WorldWideScience

Sample records for bonsai

  1. Rising Threat; Bonsai.

    Science.gov (United States)

    Aksel, Gokhan; Bozan, Oner; Kayaci, Mine; Guneysel, Ozlem; Sezgin, Seckin Bahar

    2015-06-01

    In recent years, and especially in the past few months, the number of synthetic cannabinoid (bonsai) users has increased in our country. The aim of this study was to draw attention to the consumption of bonsai among young people and reveal the demographic and basic clinical characteristics of these users. This was a retrospective study conducted at the Ümraniye Training and Research Hospital. All of the adult patients (≥18 year old) with synthetic cannabinoid intoxication who presented to the Emergency Department throughout the two years of the study (July 1(st) 2012-June 30(th) 2014) were enrolled. The frequencies were given as the median and inter-quartile range). 197 patients were included in this study, with 190 male patients (96.4%) and 7 (3.6%) female patients. Two of the four hospitalized patients were exitus, 52 left on their own will and a total of 141 patients were discharged after 6-12 hours of observation in the ED. The use of synthetic cannabinoids (bonsai) in the recent years, especially in the summer months of 2014 was investigated in this study. Although these patients can have a benign clinical course, the process can also be fatal. It should especially be noted that patients with depressed respiration, low GCS scores and high PaCO2 values are at higher risk for mortality and the necessity of early intubation should be kept in mind.

  2. Rising Threat; Bonsai

    Directory of Open Access Journals (Sweden)

    Gokhan AKSEL

    2015-06-01

    Full Text Available SUMMARY: Objectives: In recent years, and especially in the past few months, the number of synthetic cannabinoid (bonsai users has increased in our country. The aim of this study was to draw attention to the consumption of bonsai among young people and reveal the demographic and basic clinical characteristics of these users. Methods: This was a retrospective study conducted at the Ümraniye Training and Research Hospital. All of the adult patients (≥18 year old with synthetic cannabinoid intoxication who presented to the Emergency Department throughout the two years of the study (July 1st 2012–June 30th 2014 were enrolled. The frequencies were given as the median and inter-quartile range. Results: 197 patients were included in this study, with 190 male patients (96.4% and 7 (3.6% female patients. Two of the four hospitalized patients were exitus, 52 left on their own will and a total of 141 patients were discharged after 6-12 hours of observation in the ED. Conclusions: The use of synthetic cannabinoids (bonsai in the recent years, especially in the summer months of 2014 was investigated in this study. Although these patients can have a benign clinical course, the process can also be fatal. It should especially be noted that patients with depressed respiration, low GCS scores and high PaCO2 values are at higher risk for mortality and the necessity of early intubation should be kept in mind. Key words: Cannabinoid receptor agonists, emergency medicine

  3. [Bonsai induced acute myocardial infarction].

    Science.gov (United States)

    Ayhan, Hüseyin; Aslan, Abdullah Nabi; Süygün, Hakan; Durmaz, Tahir

    2014-09-01

    Incidences of drug abuse and cannabis have increased in young adults, recently. Cannabis induced myocardial infarction has rarely been reported in these people. There is no any literature about a synthetic cannabinoid, being recently most popular Bonsai, to cause myocardial infarction. In this case report we presented a 33-year-old male patient who developed acute myocardial infarction after taking high doses of Bonsai.

  4. BONSAI Garden: Parallel knowledge discovery system for amino acid sequences

    Energy Technology Data Exchange (ETDEWEB)

    Shoudai, T.; Miyano, S.; Shinohara, A.; Okazaki, T.; Arikawa, S. [Kyushu Univ., Fukuoka (Japan)] [and others

    1995-12-31

    We have developed a machine discovery system BON-SAI which receives positive and negative examples as inputs and produces as a hypothesis a pair of a decision tree over regular patterns and an alphabet indexing. This system has succeeded in discovering reasonable knowledge on transmembrane domain sequences and signal peptide sequences by computer experiments. However, when several kinds of sequences axe mixed in the data, it does not seem reasonable for a single BONSAI system to find a hypothesis of a reasonably small size with high accuracy. For this purpose, we have designed a system BONSAI Garden, in which several BONSAI`s and a program called Gardener run over a network in parallel, to partition the data into some number of classes together with hypotheses explaining these classes accurately.

