Fernández, Gabriela C; Isturiz, Martín; Ghiringhelli, Pablo D; Palermo, Marina S

    2013-01-01

    Shiga toxins (Stx) are the main virulence factors in enterohemorrhagic Escherichia coli (EHEC) infections, causing diarrhea and hemolytic uremic syndrome (HUS). The genes encoding for Shiga toxin-2 (Stx2) are located in a bacteriophage. The toxin is formed by a single A subunit and five B subunits, each of which has its own promoter sequence. We have previously reported the expression of the B subunit within the eukaryotic environment, probably driven by their own promoter. The aim of this work was to evaluate the ability of the eukaryotic machinery to recognize stx2 sequences as eukaryotic-like promoters. Vero cells were transfected with a plasmid encoding Stx2 under its own promoter. The cytotoxic effect on these cells was similar to that observed upon incubation with purified Stx2. In addition, we showed that Stx2 expression in Stx2-insensitive BHK eukaryotic cells induced drastic morphological and cytoskeletal changes. In order to directly evaluate the capacity of the wild promoter sequences of the A and B subunits to drive protein expression in mammalian cells, GFP was cloned under eukaryotic-like putative promoter sequences. GFP expression was observed in 293T cells transfected with these constructions. These results show a novel and alternative way to synthesize Stx2 that could contribute to the global understanding of EHEC infections with immediate impact on the development of treatments or vaccines against HUS.

  19. Efficient method to optimize antibodies using avian leukosis virus display and eukaryotic cells.

    Science.gov (United States)

    Yu, Changming; Pike, Gennett M; Rinkoski, Tommy A; Correia, Cristina; Kaufmann, Scott H; Federspiel, Mark J

    2015-08-11

    Antibody-based therapeutics have now had success in the clinic. The affinity and specificity of the antibody for the target ligand determines the specificity of therapeutic delivery and off-target side effects. The discovery and optimization of high-affinity antibodies to important therapeutic targets could be significantly improved by the availability of a robust, eukaryotic display technology comparable to phage display that would overcome the protein translation limitations of microorganisms. The use of eukaryotic cells would improve the diversity of the displayed antibodies that can be screened and optimized as well as more seamlessly transition into a large-scale mammalian expression system for clinical production. In this study, we demonstrate that the replication and polypeptide display characteristics of a eukaryotic retrovirus, avian leukosis virus (ALV), offers a robust, eukaryotic version of bacteriophage display. The binding affinity of a model single-chain Fv antibody was optimized by using ALV display, improving affinity >2,000-fold, from micromolar to picomolar levels. We believe ALV display provides an extension to antibody display on microorganisms and offers virus and cell display platforms in a eukaryotic expression system. ALV display should enable an improvement in the diversity of properly processed and functional antibody variants that can be screened and affinity-optimized to improve promising antibody candidates.

  20. Production of the R2 subunit of ribonucleotide reductase from herpes simplex virus with prokaryotic and eukaryotic expression systems: higher activity of R2 produced by eukaryotic cells related to higher iron-binding capacity.

    OpenAIRE

    Lamarche, N; Matton, G; Massie, B; Fontecave, M; Atta, M; Dumas, F; Gaudreau, P; Langelier, Y

    1996-01-01

    The R2 subunit of ribonucleotide reductase from herpes simplex virus type 2 was overproduced with prokaryotic and eukaryotic expression systems. The recombinant R2 purified by a two-step procedure exhibited a 3-fold higher activity when produced in eukaryotic cells. Precise quantification of the R2 concentration at each step of the purification indicated that the activity was not altered during the purification procedure. Moreover, we have observed that the level of R2 expression, in eukaryot...

  1. The evolution of eukaryotic cells from the perspective of peroxisomes: phylogenetic analyses of peroxisomal beta-oxidation enzymes support mitochondria-first models of eukaryotic cell evolution.

    Science.gov (United States)

    Bolte, Kathrin; Rensing, Stefan A; Maier, Uwe-G

    2015-02-01

    Beta-oxidation of fatty acids and detoxification of reactive oxygen species are generally accepted as being fundamental functions of peroxisomes. Additionally, these pathways might have been the driving force favoring the selection of this compartment during eukaryotic evolution. Here we performed phylogenetic analyses of enzymes involved in beta-oxidation of fatty acids in Bacteria, Eukaryota, and Archaea. These imply an alpha-proteobacterial origin for three out of four enzymes. By integrating the enzymes' history into the contrasting models on the origin of eukaryotic cells, we conclude that peroxisomes most likely evolved non-symbiotically and subsequent to the acquisition of mitochondria in an archaeal host cell. © 2015 WILEY Periodicals, Inc.

  2. Commentary: Indigenous Health Special Issue

    Science.gov (United States)

    Tonmyr, Lil; Blackstock, Cindy

    2010-01-01

    This commentary highlights indigenous public health research from a special issue of the International Journal of Mental Health and Addiction dealing with child maltreatment, mental health, substance abuse and gambling. We focus on the emerging and growing research movement in Indigenous research through three important themes: 1) worldview and…

  3. Nonobtuse simplices & special matrix classes

    NARCIS (Netherlands)

    Cihangir, A.

    2016-01-01

    This thesis focuses on the study of certain special classes of n-simplices that occur in the context of numerical analysis, linear algebra, abstract algebra, geometry, and combinatorics. The type of simplex that is of central interest is the nonobtuse simplex, a simplex without any obtuse dihedral

  4. A superfamily of archaeal, bacterial, and eukaryotic proteins homologous to animal transglutaminases.

    Science.gov (United States)

    Makarova, K S; Aravind, L; Koonin, E V

    1999-08-01

    Computer analysis using profiles generated by the PSI-BLAST program identified a superfamily of proteins homologous to eukaryotic transglutaminases. The members of the new protein superfamily are found in all archaea, show a sporadic distribution among bacteria, and were detected also in eukaryotes, such as two yeast species and the nematode Caenorhabditis elegans. Sequence conservation in this superfamily primarily involves three motifs that center around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologs of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease.

  5. Structural basis of eukaryotic cell targeting by type III secretion system (T3SS) effectors.

    Science.gov (United States)

    Tosi, Tommaso; Pflug, Alexander; Discola, Karen F; Neves, David; Dessen, Andréa

    2013-01-01

    Type III secretion systems (T3SS) are macromolecular complexes that translocate a wide number of effector proteins into eukaryotic host cells. Once within the cytoplasm, many T3SS effectors mimic the structure and/or function of eukaryotic proteins in order to manipulate signaling cascades, and thus play pivotal roles in colonization, invasion, survival and virulence. Structural biology techniques have played key roles in the unraveling of bacterial strategies employed for mimicry and targeting. This review provides an overall view of our current understanding of structure and function of T3SS effectors, as well as of the different classes of eukaryotic proteins that are targeted and the consequences for the infected cell. Copyright © 2013 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  6. Faster growth of the major prokaryotic versus eukaryotic CO2 fixers in the oligotrophic ocean.

    Science.gov (United States)

    Zubkov, Mikhail V

    2014-04-29

    Because maintenance of non-scalable cellular components--membranes and chromosomes--requires an increasing fraction of energy as cell size decreases, miniaturization comes at a considerable energetic cost for a phytoplanktonic cell. Consequently, if eukaryotes can use their superior energetic resources to acquire nutrients with more or even similar efficiency compared with prokaryotes, larger unicellular eukaryotes should be able to achieve higher growth rates than smaller cyanobacteria. Here, to test this hypothesis, we directly compare the intrinsic growth rates of phototrophic prokaryotes and eukaryotes from the equatorial to temperate South Atlantic using an original flow cytometric (14)CO2-tracer approach. At the ocean basin scale, cyanobacteria double their biomass twice as frequently as the picoeukaryotes indicating that the prokaryotes are faster growing CO2 fixers, better adapted to phototrophic living in the oligotrophic open ocean-the most extensive biome on Earth.

  7. Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

    DEFF Research Database (Denmark)

    Møller, Henrik D.; Bojsen, Rasmus Kenneth; Tachibana, Chris

    2016-01-01

    Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods...... for detecting eccDNA are needed to clarify how these elements affect genome stability and how environmental and biological factors induce their formation in eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The method encompasses column purification of circular DNA...... DNA. Validation of the Circle-Seq method on three S. cerevisiae CEN.PK populations of 10(10) cells detected hundreds of eccDNA profiles in sizes larger than 1 kilobase. Repeated findings of ASP3-1, COS111, CUP1, RSC30, HXT6, HXT7 genes on circular DNA in both S288c and CEN.PK suggests that DNA...

  8. The Evolution of Organellar Coat Complexes and Organization of the Eukaryotic Cell.

    Science.gov (United States)

    Rout, Michael P; Field, Mark C

    2017-06-20

    Eukaryotic cells possess a remarkably diverse range of organelles that provide compartmentalization for distinct cellular functions and are likely responsible for the remarkable success of these organisms. The origins and subsequent elaboration of these compartments represent a key aspect in the transition between prokaryotic and eukaryotic cellular forms. The protein machinery required to build, maintain, and define many membrane-bound compartments is encoded by several paralog families, including small GTPases, coiled-bundle proteins, and proteins with β-propeller and α-solenoid secondary structures. Together these proteins provide the membrane coats and control systems to structure and coordinate the endomembrane system. Mechanistically and evolutionarily, they unite not only secretory and endocytic organelles but also the flagellum and nucleus. The ancient origins for these families have been revealed by recent findings, providing new perspectives on the deep evolutionary processes and relationships that underlie eukaryotic cell structure.

  9. Large-scale analysis of phosphorylation site occupancy in eukaryotic proteins

    DEFF Research Database (Denmark)

    Rao, R Shyama Prasad; Møller, Ian Max

    2012-01-01

    in proteins is currently lacking. We have therefore analyzed the occurrence and occupancy of phosphorylated sites (~ 100,281) in a large set of eukaryotic proteins (~ 22,995). Phosphorylation probability was found to be much higher in both the  termini of protein sequences and this is much pronounced...... maximum randomness. An analysis of phosphorylation motifs indicated that just 40 motifs and a much lower number of associated kinases might account for nearly 50% of the known phosphorylations in eukaryotic proteins. Our results provide a broad picture of the phosphorylation sites in eukaryotic proteins.......Many recent high throughput technologies have enabled large-scale discoveries of new phosphorylation sites and phosphoproteins. Although they have provided a number of insights into protein phosphorylation and the related processes, an inclusive analysis on the nature of phosphorylated sites...

  10. The reduced kinome of Ostreococcus tauri: core eukaryotic signalling components in a tractable model species.

    Science.gov (United States)

    Hindle, Matthew M; Martin, Sarah F; Noordally, Zeenat B; van Ooijen, Gerben; Barrios-Llerena, Martin E; Simpson, T Ian; Le Bihan, Thierry; Millar, Andrew J

    2014-08-02

    The current knowledge of eukaryote signalling originates from phenotypically diverse organisms. There is a pressing need to identify conserved signalling components among eukaryotes, which will lead to the transfer of knowledge across kingdoms. Two useful properties of a eukaryote model for signalling are (1) reduced signalling complexity, and (2) conservation of signalling components. The alga Ostreococcus tauri is described as the smallest free-living eukaryote. With less than 8,000 genes, it represents a highly constrained genomic palette. Our survey revealed 133 protein kinases and 34 protein phosphatases (1.7% and 0.4% of the proteome). We conducted phosphoproteomic experiments and constructed domain structures and phylogenies for the catalytic protein-kinases. For each of the major kinases families we review the completeness and divergence of O. tauri representatives in comparison to the well-studied kinomes of the laboratory models Arabidopsis thaliana and Saccharomyces cerevisiae, and of Homo sapiens. Many kinase clades in O. tauri were reduced to a single member, in preference to the loss of family diversity, whereas TKL and ABC1 clades were expanded. We also identified kinases that have been lost in A. thaliana but retained in O. tauri. For three, contrasting eukaryotic pathways - TOR, MAPK, and the circadian clock - we established the subset of conserved components and demonstrate conserved sites of substrate phosphorylation and kinase motifs. We conclude that O. tauri satisfies our two central requirements. Several of its kinases are more closely related to H. sapiens orthologs than S. cerevisiae is to H. sapiens. The greatly reduced kinome of O. tauri is therefore a suitable model for signalling in free-living eukaryotes.

  11. Convergent use of RhoGAP toxins by eukaryotic parasites and bacterial pathogens.

    Directory of Open Access Journals (Sweden)

    Dominique Colinet

    2007-12-01

    Full Text Available Inactivation of host Rho GTPases is a widespread strategy employed by bacterial pathogens to manipulate mammalian cellular functions and avoid immune defenses. Some bacterial toxins mimic eukaryotic Rho GTPase-activating proteins (GAPs to inactivate mammalian GTPases, probably as a result of evolutionary convergence. An intriguing question remains whether eukaryotic pathogens or parasites may use endogenous GAPs as immune-suppressive toxins to target the same key genes as bacterial pathogens. Interestingly, a RhoGAP domain-containing protein, LbGAP, was recently characterized from the parasitoid wasp Leptopilina boulardi, and shown to protect parasitoid eggs from the immune response of Drosophila host larvae. We demonstrate here that LbGAP has structural characteristics of eukaryotic RhoGAPs but that it acts similarly to bacterial RhoGAP toxins in mammals. First, we show by immunocytochemistry that LbGAP enters Drosophila immune cells, plasmatocytes and lamellocytes, and that morphological changes in lamellocytes are correlated with the quantity of LbGAP they contain. Demonstration that LbGAP displays a GAP activity and specifically interacts with the active, GTP-bound form of the two Drosophila Rho GTPases Rac1 and Rac2, both required for successful encapsulation of Leptopilina eggs, was then achieved using biochemical tests, yeast two-hybrid analysis, and GST pull-down assays. In addition, we show that the overall structure of LbGAP is similar to that of eukaryotic RhoGAP domains, and we identify distinct residues involved in its interaction with Rac GTPases. Altogether, these results show that eukaryotic parasites can use endogenous RhoGAPs as virulence factors and that despite their differences in sequence and structure, eukaryotic and bacterial RhoGAP toxins are similarly used to target the same immune pathways in insects and mammals.

  12. Gene flow and biological conflict systems in the origin and evolution of eukaryotes

    Directory of Open Access Journals (Sweden)

    L eAravind

    2012-06-01

    Full Text Available The endosymbiotic origin of eukaryotes brought together two disparate genomes in the cell. Additionally, eukaryotic natural history has included other endosymbiotic events, phagotrophic consumption of organisms, and intimate interactions with viruses and endoparasites. These phenomena facilitated large-scale lateral gene transfer and biological conflicts. We synthesize information from nearly two decades of genomics to illustrate how the interplay between lateral gene transfer and biological conflicts has impacted the emergence of new adaptations in eukaryotes. Using apicomplexans as example, we illustrate how lateral transfer from animals has contributed to unique parasite-host interfaces comprised of adhesion- and O-linked glycosylation-related domains. Adaptations, emerging due to intense selection for diversity in the molecular participants in organismal and genomic conflicts, being dispersed by lateral transfer, were subsequently exapted for eukaryote-specific innovations. We illustrate this using examples relating to eukaryotic chromatin, RNAi and RNA-processing systems, signaling pathways, apoptosis and immunity. We highlight the major contributions from catalytic domains of bacterial toxin-systems to the origin of signaling enzymes (e.g. ADP-ribosylation and small-molecule messenger synthesis, mutagenic enzymes for immune receptor diversification and RNA-processing. Similarly, we discuss contributions of bacterial antibiotic/siderophore synthesis systems and intra-genomic and intra-cellular selfish elements (e.g. restriction-modification, mobile elements and lysogenic phages in the emergence of chromatin remodeling/modifying enzymes and RNA-based regulation. We develop the concept that biological conflict systems served as evolutionary nurseries for innovations in the protein world, which were delivered to eukaryotes via lateral gene flow to spur key evolutionary innovations all the way from nucleogenesis to lineage-specific adaptations

  13. Special Education and General Education--Coordinated or Separated? A Study of Curriculum Planning for Pupils with Special Educational Needs

    Science.gov (United States)

    Nilsen, Sven

    2017-01-01

    The central issue of this article is the coordination between special and general education in curriculum planning for pupils with special educational needs. The focus is on individual education plans (IEPs) in special education and work plans in general education. This is also viewed in relation to how special and general education teachers…

  14. Engineering of ribosomal shunt-modulating eukaryotic ON riboswitches by using a cell-free translation system.

    Science.gov (United States)

    Ogawa, Atsushi

    2015-01-01

    A number of natural and artificial bacterial riboswitches have been reported thus far. However, they generally function only in bacteria, not in eukaryotes. This is because of the differences of expression mechanisms (transcription, translation, and so on) between these two main types of organisms. For example, the mechanism of translation initiation is quite different between bacteria and eukaryotes, especially in ribosome loading on mRNA. While the bacterial ribosome binds to a well-conserved, internal sequence some bases before the start codon to initiate translation, the eukaryotic one is loaded on the 5' terminus with the help of certain eukaryotic initiation factors. This means not only that bacterial riboswitches regulating translation initiation are not available in eukaryotic translation systems, but also that it is physically difficult to construct eukaryotic ON riboswitches that regulate the eukaryotic canonical translation initiation, because an aptamer cannot be inserted upstream of the ribosome loading site. However, the mechanism of noncanonical translation initiation via "ribosomal shunt" enables us to design translation initiation-modulating (specifically, ribosomal shunt-modulating) eukaryotic ON riboswitches. This chapter describes a facile method for engineering these ribosomal shunt-modulating eukaryotic ON riboswitches by using a cell-free translation system. Because these riboswitches do not require hybridization switching thanks to a unique shunting mechanism, they have the major advantages of a low energy requirement for upregulation and relatively straightforward design over common hybridization switch-based ON riboswitches. © 2015 Elsevier Inc. All rights reserved.

  15. Comparative radiobiology of genetic loci of eukaryots as the basis of the general theory of mutations

    International Nuclear Information System (INIS)

    Aleksandrov, I.D.

    1983-01-01

    One of the fundamental problems of modern molecular cellular radiobiology is to reveal general and peculiar processes of the formation of gene mutations and chromosome aberrations in each stage of their formation in the irradiated genome of the higher eukaryots. The solution of the problems depends on the development of research within the framework of comparative radiobiology of genetic loci of the higher eukaryots that makes it possible to study quantitative regularities in the formation of gene (point) mutations and chromosome aberrations in one object and in the same experiment

  16. Dynamic instability--a common denominator in prokaryotic and eukaryotic DNA segregation and cell division.

    Science.gov (United States)

    Fuesler, John A; Li, Hsin-Jung Sophia

    2012-12-01

    Dynamic instability is an essential phenomenon in eukaryotic nuclear division and prokaryotic plasmid R1 segregation. Although the molecular machines used in both systems differ greatly in composition, strong similarities and requisite nuances in dynamics and segregation mechanisms are observed. This brief examination of the current literature provides a functional comparison between prokaryotic and eukaryotic dynamically unstable filaments, specifically ParM and microtubules. Additionally, this mini-review should support the notion that any dynamically unstable filament could serve as the molecular machine driving DNA segregation, but these machines possess auxiliary features to adapt to temporal and spatial disparities in either system.