  5. BONSAI Garden: parallel knowledge discovery system for amino acid sequences.

    Science.gov (United States)

    Shoudai, T; Lappe, M; Miyano, S; Shinohara, A; Okazaki, T; Arikawa, S; Uchida, T; Shimozono, S; Shinohara, T; Kuhara, S

    1995-01-01

    We have developed a machine discovery system BONSAI which receives positive and negative examples as inputs and produces as a hypothesis a pair of a decision tree over regular patterns and an alphabet indexing. This system has succeeded in discovering reasonable knowledge on transmembrane domain sequences and signal peptide sequences by computer experiments. However, when several kinds of sequences are mixed in the data, it does not seem reasonable for a single BONSAI system to find a hypothesis of a reasonably small size with high accuracy. For this purpose, we have designed a system BONSAI Garden, in which several BONSAI's and a program called Gardener run over a network in parallel, to partition the data into some number of classes together with hypotheses explaining these classes accurately.

  6. Bonsai: N-body GPU tree-code

    Science.gov (United States)

    Bédorf, Jeroen; Gaburov, Evghenii; Portegies Zwart, Simon

    2012-12-01

    Bonsai is a gravitational N-body tree-code that runs completely on the GPU. This reduces the amount of time spent on communication with the CPU. The code runs on NVIDIA GPUs and on a GTX480 it is able to integrate 2.8M particles per second. The tree construction and traverse algorithms are portable to many-core devices which have support for CUDA or OpenCL programming languages.

  7. Performance improvement in protein N-myristoyl classification by BONSAI with insignificant indexing symbol.

    Science.gov (United States)

    Sugii, Manabu; Okada, Ryo; Matsuno, Hiroshi; Miyano, Satoru

    2007-01-01

    Many N-myristoylated proteins play key roles in regulating cellular structure and function. In the previous study, we have applied the machine learning system BONSAI to predict patterns based on which positive and negative examples could be classified. Although BONSAI has helped establish 2 interesting rules regarding the requirements for N-myristoylation, the accuracy rates of these rules are not satisfactory. This paper suggests an enhancement of BONSAI by introducing an "insignificant indexing symbol" and demonstrates the efficiency of this enhancement by showing an improvement in the accuracy rates. We further examine the performance of this enhanced BONSAI by comparing the results of classification obtained the proposed method and an existing public method for the same sets of positive and negative examples.

  8. Giant J (Osborn Wave due to Bonsai Abuse: Comments on Clinical Practice

    Directory of Open Access Journals (Sweden)

    Murat Yalçın

    2017-02-01

    Full Text Available Background: Osborn wave, typically associated with hypothermia, is currently referred to as one of the J wave syndromes due to its clinical potential to develop lethal cardiac arrhythmia; it may rarely be observed in a non-hypothermic setting such as cannabis abuse. Case Report: In this paper, we presented two young cases who presented to the emergency services with unconsciousness, drowsiness, and hypoxia, and also J wave on electrocardiography (ECG due to Bonsai abuse. Conclusion: Osborn wave may be a significant criterion to initiate close monitoring in a coronary care unit, with supportive treatment and mechanical ventilation as necessary in those patients who abuse Bonsai

  9. Giant J (Osborn) Wave due to Bonsai Abuse: Comments on Clinical Practice.

    Science.gov (United States)

    Yalçın, Murat; Aparcı, Mustafa; Eroğlu, Murat; Işılak, Zafer; Özmen, Namık

    2017-01-01

    Osborn wave, typically associated with hypothermia, is currently referred to as one of the J wave syndromes due to its clinical potential to develop lethal cardiac arrhythmia; it may rarely be observed in a non-hypothermic setting such as cannabis abuse. In this paper, we presented two young cases who presented to the emergency services with unconsciousness, drowsiness, and hypoxia, and also J wave on electrocardiography (ECG) due to Bonsai abuse. Osborn wave may be a significant criterion to initiate close monitoring in a coronary care unit, with supportive treatment and mechanical ventilation as necessary in those patients who abuse Bonsai.

  10. Bionomics and formation of "Bonsai" colonies with long term rearing of Coptotermes formosanus (Isoptera: Rhinotermitidae)

    Science.gov (United States)

    This laboratory study reports the ability of Formosan subterranean termite, Coptotermes formosanus Shiraki, colonies to survive for at least 9-yr while restricted to a sweater box. Colonies survived by limiting queen size and worker numbers, allowing these bonsai colonies to thrive. Queen physogastr...