  17. Use of prokaryotic transcriptional activators as metabolite biosensors in eukaryotic cells

    DEFF Research Database (Denmark)

    2018-01-01

    The present invention relates to the use of transcriptional activators from prokaryotic organisms for use in eukaryotic cells, such as yeast as sensors of intracellular and extracellular accumulation of a ligand or metabolite specifically activating this transcriptional activator in a eukaryot......, such as yeast cell, such as a cell engineered to produce this ligand. The transcriptional activator controls a promoter upstream of one or more gene, which may include e.g. a reporter gene that may be a fluorescence marker, such as luciferase, green fluorescent protein or a gnee encoding antibiotic resistance....

  18. Once in a lifetime: strategies for preventing re-replication in prokaryotic and eukaryotic cells

    DEFF Research Database (Denmark)

    Nielsen, Olaf; Løbner-Olesen, Anders

    2008-01-01

    DNA replication is an extremely accurate process and cells have evolved intricate control mechanisms to ensure that each region of their genome is replicated only once during S phase. Here, we compare what is known about the processes that prevent re-replication in prokaryotic and eukaryotic cells...... prokaryotes and eukaryotes are inactivated until the next cell cycle. Furthermore, in both systems the beta-clamp of the replicative polymerase associates with enzymatic activities that contribute to the inactivation of the helicase loaders. Finally, recent studies suggest that the control mechanism...

  19. Molecular analyses reveal high levels of eukaryotic richness associated with enigmatic deep-sea protists (Komokiacea)

    DEFF Research Database (Denmark)

    Lecroq, Beatrice; Gooday, Andrew John; Cedhagen, Tomas

    2009-01-01

    morphological features. To examine their taxonomic position at the molecular level, we analysed the SSU rDNA sequences of two species, Normanina conferta and Septuma ocotillo, obtained either with specific foraminiferal or universal eukaryotic primers. Many different sequences resulted from this investigation...... but none of them could clearly be attributed to komokiaceans. Although our study failed to confirm univocally that Komokiacea are foraminiferans, it revealed a huge eukaryotic richness associated with these organisms, comparable with the richness in the overall surrounding sediment. These observations...

  20. Evolution of specialization and ecological character displacement: metabolic plasticity matters.

    NARCIS (Netherlands)

    Egas, C.J.M.; Reydon, Th.A.C.; Hemerik, L.

    2005-01-01

    An important question in evolutionary biology, especially with respect to herbivorous arthropods, is the evolution of specialization. In a previous paper, the combined evolutionary dynamics of specialization and ecological character displacement was studied, focusing on the role of herbivore

  1. Towards a palaeoecological model of the Mesoproterozoic Taoudeni Basin, Mauritania, Northwestern Africa: implications for early eukaryote evolution

    Science.gov (United States)

    Beghin, Jérémie; Guilbaud, Romain; Poulton, Simon W.; Gueneli, Nur; Brocks, Jochen J.; Storme, Jean-Yves; Blanpied, Christian; Javaux, Emmanuelle J.

    2016-04-01

    The mid-Proterozoic rock record preserves a relatively moderate diversity of early eukaryotes, despite the early evolution of fundamental features of the eukaryotic cell. Common hypotheses involve the redox state of stratified oceans with oxic shallow waters, euxinic mid-depth waters, and anoxic and ferruginous deep waters during this time period. Mid-Proterozoic eukaryotes would have found suitable ecological niches in estuarine, fluvio-deltaic and coastal shallow marine environments near nutrient sources, while N2-fixing photoautotrophs bacteria would have been better competitors than eukaryotic algae in nutrient-poor niches. Here, we present the first palaeoecological model of the late Mesoproterozoic Taoudeni Basin, Mauritania, Northwestern Africa. Previous palaeontological studies in the basin reported stromatolites, a low diversity of microfossils - including one species of presumed eukaryotes: verrucae-bearing acritarch - and biomarkers of anoxygenic phototrophic purple and green sulfur bacteria, cyanobacteria and microaerophilic methanotrophs. However, no biomarkers diagnostic for crown group eukaryotes were reported so far. In addition to exceptionally well preserved microbial mats showing chain-like aggregates of pyrite grains, we observed a total of sixty-two morphotaxa including nine presumed prokaryotes, thirty-five possible prokaryotes or eukaryotes, fifteen unambiguous species of eukaryotes - ornamented and process-bearing acritarchs, multicellular morphotaxon, putative VSMs, large budding vesicles, and vesicles with a sophisticated excystment structure: the pylome - and three remains of structured kerogen. Here, we combined the geological context (sedimentological features and lithofacies), iron speciation (n = 156) - with the aim of reconstructing palaeoredox environmental conditions -, and microfossils quantitative analysis (n = 61). Sediments were deposited under shallow waters in pericratonic (western basin) and epicratonic (eastern basin

  2. The Special Olympics: Sporting or Social Event?

    Science.gov (United States)

    Hughes, Carolyn; McDonald, Meghan L.

    2008-01-01

    Storey (2008), in his eloquent and timely critique of the Special Olympics and his call to close it down, focuses on the failure of the Special Olympics to achieve the goal of social integration and sustained social interaction among people with intellectual disabilities and their peers without a disability label. The authors wholeheartedly agree…

  3. Teaching Science to Learners with Special Needs

    Science.gov (United States)

    McGinnis, J. Randy

    2013-01-01

    A fundamental social justice issue worldwide is how to meet the needs of all learners, especially those with special needs who historically have faced discrimination, exclusion, and oppression due to special needs (physical, cognitive, or behavioral dimensions). This article focuses on the key questions that researchers interested in improving…

  4. The Training of Teachers in Special Education.

    Science.gov (United States)

    Gulliford, Ronald

    1986-01-01

    As special needs children are integrated into regular education, new needs in teacher training have become apparent. Focusing on the United Kingdom, this paper discusses the training of special education teachers and the preservice education and inservice training of all teachers. (Author/JDD)

  5. Developing Adaptive Proficiency in Special Forces Officers

    National Research Council Canada - National Science Library

    White, Susan S; Mueller-Hanson, Rose A; Dorsey, David W; Pulakos, Elaine D; Wisecarver, Michelle M; Deagle, Edwin A., III; Mendini, Kip G

    2005-01-01

    Adaptive proficiency is critical for operating in the dynamic Special Forces (SF) mission environment and a recent focus on this requirement has resulted in a greater emphasis on adaptability in current training for SF...

  6. The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists

    Science.gov (United States)

    SINA M. ADL; ALASTAIR G. B. SIMPSON; MARK A. FARMER; ROBERT A. ANDERSEN; O. ROGER ANDERSON; JOHN R. BARTA; SAMUEL S. BOWSER; GUY BRUGEROLLE; ROBERT A. FENSOME; SUZANNE FREDERICQ; TIMOTHY Y. JAMES; SERGEI KARPOV; PAUL KUGRENS; JOHN KRUG; CHRISTOPHER E. LANE; LOUISE A. LEWIS; JEAN LODGE; DENIS H. LYNN; DAVID G. MANN; RICHARD M. MCCOURT; LEONEL MENDOZA; ØJVIND MOESTRUP; SHARON E. MOZLEY-STANDRIDGE; THOMAS A. NERAD; CAROL A. SHEARER; ALEXEY V. SMIRNOV; FREDERICK W. SPIEGEL; MAX F.J.R. TAYLOR

    2005-01-01

    This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic...

  7. Production of yeastolates for uniform stable isotope labelling in eukaryotic cell culture.

    NARCIS (Netherlands)

    Egorova-Zachernyuk, T.A.; Bosman, G.J.C.G.M.; Pistorius, A.M.A.; Grip, W.J. de

    2009-01-01

    Preparation of stable isotope-labelled yeastolates opens up ways to establish more cost-effective stable isotope labelling of biomolecules in insect and mammalian cell lines and hence to employ higher eukaryotic cell lines for stable isotope labelling of complex recombinant proteins. Therefore, we

  8. The Ancient Gamete Fusogen HAP2 Is a Eukaryotic Class II Fusion Protein.

    Science.gov (United States)

    Fédry, Juliette; Liu, Yanjie; Péhau-Arnaudet, Gérard; Pei, Jimin; Li, Wenhao; Tortorici, M Alejandra; Traincard, François; Meola, Annalisa; Bricogne, Gérard; Grishin, Nick V; Snell, William J; Rey, Félix A; Krey, Thomas

    2017-02-23

    Sexual reproduction is almost universal in eukaryotic life and involves the fusion of male and female haploid gametes into a diploid cell. The sperm-restricted single-pass transmembrane protein HAP2-GCS1 has been postulated to function in membrane merger. Its presence in the major eukaryotic taxa-animals, plants, and protists (including important human pathogens like Plasmodium)-suggests that many eukaryotic organisms share a common gamete fusion mechanism. Here, we report combined bioinformatic, biochemical, mutational, and X-ray crystallographic studies on the unicellular alga Chlamydomonas reinhardtii HAP2 that reveal homology to class II viral membrane fusion proteins. We further show that targeting the segment corresponding to the fusion loop by mutagenesis or by antibodies blocks gamete fusion. These results demonstrate that HAP2 is the gamete fusogen and suggest a mechanism of action akin to viral fusion, indicating a way to block Plasmodium transmission and highlighting the impact of virus-cell genetic exchanges on the evolution of eukaryotic life. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  9. Eukaryotes in the gut microbiota in myalgic encephalomyelitis/chronic fatigue syndrome

    Directory of Open Access Journals (Sweden)

    Alexandra H. Mandarano

    2018-01-01

    Full Text Available Patients with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS often suffer from gastrointestinal symptoms and many are diagnosed with irritable bowel syndrome (IBS. Previous studies, including from our laboratory, have demonstrated that the ME/CFS gut bacterial composition is altered and less diverse when compared to healthy individuals. Patients have increased biomarkers of inflammation and leaky gut syndrome. To further investigate dysbiosis in the ME/CFS gut microbiome, we sought to characterize the eukaryotes present in the gut of 49 individuals with ME/CFS and 39 healthy controls. Using 18S rRNA sequencing, we have identified eukaryotes in stool samples of 17 healthy individuals and 17 ME/CFS patients. Our analysis demonstrates a small, nonsignificant decrease in eukaryotic diversity in ME/CFS patients compared to healthy individuals. In addition, ME/CFS patients show a nonsignificant increase in the ratio of fungal phyla Basidiomycota to Ascomycota, which is consistent with ongoing inflammation in ME/CFS. We did not identify specific eukaryotic taxa that are associated with ME/CFS disease status.

  10. SUMO fusion technology for enhanced protein production in prokaryotic and eukaryotic expression systems.

    Science.gov (United States)

    Panavas, Tadas; Sanders, Carsten; Butt, Tauseef R

    2009-01-01

    In eukaryotic cells, the reversible attachment of small ubiquitin-like modifier (SUMO) protein is a post-translational modification that has been demonstrated to play an important role in various cellular processes. Moreover, it has been found that SUMO as an N-terminal fusion partner enhances functional protein production in prokaryotic and eukaryotic expression systems, based upon significantly improved protein stability and solubility. Following the expression and purification of the fusion protein, the SUMO-tag can be cleaved by specific (SUMO) proteases via their endopeptidase activity in vitro to generate the desired N-terminus of the released protein partner. In addition to its physiological relevance in eukaryotes, SUMO can, thus, be used as a powerful biotechnological tool for protein expression in prokaryotic and eukaryotic cell systems.In this chapter, we will describe the construction of a fusion protein with the SUMO-tag, its expression in Escherichia coli, and its purification followed by the removal of the SUMO-tag by a SUMO-specific protease in vitro.

  11. Eukaryotic Ribonucleases P/MRP: the Crystal Structure of the P3 Domain

    Energy Technology Data Exchange (ETDEWEB)

    Perederina, A.; Esakova, O; Quan, C; Khanova, E; Krasilnikov, A

    2010-01-01

    Ribonuclease (RNase) P is a site-specific endoribonuclease found in all kingdoms of life. Typical RNase P consists of a catalytic RNA component and a protein moiety. In the eukaryotes, the RNase P lineage has split into two, giving rise to a closely related enzyme, RNase MRP, which has similar components but has evolved to have different specificities. The eukaryotic RNases P/MRP have acquired an essential helix-loop-helix protein-binding RNA domain P3 that has an important function in eukaryotic enzymes and distinguishes them from bacterial and archaeal RNases P. Here, we present a crystal structure of the P3 RNA domain from Saccharomyces cerevisiae RNase MRP in a complex with RNase P/MRP proteins Pop6 and Pop7 solved to 2.7 {angstrom}. The structure suggests similar structural organization of the P3 RNA domains in RNases P/MRP and possible functions of the P3 domains and proteins bound to them in the stabilization of the holoenzymes' structures as well as in interactions with substrates. It provides the first insight into the structural organization of the eukaryotic enzymes of the RNase P/MRP family.

  12. Revealing genetic diversity of eukaryotic microorganisms in aquatic environments by denaturing gradient gel electrophoresis

    NARCIS (Netherlands)

    Van Hannen, E.J.; Van Agterveld, M.P.; Gons, H.J.; Laanbroek, H.J.

    1998-01-01

    A new Eucarya-specific 18S rDNA primer set was constructed and tested using denaturing gradient gel electrophoresis to analyze the genetic diversity of eukaryotic microorganisms in aquatic environments. All eukaryal lines of descent exhibited four or fewer nucleotide mismatches in the forward primer

  13. Studying NK cell lectin receptors and their interactions using HEK293T eukaryotic expression system

    Czech Academy of Sciences Publication Activity Database

    Vaněk, O.; Celadová, P.; Kolenko, Petr; Dohnálek, Jan; Bezouška, Karel

    2009-01-01

    Roč. 276, Suppl. 1 (2009), s. 170 ISSN 1742-464X. [FEBS Congress "Life´s Molecular Interactions /34./. 04.07.2009-09.07.2009, Praha] Institutional research plan: CEZ:AV0Z40500505 Keywords : NK cell lectin receptors * HEK293T * eukaryotic expression system Subject RIV: CD - Macromolecular Chemistry

  14. A complex cell division machinery was present in the last common ancestor of eukaryotes.

    Directory of Open Access Journals (Sweden)

    Laura Eme

    Full Text Available BACKGROUND: The midbody is a transient complex structure containing proteins involved in cytokinesis. Up to now, it has been described only in Metazoa. Other eukaryotes present a variety of structures implied in the last steps of cell division, such as the septum in fungi or the phragmoplast in plants. However, it is unclear whether these structures are homologous (derive from a common ancestral structure or analogous (have distinct evolutionary origins. Recently, the proteome of the hamster midbody has been characterized and 160 proteins identified. METHODOLOGY/PRINCIPAL FINDINGS: Using phylogenomic approaches, we show here that nearly all of these 160 proteins (95% are conserved across metazoan lineages. More surprisingly, we show that a large part of the mammalian midbody components (91 proteins were already present in the last common ancestor of all eukaryotes (LECA and were most likely involved in the construction of a complex multi-protein assemblage acting in cell division. CONCLUSIONS/SIGNIFICANCE: Our results indicate that the midbodies of non-mammalian metazoa are likely very similar to the mammalian one and that the ancestor of Metazoa possessed a nearly modern midbody. Moreover, our analyses support the hypothesis that the midbody and the structures involved in cytokinesis in other eukaryotes derive from a large and complex structure present in LECA, likely involved in cytokinesis. This is an additional argument in favour of the idea of a complex ancestor for all contemporary eukaryotes.

  15. Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling.

    Science.gov (United States)

    Gutierrez, Jahir M; Lewis, Nathan E

    2015-07-01

    Eukaryotic cell lines, including Chinese hamster ovary cells, yeast, and insect cells, are invaluable hosts for the production of many recombinant proteins. With the advent of genomic resources, one can now leverage genome-scale computational modeling of cellular pathways to rationally engineer eukaryotic host cells. Genome-scale models of metabolism include all known biochemical reactions occurring in a specific cell. By describing these mathematically and using tools such as flux balance analysis, the models can simulate cell physiology and provide targets for cell engineering that could lead to enhanced cell viability, titer, and productivity. Here we review examples in which metabolic models in eukaryotic cell cultures have been used to rationally select targets for genetic modification, improve cellular metabolic capabilities, design media supplementation, and interpret high-throughput omics data. As more comprehensive models of metabolism and other cellular processes are developed for eukaryotic cell culture, these will enable further exciting developments in cell line engineering, thus accelerating recombinant protein production and biotechnology in the years to come. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins

    Science.gov (United States)

    Li, Sanshu; Smith, Kathryn D.; Davis, Jared H.; Gordon, Patricia B.; Breaker, Ronald R.; Strobel, Scott A.

    2013-01-01

    Fluorine is an abundant element and is toxic to organisms from bacteria to humans, but the mechanisms by which eukaryotes resist fluoride toxicity are unknown. The Escherichia coli gene crcB was recently shown to be regulated by a fluoride-responsive riboswitch, implicating it in fluoride response. There are >8,000 crcB homologs across all domains of life, indicating that it has an important role in biology. Here we demonstrate that eukaryotic homologs [renamed FEX (fluoride exporter)] function in fluoride export. FEX KOs in three eukaryotic model organisms, Neurospora crassa, Saccharomyces cerevisiae, and Candida albicans, are highly sensitized to fluoride (>200-fold) but not to other halides. Some of these KO strains are unable to grow in fluoride concentrations found in tap water. Using the radioactive isotope of fluoride, 18F, we developed an assay to measure the intracellular fluoride concentration and show that the FEX deletion strains accumulate fluoride in excess of the external concentration, providing direct evidence of FEX function in fluoride efflux. In addition, they are more sensitive to lower pH in the presence of fluoride. These results demonstrate that eukaryotic FEX genes encode a previously unrecognized class of fluoride exporter necessary for survival in standard environmental conditions. PMID:24173035

  17. Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain.