  11. Bonsai: An event-based framework for processing and controlling data streams

    Directory of Open Access Journals (Sweden)

    Gonçalo eLopes

    2015-04-01

    Full Text Available The design of modern scientific experiments requires the control and monitoring of many different data streams. However, the serial execution of programming instructions in a computer makes it a challenge to develop software that can deal with the asynchronous, parallel nature of scientific data. Here we present Bonsai, a modular, high-performance, open-source visual programming framework for the acquisition and online processing of data streams. We describe Bonsai's core principles and architecture and demonstrate how it allows for the rapid and flexible prototyping of integrated experimental designs in neuroscience. We specifically highlight some applications that require the combination of many different hardware and software components, including video tracking of behavior, electrophysiology and closed-loop control of stimulation.

  12. Bonsai: an event-based framework for processing and controlling data streams.

    Science.gov (United States)

    Lopes, Gonçalo; Bonacchi, Niccolò; Frazão, João; Neto, Joana P; Atallah, Bassam V; Soares, Sofia; Moreira, Luís; Matias, Sara; Itskov, Pavel M; Correia, Patrícia A; Medina, Roberto E; Calcaterra, Lorenza; Dreosti, Elena; Paton, Joseph J; Kampff, Adam R

    2015-01-01

    The design of modern scientific experiments requires the control and monitoring of many different data streams. However, the serial execution of programming instructions in a computer makes it a challenge to develop software that can deal with the asynchronous, parallel nature of scientific data. Here we present Bonsai, a modular, high-performance, open-source visual programming framework for the acquisition and online processing of data streams. We describe Bonsai's core principles and architecture and demonstrate how it allows for the rapid and flexible prototyping of integrated experimental designs in neuroscience. We specifically highlight some applications that require the combination of many different hardware and software components, including video tracking of behavior, electrophysiology and closed-loop control of stimulation.

  13. Efficient, reliable and fast high-level triggering using a bonsai boosted decision tree

    CERN Document Server

    Gligorov, V.V.

    2013-01-01

    High-level triggering is a vital component in many modern particle physics experiments. This paper describes a modification to the standard boosted decision tree (BDT) classifier, the so-called "bonsai" BDT, that has the following important properties: it is more efficient than traditional cut-based approaches; it is robust against detector instabilities, and it is very fast. Thus, it is fit-for-purpose for the online running conditions faced by any large-scale data acquisition system.

  14. Efficient, reliable and fast high-level triggering using a bonsai boosted decision tree

    Science.gov (United States)

    Gligorov, V. V.; Williams, M.

    2013-02-01

    High-level triggering is a vital component of many modern particle physics experiments. This paper describes a modification to the standard boosted decision tree (BDT) classifier, the so-called bonsai BDT, that has the following important properties: it is more efficient than traditional cut-based approaches; it is robust against detector instabilities, and it is very fast. Thus, it is fit-for-purpose for the online running conditions faced by any large-scale data acquisition system.

  15. Efficient, reliable and fast high-level triggering using a bonsai boosted decision tree

    International Nuclear Information System (INIS)

    Gligorov, V V; Williams, M

    2013-01-01

    High-level triggering is a vital component of many modern particle physics experiments. This paper describes a modification to the standard boosted decision tree (BDT) classifier, the so-called bonsai BDT, that has the following important properties: it is more efficient than traditional cut-based approaches; it is robust against detector instabilities, and it is very fast. Thus, it is fit-for-purpose for the online running conditions faced by any large-scale data acquisition system.

  16. Clinician accessible tools for GUI computational models of transcranial electrical stimulation: BONSAI and SPHERES.

    Science.gov (United States)

    Truong, Dennis Q; Hüber, Mathias; Xie, Xihe; Datta, Abhishek; Rahman, Asif; Parra, Lucas C; Dmochowski, Jacek P; Bikson, Marom

    2014-01-01

    Computational models of brain current flow during transcranial electrical stimulation (tES), including transcranial direct current stimulation (tDCS) and transcranial alternating current stimulation (tACS), are increasingly used to understand and optimize clinical trials. We propose that broad dissemination requires a simple graphical user interface (GUI) software that allows users to explore and design montages in real-time, based on their own clinical/experimental experience and objectives. We introduce two complimentary open-source platforms for this purpose: BONSAI and SPHERES. BONSAI is a web (cloud) based application (available at neuralengr.com/bonsai) that can be accessed through any flash-supported browser interface. SPHERES (available at neuralengr.com/spheres) is a stand-alone GUI application that allow consideration of arbitrary montages on a concentric sphere model by leveraging an analytical solution. These open-source tES modeling platforms are designed go be upgraded and enhanced. Trade-offs between open-access approaches that balance ease of access, speed, and flexibility are discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. Use of BONSAI decision trees for the identification of potential MHC class I peptide epitope motifs.