    Science.gov (United States)

    Perederina, Anna; Esakova, Olga; Quan, Chao; Khanova, Elena; Krasilnikov, Andrey S

    2010-02-17

    Ribonuclease (RNase) P is a site-specific endoribonuclease found in all kingdoms of life. Typical RNase P consists of a catalytic RNA component and a protein moiety. In the eukaryotes, the RNase P lineage has split into two, giving rise to a closely related enzyme, RNase MRP, which has similar components but has evolved to have different specificities. The eukaryotic RNases P/MRP have acquired an essential helix-loop-helix protein-binding RNA domain P3 that has an important function in eukaryotic enzymes and distinguishes them from bacterial and archaeal RNases P. Here, we present a crystal structure of the P3 RNA domain from Saccharomyces cerevisiae RNase MRP in a complex with RNase P/MRP proteins Pop6 and Pop7 solved to 2.7 A. The structure suggests similar structural organization of the P3 RNA domains in RNases P/MRP and possible functions of the P3 domains and proteins bound to them in the stabilization of the holoenzymes' structures as well as in interactions with substrates. It provides the first insight into the structural organization of the eukaryotic enzymes of the RNase P/MRP family.

  18. Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life

    Czech Academy of Sciences Publication Activity Database

    Speijer, D.; Lukeš, Julius; Eliáš, M.

    2015-01-01

    Roč. 112, č. 29 (2015), s. 8827-8834 ISSN 0027-8424 R&D Projects: GA MŠk LH12104; GA ČR GA15-21974S Institutional support: RVO:60077344 Keywords : reactive oxygen species * evolution * protists * eukaryotes * sex Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.423, year: 2015

  19. High Genetic Diversity and Novelty in Eukaryotic Plankton Assemblages Inhabiting Saline Lakes in the Qaidam Basin

    Science.gov (United States)

    Wang, Jiali; Wang, Fang; Chu, Limin; Wang, Hao; Zhong, Zhiping; Liu, Zhipei; Gao, Jianyong; Duan, Hairong

    2014-01-01

    Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution. PMID:25401703

  20. Function of Rad51 paralogs in eukaryotic homologous recombinational repair

    International Nuclear Information System (INIS)

    Liu, N.; Skowronek, K.

    2003-01-01

    Full text: Homologous recombinational repair (HRR) is an important mechanism for maintaining genetic integrity and cancer prevention by accurately repair of DNA double strand breaks induced by environmental insults or occurred in DNA replication. A critical step in HRR is the polymerization of Rad51 on single stranded DNA to form nuclear protein filaments, the later conduct DNA strand paring and exchange between homologous strands. A number of proteins, including replication protein A (RPA), Rad52 and Rad51 paralogs, are suggested to modulate or facilitate the process of Rad51 filament formation. Five Rad51 paralogs, namely XRCC2, XRCC3, Rad51B, Rad51C and Rad51D have been identified in eucaryotic cells. These proteins show distant protein sequence identity to Rad51, to yeast Rad51 paralogs (Rad55 and Rad57) and to each other. Hamster or chicken mutants of Rad51 paralogs exhibit hypersensitivity to a variety of DNA damaging agents, especially cross-linking agents, and are defective in assembly of Rad51 onto HRR site after DNA damage. Recent data from our and other labs showed that Rad51 paralogs constitute two distinct complexes in cell extracts, one contains XRCC2, Rad51B, Rad51C and Rad51D, and the other contains Rad51C and XRCC3. Rad51C is involved in both complexes. Our results also showed that XRCC3-Rad51C complex interacts with Rad51 in vivo. Furthermore, overexpression of Rad52 can partially suppress the hypersensitivity of XRCC2 mutant irs1 to ionizing radiation and corrected the defects in Rad51 focus formation. These results suggest that XRCC2 and other Rad51 paralogs play a mediator function to Rad51 in the early stage of HRR

  1. Bacterial Signaling Nucleotides Inhibit Yeast Cell Growth by Impacting Mitochondrial and Other Specifically Eukaryotic Functions.

    Science.gov (United States)

    Hesketh, Andy; Vergnano, Marta; Wan, Chris; Oliver, Stephen G

    2017-07-25

    We have engineered Saccharomyces cerevisiae to inducibly synthesize the prokaryotic signaling nucleotides cyclic di-GMP (cdiGMP), cdiAMP, and ppGpp in order to characterize the range of effects these nucleotides exert on eukaryotic cell function during bacterial pathogenesis. Synthetic genetic array (SGA) and transcriptome analyses indicated that, while these compounds elicit some common reactions in yeast, there are also complex and distinctive responses to each of the three nucleotides. All three are capable of inhibiting eukaryotic cell growth, with the guanine nucleotides exhibiting stronger effects than cdiAMP. Mutations compromising mitochondrial function and chromatin remodeling show negative epistatic interactions with all three nucleotides. In contrast, certain mutations that cause defects in chromatin modification and ribosomal protein function show positive epistasis, alleviating growth inhibition by at least two of the three nucleotides. Uniquely, cdiGMP is lethal both to cells growing by respiration on acetate and to obligately fermentative petite mutants. cdiGMP is also synthetically lethal with the ribonucleotide reductase (RNR) inhibitor hydroxyurea. Heterologous expression of the human ppGpp hydrolase Mesh1p prevented the accumulation of ppGpp in the engineered yeast and restored cell growth. Extensive in vivo interactions between bacterial signaling molecules and eukaryotic gene function occur, resulting in outcomes ranging from growth inhibition to death. cdiGMP functions through a mechanism that must be compensated by unhindered RNR activity or by functionally competent mitochondria. Mesh1p may be required for abrogating the damaging effects of ppGpp in human cells subjected to bacterial infection. IMPORTANCE During infections, pathogenic bacteria can release nucleotides into the cells of their eukaryotic hosts. These nucleotides are recognized as signals that contribute to the initiation of defensive immune responses that help the infected

  2. Evolutionary Origins of the Eukaryotic Shikimate Pathway: Gene Fusions, Horizontal Gene Transfer, and Endosymbiotic Replacements†

    Science.gov (United States)

    Richards, Thomas A.; Dacks, Joel B.; Campbell, Samantha A.; Blanchard, Jeffrey L.; Foster, Peter G.; McLeod, Rima; Roberts, Craig W.

    2006-01-01

    Currently the shikimate pathway is reported as a metabolic feature of prokaryotes, ascomycete fungi, apicomplexans, and plants. The plant shikimate pathway enzymes have similarities to prokaryote homologues and are largely active in chloroplasts, suggesting ancestry from the plastid progenitor genome. Toxoplasma gondii, which also possesses an alga-derived plastid organelle, encodes a shikimate pathway with similarities to ascomycete genes, including a five-enzyme pentafunctional arom. These data suggests that the shikimate pathway and the pentafunctional arom either had an ancient origin in the eukaryotes or was conveyed by eukaryote-to-eukaryote horizontal gene transfer (HGT). We expand sampling and analyses of the shikimate pathway genes to include the oomycetes, ciliates, diatoms, basidiomycetes, zygomycetes, and the green and red algae. Sequencing of cDNA from Tetrahymena thermophila confirmed the presence of a pentafused arom, as in fungi and T. gondii. Phylogenies and taxon distribution suggest that the arom gene fusion event may be an ancient eukaryotic innovation. Conversely, the Plantae lineage (represented here by both Viridaeplantae and the red algae) acquired different prokaryotic genes for all seven steps of the shikimate pathway. Two of the phylogenies suggest a derivation of the Plantae genes from the cyanobacterial plastid progenitor genome, but if the full Plantae pathway was originally of cyanobacterial origin, then the five other shikimate pathway genes were obtained from a minimum of two other eubacterial genomes. Thus, the phylogenies demonstrate both separate HGTs and shared derived HGTs within the Plantae clade either by primary HGT transfer or secondarily via the plastid progenitor genome. The shared derived characters support the holophyly of the Plantae lineage and a single ancestral primary plastid endosymbiosis. Our analyses also pinpoints a minimum of 50 gene/domain loss events, demonstrating that loss and replacement events have been

  3. A tree of life based on ninety-eight expressed genes conserved across diverse eukaryotic species.

    Directory of Open Access Journals (Sweden)

    Pawan Kumar Jayaswal

    Full Text Available Rapid advances in DNA sequencing technologies have resulted in the accumulation of large data sets in the public domain, facilitating comparative studies to provide novel insights into the evolution of life. Phylogenetic studies across the eukaryotic taxa have been reported but on the basis of a limited number of genes. Here we present a genome-wide analysis across different plant, fungal, protist, and animal species, with reference to the 36,002 expressed genes of the rice genome. Our analysis revealed 9831 genes unique to rice and 98 genes conserved across all 49 eukaryotic species analysed. The 98 genes conserved across diverse eukaryotes mostly exhibited binding and catalytic activities and shared common sequence motifs; and hence appeared to have a common origin. The 98 conserved genes belonged to 22 functional gene families including 26S protease, actin, ADP-ribosylation factor, ATP synthase, casein kinase, DEAD-box protein, DnaK, elongation factor 2, glyceraldehyde 3-phosphate, phosphatase 2A, ras-related protein, Ser/Thr protein phosphatase family protein, tubulin, ubiquitin and others. The consensus Bayesian eukaryotic tree of life developed in this study demonstrated widely separated clades of plants, fungi, and animals. Musa acuminata provided an evolutionary link between monocotyledons and dicotyledons, and Salpingoeca rosetta provided an evolutionary link between fungi and animals, which indicating that protozoan species are close relatives of fungi and animals. The divergence times for 1176 species pairs were estimated accurately by integrating fossil information with synonymous substitution rates in the comprehensive set of 98 genes. The present study provides valuable insight into the evolution of eukaryotes.

  4. Ion Channels Activated by Mechanical Forces in Bacterial and Eukaryotic Cells.

    Science.gov (United States)

    Sokabe, Masahiro; Sawada, Yasuyuki; Kobayashi, Takeshi

    2015-01-01

    Since the first discovery of mechanosensitive ion channel (MSC) in non-sensory cells in 1984, a variety of MSCs has been identified both in prokaryotic and eukaryotic cells. One of the central issues concerning MSCs is to understand the molecular and biophysical mechanisms of how mechanical forces activate/open MSCs. It has been well established that prokaryotic (mostly bacterial) MSCs are activated exclusively by membrane tension. Thus the problem to be solved with prokaryotic MSCs is the mechanisms how the MSC proteins receive tensile forces from the lipid bilayer and utilize them for channel opening. On the other hand, the activation of many eukaryotic MSCs crucially depends on tension in the actin cytoskeleton. By using the actin cytoskeleton as a force sensing antenna, eukaryotic MSCs have obtained sophisticated functions such as remote force sensing and force-direction sensing, which bacterial MSCs do not have. Actin cytoskeletons also give eukaryotic MSCs an interesting and important function called "active touch sensing", by which cells can sense rigidity of their substrates. The contractile actin cytoskeleton stress fiber (SF) anchors its each end to a focal adhesion (FA) and pulls the substrate to generate substrate-rigidity-dependent stresses in the FA. It has been found that those stresses are sensed by some Ca2+-permeable MSCs existing in the vicinity of FAs, thus the MSCs work as a substrate rigidity sensor that can transduce the rigidity into intracellular Ca2+ levels. This short review, roughly constituting of two parts, deals with molecular and biophysical mechanisms underlying the MSC activation process mostly based on our recent studies; (1) structure-function in bacterial MSCs activation at the atomic level, and (2) roles of actin cytoskeletons in the activation of eukaryotic MSCs.

  5. Did group II intron proliferation in an endosymbiont-bearing archaeon create eukaryotes?

    Directory of Open Access Journals (Sweden)

    Poole Anthony M

    2006-12-01

    Full Text Available Abstract Martin & Koonin recently proposed that the eukaryote nucleus evolved as a quality control mechanism to prevent ribosome readthrough into introns. In their scenario, the bacterial ancestor of mitochondria was resident in an archaeal cell, and group II introns (carried by the fledgling mitochondrion inserted into coding regions in the archaeal host genome. They suggest that if transcription and translation were coupled, and because splicing is expected to have been slower than translation, the effect of insertion would have been ribosome readthrough into introns, resulting in production of aberrant proteins. The emergence of the nuclear compartment would thus have served to separate transcription and splicing from translation, thereby alleviating this problem. In this article, I argue that Martin & Koonin's model is not compatible with current knowledge. The model requires that group II introns would spread aggressively through an archaeal genome. It is well known that selfish elements can spread through an outbreeding sexual population despite a substantial fitness cost to the host. The same is not true for asexual lineages however, where both theory and observation argue that such elements will be under pressure to reduce proliferation, and may be lost completely. The recent introduction of group II introns into archaea by horizontal transfer provides a natural test case with which to evaluate Martin & Koonin's model. The distribution and behaviour of these introns fits prior theoretical expectations, not the scenario of aggressive proliferation advocated by Martin & Koonin. I therefore conclude that the mitochondrial seed hypothesis for the origin of eukaryote introns, on which their model is based, better explains the early expansion of introns in eukaryotes. The mitochondrial seed hypothesis has the capacity to separate the origin of eukaryotes from the origin of introns, leaving open the possibility that the cell that engulfed the

  6. Special dossier: new energies

    International Nuclear Information System (INIS)

    Cassin, Fabrice; His, Stephane; Le Lidec, Frederic; Paillard, Michel; Vandevoorde, Patrick; Huby, Jean; Soetaert, Emmanuel; Bertiere, Francois; Zwierski, Didier; Kuntz, Michel; Mallet, Pierre; Leboucher, Nathalie; Isikveren, Murat; Vacher, Romain

    2012-01-01

    This special dossier about renewable energies is made of 14 contributions dealing with: wind turbines against radars, legal constraints on wind farms location (Fabrice Cassin); the sea, an ocean of wind energy (Stephane His); marine energies, a promising sector (Frederic Le Lidec); Gamesa, an integrated actor of the wind power industry; the great future of renewable marine energies (Michel Paillard); focus on wind power (Patrick Vandevoorde); wind power, a new industrial adventure (Jean Huby); hydropower, a renewed modernity (Emmanuel Soetaert); the new needs of tomorrows' cities (Francois Bertiere); the control of power consumption, a huge market in progress (Didier Zwierski, Michel Kuntz); in the heart of the smart grids revolution (Pierre Mallet); the smart-city, an established reality (Nathalie Leboucher); imagining solutions for the environment (Murat Isikveren); energy: towards a smart consumption (Romain Vacher)

  7. The TULIP superfamily of eukaryotic lipid-binding proteins as a mediator of lipid sensing and transport.

    Science.gov (United States)

    Alva, Vikram; Lupas, Andrei N

    2016-08-01

    The tubular lipid-binding (TULIP) superfamily has emerged in recent years as a major mediator of lipid sensing and transport in eukaryotes. It currently encompasses three protein families, SMP-like, BPI-like, and Takeout-like, which share a common fold. This fold consists of a long helix wrapped in a highly curved anti-parallel β-sheet, enclosing a central, lipophilic cavity. The SMP-like proteins, which include subunits of the ERMES complex and the extended synaptotagmins (E-Syts), appear to be mainly located at membrane contacts sites (MCSs) between organelles, mediating inter-organelle lipid exchange. The BPI-like proteins, which include the bactericidal/permeability-increasing protein (BPI), the LPS (lipopolysaccharide)-binding protein (LBP), the cholesteryl ester transfer protein (CETP), and the phospholipid transfer protein (PLTP), are either involved in innate immunity against bacteria through their ability to sense lipopolysaccharides, as is the case for BPI and LBP, or in lipid exchange between lipoprotein particles, as is the case for CETP and PLTP. The Takeout-like proteins, which are comprised of insect juvenile hormone-binding proteins and arthropod allergens, transport, where known, lipid hormones to target tissues during insect development. In all cases, the activity of these proteins is underpinned by their ability to bind large, hydrophobic ligands in their central cavity and segregate them away from the aqueous environment. Furthermore, where they are involved in lipid exchange, recent structural studies have highlighted their ability to establish lipophilic, tubular channels, either between organelles in the case of SMP domains or between lipoprotein particles in the case of CETP. Here, we review the current knowledge on the structure, versatile functions, and evolution of the TULIP superfamily. We propose a deep evolutionary split in this superfamily, predating the Last Eukaryotic Common Ancestor, between the SMP-like proteins, which act on

  8. Trends in Special Education

    Science.gov (United States)

    Gulliford, R.

    1977-01-01

    A broader concept of special education is developing--one that recognizes the relative frequency of special needs and the necessity for a range of alternative forms of special educational provision extending the idea into pre-school years and adult education with special methods of teaching and curricula required for the most handicapped students.…

  9. The Special Court for Sierra Leone

    DEFF Research Database (Denmark)

    Damgaard, Ciara Therése

    2004-01-01

    The focus of this article is the Special Court for Sierra Leone and the extent to which it can be said that the Special Court has already challenged, or will, in the future, challenge the tradition of impunity for gender-based crimes. In this regard, an analysis is undertaken of the Special Court......'s Statute, Rules of Procedure and Evidence and practice to date, in order to determine its treatment of gender-based crimes and whether it can be said that the Special Court for Sierra Leone challenges the tradition of impunity for gender-based crimes. Udgivelsesdato: december 2004...

  10. The Special Court for Sierra Leone

    DEFF Research Database (Denmark)

    Damgaard, Ciara Therése

    2004-01-01

    's Statute, Rules of Procedure and Evidence and practice to date, in order to determine its treatment of gender-based crimes and whether it can be said that the Special Court for Sierra Leone challenges the tradition of impunity for gender-based crimes. Udgivelsesdato: december 2004......The focus of this article is the Special Court for Sierra Leone and the extent to which it can be said that the Special Court has already challenged, or will, in the future, challenge the tradition of impunity for gender-based crimes. In this regard, an analysis is undertaken of the Special Court...

  11. Perspective plasma focus

    International Nuclear Information System (INIS)

    Lakicevic, I. S.