    Science.gov (United States)

    Savoie, C J; Kamikawaji, N; Sasazuki, T; Kuhara, S

    1999-01-01

    Recognition of short peptides of 8 to 10 mer bound to MHC class I molecules by cytotoxic T lymphocytes forms the basis of cellular immunity. While the sequence motifs necessary for binding of intracellular peptides to MHC have been well studied, little is known about sequence motifs that may cause preferential affinity to the T cell receptor and/or preferential recognition and response by T cells. Here we demonstrate that computational learning systems can be useful to elucidate sequence motifs that affect T cell activation. Knowledge of T cell activation motifs could be useful for targeted vaccine design or immunotherapy. With the BONSAI computational learning algorithm, using a database of previously reported MHC bound peptides that had positive or negative T cell responses, we were able to identify sequence motif rules that explain 70% of positive T cell responses and 84% of negative T cell responses.

  18. Effects of Visual Stimulation with Bonsai Trees on Adult Male Patients with Spinal Cord Injury.

    Science.gov (United States)

    Ochiai, Hiroko; Song, Chorong; Ikei, Harumi; Imai, Michiko; Miyazaki, Yoshifumi

    2017-09-05

    Nature therapy has been demonstrated to induce physiological relaxation. The psychophysiological effects of nature therapy (stimulation with bonsai trees) on adult male patients with spinal cord injury (SCI) were examined. Oxyhemoglobin concentration changes in the prefrontal cortex were measured using near-infrared spectroscopy, and heart rate variability was analyzed. Psychological responses were evaluated using the modified semantic differential method and Profile of Mood States (POMS) subscale scores. Visual stimulation of adult male patients with SCI elicited significantly decreased left prefrontal cortex activity, increased parasympathetic nervous activity, decreased sympathetic nervous activity, increased positive feelings, and resulted in lower negative POMS subscale scores. Nature therapy can lead to a state of physiological and psychological relaxation in patients with SCI.

  19. Clinical Characteristics of Patients Diagnosed with Synthetic Cannabinoid (Bonsai Intoxication in Intensive Care Unit

    Directory of Open Access Journals (Sweden)

    Hatice Betül Altınışık

    2015-12-01

    Full Text Available Objective: In recent years, synthetic cannabinoids (bonsai poisoning is a widely seen case that needs to be treated in intensive care unit (ICU in our country. In this study, it was aimed to discuss the clinical characteristics of patients diagnosed with synthetic cannabinoid intoxication followed in ICU. Material and Method: Patients followed in ICU of Çanakkale Onsekiz Mart University and Çanakkale State Hospital between 2014 and 2015 were studied retrospectively. Results: Twelve cases were included. In neurological system; confusions (n=4, drowsiness (n=7, restlessness/agitations (n=5, hallucinations (n=2, anxieties/panics (n=3, acute psychosis (n=1 and amnesias (n=11 were detected. One patient was intubated. In cardiovascular system; tachycardias (n=3, bradycardias (n=2, hypertensions (n=2, hypotension (n=1, and arrhythmias (n=2 were observed. In laboratory tests, leukocytosis (n=4, leukopenia (n=1, hypoglycemias (n=3, elevation in liver and renal function tests (n=1 were identified. The average recovery time was 19.3-hours and the average ICU stay was 3-days. Conclusion: In the synthetic cannabinoid intoxication cases; it should be kept in mind that seizure activities may occur in the first hours, myocardial infarction risk in the first 3-days. Liver-kidney functions should be monitored. Hypopotasemia is the most common electrolyte disorder. Cases without any complication are expected to recover in 24-hours. However, new types of synthetic cannabinoids are put on the market every day.