    1997-01-01

    Experimental results of the plasma focus have been analyzed and compared with theoretical regularities of the plasma force-free state. It has been shown that the plasma focus vortex filaments structures, which are closing in itself forming hot spots, have to be unstable, and so they are quickly destroying. That is the reason why in the plasma focus the controlled thermonuclear fusion can not be realized. (author)

  12. Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility

    Directory of Open Access Journals (Sweden)

    Hoeppner Marc P

    2012-09-01

    Full Text Available Abstract Background Small nucleolar (snoRNAs are required for posttranscriptional processing and modification of ribosomal, spliceosomal and messenger RNAs. Their presence in both eukaryotes and archaea indicates that snoRNAs are evolutionarily ancient. The location of some snoRNAs within the introns of ribosomal protein genes has been suggested to belie an RNA world origin, with the exons of the earliest protein-coding genes having evolved around snoRNAs after the advent of templated protein synthesis. Alternatively, this intronic location may reflect more recent selection for coexpression of snoRNAs and ribosomal components, ensuring rRNA modification by snoRNAs during ribosome synthesis. To gain insight into the evolutionary origins of this genetic organization, we examined the antiquity of snoRNA families and the stability of their genomic location across 44 eukaryote genomes. Results We report that dozens of snoRNA families are traceable to the Last Eukaryotic Common Ancestor (LECA, but find only weak similarities between the oldest eukaryotic snoRNAs and archaeal snoRNA-like genes. Moreover, many of these LECA snoRNAs are located within the introns of host genes independently traceable to the LECA. Comparative genomic analyses reveal the intronic location of LECA snoRNAs is not ancestral however, suggesting the pattern we observe is the result of ongoing intragenomic mobility. Analysis of human transcriptome data indicates that the primary requirement for hosting intronic snoRNAs is a broad expression profile. Consistent with ongoing mobility across broadly-expressed genes, we report a case of recent migration of a non-LECA snoRNA from the intron of a ubiquitously expressed non-LECA host gene into the introns of two LECA genes during the evolution of primates. Conclusions Our analyses show that snoRNAs were a well-established family of RNAs at the time when eukaryotes began to diversify. While many are intronic, this association is not

  13. Composition of Micro-eukaryotes on the Skin of the Cascades Frog (Rana cascadae and Patterns of Correlation between Skin Microbes and Batrachochytrium dendrobatidis

    Directory of Open Access Journals (Sweden)

    Jordan G. Kueneman

    2017-12-01

    Full Text Available Global amphibian decline linked to fungal pathogens has galvanized research on applied amphibian conservation. Skin-associated bacterial communities of amphibians have been shown to mediate fungal skin infections and the development of probiotic treatments with antifungal bacteria has become an emergent area of research. While exploring the role of protective bacteria has been a primary focus for amphibian conservation, we aim to expand and study the other microbes present in amphibian skin communities including fungi and other micro-eukaryotes. Here, we characterize skin-associated bacteria and micro-eukaryotic diversity found across life stages of Cascades frog (Rana cascadae and their associated aquatic environments using culture independent 16S and 18S rRNA marker-gene sequencing. Individuals of various life stages of Cascades frogs were sampled from a population located in the Trinity Alps in Northern California during an epidemic of the chytrid fungus, Batrachochytrium dendrobatidis. We filtered the bacterial sequences against a published database of bacteria known to inhibit B. dendrobatidis in co-culture to estimate the proportion of the skin bacterial community that is likely to provide defense against B. dendrobatidis. Tadpoles had a significantly higher proportion of B. dendrobatidis-inhibitory bacterial sequence matches relative to subadult and adult Cascades frogs. We applied a network analysis to examine patterns of correlation between bacterial taxa and B. dendrobatidis, as well as micro-eukaryotic taxa and B. dendrobatidis. Combined with the published database of bacteria known to inhibit B. dendrobatidis, we used the network analysis to identify bacteria that negatively correlated with B. dendrobatidis and thus could be good probiotic candidates in the Cascades frog system.

  14. Focusing Automatic Code Inspections

    NARCIS (Netherlands)

    Boogerd, C.J.

    2010-01-01

    Automatic Code Inspection tools help developers in early detection of defects in software. A well-known drawback of many automatic inspection approaches is that they yield too many warnings and require a clearer focus. In this thesis, we provide such focus by proposing two methods to prioritize

  15. Space Focus Lead Report

    Energy Technology Data Exchange (ETDEWEB)

    Reeves, Geoffrey D. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-08-10

    The Space Focus team is tasked with the definition of the Space Focused Science Topics, and with the review and ranking of the CSES proposals received in all the program areas. This is achieved by dedicated meetings or a series of informal discussions and/or e-mail reviews.

  16. Focus and VP Ellipsis

    Science.gov (United States)

    Frazier, Lyn; Clifton, Charles, Jr.; Carlson, Katy

    2007-01-01

    In spoken English, pitch accents can convey the focus associated with new or contrasted constituents. Two listening experiments were conducted to determine whether accenting a subject makes its predicate a more tempting antecedent for an elided verb phrase, presumably because the accent helps focus the subject of the antecedent clause, increasing…

  17. Shedding light on the expansion and diversification of the Cdc48 protein family during the rise of the eukaryotic cell.

    Science.gov (United States)

    Kienle, Nickias; Kloepper, Tobias H; Fasshauer, Dirk

    2016-10-18

    A defining feature of eukaryotic cells is the presence of various distinct membrane-bound compartments with different metabolic roles. Material exchange between most compartments occurs via a sophisticated vesicle trafficking system. This intricate cellular architecture of eukaryotes appears to have emerged suddenly, about 2 billion years ago, from much less complex ancestors. How the eukaryotic cell acquired its internal complexity is poorly understood, partly because no prokaryotic precursors have been found for many key factors involved in compartmentalization. One exception is the Cdc48 protein family, which consists of several distinct classical ATPases associated with various cellular activities (AAA+) proteins with two consecutive AAA domains. Here, we have classified the Cdc48 family through iterative use of hidden Markov models and tree building. We found only one type, Cdc48, in prokaryotes, although a set of eight diverged members that function at distinct subcellular compartments were retrieved from eukaryotes and were probably present in the last eukaryotic common ancestor (LECA). Pronounced changes in sequence and domain structure during the radiation into the LECA set are delineated. Moreover, our analysis brings to light lineage-specific losses and duplications that often reflect important biological changes. Remarkably, we also found evidence for internal duplications within the LECA set that probably occurred during the rise of the eukaryotic cell. Our analysis corroborates the idea that the diversification of the Cdc48 family is closely intertwined with the development of the compartments of the eukaryotic cell.

  18. The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups.

    Science.gov (United States)

    Koonin, Eugene V; Wolf, Yuri I; Nagasaki, Keizo; Dolja, Valerian V

    2008-12-01

    The recent discovery of RNA viruses in diverse unicellular eukaryotes and developments in evolutionary genomics have provided the means for addressing the origin of eukaryotic RNA viruses. The phylogenetic analyses of RNA polymerases and helicases presented in this Analysis article reveal close evolutionary relationships between RNA viruses infecting hosts from the Chromalveolate and Excavate supergroups and distinct families of picorna-like viruses of plants and animals. Thus, diversification of picorna-like viruses probably occurred in a 'Big Bang' concomitant with key events of eukaryogenesis. The origins of the conserved genes of picorna-like viruses are traced to likely ancestors including bacterial group II retroelements, the family of HtrA proteases and DNA bacteriophages.

  19. Once in a lifetime: strategies for preventing re-replication in prokaryotic and eukaryotic cells.

    Science.gov (United States)

    Nielsen, Olaf; Løbner-Olesen, Anders

    2008-02-01

    DNA replication is an extremely accurate process and cells have evolved intricate control mechanisms to ensure that each region of their genome is replicated only once during S phase. Here, we compare what is known about the processes that prevent re-replication in prokaryotic and eukaryotic cells by using the model organisms Escherichia coli and Schizosaccharomyces pombe as examples. Although the underlying molecular details are different, the logic behind the control mechanisms is similar. For example, after initiation, crucial molecules required for the loading of replicative helicases in both prokaryotes and eukaryotes are inactivated until the next cell cycle. Furthermore, in both systems the beta-clamp of the replicative polymerase associates with enzymatic activities that contribute to the inactivation of the helicase loaders. Finally, recent studies suggest that the control mechanism that prevents re-replication in both systems also increases the synthesis of DNA building blocks.

  20. Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases

    Science.gov (United States)

    Buey, Rubén M.; Ledesma-Amaro, Rodrigo; Velázquez-Campoy, Adrián; Balsera, Mónica; Chagoyen, Mónica; de Pereda, José M.; Revuelta, José L.

    2015-11-01

    Inosine-5'-monophosphate dehydrogenase (IMPDH) plays key roles in purine nucleotide metabolism and cell proliferation. Although IMPDH is a widely studied therapeutic target, there is limited information about its physiological regulation. Using Ashbya gossypii as a model, we describe the molecular mechanism and the structural basis for the allosteric regulation of IMPDH by guanine nucleotides. We report that GTP and GDP bind to the regulatory Bateman domain, inducing octamers with compromised catalytic activity. Our data suggest that eukaryotic and prokaryotic IMPDHs might have developed different regulatory mechanisms, with GTP/GDP inhibiting only eukaryotic IMPDHs. Interestingly, mutations associated with human retinopathies map into the guanine nucleotide-binding sites including a previously undescribed non-canonical site and disrupt allosteric inhibition. Together, our results shed light on the mechanisms of the allosteric regulation of enzymes mediated by Bateman domains and provide a molecular basis for certain retinopathies, opening the door to new therapeutic approaches.

  1. EVpedia: A community web resource for prokaryotic and eukaryotic extracellular vesicles research.

    Science.gov (United States)

    Kim, Dae-Kyum; Lee, Jaewook; Simpson, Richard J; Lötvall, Jan; Gho, Yong Song

    2015-04-01

    For cell-to-cell communication, all living cells including archaea, bacteria, and eukaryotes secrete nano-sized membrane vesicles into the extracellular space. These extracellular vesicles harbor specific subsets of proteins, mRNAs, miRNAs, lipids, and metabolites that represent their cellular status. These vesicle-specific cargos are considered as novel diagnostic biomarkers as well as therapeutic targets. With the advancement in high-throughput technologies on multiomics studies and improvements in bioinformatics approaches, a huge number of vesicular proteins, mRNAs, miRNAs, lipids, and metabolites have been identified, and our understanding of these complex extracellular organelles has considerably increased during these past years. In this review, we highlight EVpedia (http://evpedia.info), a community web portal for systematic analyses of prokaryotic and eukaryotic extracellular vesicles research. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Production of isotopically labeled heterologous proteins in non-E. coli prokaryotic and eukaryotic cells.

    Science.gov (United States)

    Takahashi, Hideo; Shimada, Ichio

    2010-01-01

    The preparation of stable isotope-labeled proteins is necessary for the application of a wide variety of NMR methods, to study the structures and dynamics of proteins and protein complexes. The E. coli expression system is generally used for the production of isotope-labeled proteins, because of the advantages of ease of handling, rapid growth, high-level protein production, and low cost for isotope-labeling. However, many eukaryotic proteins are not functionally expressed in E. coli, due to problems related to disulfide bond formation, post-translational modifications, and folding. In such cases, other expression systems are required for producing proteins for biomolecular NMR analyses. In this paper, we review the recent advances in expression systems for isotopically labeled heterologous proteins, utilizing non-E. coli prokaryotic and eukaryotic cells.

  3. Origins of robustness in translational control via eukaryotic translation initiation factor (eIF) 2.

    Science.gov (United States)

    Khan, Mohammad Farhan; Spurgeon, Sarah; von der Haar, Tobias

    2018-05-14

    Phosphorylation of eukaryotic translation initiation factor 2 (eIF2) is one of the best studied and most widely used means for regulating protein synthesis activity in eukaryotic cells. This pathway regulates protein synthesis in response to stresses, viral infections, and nutrient depletion, among others. We present analyses of an ordinary differential equation-based model of this pathway, which aim to identify its principal robustness-conferring features. Our analyses indicate that robustness is a distributed property, rather than arising from the properties of any one individual pathway species. However, robustness-conferring properties are unevenly distributed between the different species, and we identify a guanine nucleotide dissociation inhibitor (GDI) complex as a species that likely contributes strongly to the robustness of the pathway. Our analyses make further predictions on the dynamic response to different types of kinases that impinge on eIF2. Copyright © 2018 Elsevier Ltd. All rights reserved.

  4. Diversity of eukaryotic microorganisms: computer-based resources, "The Handbook of Protoctista" and its "Glossary"

    Science.gov (United States)

    Margulis, L.; Olendzenski, L.; Dolan, M.; MacIntyre, F.

    1996-01-01

    The kingdom Protoctista comprises some 30 phyla, including the eukaryotic anaerobes that permanently lack mitochondria, the Phylum Archaeprotista, with its three classes: (i) Archamoebae, e.g., Pelomyxa, Mastigina, (ii) Metamonada, e.g., Giardia, Pyrsonympha, and (iii) Parabasalia, e.g., Trichomonas, Calonympha, and the Phylum Microspora (Microsporidia), e.g., Vairimorpha. These and all algae, protozoa, labyrinthulids, "water molds" (oomycota, plasmodiophorans, hyphochytrids, chytrids, etc.) and other eukaryotes excluded from plants, animals and fungi are detailed in the Handbook of Protoctista. The Illustrated Glossary of Protoctista contains descriptions of the morphology and taxonomy of these microorganisms, including the many equivalent and homologous structures with different names. The Glossary has also been made into a Macintosh-compatible CD-ROM disk.

  5. On eukaryotic intelligence: signaling system's guidance in the evolution of multicellular organization.

    Science.gov (United States)

    Marijuán, Pedro C; del Moral, Raquel; Navarro, Jorge

    2013-10-01

    Communication with the environment is an essential characteristic of the living cell, even more when considering the origins and evolution of multicellularity. A number of changes and tinkering inventions were necessary in the evolutionary transition between prokaryotic and eukaryotic cells, which finally made possible the appearance of genuine multicellular organisms. In the study of this process, however, the transformations experimented by signaling systems themselves have been rarely object of analysis, obscured by other more conspicuous biological traits: incorporation of mitochondria, segregated nucleus, introns/exons, flagellum, membrane systems, etc. Herein a discussion of the main avenues of change from prokaryotic to eukaryotic signaling systems and a review of the signaling resources and strategies underlying multicellularity will be attempted. In the expansion of prokaryotic signaling systems, four main systemic resources were incorporated: molecular tools for detection of solutes, molecular tools for detection of solvent (Donnan effect), the apparatuses of cell-cycle control, and the combined system endocytosis/cytoskeleton. The multiple kinds of enlarged, mixed pathways that emerged made possible the eukaryotic revolution in morphological and physiological complexity. The massive incorporation of processing resources of electro-molecular nature, derived from the osmotic tools counteracting the Donnan effect, made also possible the organization of a computational tissue with huge information processing capabilities: the nervous system. In the central nervous systems of vertebrates, and particularly in humans, neurons have achieved both the highest level of molecular-signaling complexity and the highest degree of information-processing adaptability. Theoretically, it can be argued that there has been an accelerated pace of evolutionary change in eukaryotic signaling systems, beyond the other general novelties introduced by eukaryotic cells in their

  6. Modeling cytokinesis of eukaryotic cells driven by the actomyosin contractile ring.

    Science.gov (United States)

    Zhao, Jia; Wang, Qi

    2016-12-01

    A three-dimensional (3D) hydrodynamic model for cytokinesis of eukaryotic cells is developed, in which we model dynamics of actomyosins in the cell cortex, in particular, along the cytokinetic ring formed in the cortex and in the neighborhood of the cell's division plane explicitly. Specifically, the active force actuated by the actomyosin's activity along the cytokinetic ring is modeled by a surface force whose strength is proportional to the actomyosin concentration while the cell morphology is tracked by a phase field model. The model is then solved in 3D space and time using a finite difference method on graphic processing units. Dynamical morphological patterns of eukaryotic cells during cytokinesis are numerically simulated with the model. These simulated morphological patterns agree quantitatively with experimental observations. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  7. Role for RNA:DNA hybrids in origin-independent replication priming in a eukaryotic system.

    Science.gov (United States)

    Stuckey, Ruth; García-Rodríguez, Néstor; Aguilera, Andrés; Wellinger, Ralf Erik

    2015-05-05

    DNA replication initiates at defined replication origins along eukaryotic chromosomes, ensuring complete genome duplication within a single S-phase. A key feature of replication origins is their ability to control the onset of DNA synthesis mediated by DNA polymerase-α and its intrinsic RNA primase activity. Here, we describe a novel origin-independent replication process that is mediated by transcription. RNA polymerase I transcription constraints lead to persistent RNA:DNA hybrids (R-loops) that prime replication in the ribosomal DNA locus. Our results suggest that eukaryotic genomes have developed tools to prevent R-loop-mediated replication events that potentially contribute to copy number variation, particularly relevant to carcinogenesis.

  8. DNA structural features of eukaryotic TATA-containing and TATA-less promoters.

    Science.gov (United States)

    Yella, Venkata Rajesh; Bansal, Manju

    2017-03-01

    Eukaryotic genes can be broadly classified as TATA-containing and TATA-less based on the presence of TATA box in their promoters. Experiments on both classes of genes have revealed a disparity in the regulation of gene expression and cellular functions between the two classes. In this study, we report characteristic differences in promoter sequences and associated structural properties of the two categories of genes in six different eukaryotes. We have analyzed three structural features, DNA duplex stability, bendability, and curvature along with the distribution of A-tracts, G-quadruplex motifs, and CpG islands. The structural feature analyses reveal that while the two classes of gene promoters are distinctly different from each other, the properties are also distinguishable across the six organisms.

  9. Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA

    Science.gov (United States)

    Zhu, Yanglong; Stribinskis, Vilius; Ramos, Kenneth S.; Li, Yong

    2006-01-01

    RNase MRP is a eukaryote-specific endoribonuclease that generates RNA primers for mitochondrial DNA replication and processes precursor rRNA. RNase P is a ubiquitous endoribonuclease that cleaves precursor tRNA transcripts to produce their mature 5′ termini. We found extensive sequence homology of catalytic domains and specificity domains between their RNA subunits in many organisms. In Candida glabrata, the internal loop of helix P3 is 100% conserved between MRP and P RNAs. The helix P8 of MRP RNA from microsporidia Encephalitozoon cuniculi is identical to that of P RNA. Sequence homology can be widely spread over the whole molecule of MRP RNA and P RNA, such as those from Dictyostelium discoideum. These conserved nucleotides between the MRP and P RNAs strongly support the hypothesis that the MRP RNA is derived from the P RNA molecule in early eukaryote evolution. PMID:16540690

  10. Production of isotopically labeled heterologous proteins in non-E. coli prokaryotic and eukaryotic cells

    International Nuclear Information System (INIS)

    Takahashi, Hideo; Shimada, Ichio

    2010-01-01

    The preparation of stable isotope-labeled proteins is necessary for the application of a wide variety of NMR methods, to study the structures and dynamics of proteins and protein complexes. The E. coli expression system is generally used for the production of isotope-labeled proteins, because of the advantages of ease of handling, rapid growth, high-level protein production, and low cost for isotope-labeling. However, many eukaryotic proteins are not functionally expressed in E. coli, due to problems related to disulfide bond formation, post-translational modifications, and folding. In such cases, other expression systems are required for producing proteins for biomolecular NMR analyses. In this paper, we review the recent advances in expression systems for isotopically labeled heterologous proteins, utilizing non-E. coli prokaryotic and eukaryotic cells.

  11. Eukaryotic diversity in late Pleistocene marine sediments around a shallow methane hydrate deposit in the Japan Sea.

    Science.gov (United States)

    Kouduka, M; Tanabe, A S; Yamamoto, S; Yanagawa, K; Nakamura, Y; Akiba, F; Tomaru, H; Toju, H; Suzuki, Y

    2017-09-01

    Marine sediments contain eukaryotic DNA deposited from overlying water columns. However, a large proportion of deposited eukaryotic DNA is aerobically biodegraded in shallow marine sediments. Cold seep sediments are often anaerobic near the sediment-water interface, so eukaryotic DNA in such sediments is expected to be preserved. We investigated deeply buried marine sediments in the Japan Sea, where a methane hydrate deposit is associated with cold seeps. Quantitative PCR analysis revealed the reproducible recovery of eukaryotic DNA in marine sediments at depths up to 31.0 m in the vicinity of the methane hydrate deposit. In contrast, the reproducible recovery of eukaryotic DNA was limited to a shallow depth (8.3 m) in marine sediments not adjacent to the methane hydrate deposit in the same area. Pyrosequencing of an 18S rRNA gene variable region generated 1,276-3,307 reads per sample, which was sufficient to cover the biodiversity based on rarefaction curves. Phylogenetic analysis revealed that most of the eukaryotic DNA originated from radiolarian genera of the class Chaunacanthida, which have SrSO 4 skeletons, the sea grass genus Zostera, and the seaweed genus Sargassum. Eukaryotic DNA originating from other planktonic fauna and land plants was also detected. Diatom sequences closely related to Thalassiosira spp., indicative of cold climates, were obtained from sediments deposited during the last glacial period (MIS-2). Plant sequences of the genera Alnus, Micromonas, and Ulmus were found in sediments deposited during the warm interstadial period (MIS-3). These results suggest the long-term persistence of eukaryotic DNA from terrestrial and aquatic sources in marine sediments associated with cold seeps, and that the genetic information from eukaryotic DNA from deeply buried marine sediments associated with cold seeps can be used to reconstruct environments and ecosystems from the past. © 2017 John Wiley & Sons Ltd.

  12. DESY: focuses on HERA

    International Nuclear Information System (INIS)

    Anon.

    1992-01-01

    On 1 October, a special 'FestKolloquium' at DESY marked the official start of the research programme at the new HERA electron-proton collider, which began operations earlier this year. The timing could not have been better, as HERA performance had improved by a factor of ten during the two weeks beforehand. More than 600 guests assembled in one of the big halls previously used for assembly of major components for HERA experiments

  13. Morphology of the Proterozoic eukaryotic microfossils as a reflection of their intracellular complexity

    OpenAIRE

    Agić, Heda; Moczydłowska, Małgorzata; Yin, Leiming

    2014-01-01

    Mesoproterozoic is a time of increasing diversity of microscopic life and appearance of intricate new cell morphologies. First eukaryotes may have evolved around 2.4 Ga, but the first microbiota with intricate sculpture and ornamentation are found in the younger, 1.8.-1.6 Ga successions worldwide. Such microfossils were uncovered from the Ruyang Formation in Shanxi, China and Roper Group, Northern Territories, Australia, dating back to 1.6-1.0 Ga ago. Some of these unicellular organic-walled ...

  14. Expression of the lysostaphin gene of Staphylococcus simulans in a eukaryotic system.

    OpenAIRE

    Williamson, C M; Bramley, A J; Lax, A J

    1994-01-01

    The lysostaphin gene of Staphylococcus simulans was cloned into Escherichia coli. The 5' end of the gene was modified to include a eukaryotic start codon, the Kozak expression start site consensus sequence, and an enzyme site to facilitate manipulation of the gene. Transcription of the modified gene in vitro yielded an RNA transcript which, when added to a rabbit reticulocyte cell-free translation system, directed the synthesis of several products. The largest product, migrating at approximat...

  15. Mitochondria, the Cell Cycle, and the Origin of Sex via a Syncytial Eukaryote Common Ancestor

    OpenAIRE

    Garg, Sriram G.; Martin, William F.

    2016-01-01

    Theories for the origin of sex traditionally start with an asexual mitosing cell and add recombination, thereby deriving meiosis from mitosis. Though sex was clearly present in the eukaryote common ancestor, the order of events linking the origin of sex and the origin of mitosis is unknown. Here, we present an evolutionary inference for the origin of sex starting with a bacterial ancestor of mitochondria in the cytosol of its archaeal host. We posit that symbiotic association led to the origi...

  16. Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells

    OpenAIRE

    Weghuber, Julian; Aichinger, Michael C.; Brameshuber, Mario; Wieser, Stefan; Ruprecht, Verena; Plochberger, Birgit; Madl, Josef; Horner, Andreas; Reipert, Siegfried; Lohner, Karl; Henics, Tamas; Schuetz, Gerhard J

    2011-01-01

    Cationic antimicrobial peptides (CAMPs) selectively target bacterial membranes by electrostatic interactions with negatively charged lipids. It turned out that for inhibition of microbial growth a high CAMP membrane concentration is required, which can be realized by the incorporation of hydrophobic groups within the peptide. Increasing hydrophobicity, however, reduces the CAMP selectivity for bacterial over eukaryotic host membranes, thereby causing the risk of detrimental side-effects. In t...

  17. IRES-mediated translation of membrane proteins and glycoproteins in eukaryotic cell-free systems.

    Directory of Open Access Journals (Sweden)

    Andreas K Brödel

    Full Text Available Internal ribosome entry site (IRES elements found in the 5' untranslated region of mRNAs enable translation initiation in a cap-independent manner, thereby representing an alternative to cap-dependent translation in cell-free protein expression systems. However, IRES function is largely species-dependent so their utility in cell-free systems from different species is rather limited. A promising approach to overcome these limitations would be the use of IRESs that are able to recruit components of the translation initiation apparatus from diverse origins. Here, we present a solution to this technical problem and describe the ability of a number of viral IRESs to direct efficient protein expression in different eukaryotic cell-free expression systems. The IRES from the intergenic region (IGR of the Cricket paralysis virus (CrPV genome was shown to function efficiently in four different cell-free systems based on lysates derived from cultured Sf21, CHO and K562 cells as well as wheat germ. Our results suggest that the CrPV IGR IRES-based expression vector is universally applicable for a broad range of eukaryotic cell lysates. Sf21, CHO and K562 cell-free expression systems are particularly promising platforms for the production of glycoproteins and membrane proteins since they contain endogenous microsomes that facilitate the incorporation of membrane-spanning proteins and the formation of post-translational modifications. We demonstrate the use of the CrPV IGR IRES-based expression vector for the enhanced synthesis of various target proteins including the glycoprotein erythropoietin and the membrane proteins heparin-binding EGF-like growth factor receptor as well as epidermal growth factor receptor in the above mentioned eukaryotic cell-free systems. CrPV IGR IRES-mediated translation will facilitate the development of novel eukaryotic cell-free expression platforms as well as the high-yield synthesis of desired proteins in already established

  18. This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes.

    Directory of Open Access Journals (Sweden)

    Christian M Zmasek

    Full Text Available Evolutionary innovation in eukaryotes and especially animals is at least partially driven by genome rearrangements and the resulting emergence of proteins with new domain combinations, and thus potentially novel functionality. Given the random nature of such rearrangements, one could expect that proteins with particularly useful multidomain combinations may have been rediscovered multiple times by parallel evolution. However, existing reports suggest a minimal role of this phenomenon in the overall evolution of eukaryotic proteomes. We assembled a collection of 172 complete eukaryotic genomes that is not only the largest, but also the most phylogenetically complete set of genomes analyzed so far. By employing a maximum parsimony approach to compare repertoires of Pfam domains and their combinations, we show that independent evolution of domain combinations is significantly more prevalent than previously thought. Our results indicate that about 25% of all currently observed domain combinations have evolved multiple times. Interestingly, this percentage is even higher for sets of domain combinations in individual species, with, for instance, 70% of the domain combinations found in the human genome having evolved independently at least once in other species. We also show that previous, much lower estimates of this rate are most likely due to the small number and biased phylogenetic distribution of the genomes analyzed. The process of independent emergence of identical domain combination is widespread, not limited to domains with specific functional categories. Besides data from large-scale analyses, we also present individual examples of independent domain combination evolution. The surprisingly large contribution of parallel evolution to the development of the domain combination repertoire in extant genomes has profound consequences for our understanding of the evolution of pathways and cellular processes in eukaryotes and for comparative

  19. New insights into the structural organization of eukaryotic and prokaryotic cytoskeletons using cryo-electron tomography

    International Nuclear Information System (INIS)

    Kuerner, Julia; Medalia, Ohad; Linaroudis, Alexandros A.; Baumeister, Wolfgang

    2004-01-01

    Cryo-electron tomography (cryo-ET) is an emerging imaging technology that combines the potential of three-dimensional (3-D) imaging at molecular resolution (<5 nm) with a close-to-life preservation of the specimen. In conjunction with pattern recognition techniques, it enables us to map the molecular landscape inside cells. The application of cryo-ET to intact cells provides novel insights into the structure and the spatial organization of the cytoskeleton in prokaryotic and eukaryotic cells

  20. Once in a lifetime: strategies for preventing re-replication in prokaryotic and eukaryotic cells.

    OpenAIRE

    Nielsen, Olaf; Løbner-Olesen, Anders

    2008-01-01

    Udgivelsesdato: 2008-Feb DNA replication is an extremely accurate process and cells have evolved intricate control mechanisms to ensure that each region of their genome is replicated only once during S phase. Here, we compare what is known about the processes that prevent re-replication in prokaryotic and eukaryotic cells by using the model organisms Escherichia coli and Schizosaccharomyces pombe as examples. Although the underlying molecular details are different, the logic behind the con...

  1. Intra-plastid protein trafficking: How plant cells adapted prokaryotic mechanisms to the eukaryotic condition

    OpenAIRE

    Celedon, Jose M.; Cline, Kenneth

    2013-01-01

    Protein trafficking and localization in plastids involves a complex interplay between ancient (prokaryotic) and novel (eukaryotic) translocases and targeting machineries. During evolution, ancient systems acquired new functions and novel translocation machineries were developed to facilitate the correct localization of nuclear encoded proteins targeted to the chloroplast. Because of its post-translational nature, targeting and integration of membrane proteins posed the biggest challenge to th...

  2. IRES-Mediated Translation of Membrane Proteins and Glycoproteins in Eukaryotic Cell-Free Systems

    Science.gov (United States)

    Brödel, Andreas K.; Sonnabend, Andrei; Roberts, Lisa O.; Stech, Marlitt; Wüstenhagen, Doreen A.; Kubick, Stefan

    2013-01-01

    Internal ribosome entry site (IRES) elements found in the 5′ untranslated region of mRNAs enable translation initiation in a cap-independent manner, thereby representing an alternative to cap-dependent translation in cell-free protein expression systems. However, IRES function is largely species-dependent so their utility in cell-free systems from different species is rather limited. A promising approach to overcome these limitations would be the use of IRESs that are able to recruit components of the translation initiation apparatus from diverse origins. Here, we present a solution to this technical problem and describe the ability of a number of viral IRESs to direct efficient protein expression in different eukaryotic cell-free expression systems. The IRES from the intergenic region (IGR) of the Cricket paralysis virus (CrPV) genome was shown to function efficiently in four different cell-free systems based on lysates derived from cultured Sf21, CHO and K562 cells as well as wheat germ. Our results suggest that the CrPV IGR IRES-based expression vector is universally applicable for a broad range of eukaryotic cell lysates. Sf21, CHO and K562 cell-free expression systems are particularly promising platforms for the production of glycoproteins and membrane proteins since they contain endogenous microsomes that facilitate the incorporation of membrane-spanning proteins and the formation of post-translational modifications. We demonstrate the use of the CrPV IGR IRES-based expression vector for the enhanced synthesis of various target proteins including the glycoprotein erythropoietin and the membrane proteins heparin-binding EGF-like growth factor receptor as well as epidermal growth factor receptor in the above mentioned eukaryotic cell-free systems. CrPV IGR IRES-mediated translation will facilitate the development of novel eukaryotic cell-free expression platforms as well as the high-yield synthesis of desired proteins in already established systems. PMID

  3. Evolution and function of eukaryotic-like proteins from sponge symbionts.

    Science.gov (United States)

    Reynolds, David; Thomas, Torsten

    2016-10-01

    Sponges (Porifera) are ancient metazoans that harbour diverse microorganisms, whose symbiotic interactions are essential for the host's health and function. Although symbiosis between bacteria and sponges are ubiquitous, the molecular mechanisms that control these associations are largely unknown. Recent (meta-) genomic analyses discovered an abundance of genes encoding for eukaryotic-like proteins (ELPs) in bacterial symbionts from different sponge species. ELPs belonging to the ankyrin repeat (AR) class from a bacterial symbiont of the sponge Cymbastela concentrica were subsequently found to modulate amoebal phagocytosis. This might be a molecular mechanism, by which symbionts can control their interaction with the sponge. In this study, we investigated the evolution and function of ELPs from other classes and from symbionts found in other sponges to better understand the importance of ELPs for bacteria-eukaryote interactions. Phylogenetic analyses showed that all of the nine ELPs investigated were most closely related to proteins found either in eukaryotes or in bacteria that can live in association with eukaryotes. ELPs were then recombinantly expressed in Escherichia coli and exposed to the amoeba Acanthamoeba castellanii, which is functionally analogous to phagocytic cells in sponges. Phagocytosis assays with E. coli containing three ELP classes (AR, TPR-SEL1 and NHL) showed a significantly higher percentage of amoeba containing bacteria and average number of intracellular bacteria per amoeba when compared to negative controls. The result that various classes of ELPs found in symbionts of different sponges can modulate phagocytosis indicates that they have a broader function in mediating bacteria-sponge interactions. © 2016 John Wiley & Sons Ltd.

  4. Construction of sized eukaryotic cDNA libraries using low input of total environmental metatranscriptomic RNA

    OpenAIRE

    Yadav, Rajiv Kumar; Barbi, Florian; Ziller, Antoine; Luis, Patricia; Marmeisse, Roland; Reddy, M Sudhakara; Fraissinet-Tachet, Laurence

    2014-01-01

    Background: Construction of high quality cDNA libraries from the usually low amounts of eukaryotic mRNA extracted from environmental samples is essential in functional metatranscriptomics for the selection of functional, full-length genes encoding proteins of interest. Many of the inserts in libraries constructed by standard methods are represented by truncated cDNAs due to premature stoppage of reverse transcriptase activity and preferential cloning of short cDNAs. Results: We report here a ...

  5. Metabolism in anoxic permeable sediments is dominated by eukaryotic dark fermentation

    DEFF Research Database (Denmark)

    Bourke, Michael F.; Marriott, Philip J; Glud, Ronnie N.

    2017-01-01

    Permeable sediments are common across continental shelves and are critical contributors to marine biogeochemical cycling. Organic matter in permeable sediments is dominated by microalgae, which as eukaryotes have different anaerobic metabolic pathways to prokaryotes such as bacteria and archaea....... Cell counts revealed a predominance of microalgae in the sediments. H2 production was observed in dark anoxic cultures of diatoms (Fragilariopsis sp.) and a chlorophyte (Pyramimonas) isolated from the study site, substantiating the hypothesis that microalgae undertake fermentation. We conclude...

  6. Genomic and experimental evidence suggests that Verrucomicrobium spinosum interacts with eukaryotes

    Directory of Open Access Journals (Sweden)

    Michelle eSait

    2011-10-01

    Full Text Available Our knowledge of pathogens and symbionts is heavily biased towards phyla containing species that are straightforward to isolate in pure culture. Novel bacterial phyla are often represented by a handful of strains, and the number of species interacting with eukaryotes is likely underestimated. Identification of predicted pathogenesis and symbiosis determinants such as the Type III Secretion System (T3SS in the genomes of ‘free-living’ bacteria suggests that these microbes participate in uncharacterized interactions with eukaryotes. Our study aimed to test this hypothesis on Verrucomicrobium spinosum (phylum Verrucomicrobia and to begin characterization of its predicted T3SS. We showed the putative T3SS structural genes to be transcriptionally active, and that expression of predicted effector proteins was toxic to yeast in an established functional screen. Our results suggest that the predicted T3SS genes of V. spinosum could encode a functional T3SS, although further work is needed to determine whether V. spinosum produces a T3SS injectisome that delivers the predicted effectors. In the absence of a known eukaryotic host, we made use of invertebrate infection models. The injection or feeding of V. spinosum to Drosophila melanogaster and Caenorhabiditis elegans, respectively, was shown to result in increased mortality rates relative to controls, a phenomenon exaggerated in C. elegans mutants hypersensitive to pathogen infection. This finding, although not conclusively demonstrating pathogenesis, suggests that V. spinosum is capable of pathogenic activity towards an invertebrate host. Symbiotic interactions with a natural host provide an alternative explanation for the results seen in the invertebrate models. Further work is needed to determine whether V. spinosum can establish and maintain interactions with eukaryotic species found in its natural habitat, and whether the predicted T3SS is directly involved in pathogenic or symbiotic activity.

  7. Viruses of eukaryotic green algae. Final technical report, June 1, 1989--February 1, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Van Etten, J.L.

    1992-12-31

    We have isolated and partially characterized many large, polyhedral, DNA containing, plaque forming viruses which infect certain unicellular, eukaryotic, chlorella-like green algae. These viruses have several unique features, including the fact that they code for DNA site-specific endonucleases and DNA methyltransferases. The primary objectives of this study were to identify, clone, and characterize some of the virus-encoded DNA methyltransferases and DNA restriction endonucleases in order to understand their biological function.

  8. Functional and evolutionary characterization of Ohr proteins in eukaryotes reveals many active homologs among pathogenic fungi

    Directory of Open Access Journals (Sweden)

    D.A. Meireles

    2017-08-01

    Full Text Available Ohr and OsmC proteins comprise two subfamilies within a large group of proteins that display Cys-based, thiol dependent peroxidase activity. These proteins were previously thought to be restricted to prokaryotes, but we show here, using iterated sequence searches, that Ohr/OsmC homologs are also present in 217 species of eukaryotes with a massive presence in Fungi (186 species. Many of these eukaryotic Ohr proteins possess an N-terminal extension that is predicted to target them to mitochondria. We obtained recombinant proteins for four eukaryotic members of the Ohr/OsmC family and three of them displayed lipoyl peroxidase activity. Further functional and biochemical characterization of the Ohr homologs from the ascomycete fungus Mycosphaerella fijiensis Mf_1 (MfOhr, the causative agent of Black Sigatoka disease in banana plants, was pursued. Similarly to what has been observed for the bacterial proteins, we found that: (i the peroxidase activity of MfOhr was supported by DTT or dihydrolipoamide (dithiols, but not by β-mercaptoethanol or GSH (monothiols, even in large excess; (ii MfOhr displayed preference for organic hydroperoxides (CuOOH and tBOOH over hydrogen peroxide; (iii MfOhr presented extraordinary reactivity towards linoleic acid hydroperoxides (k=3.18 (±2.13×108 M−1 s−1. Both Cys87 and Cys154 were essential to the peroxidase activity, since single mutants for each Cys residue presented no activity and no formation of intramolecular disulfide bond upon treatment with hydroperoxides. The pKa value of the Cysp residue was determined as 5.7±0.1 by a monobromobimane alkylation method. Therefore, eukaryotic Ohr peroxidases share several biochemical features with prokaryotic orthologues and are preferentially located in mitochondria. Keywords: Ohr/OsmC, Thiol-dependent peroxidases, Phylogeny

  9. Functional and evolutionary characterization of Ohr proteins in eukaryotes reveals many active homologs among pathogenic fungi.