  20. LimsPortal and BonsaiLIMS: development of a lab information management system for translational medicine

    Directory of Open Access Journals (Sweden)

    Afzal Vackar

    2011-05-01

    Full Text Available Abstract Background Laboratory Information Management Systems (LIMS are an increasingly important part of modern laboratory infrastructure. As typically very sophisticated software products, LIMS often require considerable resources to select, deploy and maintain. Larger organisations may have access to specialist IT support to assist with requirements elicitation and software customisation, however smaller groups will often have limited IT support to perform the kind of iterative development that can resolve the difficulties that biologists often have when specifying requirements. Translational medicine aims to accelerate the process of treatment discovery by bringing together multiple disciplines to discover new approaches to treating disease, or novel applications of existing treatments. The diverse set of disciplines and complexity of processing procedures involved, especially with the use of high throughput technologies, bring difficulties in customizing a generic LIMS to provide a single system for managing sample related data within a translational medicine research setting, especially where limited IT support is available. Results We have designed and developed a LIMS, BonsaiLIMS, around a very simple data model that can be easily implemented using a variety of technologies, and can be easily extended as specific requirements dictate. A reference implementation using Oracle 11 g database and the Python framework, Django is presented. Conclusions By focusing on a minimal feature set and a modular design we have been able to deploy the BonsaiLIMS system very quickly. The benefits to our institute have been the avoidance of the prolonged implementation timescales, budget overruns, scope creep, off-specifications and user fatigue issues that typify many enterprise software implementations. The transition away from using local, uncontrolled records in spreadsheet and paper formats to a centrally held, secured and backed-up database brings the

  1. LimsPortal and BonsaiLIMS: development of a lab information management system for translational medicine.

    Science.gov (United States)

    Bath, Timothy G; Bozdag, Selcuk; Afzal, Vackar; Crowther, Daniel

    2011-05-13

    Laboratory Information Management Systems (LIMS) are an increasingly important part of modern laboratory infrastructure. As typically very sophisticated software products, LIMS often require considerable resources to select, deploy and maintain. Larger organisations may have access to specialist IT support to assist with requirements elicitation and software customisation, however smaller groups will often have limited IT support to perform the kind of iterative development that can resolve the difficulties that biologists often have when specifying requirements. Translational medicine aims to accelerate the process of treatment discovery by bringing together multiple disciplines to discover new approaches to treating disease, or novel applications of existing treatments. The diverse set of disciplines and complexity of processing procedures involved, especially with the use of high throughput technologies, bring difficulties in customizing a generic LIMS to provide a single system for managing sample related data within a translational medicine research setting, especially where limited IT support is available. We have designed and developed a LIMS, BonsaiLIMS, around a very simple data model that can be easily implemented using a variety of technologies, and can be easily extended as specific requirements dictate. A reference implementation using Oracle 11 g database and the Python framework, Django is presented. By focusing on a minimal feature set and a modular design we have been able to deploy the BonsaiLIMS system very quickly. The benefits to our institute have been the avoidance of the prolonged implementation timescales, budget overruns, scope creep, off-specifications and user fatigue issues that typify many enterprise software implementations. The transition away from using local, uncontrolled records in spreadsheet and paper formats to a centrally held, secured and backed-up database brings the immediate benefits of improved data visibility, audit and

  2. Bonsai: A GPU Tree-Code

    Science.gov (United States)

    Bédorf, J.; Gaburov, E.; Portegies Zwart, S.

    2012-07-01

    We present a gravitational hierarchical N-body code that is designed to run efficiently on Graphics Processing Units (GPUs). All parts of the algorithm are exectued on the GPU which eliminates the need for data transfer between the Central Processing Unit (CPU) and the GPU. Our tests indicate that the gravitational tree-code outperforms tuned CPU code for all parts of the algorithm and show an overall performance improvement of more than a factor 20, resulting in a processing rate of more than 2.8 million particles per second.

  3. Teaching Culturally Different Students: Growing Pine Trees or Bonsai Trees.

    Science.gov (United States)

    Locke, Don C.

    1988-01-01

    This article reviews educational inequalities based on cultural heritage and proposes a model for teachers to become more effective in teaching culturally diverse students. The cross-cultural awareness continuum is described and the stages through which a teacher must pass to achieve such awareness are discussed. (JL)

  4. Boosting bonsai trees for handwritten/printed text discrimination

    Science.gov (United States)

    Ricquebourg, Yann; Raymond, Christian; Poirriez, Baptiste; Lemaitre, Aurélie; Coüasnon, Bertrand

    2013-12-01

    Boosting over decision-stumps proved its efficiency in Natural Language Processing essentially with symbolic features, and its good properties (fast, few and not critical parameters, not sensitive to over-fitting) could be of great interest in the numeric world of pixel images. In this article we investigated the use of boosting over small decision trees, in image classification processing, for the discrimination of handwritten/printed text. Then, we conducted experiments to compare it to usual SVM-based classification revealing convincing results with very close performance, but with faster predictions and behaving far less as a black-box. Those promising results tend to make use of this classifier in more complex recognition tasks like multiclass problems.