    Science.gov (United States)

    Meireles, D A; Domingos, R M; Gaiarsa, J W; Ragnoni, E G; Bannitz-Fernandes, R; da Silva Neto, J F; de Souza, R F; Netto, L E S

    2017-08-01

    Ohr and OsmC proteins comprise two subfamilies within a large group of proteins that display Cys-based, thiol dependent peroxidase activity. These proteins were previously thought to be restricted to prokaryotes, but we show here, using iterated sequence searches, that Ohr/OsmC homologs are also present in 217 species of eukaryotes with a massive presence in Fungi (186 species). Many of these eukaryotic Ohr proteins possess an N-terminal extension that is predicted to target them to mitochondria. We obtained recombinant proteins for four eukaryotic members of the Ohr/OsmC family and three of them displayed lipoyl peroxidase activity. Further functional and biochemical characterization of the Ohr homologs from the ascomycete fungus Mycosphaerella fijiensis Mf_1 (MfOhr), the causative agent of Black Sigatoka disease in banana plants, was pursued. Similarly to what has been observed for the bacterial proteins, we found that: (i) the peroxidase activity of MfOhr was supported by DTT or dihydrolipoamide (dithiols), but not by β-mercaptoethanol or GSH (monothiols), even in large excess; (ii) MfOhr displayed preference for organic hydroperoxides (CuOOH and tBOOH) over hydrogen peroxide; (iii) MfOhr presented extraordinary reactivity towards linoleic acid hydroperoxides (k=3.18 (±2.13)×10 8 M -1 s -1 ). Both Cys 87 and Cys 154 were essential to the peroxidase activity, since single mutants for each Cys residue presented no activity and no formation of intramolecular disulfide bond upon treatment with hydroperoxides. The pK a value of the Cys p residue was determined as 5.7±0.1 by a monobromobimane alkylation method. Therefore, eukaryotic Ohr peroxidases share several biochemical features with prokaryotic orthologues and are preferentially located in mitochondria. Copyright © 2017. Published by Elsevier B.V.

  10. IRES-mediated translation of membrane proteins and glycoproteins in eukaryotic cell-free systems.

    Science.gov (United States)

    Brödel, Andreas K; Sonnabend, Andrei; Roberts, Lisa O; Stech, Marlitt; Wüstenhagen, Doreen A; Kubick, Stefan

    2013-01-01

    Internal ribosome entry site (IRES) elements found in the 5' untranslated region of mRNAs enable translation initiation in a cap-independent manner, thereby representing an alternative to cap-dependent translation in cell-free protein expression systems. However, IRES function is largely species-dependent so their utility in cell-free systems from different species is rather limited. A promising approach to overcome these limitations would be the use of IRESs that are able to recruit components of the translation initiation apparatus from diverse origins. Here, we present a solution to this technical problem and describe the ability of a number of viral IRESs to direct efficient protein expression in different eukaryotic cell-free expression systems. The IRES from the intergenic region (IGR) of the Cricket paralysis virus (CrPV) genome was shown to function efficiently in four different cell-free systems based on lysates derived from cultured Sf21, CHO and K562 cells as well as wheat germ. Our results suggest that the CrPV IGR IRES-based expression vector is universally applicable for a broad range of eukaryotic cell lysates. Sf21, CHO and K562 cell-free expression systems are particularly promising platforms for the production of glycoproteins and membrane proteins since they contain endogenous microsomes that facilitate the incorporation of membrane-spanning proteins and the formation of post-translational modifications. We demonstrate the use of the CrPV IGR IRES-based expression vector for the enhanced synthesis of various target proteins including the glycoprotein erythropoietin and the membrane proteins heparin-binding EGF-like growth factor receptor as well as epidermal growth factor receptor in the above mentioned eukaryotic cell-free systems. CrPV IGR IRES-mediated translation will facilitate the development of novel eukaryotic cell-free expression platforms as well as the high-yield synthesis of desired proteins in already established systems.

  11. A Polycomb complex remains bound through DNA replication in the absence of other eukaryotic proteins

    KAUST Repository

    Lengsfeld, Bettina M.

    2012-09-17

    Propagation of chromatin states through DNA replication is central to epigenetic regulation and can involve recruitment of chromatin proteins to replicating chromatin through interactions with replication fork components. Here we show using a fully reconstituted T7 bacteriophage system that eukaryotic proteins are not required to tether the Polycomb complex PRC1 to templates during DNA replication. Instead, DNA binding by PRC1 can withstand passage of a simple replication fork.

  12. Doing focus group research

    DEFF Research Database (Denmark)

    Lindegaard, Laura Bang

    2014-01-01

    Scholars of ethnomethodologically informed discourse studies are often sceptical of the use of interview data such as focus group data. Some scholars quite simply reject interview data with reference to a general preference for so-called naturally occurring data. Other scholars acknowledge......, not as something that pre-exists or goes beyond the situated interaction. This article, however, challenges not only the first, but also the second position and suggests that it is, after all, possible to do committedly ethnomethodological studies of focus group data that demonstrate how members of a focus group...

  13. Alternative Eukaryotic Expression Systems for the Production of Proteins and Protein Complexes.

    Science.gov (United States)

    Gómez, Sara; López-Estepa, Miguel; Fernández, Francisco J; Suárez, Teresa; Vega, M Cristina

    2016-01-01

    Besides the most established expression hosts, several eukaryotic microorganisms and filamentous fungi have also been successfully used as platforms for the production of foreign proteins. Filamentous fungi and Dictyostelium discoideum are two prominent examples. Filamentous fungi, typically Aspergillus and Trichoderma, are usually employed for the industrial production of enzymes and secondary metabolites for food processing, pharmaceutical drugs production, and textile and paper applications, with multiple products already accepted for their commercialization. The low cost of culture medium components, high secretion capability directly to the extracellular medium, and the intrinsic ability to produce post-translational modifications similar to the mammalian type, have promoted this group as successful hosts for the expression of proteins, including examples from phylogenetically distant groups: humans proteins such as IL-2, IL-6 or epithelial growth factor; α-galactosidase from plants; or endoglucanase from Cellulomonas fimi, among others. D. discoideum is a social amoeba that can be used as an expression platform for a variety of proteins, which has been extensively illustrated for cytoskeletal proteins. New vectors for heterologous expression in D. discoideum have been recently developed that might increase the usefulness of this system and expand the range of protein classes that can be tackled. Continuous developments are ongoing to improve strains, promoters, production and downstream processes for filamentous fungi, D. discoideum, and other alternative eukaryotic hosts. Either for the overexpression of individual genes, or in the coexpression of multiples genes, this chapter illustrates the enormous possibilities offered by these groups of eukaryotic organisms.

  14. Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME.

    Science.gov (United States)

    Leray, Matthieu; Knowlton, Nancy

    2016-01-01

    PCR amplification followed by deep sequencing of homologous gene regions is increasingly used to characterize the diversity and taxonomic composition of marine eukaryotic communities. This approach may generate millions of sequences for hundreds of samples simultaneously. Therefore, tools that researchers can use to visualize complex patterns of diversity for these massive datasets are essential. Efforts by microbiologists to understand the Earth and human microbiomes using high-throughput sequencing of the 16S rRNA gene has led to the development of several user-friendly, open-source software packages that can be similarly used to analyze eukaryotic datasets. Quantitative Insights Into Microbial Ecology (QIIME) offers some of the most helpful data visualization tools. Here, we describe functionalities to import OTU tables generated with any molecular marker (e.g., 18S, COI, ITS) and associated metadata into QIIME. We then present a range of analytical tools implemented within QIIME that can be used to obtain insights about patterns of alpha and beta diversity for marine eukaryotes.

  15. [Expression of interferon alpha family gene of Chinese marmot in eukaryotic and prokaryotic cells].

    Science.gov (United States)

    Lu, Yin-ping; Wang, Bao-ju; Huang, Hong-ping; Tian, Yong-jun; Yang, Yan; Dong, Ji-hua; Lu, Meng-ji; Yang, Dong-liang

    2006-02-01

    To investigate the function of interferon alpha (IFNalpha) in a Chinese marmot model of hepatitis B, we expressed the Chinese marmot (Marmota himalayana) IFNalpha family gene (IFNA) in eukaryotic cells and prokaryotic cells. Eukaryotic and prokaryotic expression plasmids harboring Chinese marmot interferon alpha gene with different genotypes were generated using molecular cloning technology. We detected the biological activity of all expression products by viral protection assay, and analyzed their differences and species restriction of the biological activity. The Chinese marmot functional genotype IFNalpha was expressed in the baby hamster kidney (BHK) cell line, and these products protected WH12/6 cells challenged by encephalomyocarditis virus (EMCV). The Chinese marmot IFN-alpha5 also expressed in E. Coli induced by IPTG, and purified fusion protein had antiviral biological activity. The biologic activity displayed differences among different subtype IFNalpha, and it had strict species restriction. The IFNalpha family gene of the Chinese marmot can be expressed in both eukaryotic and prokaryotic cells, and the expression products show antiviral activity in a protection assay. This study provides, for the first time, evidence that IFNalpha from the Chinese marmot has an antiviral function in vitro and can be used to improve the efficacy of current therapies for HBV infection in our Chinese marmot model.

  16. A Pseudomonas aeruginosa type VI secretion phospholipase D effector targets both prokaryotic and eukaryotic cells.

    Science.gov (United States)

    Jiang, Feng; Waterfield, Nicholas R; Yang, Jian; Yang, Guowei; Jin, Qi

    2014-05-14

    Widely found in animal and plant-associated proteobacteria, type VI secretion systems (T6SSs) are potentially capable of facilitating diverse interactions with eukaryotes and/or other bacteria. Pseudomonas aeruginosa encodes three distinct T6SS haemolysin coregulated protein (Hcp) secretion islands (H1, H2, and H3-T6SS), each involved in different aspects of the bacterium's interaction with other organisms. Here we describe the characterization of a P. aeruginosa H3-T6SS-dependent phospholipase D effector, PldB, and its three tightly linked cognate immunity proteins. PldB targets the periplasm of prokaryotic cells and exerts an antibacterial activity. Surprisingly, PldB also facilitates intracellular invasion of host eukaryotic cells by activation of the PI3K/Akt pathway, revealing it to be a trans-kingdom effector. Our findings imply a potentially widespread T6SS-mediated mechanism, which deploys a single phospholipase effector to influence both prokaryotic cells and eukaryotic hosts. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. Conservation of coevolving protein interfaces bridges prokaryote–eukaryote homologies in the twilight zone

    Science.gov (United States)

    Rodriguez-Rivas, Juan; Marsili, Simone; Juan, David; Valencia, Alfonso

    2016-01-01

    Protein–protein interactions are fundamental for the proper functioning of the cell. As a result, protein interaction surfaces are subject to strong evolutionary constraints. Recent developments have shown that residue coevolution provides accurate predictions of heterodimeric protein interfaces from sequence information. So far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compiled. We explore the hypothesis that coevolution points to structurally conserved contacts at protein–protein interfaces, which can be reliably projected to homologous complexes with distantly related sequences. We introduce a domain-centered protocol to study the interplay between residue coevolution and structural conservation of protein–protein interfaces. We show that sequence-based coevolutionary analysis systematically identifies residue contacts at prokaryotic interfaces that are structurally conserved at the interface of their eukaryotic counterparts. In turn, this allows the prediction of conserved contacts at eukaryotic protein–protein interfaces with high confidence using solely mutational patterns extracted from prokaryotic genomes. Even in the context of high divergence in sequence (the twilight zone), where standard homology modeling of protein complexes is unreliable, our approach provides sequence-based accurate information about specific details of protein interactions at the residue level. Selected examples of the application of prokaryotic coevolutionary analysis to the prediction of eukaryotic interfaces further illustrate the potential of this approach. PMID:27965389

  18. Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans

    KAUST Repository

    Pernice, Massimo C.

    2015-10-09

    In this work, we study the diversity of bathypelagic microbial eukaryotes (0.8–20 μm) in the global ocean. Seawater samples from 3000 to 4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S ribosomal DNA. The relative abundance of the most abundant operational taxonomic units agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.

    The ISME Journal advance online publication, 9 October 2015; doi:10.1038/ismej.2015.170

  19. Type VI secretion system MIX-effectors carry both antibacterial and anti-eukaryotic activities.

    Science.gov (United States)

    Ray, Ann; Schwartz, Nika; de Souza Santos, Marcela; Zhang, Junmei; Orth, Kim; Salomon, Dor

    2017-11-01

    Most type VI secretion systems (T6SSs) described to date are protein delivery apparatuses that mediate bactericidal activities. Several T6SSs were also reported to mediate virulence activities, although only few anti-eukaryotic effectors have been described. Here, we identify three T6SSs in the marine bacterium Vibrio proteolyticus and show that T6SS1 mediates bactericidal activities under warm marine-like conditions. Using comparative proteomics, we find nine potential T6SS1 effectors, five of which belong to the polymorphic MIX-effector class. Remarkably, in addition to six predicted bactericidal effectors, the T6SS1 secretome includes three putative anti-eukaryotic effectors. One of these is a MIX-effector containing a cytotoxic necrotizing factor 1 domain. We demonstrate that T6SS1 can use this MIX-effector to target phagocytic cells, resulting in morphological changes and actin cytoskeleton rearrangements. In conclusion, the V. proteolyticus T6SS1, a system homologous to one found in pathogenic vibrios, uses a suite of polymorphic effectors that target both bacteria and eukaryotic neighbors. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

  20. Heterologous Expression of Toxins from Bacterial Toxin-Antitoxin Systems in Eukaryotic Cells: Strategies and Applications

    Directory of Open Access Journals (Sweden)

    Chew Chieng Yeo

    2016-02-01

    Full Text Available Toxin-antitoxin (TA systems are found in nearly all prokaryotic genomes and usually consist of a pair of co-transcribed genes, one of which encodes a stable toxin and the other, its cognate labile antitoxin. Certain environmental and physiological cues trigger the degradation of the antitoxin, causing activation of the toxin, leading either to the death or stasis of the host cell. TA systems have a variety of functions in the bacterial cell, including acting as mediators of programmed cell death, the induction of a dormant state known as persistence and the stable maintenance of plasmids and other mobile genetic elements. Some bacterial TA systems are functional when expressed in eukaryotic cells and this has led to several innovative applications, which are the subject of this review. Here, we look at how bacterial TA systems have been utilized for the genetic manipulation of yeasts and other eukaryotes, for the containment of genetically modified organisms, and for the engineering of high expression eukaryotic cell lines. We also examine how TA systems have been adopted as an important tool in developmental biology research for the ablation of specific cells and the potential for utility of TA systems in antiviral and anticancer gene therapies.

  1. Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments.

    Science.gov (United States)

    Broman, Elias; Sachpazidou, Varvara; Dopson, Mark; Hylander, Samuel

    2017-10-11

    An important characteristic of marine sediments is the oxygen concentration that affects many central metabolic processes. There has been a widespread increase in hypoxia in coastal systems (referred to as 'dead zones') mainly caused by eutrophication. Hence, it is central to understand the metabolism and ecology of eukaryotic life in sediments during changing oxygen conditions. Therefore, we sampled coastal 'dead zone' Baltic Sea sediment during autumn and spring, and analysed the eukaryotic metatranscriptome from field samples and after incubation in the dark under oxic or anoxic conditions. Bacillariophyta (diatoms) dominated the eukaryotic metatranscriptome in spring and were also abundant during autumn. A large fraction of the diatom RNA reads was associated with the photosystems suggesting a constitutive expression in darkness. Microscope observation showed intact diatom cells and these would, if hatched, represent a significant part of the pelagic phytoplankton biomass. Oxygenation did not significantly change the relative proportion of diatoms nor resulted in any major shifts in metabolic 'signatures'. By contrast, diatoms rapidly responded when exposed to light suggesting that light is limiting diatom development in hypoxic sediments. Hence, it is suggested that diatoms in hypoxic sediments are on 'standby' to exploit the environment if they reach suitable habitats. © 2017 The Author(s).

  2. 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.

    2015-01-01

    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

  3. Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi.

    Science.gov (United States)

    Taylor, John W; Turner, Elizabeth; Townsend, Jeffrey P; Dettman, Jeremy R; Jacobson, David

    2006-11-29

    The claim that eukaryotic micro-organisms have global geographic ranges, constituting a significant departure from the situation with macro-organisms, has been supported by studies of morphological species from protistan kingdoms. Here, we examine this claim by reviewing examples from another kingdom of eukaryotic microbes, the Fungi. We show that inferred geographic range of a fungal species depends upon the method of species recognition. While some fungal species defined by morphology show global geographic ranges, when fungal species are defined by phylogenetic species recognition they are typically shown to harbour several to many endemic species. We advance two non-exclusive reasons to explain the perceived difference between the size of geographic ranges of microscopic and macroscopic eukaryotic species when morphological methods of species recognition are used. These reasons are that microbial organisms generally have fewer morphological characters, and that the rate of morphological change will be slower for organisms with less elaborate development and fewer cells. Both of these reasons result in fewer discriminatory morphological differences between recently diverged lineages. The rate of genetic change, moreover, is similar for both large and small organisms, which helps to explain why phylogenetic species of large and small organisms show a more similar distribution of geographic ranges. As a consequence of the different rates in fungi of genetic and morphological changes, genetic isolation precedes a recognizable morphological change. The final step in speciation, reproductive isolation, also follows genetic isolation and may precede morphological change.

  4. Evolution of domain promiscuity in eukaryotic genomes—a perspective from the inferred ancestral domain architectures†

    Science.gov (United States)

    Cohen-Gihon, Inbar; Fong, Jessica H.; Sharan, Roded; Nussinov, Ruth

    2012-01-01

    Most eukaryotic proteins are composed of two or more domains. These assemble in a modular manner to create new proteins usually by the acquisition of one or more domains to an existing protein. Promiscuous domains which are found embedded in a variety of proteins and co-exist with many other domains are of particular interest and were shown to have roles in signaling pathways and mediating network communication. The evolution of domain promiscuity is still an open problem, mostly due to the lack of sequenced ancestral genomes. Here we use inferred domain architectures of ancestral genomes to trace the evolution of domain promiscuity in eukaryotic genomes. We find an increase in average promiscuity along many branches of the eukaryotic tree. Moreover, domain promiscuity can proceed at almost a steady rate over long evolutionary time or exhibit lineage-specific acceleration. We also observe that many signaling and regulatory domains gained domain promiscuity around the Bilateria divergence. In addition we show that those domains that played a role in the creation of two body axes and existed before the divergence of the bilaterians from fungi/metazoan achieve a boost in their promiscuities during the bilaterian evolution. PMID:21127809

  5. Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures.

    Science.gov (United States)

    Cohen-Gihon, Inbar; Fong, Jessica H; Sharan, Roded; Nussinov, Ruth; Przytycka, Teresa M; Panchenko, Anna R

    2011-03-01

    Most eukaryotic proteins are composed of two or more domains. These assemble in a modular manner to create new proteins usually by the acquisition of one or more domains to an existing protein. Promiscuous domains which are found embedded in a variety of proteins and co-exist with many other domains are of particular interest and were shown to have roles in signaling pathways and mediating network communication. The evolution of domain promiscuity is still an open problem, mostly due to the lack of sequenced ancestral genomes. Here we use inferred domain architectures of ancestral genomes to trace the evolution of domain promiscuity in eukaryotic genomes. We find an increase in average promiscuity along many branches of the eukaryotic tree. Moreover, domain promiscuity can proceed at almost a steady rate over long evolutionary time or exhibit lineage-specific acceleration. We also observe that many signaling and regulatory domains gained domain promiscuity around the Bilateria divergence. In addition we show that those domains that played a role in the creation of two body axes and existed before the divergence of the bilaterians from fungi/metazoan achieve a boost in their promiscuities during the bilaterian evolution.

  6. Heterologous Expression of Toxins from Bacterial Toxin-Antitoxin Systems in Eukaryotic Cells: Strategies and Applications.

    Science.gov (United States)

    Yeo, Chew Chieng; Abu Bakar, Fauziah; Chan, Wai Ting; Espinosa, Manuel; Harikrishna, Jennifer Ann

    2016-02-19

    Toxin-antitoxin (TA) systems are found in nearly all prokaryotic genomes and usually consist of a pair of co-transcribed genes, one of which encodes a stable toxin and the other, its cognate labile antitoxin. Certain environmental and physiological cues trigger the degradation of the antitoxin, causing activation of the toxin, leading either to the death or stasis of the host cell. TA systems have a variety of functions in the bacterial cell, including acting as mediators of programmed cell death, the induction of a dormant state known as persistence and the stable maintenance of plasmids and other mobile genetic elements. Some bacterial TA systems are functional when expressed in eukaryotic cells and this has led to several innovative applications, which are the subject of this review. Here, we look at how bacterial TA systems have been utilized for the genetic manipulation of yeasts and other eukaryotes, for the containment of genetically modified organisms, and for the engineering of high expression eukaryotic cell lines. We also examine how TA systems have been adopted as an important tool in developmental biology research for the ablation of specific cells and the potential for utility of TA systems in antiviral and anticancer gene therapies.

  7. Tetrapyrroles as Endogenous TSPO Ligands in Eukaryotes and Prokaryotes: Comparisons with Synthetic Ligands

    Directory of Open Access Journals (Sweden)

    Leo Veenman

    2016-06-01

    Full Text Available The 18 kDa translocator protein (TSPO is highly 0conserved in eukaryotes and prokaryotes. Since its discovery in 1977, numerous studies established the TSPO’s importance for life essential functions. For these studies, synthetic TSPO ligands typically are applied. Tetrapyrroles present endogenous ligands for the TSPO. Tetrapyrroles are also evolutionarily conserved and regulate multiple functions. TSPO and tetrapyrroles regulate each other. In animals TSPO-tetrapyrrole interactions range from effects on embryonic development to metabolism, programmed cell death, response to stress, injury and disease, and even to life span extension. In animals TSPOs are primarily located in mitochondria. In plants TSPOs are also present in plastids, the nuclear fraction, the endoplasmic reticulum, and Golgi stacks. This may contribute to translocation of tetrapyrrole intermediates across organelles’ membranes. As in animals, plant TSPO binds heme and protoporphyrin IX. TSPO-tetrapyrrole interactions in plants appear to relate to development as well as stress conditions, including salt tolerance, abscisic acid-induced stress, reactive oxygen species homeostasis, and finally cell death regulation. In bacteria, TSPO is important for switching from aerobic to anaerobic metabolism, including the regulation of photosynthesis. As in mitochondria, in bacteria TSPO is located in the outer membrane. TSPO-tetrapyrrole interactions may be part of the establishment of the bacterial-eukaryote relationships, i.e., mitochondrial-eukaryote and plastid-plant endosymbiotic relationships.

  8. Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils.

    Science.gov (United States)

    Baldwin, Darren S; Colloff, Matthew J; Rees, Gavin N; Chariton, Anthony A; Watson, Garth O; Court, Leon N; Hartley, Diana M; Morgan, Matthew J; King, Andrew J; Wilson, Jessica S; Hodda, Michael; Hardy, Christopher M

    2013-03-01

    Floodplain ecosystems are characterized by alternating wet and dry phases and periodic inundation defines their ecological character. Climate change, river regulation and the construction of levees have substantially altered natural flooding and drying regimes worldwide with uncertain effects on key biotic groups. In southern Australia, we hypothesized that soil eukaryotic communities in climate change affected areas of a semi-arid floodplain would transition towards comprising mainly dry-soil specialist species with increasing drought severity. Here, we used 18S rRNA amplicon pyrosequencing to measure the eukaryote community composition in soils that had been depleted of water to varying degrees to confirm that reproducible transitional changes occur in eukaryotic biodiversity on this floodplain. Interflood community structures (3 years post-flood) were dominated by persistent rather than either aquatic or dry-specialist organisms. Only 2% of taxa were unique to dry locations by 8 years post-flood, and 10% were restricted to wet locations (inundated a year to 2 weeks post-flood). Almost half (48%) of the total soil biota were detected in both these environments. The discovery of a large suite of organisms able to survive nearly a decade of drought, and up to a year submerged supports the concept of inherent resilience of Australian semi-arid floodplain soil communities under increasing pressure from climatic induced changes in water availability. © 2013 Blackwell Publishing Ltd.

  9. Cultivating a Community of Effective Special Education Teachers: Local Special Education Administrators' Roles

    Science.gov (United States)

    Bettini, Elizabeth; Benedict, Amber; Thomas, Rachel; Kimerling, Jenna; Choi, Nari; McLeskey, James

    2017-01-01

    Evidence of the powerful impact teachers have on student achievement has led to an intensive focus on cultivating effective teachers, including special education teachers (SETs). Local special education administrators (LSEAs) share responsibility for cultivating effective SETs throughout their districts. However, the roles LSEAs play in this…

  10. Focus group discussions

    CERN Document Server

    Hennink, Monique M

    2014-01-01

    The Understanding Research series focuses on the process of writing up social research. The series is broken down into three categories: Understanding Statistics, Understanding Measurement, and Understanding Qualitative Research. The books provide researchers with guides to understanding, writing, and evaluating social research. Each volume demonstrates how research should be represented, including how to write up the methodology as well as the research findings. Each volume also reviews how to appropriately evaluate published research. Focus Group Discussions addresses the challenges associated with conducting and writing focus group research. It provides detailed guidance on the practical and theoretical considerations in conducting focus group discussions including: designing the discussion guide, recruiting participants, training a field team, moderating techniques and ethical considerations. Monique Hennink describes how a methodology section is read and evaluated by others, such as journal reviewers or ...

  11. Final focus nomenclature

    International Nuclear Information System (INIS)

    Erickson, R.

    1986-01-01

    The formal names and common names for all devices in the final focus system of the SLC are listed. The formal names consist of a device type designator, microprocessor designator, and a four-digit unit number

  12. Final focus test beam

    International Nuclear Information System (INIS)

    1991-03-01

    This report discusses the following: the Final Focus Test Beam Project; optical design; magnets; instrumentation; magnetic measurement and BPM calibration; mechanical alignment and stabilization; vacuum system; power supplies; control system; radiation shielding and personnel protection; infrastructure; and administration

  13. BrightFocus Foundation

    Science.gov (United States)

    ... announcement by Bill Gates of his $50 million investment in the Dementia Discovery Fund. A charitable act ... under section 501(c)(3) of the Internal Revenue Code of the United States.Copyright 2017 BrightFocus ...

  14. Final focus nomenclature

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, R.

    1986-08-08

    The formal names and common names for all devices in the final focus system of the SLC are listed. The formal names consist of a device type designator, microprocessor designator, and a four-digit unit number. (LEW)

  15. Special interests and subjective wellbeing in autistic adults

    NARCIS (Netherlands)

    Grove, Rachel; Hoekstra, Rosa A; Wierda, Marlies; Begeer, Sander

    2018-01-01

    Special interests form part of the core features of autism. However, to date there has been limited research focusing on the role of special interests in the lives of autistic adults. This study surveyed autistic adults on their special interest topics, intensity, and motivation. It also assessed

  16. Introduction to "PIQ"'s Special Ethics Section.

    Science.gov (United States)

    Hatcher, Tim

    2003-01-01

    Introduces "Performance Improvement Quarterly's" special section on ethics. The focus of this special section is to explore ethics and the field of human performance improvement in a broad sense by encouraging an examination of ethical concepts and responsibilities in the profession. This special section includes three critical views of…

  17. High harmonics focusing undulator

    Energy Technology Data Exchange (ETDEWEB)

    Varfolomeev, A.A.; Hairetdinov, A.H.; Smirnov, A.V.; Khlebnikov, A.S. [Kurchatov Institute, Moscow (Russian Federation)

    1995-12-31

    It was shown in our previous work that there exist a possibility to enhance significantly the {open_quote}natural{close_quote} focusing properties of the hybrid undulator. Here we analyze the actual undulator configurations which could provide such field structure. Numerical simulations using 2D code PANDIRA were carried out and the enhanced focusing properties of the undulator were demonstrated. The obtained results provide the solution for the beam transport in a very long (short wavelength) undulator schemes.

  18. Plutonium focus area

    International Nuclear Information System (INIS)

    1996-08-01

    To ensure research and development programs focus on the most pressing environmental restoration and waste management problems at the U.S. Department of Energy (DOE), the Assistant Secretary for the Office of Environmental Management (EM) established a working group in August 1993 to implement a new approach to research and technology development. As part of this new approach, EM developed a management structure and principles that led to the creation of specific Focus Areas. These organizations were designed to focus the scientific and technical talent throughout DOE and the national scientific community on the major environmental restoration and waste management problems facing DOE. The Focus Area approach provides the framework for intersite cooperation and leveraging of resources on common problems. After the original establishment of five major Focus Areas within the Office of Technology Development (EM-50, now called the Office of Science and Technology), the Nuclear Materials Stabilization Task Group (EM-66) followed the structure already in place in EM-50 and chartered the Plutonium Focus Area (PFA). The following information outlines the scope and mission of the EM, EM-60, and EM-66 organizations as related to the PFA organizational structure

  19. Plutonium focus area

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-08-01

    To ensure research and development programs focus on the most pressing environmental restoration and waste management problems at the U.S. Department of Energy (DOE), the Assistant Secretary for the Office of Environmental Management (EM) established a working group in August 1993 to implement a new approach to research and technology development. As part of this new approach, EM developed a management structure and principles that led to the creation of specific Focus Areas. These organizations were designed to focus the scientific and technical talent throughout DOE and the national scientific community on the major environmental restoration and waste management problems facing DOE. The Focus Area approach provides the framework for intersite cooperation and leveraging of resources on common problems. After the original establishment of five major Focus Areas within the Office of Technology Development (EM-50, now called the Office of Science and Technology), the Nuclear Materials Stabilization Task Group (EM-66) followed the structure already in place in EM-50 and chartered the Plutonium Focus Area (PFA). The following information outlines the scope and mission of the EM, EM-60, and EM-66 organizations as related to the PFA organizational structure.

  20. Plasma focus matching conditions

    International Nuclear Information System (INIS)

    Soliman, H.M.; Masoud, M.M.; Elkhalafawy, T.A.

    1988-01-01

    A snow-plough and slug models have been used to obtain the optimum matching conditions of the plasma in the focus. The dimensions of the plasma focus device are, inner electrode radius = 2 cm, outer electrode radius = 5.5 cm, and its length = 8 cm. It was found that the maximum magnetic energy of 12.26 kJ has to be delivered to plasma focus whose density is 10 19 /cm 3 at focusing time of 2.55 μs and with total external inductance of 24.2 n H. The same method is used to evaluate the optimum matching conditions for the previous coaxial discharge system which had inner electrode radius = 1.6 cm, outer electrode radius = 3.3 cm and its length = 31.5 cm. These conditions are charging voltage = 12 kV, capacity of the condenser bank = 430 μf, plasma focus density = 10 19 /cm 3 focusing time = 8 μs and total external inductance = 60.32 n H.3 fig., 2 tab

  1. A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes

    Directory of Open Access Journals (Sweden)

    Koonin Eugene V

    2011-05-01

    Full Text Available Abstract Background Accurate estimation of the divergence time of the extant eukaryotes is a fundamentally important but extremely difficult problem owing primarily to gross violations of the molecular clock at long evolutionary distances and the lack of appropriate calibration points close to the date of interest. These difficulties are intrinsic to the dating of ancient divergence events and are reflected in the large discrepancies between estimates obtained with different approaches. Estimates of the age of Last Eukaryotic Common Ancestor (LECA vary approximately twofold, from ~1,100 million years ago (Mya to ~2,300 Mya. Results We applied the genome-wide analysis of rare genomic changes associated with conserved amino acids (RGC_CAs and used several independent techniques to obtain date estimates for the divergence of the major lineages of eukaryotes with calibration intervals for insects, land plants and vertebrates. The results suggest an early divergence of monocot and dicot plants, approximately 340 Mya, raising the possibility of plant-insect coevolution. The divergence of bilaterian animal phyla is estimated at ~400-700 Mya, a range of dates that is consistent with cladogenesis immediately preceding the Cambrian explosion. The origin of opisthokonts (the supergroup of eukaryotes that includes metazoa and fungi is estimated at ~700-1,000 Mya, and the age of LECA at ~1,000-1,300 Mya. We separately analyzed the red algal calibration interval which is based on single fossil. This analysis produced time estimates that were systematically older compared to the other estimates. Nevertheless, the majority of the estimates for the age of the LECA using the red algal data fell within the 1,200-1,400 Mya interval. Conclusion The inference of a "young LECA" is compatible with the latest of previously estimated dates and has substantial biological implications. If these estimates are valid, the approximately 1 to 1.4 billion years of evolution of

  2. EDITORIAL: Focus on Plasmonics FOCUS ON PLASMONICS

    Science.gov (United States)

    Bozhevolnyi, Sergey; García-Vidal, Francisco

    2008-10-01

    Plasmonics is an emerging field in optics dealing with the so-called surface plasmons whose extraordinary properties are being both analyzed from a fundamental point of view and exploited for numerous technological applications. Surface plasmons associated with surface electron density oscillations decorating metal-dielectric interfaces were discovered by Rufus Ritchie in the 1950s. Since the seventies, the subwavelength confinement of electromagnetic fields as well as their enhancement inherent to the surface plasmon excitation has been widely used for spectroscopic purposes. Recent advances in nano-fabrication, characterization and modelling techniques have allowed unique properties of these surface electromagnetic modes to be explored with respect to subwavelength field localization and waveguiding, opening the path to truly nanoscale plasmonic optical devices. This area of investigation also has interesting links with research on photonic band gap materials and the field of optical metamaterials. Nowadays, plasmonics can be seen as a mature interdisciplinary area of research in which scientists coming from different backgrounds (chemistry, physics, optics and engineering) strive to discover and exploit new and exciting phenomena associated with surface plasmons. The already made and forthcoming discoveries will have impacts in many fields of science and technology, including not only photonics and materials science but also computation, biology and medicine, among others. This focus issue of New Journal of Physics is intended to cover all the aforementioned capabilities of surface plasmons by presenting a current overview of state-of-the-art advances achieved by the leading groups in this field of research. The below list of articles represents the first contributions to the collection and further additions will appear soon. Focus on Plasmonics Contents Nanoantenna array-induced fluorescence enhancement and reduced lifetimes Reuben M Bakker, Vladimir P Drachev

  3. Comparative genomic analysis of multi-subunit tethering complexes demonstrates an ancient pan-eukaryotic complement and sculpting in Apicomplexa.

    Directory of Open Access Journals (Sweden)

    Christen M Klinger

    Full Text Available Apicomplexa are obligate intracellular parasites that cause tremendous disease burden world-wide. They utilize a set of specialized secretory organelles in their invasive process that require delivery of components for their biogenesis and function, yet the precise mechanisms underpinning such processes remain unclear. One set of potentially important components is the multi-subunit tethering complexes (MTCs, factors increasingly implicated in all aspects of vesicle-target interactions. Prompted by the results of previous studies indicating a loss of membrane trafficking factors in Apicomplexa, we undertook a bioinformatic analysis of MTC conservation. Building on knowledge of the ancient presence of most MTC proteins, we demonstrate the near complete retention of MTCs in the newly available genomes for Guillardiatheta and Bigelowiellanatans. The latter is a key taxonomic sampling point as a basal sister taxa to the group including Apicomplexa. We also demonstrate an ancient origin of the CORVET complex subunits Vps8 and Vps3, as well as the TRAPPII subunit Tca17. Having established that the lineage leading to Apicomplexa did at one point possess the complete eukaryotic complement of MTC components, we undertook a deeper taxonomic investigation in twelve apicomplexan genomes. We observed excellent conservation of the VpsC core of the HOPS and CORVET complexes, as well as the core TRAPP subunits, but sparse conservation of TRAPPII, COG, Dsl1, and HOPS/CORVET-specific subunits. However, those subunits that we did identify appear to be expressed with similar patterns to the fully conserved MTC proteins, suggesting that they may function as minimal complexes or with analogous partners. Strikingly, we failed to identify any subunits of the exocyst complex in all twelve apicomplexan genomes, as well as the dinoflagellate Perkinsus marinus. Overall, we demonstrate reduction of MTCs in Apicomplexa and their ancestors, consistent with modification during

  4. Decontamination & decommissioning focus area

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-08-01

    In January 1994, the US Department of Energy Office of Environmental Management (DOE EM) formally introduced its new approach to managing DOE`s environmental research and technology development activities. The goal of the new approach is to conduct research and development in critical areas of interest to DOE, utilizing the best talent in the Department and in the national science community. To facilitate this solutions-oriented approach, the Office of Science and Technology (EM-50, formerly the Office of Technology Development) formed five Focus AReas to stimulate the required basic research, development, and demonstration efforts to seek new, innovative cleanup methods. In February 1995, EM-50 selected the DOE Morgantown Energy Technology Center (METC) to lead implementation of one of these Focus Areas: the Decontamination and Decommissioning (D & D) Focus Area.