  5. Bonsai fires for small incinerators. Flexible incinerators for low throughput; Bonsai-Feuer fuer die Kleinen. Flexible Muellverbrennungstechnik zielt auf geringen Durchsatz

    Energy Technology Data Exchange (ETDEWEB)

    Kerres, K.; Paassen, P. [RWE Umwelt Services Deutschland GmbH (Germany); Napp, M. [Roll Inova GmbH (Germany)

    2000-09-01

    RWE Umwelt and von Roll cooperated in constructing small-scale incinerators for a target group comprising about 100 regional utilities. Standardisation and a well-tried technology have kept the cost at an acceptable level. [German] Die Entwickler haben ihre Zielgruppe bereits fest im Auge. Rund 100 Gebietskoerperschaften kommen fuer Zwerg-MVA in Frage, die in Zusammenarbeit aus RWE Umwelt und von Roll entstanden. Standardisierung und Rueckgriff auf bewaehrte Technik machen diese MVA auch finanzierbar. (orig.)

  6. Spontaneous Mediastinal Emphysema Associated with the Use of Synthetic Cannabinoid (Bonsai).

    Science.gov (United States)

    Chousein, Efsun Gonca Uğur; İliaz, Sinem; Nizam, Merve; Öztürk, Sakine; Çağlar, Emel

    2016-01-01

    Spontaneous Mediastinal Emphysema (SME), which is a rarely seen case is defined as the detection of free air in the mediastinum without any trauma. Although rare, some cases secondary to drug use have been reported. In this study, two SME cases that developed due to the use of a synthetic cannabinoid known as "bonzai", which has recently become widespread in Turkey, are presented. We would like to emphasize that SME should also be considered in the differential diagnosis of patients who present with the symptoms of chest pain and dyspnea and have a history of drug use.

  7. Bonsai trees in your head: how the pavlovian system sculpts goal-directed choices by pruning decision trees.

    Science.gov (United States)

    Huys, Quentin J M; Eshel, Neir; O'Nions, Elizabeth; Sheridan, Luke; Dayan, Peter; Roiser, Jonathan P

    2012-01-01

    When planning a series of actions, it is usually infeasible to consider all potential future sequences; instead, one must prune the decision tree. Provably optimal pruning is, however, still computationally ruinous and the specific approximations humans employ remain unknown. We designed a new sequential reinforcement-based task and showed that human subjects adopted a simple pruning strategy: during mental evaluation of a sequence of choices, they curtailed any further evaluation of a sequence as soon as they encountered a large loss. This pruning strategy was Pavlovian: it was reflexively evoked by large losses and persisted even when overwhelmingly counterproductive. It was also evident above and beyond loss aversion. We found that the tendency towards Pavlovian pruning was selectively predicted by the degree to which subjects exhibited sub-clinical mood disturbance, in accordance with theories that ascribe Pavlovian behavioural inhibition, via serotonin, a role in mood disorders. We conclude that Pavlovian behavioural inhibition shapes highly flexible, goal-directed choices in a manner that may be important for theories of decision-making in mood disorders.

  8. Bonsai trees in your head: how the pavlovian system sculpts goal-directed choices by pruning decision trees.

    Directory of Open Access Journals (Sweden)

    Quentin J M Huys

    Full Text Available When planning a series of actions, it is usually infeasible to consider all potential future sequences; instead, one must prune the decision tree. Provably optimal pruning is, however, still computationally ruinous and the specific approximations humans employ remain unknown. We designed a new sequential reinforcement-based task and showed that human subjects adopted a simple pruning strategy: during mental evaluation of a sequence of choices, they curtailed any further evaluation of a sequence as soon as they encountered a large loss. This pruning strategy was Pavlovian: it was reflexively evoked by large losses and persisted even when overwhelmingly counterproductive. It was also evident above and beyond loss aversion. We found that the tendency towards Pavlovian pruning was selectively predicted by the degree to which subjects exhibited sub-clinical mood disturbance, in accordance with theories that ascribe Pavlovian behavioural inhibition, via serotonin, a role in mood disorders. We conclude that Pavlovian behavioural inhibition shapes highly flexible, goal-directed choices in a manner that may be important for theories of decision-making in mood disorders.

  9. Scientific Opinion on a technical file submitted by the Japanese Authorities to support a derogation request from the EU import requirements for bonsai and topiary trees that are host plants of Anoplophora chinensis

    DEFF Research Database (Denmark)

    Baker, R.; Candresse, T.; Dormannsné Simon, E.

    2010-01-01

    Following a request from the EU Commission, the EFSA PLH Panel conducted a scientific opinion on risk analysis and supporting documents provided by APHIS/USDA in support of the request to remove the Union's plant health import requirement that citrus fruit imported into the EU be sourced from gro...

  10. A generalization of Connes-Kreimer Hopf algebra

    Science.gov (United States)

    Byun, Jungyoon

    2005-07-01

    "Bonsai" Hopf algebras, introduced here, are generalizations of Connes-Kreimer Hopf algebras, which are motivated by Feynman diagrams and renormalization. We show that we can find operad structure on the set of bonsais. We introduce a new differential on these bonsai Hopf algebras, which is inspired by the tree differential. The cohomologies of these are computed here, and the relationship of this differential with the appending operation * of Connes-Kreimer Hopf algebras is investigated.

  11. A generalization of Connes-Kreimer Hopf algebra

    International Nuclear Information System (INIS)

    Byun, Jungyoon

    2005-01-01

    'Bonsai' Hopf algebras, introduced here, are generalizations of Connes-Kreimer Hopf algebras, which are motivated by Feynman diagrams and renormalization. We show that we can find operad structure on the set of bonsais. We introduce a differential on these bonsai Hopf algebras, which is inspired by the tree differential. The cohomologies of these are computed here, and the relationship of this differential with the appending operation * of Connes-Kreimer Hopf algebras is investigated

  12. GETDB: 103729 [GETDB

    Lifescience Database Archive (English)

    Full Text Available 103729 Link to Original w[*]; P{GawB}NP0727 / CyO 58F3 Link to DGRC Genome Viewer: 103729 CG17807 bonsai...*]; P{GawB}NP0727 / CyO Insertion Site 58F3 Map Viewer Link to DGRC Genome Viewer: 103729 Related Genes CG17807 bonsai

  13. A collector's passion from catching the stone to sharing the view

    Science.gov (United States)

    This is an introduction to a second edition of the catalogue for the groundbreaking 2008 exhibition at the U.S. National Arboretum's National Bonsai & Penjing Museum - Beyond the Black Mountain: Color, Pattern, and Form in American Viewing Stones. The National Bonsai & Penjing Museum is one of the f...

  14. CosmoBon, tree research team, for studying utilization of woody plant in space environment

    Science.gov (United States)

    Tomita-Yokotani, Kaori; Yamashita, Masamichi; Hashimoto, Hirofumi; Sato, Seigo; Baba, Keiichi; Chida, Yukari

    2012-07-01

    We are proposing to raise woody plants in space for several applications and plant science, as Tree research team, TRT. Trees produce excess oxygen, wooden materials for living cabin, and provide biomass for cultivating mushroom and insect as for the space agriculture. Excellent tree shapes which would be deeply related to wood formation improve quality of life under stressful environment in outer space. We have the serious problem about their size. Bonsai is one of the Japanese traditional arts. We have been investigating the tension wood formation under exotic gravitational environment using Bonsai. CosmoBon is the small tree Bonsai for our space experiment. The tension wood formation in CosmoBon was confirmed as the same as that in the natural trees. Our goal is to examine feasibility to grow various species of trees in space as bioresource for space agriculture.

  15. Alejandro Zambra. The Art of Planting a Novel

    Directory of Open Access Journals (Sweden)

    Felipe Oliver

    2016-12-01

    Full Text Available The appearance of Bonsai in 2006, immediately placed Alejandro Zambra as one of the most representative writers of contemporary young Latin American literature. This novel of an absolute simplicity proposes however a very rich and complex framework of intertextuality. The title in fact is particularly relevant as far as it suggests a parallel between the complex technical of writing with the ancient Oriental practice of growing miniature trees. This paper seeks a reading of the novel of Zambra through its Bonsai symbolism.

  16. Street Drug Use among Emergency Patients in a Public Hospital in ...

    African Journals Online (AJOL)

    Conclusions: Selfreported SD users were mostly young males who were treated symptomatically and discharged. Almost one-third-mostly ecstasy and bonsai users-had depressed level of consciousness and required resuscitation. Keywords: Adverse drug effect, cannabis, ecstasy, emergency medicine, street drug user ...