  5. Radiological focusing techniques

    International Nuclear Information System (INIS)

    Husmann, K.; Mehrkens, A.; Hancken, G.

    1995-01-01

    The textbook explains the most common and essential radiological focusing techniques and gives the relevant theory and technical fundamentals. The theory does not consume much space in this book, the theoretical part briefly addressing such aspects as film-screen combinations, doses administered by X-ray radiography, quality assurance, radiological protection, and potential patient reactions to contrast media applied. The textbook primarily is a practical guide giving general advice and guidance on focusing techniques, accompanied by an illustrative compilation of frequent mistakes. Arranged by body regions, the well over 80 examples of focusing techniques are presented by systematic texts and illustrations. There is an annex giving a glossary of terms, a bibliography, and a list of useful addresses. (orig./MG) [de

  6. Differentiated Instruction Practice Video Series. A Focus on Inclusion [and] A Focus on the Gifted. [Videotapes].

    Science.gov (United States)

    Iervolino, Constance W.; Hanson, Helene M.

    This document contains: 2 videotapes and an accompanying viewer's guide that provide information for differentiating instruction for gifted learners and for students with special needs in inclusive classrooms. The first 50-minute videotape, "A Focus on Inclusion," discusses how to deliver appropriate curriculum to children with special…

  7. Keeping Special Forces Special: Regional Proficiency in Special Forces

    Science.gov (United States)

    2011-12-01

    communicating and teaching across intercultural barriers. Special Forces Soldiers use their interpersonal skills to obtain and maintain appropriate...or in a simulated environment with native speakers .”258 Immersion programs were “overwhelmingly described as effective and useful” by the LCNA...target language increases intercultural adjustment.”263

  8. The Upgraded Plasma Focus Installation > - The Installation >

    International Nuclear Information System (INIS)

    Krokhin, O.N.; Nikulin, V.Ya.; Babenko, B.A.; Gorbunov, D.N.; Gurei, A.E.; Kalachev, N.V.; Kozlova, T.A.; Malafeev, Yu.S.; Polukhin, S.N.; Sychev, A.A.; Tikhomirov, A.A.; Tsybenko, S.P.; Volobuev, I.V.

    1999-01-01

    The paper presents the upgraded plasma focus installation > - the installation > and some preliminary experimental results. The total energy stored in capacity bank is now 400 kJ, current - 5 MA with the rise time 3.5 μs. The investigation is targeted on the study of near electrode processes and its influence on plasma dynamics in a special operating regime of Filippov type PF - Hard X-ray regime. (author)

  9. X-Ray Focusing: Techniques and Applications

    International Nuclear Information System (INIS)

    Khounsary, A.; O'Dell, S.L.; Ice, G.

    2010-01-01

    This Special Issue of X-Ray Optics and Instrumentation comprises ten review papers and six research articles, which collectively offer a broad overview of X-ray focusing techniques and applications in laboratory measurements, in synchrotron beamlines, and in X-ray astronomy. Focusing enables not only more intense illumination for reduced exposure time and higher signal-to-noise ratio, but higher spatial resolution through true imaging. Although X-ray focusing is accomplished through the application of some basic physical principles, such as reflection (mirrors), refraction (lenses), and diffraction (crystals or zone plates), stringent performance requirements coupled with physical, mechanical, environmental, and manufacturability imperatives or limitations make the task technically challenging. The diverse X-ray focusing techniques and applications covered in this Volume provide a glimpse into the scope, challenges, and future of this expanding field.

  10. Homework. Focus On

    Science.gov (United States)

    Rahal, Michelle Layer

    2010-01-01

    Homework has been an integral part of the educational system for over 100 years. What likely began as simple memorization tasks has evolved into complex projects and sparked an increasingly heated debate over the purpose and value of homework assignments. This "Focus On" examines the purpose of homework, how to create homework that has value,…

  11. Collective focusing ion accelerator

    International Nuclear Information System (INIS)

    Goldin, F.J.

    1986-01-01

    The principal subject of this dissertation is the trapping confinement of pure electron plasmas in bumpy toroidal magnetic fields, with particular attention given to the trapping procedure and the behavior of the plasma during the final equilibrium. The most important aspects of the equilibrium studied were the qualitative nature of the plasma configuration and motion and its density, distribution and stability. The motivation for this study was that an unneutralized cloud of electrons contained in a toroidal system, sufficiently dense and stable, may serve to electrostatically focus ions (against centrifugal and self space charge forces) in a cyclic ion accelerator. Such an accelerator, known as a Collective Focusing Ion Accelerator (CFIA) could be far smaller than conventional designs (which use external magnetic fields directly to focus the ions) due to the smaller gyro-radium of an electron in a magnetic field of given strength. The electron cloud generally drifted poloidally at a finite radius from the toroidal minor axis. As this would preclude focusing ions with such clouds, damping this motion was investigated. Finite resistance in the normally perfectly conductive vessel wall did this. In further preparation for a working CFIA, additional experiments studied the effect of ions on the stability of the electron cloud

  12. Introduction to the special issue

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    Gorka Elordieta

    2007-06-01

    Full Text Available For the past few years there has been an intense and increasing collaboration effort between researchers working on the Iberian languages, and this is particularly true in the realm of phonetics and phonology. The 'Journal of Portuguese Linguistics 'has played a role in contributing to stimulate such a collaborative research focusing on the Iberian languages: first with a Special Issue on 'Variation and Change in the Iberian Languages: the Peninsula and Beyond', and now with a Special Issue on the 'Prosody of Ibero-Romance and Related Languages'. In fact, to broaden its scope of coverage to the Iberian languages has become an explicit goal of the journal. As guest-editors of this issue, we are very pleased to be able to contribute to this objective, which we find an extremely fruitful one.

  13. FATHER PLAY: IS IT SPECIAL?

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    Cabrera, Natasha J; Roggman, Lori

    2017-11-01

    Both mothers and fathers play with their children, but research on parent-child play interactions is conducted with mothers three times more often than it is with fathers. The articles in this special issue address this gap by focusing on the nature and quality of father-child play, across cultural contexts, and considering whether father play offers something unique and special for early human development, in infancy or early childhood. The studies show that fathers can be just as developmentally supportive as are mothers in terms of being playful and engaged with their children in ways that are related to greater child socioemotional competence, emotion regulation, and vocabulary, and to less aggression, anxiety, and negativity. We encourage future research to examine the cultural influences, family system dynamics, and specificity of timing and types of father-child play in relation to children's developmental competence. © 2017 Michigan Association for Infant Mental Health.

  14. [Construction and expression of eukaryotic expression plasmid pcDNA3.1-smac].

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    Qin, Si-da; Ren, Hong; Li, Xiao-Jun; Yang, Cheng-Cheng; Yang, Bin; Zhang, Xiang-Zhong; Li, Shi-Sen; Hu, Li-Juan

    2011-02-01

    To construct the eukaryotic expression vector of human gene Smac pcDNA3.1-Smac and express it in the lung adenocarcinoma A549 cells. The Smac was amplified from human testis tissue by reverse transcriptase polymerase chain reaction (RT-PCR). Then recombined eukaryotic expression vector pcDNA3.1-Smac was constructed. After the reconbinant plasmid was proved to be constructed correctly by endonucleases digesting and DNA sequencing, we trasfected it into lung adenocarcinama cells A549 through liposome inducing. The expression of Smac in transfectant A549 was detected by RT-PCR and Western blot. And the cell growth inhibition ratio after trasfection was detected by MTT. The amplified fragment by PCR was coincident with the anticipated result, and its sequence was in concordance with that published on GenBank.Therefore, the gene Smac was cloned successfully, and the recombinant plasmid pcDNA3.1-Smac was also constructed successfully. Both on the mRNA level and the protein level, the expression of Smac gene was increased obviously in the transfected A549 detected by RT-PCR and Western blot respectively. The cell growth inhibition ratio in the group transfected pcDNA3.1-Smac was significantly higher compared with the pcDNA3.1 group after 72 hours. The recombinant eukaryotic expression vector pcDNA3.1-Smac was constructed, and it could be obviously expressed in lung adenocarcinoma cells A549. It is also proven that Smac has the function of growth inhibition.

  15. Relative role of eukaryotic and prokaryotic microorganisms in phenanthrene transformation in coastal sediments

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    MacGillivray, A.R.; Shiaris, M.P. (Univ. of Massachusetts, Boston, MA (United States))

    1994-04-01

    The relative role of eukaryotic versus prokaryotic microorganisms in phenanthrene transformation was measured in slurries of coastal sediment by two different approaches: detection of marker metabolites and use of selective inhibitors on phenanthrene biotransformation. Phenanthrene biotransformation was measured by polar metabolite formation and CO[sub 2] evolution from [9-[sup 14]C]phenanthrene. Both yeasts and bacteria transformed phenanthrene in slurries of coastal sediment. Two products of phenanthrene oxidation by fungi, phenanthrene trans-3,4-dihydrodiol and 3-phenanthrol, were produced in yeast-inoculated sterile sediment. However, only products of phenanthrene oxidation typical of bacterial transformation, 1-hydroxy-2-naphthoic acid and phenanthrene cis-3,4-dihydrodiol, were isolated from slurries of coastal sediment with natural microbial populations. Phenanthrene trans-dihydrodiols or other products of fungal oxidation of phenanthrene were not detected in the slurry containing a natural microbial population. A predominant role for bacterial transformation of phenanthrene was also suggested from selective inhibitor experiments. Addition of streptomycin to slurries, at a concentration which suppressed bacterial viable counts and rates of [methyl-[sup 3]H]thymidine uptake, completely inhibited phenanthrene transformation. Treatment with colchicine, at a concentration which suppressed yeast viable counts, depressed phenanthrene transformation by 40%, and this was likely due to nontarget inhibition of bacterial activity. The relative contribution of eukaryotic microorganisms to phenanthrene transformation in inoculated sterile sediment was estimated to be less than 3% of the total activity. We conclude that the predominant degraders of phenanthrene in muddy coastal sediments are bacteria and not eukaryotic microorganisms. 35 refs., 2 figs., 1 tab.

  16. Functional prokaryotic-eukaryotic chimera from the pentameric ligand-gated ion channel family.

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    Duret, Guillaume; Van Renterghem, Catherine; Weng, Yun; Prevost, Marie; Moraga-Cid, Gustavo; Huon, Christèle; Sonner, James M; Corringer, Pierre-Jean

    2011-07-19

    Pentameric ligand-gated ion channels (pLGICs), which mediate chemo-electric signal transduction in animals, have been recently found in bacteria. Despite clear sequence and 3D structure homology, the phylogenetic distance between prokaryotic and eukaryotic homologs suggests significant structural divergences, especially at the interface between the extracellular (ECD) and the transmembrane (TMD) domains. To challenge this possibility, we constructed a chimera in which the ECD of the bacterial protein GLIC is fused to the TMD of the human α1 glycine receptor (α1GlyR). Electrophysiology in Xenopus oocytes shows that it functions as a proton-gated ion channel, thereby locating the proton activation site(s) of GLIC in its ECD. Patch-clamp experiments in BHK cells show that the ion channel displays an anionic selectivity with a unitary conductance identical to that of the α1GlyR. In addition, pharmacological investigations result in transmembrane allosteric modulation similar to the one observed on α1GlyR. Indeed, the clinically active drugs propofol, four volatile general anesthetics, alcohols, and ivermectin all potentiate the chimera while they inhibit GLIC. Collectively, this work shows the compatibility between GLIC and α1GlyR domains and points to conservation of the ion channel and transmembrane allosteric regulatory sites in the chimera. This provides evidence that GLIC and α1GlyR share a highly homologous 3D structure. GLIC is thus a relevant model of eukaryotic pLGICs, at least from the anionic type. In addition, the chimera is a good candidate for mass production in Escherichia coli, opening the way for investigations of "druggable" eukaryotic allosteric sites by X-ray crystallography.

  17. Bacterial Signaling Nucleotides Inhibit Yeast Cell Growth by Impacting Mitochondrial and Other Specifically Eukaryotic Functions

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    Andy Hesketh

    2017-07-01

    Full Text Available We have engineered Saccharomyces cerevisiae to inducibly synthesize the prokaryotic signaling nucleotides cyclic di-GMP (cdiGMP, cdiAMP, and ppGpp in order to characterize the range of effects these nucleotides exert on eukaryotic cell function during bacterial pathogenesis. Synthetic genetic array (SGA and transcriptome analyses indicated that, while these compounds elicit some common reactions in yeast, there are also complex and distinctive responses to each of the three nucleotides. All three are capable of inhibiting eukaryotic cell growth, with the guanine nucleotides exhibiting stronger effects than cdiAMP. Mutations compromising mitochondrial function and chromatin remodeling show negative epistatic interactions with all three nucleotides. In contrast, certain mutations that cause defects in chromatin modification and ribosomal protein function show positive epistasis, alleviating growth inhibition by at least two of the three nucleotides. Uniquely, cdiGMP is lethal both to cells growing by respiration on acetate and to obligately fermentative petite mutants. cdiGMP is also synthetically lethal with the ribonucleotide reductase (RNR inhibitor hydroxyurea. Heterologous expression of the human ppGpp hydrolase Mesh1p prevented the accumulation of ppGpp in the engineered yeast and restored cell growth. Extensive in vivo interactions between bacterial signaling molecules and eukaryotic gene function occur, resulting in outcomes ranging from growth inhibition to death. cdiGMP functions through a mechanism that must be compensated by unhindered RNR activity or by functionally competent mitochondria. Mesh1p may be required for abrogating the damaging effects of ppGpp in human cells subjected to bacterial infection.

  18. How MCM loading and spreading specify eukaryotic DNA replication initiation sites [version 1; referees: 4 approved

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    Olivier Hyrien

    2016-08-01

    Full Text Available DNA replication origins strikingly differ between eukaryotic species and cell types. Origins are localized and can be highly efficient in budding yeast, are randomly located in early fly and frog embryos, which do not transcribe their genomes, and are clustered in broad (10-100 kb non-transcribed zones, frequently abutting transcribed genes, in mammalian cells. Nonetheless, in all cases, origins are established during the G1-phase of the cell cycle by the loading of double hexamers of the Mcm 2-7 proteins (MCM DHs, the core of the replicative helicase. MCM DH activation in S-phase leads to origin unwinding, polymerase recruitment, and initiation of bidirectional DNA synthesis. Although MCM DHs are initially loaded at sites defined by the binding of the origin recognition complex (ORC, they ultimately bind chromatin in much greater numbers than ORC and only a fraction are activated in any one S-phase. Data suggest that the multiplicity and functional redundancy of MCM DHs provide robustness to the replication process and affect replication time and that MCM DHs can slide along the DNA and spread over large distances around the ORC. Recent studies further show that MCM DHs are displaced along the DNA by collision with transcription complexes but remain functional for initiation after displacement. Therefore, eukaryotic DNA replication relies on intrinsically mobile and flexible origins, a strategy fundamentally different from bacteria but conserved from yeast to human. These properties of MCM DHs likely contribute to the establishment of broad, intergenic replication initiation zones in higher eukaryotes.

  19. Differential gene expression in Giardia lamblia under oxidative stress: significance in eukaryotic evolution.

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    Raj, Dibyendu; Ghosh, Esha; Mukherjee, Avik K; Nozaki, Tomoyoshi; Ganguly, Sandipan

    2014-02-10

    Giardia lamblia is a unicellular, early branching eukaryote causing giardiasis, one of the most common human enteric diseases. Giardia, a microaerophilic protozoan parasite has to build up mechanisms to protect themselves against oxidative stress within the human gut (oxygen concentration 60 μM) to establish its pathogenesis. G. lamblia is devoid of the conventional mechanisms of the oxidative stress management system, including superoxide dismutase, catalase, peroxidase, and glutathione cycling, which are present in most eukaryotes. NADH oxidase is a major component of the electron transport chain of G. lamblia, which in concurrence with disulfide reductase, protects oxygen-labile proteins such as pyruvate: ferredoxin oxidoreductase against oxidative stress by sustaining a reduced intracellular environment. It also contains the arginine dihydrolase pathway, which occurs in a number of anaerobic prokaryotes, includes substrate level phosphorylation and adequately active to make a major contribution to ATP production. To study differential gene expression under three types of oxidative stress, a Giardia genomic DNA array was constructed and hybridized with labeled cDNA of cells with or without stress. The transcriptomic data has been analyzed and further validated using real time PCR. We identified that out of 9216 genes represented on the array, more than 200 genes encoded proteins with functions in metabolism, oxidative stress management, signaling, reproduction and cell division, programmed cell death and cytoskeleton. We recognized genes modulated by at least ≥ 2 fold at a significant time point in response to oxidative stress. The study has highlighted the genes that are differentially expressed during the three experimental conditions which regulate the stress management pathway differently to achieve redox homeostasis. Identification of some unique genes in oxidative stress regulation may help in new drug designing for this common enteric parasite prone to

  20. How and why DNA barcodes underestimate the diversity of microbial eukaryotes.

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    Gwenael Piganeau

    Full Text Available BACKGROUND: Because many picoplanktonic eukaryotic species cannot currently be maintained in culture, direct sequencing of PCR-amplified 18S ribosomal gene DNA fragments from filtered sea-water has been successfully used to investigate the astounding diversity of these organisms. The recognition of many novel planktonic organisms is thus based solely on their 18S rDNA sequence. However, a species delimited by its 18S rDNA sequence might contain many cryptic species, which are highly differentiated in their protein coding sequences. PRINCIPAL FINDINGS: Here, we investigate the issue of species identification from one gene to the whole genome sequence. Using 52 whole genome DNA sequences, we estimated the global genetic divergence in protein coding genes between organisms from different lineages and compared this to their ribosomal gene sequence divergences. We show that this relationship between proteome divergence and 18S divergence is lineage dependent. Unicellular lineages have especially low 18S divergences relative to their protein sequence divergences, suggesting that 18S ribosomal genes are too conservative to assess planktonic eukaryotic diversity. We provide an explanation for this lineage dependency, which suggests that most species with large effective population sizes will show far less divergence in 18S than protein coding sequences. CONCLUSIONS: There is therefore a trade-off between using genes that are easy to amplify in all species, but which by their nature are highly conserved and underestimate the true number of species, and using genes that give a better description of the number of species, but which are more difficult to amplify. We have shown that this trade-off differs between unicellular and multicellular organisms as a likely consequence of differences in effective population sizes. We anticipate that biodiversity of microbial eukaryotic species is underestimated and that numerous "cryptic species" will become