  17. Jaapanist mõeldes / Tiina Tammet

    Index Scriptorium Estoniae

    Tammet, Tiina, 1971-

    2003-01-01

    Keraami Annika Tedre jaapanipärane ridamaja aed Tallinna aedlinnas loob majaga (arhitekt Martin Aunin, sisearhitekt Enn Kivi) hästisobiva koosluse. Maja on viimistletud läbikumava sinisega toonitud kuusevineeriga. Aiakujundaja Liina Rehepapp. Siseruumist, bonsai-mändidest, kividest, veest, taimedest. 15 ill

  18. An Evaluation of OCLC's EPIC as a Resource for Subject Access to Videos.

    Science.gov (United States)

    Palmer, Joseph W.

    1992-01-01

    An examination of OCLC's EPIC service and standard video reference tools revealed that EPIC was more comprehensive in finding video titles on the popular or specialized topics of bonsai, genealogy, karate, and holography, because of its keyword searching ability on the massive OCLC database. (11 references) (EA)

  19. 24.77 Pflops on a Gravitational Tree-Code to Simulate the Milky Way Galaxy with 18600 GPUs

    Science.gov (United States)

    Bédorf, Jeroen; Gaburov, Evghenii; Fujii, Michiko S.; Nitadori, Keigo; Ishiyama, Tomoaki; Portegies Zwart, Simon

    2014-11-01

    We have simulated, for the first time, the long term evolution of the Milky Way Galaxy using 51 billion particles on the Swiss Piz Daint supercomputer with our N-body gravitational tree-code Bonsai. Herein, we describe the scientific motivation and numerical algorithms. The Milky Way model was simulated for 6 billion years, during which the bar structure and spiral arms were fully formed. This improves upon previous simulations by using 1000 times more particles, and provides a wealth of new data that can be directly compared with observations. We also report the scalability on both the Swiss Piz Daint and the US ORNL Titan. On Piz Daint the parallel efficiency of Bonsai was above 95%. The highest performance was achieved with a 242 billion particle Milky Way model using 18600 GPUs on Titan, thereby reaching a sustained GPU and application performance of 33.49 Pflops and 24.77 Pflops respectively.

  20. Suitable utilization of woody plants for hibitation on Mars

    Science.gov (United States)

    Tomita-Yokotani, Kaori; Baba, Keiichi; Suzuki, Toshisada; Kimura, Shunta; Sato, Seigo; Katoh, Hiroshi; Abe, Yusuke; Katayama, Takeshi

    2016-07-01

    We have been investigating the usefulness of woody plants for habitation on Mars. During our research, we have found that woody plants have several properties which can be utilized for therapy and materials for enrage and construction even on Mars. Japanese people traditionally believe that "Bonsai" have therapeudic properties. Trees can become carbon fuel which can be used as energy on Mars. Tree materials could be used as a tool in closed bio-ecosystems such as for the purification and/or separation of solutions in an environment in space. Here, we will show some results of their abilities, the water leakage and vacuum seal test, separation of solutions using carbon materials made from trees. At the initiation of this research, we named the trees used as material for the experiment related to space environments "CosmoBon", small bonsai tree. To establish our research, as the first step, we will try to do the experiment using "CosmoBon".

  1. CosmoBon for studying wood formation under exotic gravitational environment for future space agriculture

    Science.gov (United States)

    Tomita-Yokotani, Kaori; Baba, Keiichi; Suzuki, Toshisada; Funada, Ryo; Nakamura, Teruko; Hashimoto, Hirofumi; Yamashita, Masamichi; Cosmobon, Jstwg

    We are proposing to raise woody plants in space for several applications and plant science. Japanese flowering cherry tree is one of a candidate for these studies. Mechanism behind sensing gravity and controlling shape of tree has been studied quite extensively. Even molecular mechanism for the response of plant against gravity has been investigated quite intensively for various species, woody plants are left behind. Morphology of woody branch growth is different from that of stem growth in herbs. Morphology in tree is strongly dominated by the secondary xylem formation. Nobody knows the tree shape grown under the space environment. If whole tree could be brought up to space as research materials, it might provide important scientific knowledge. Furthermore, trees produce excess oxygen, wooden materials for living cabin, and provide biomass for cultivating mushroom and insect as for the space agriculture. Excellent tree shapes which would be deeply related to wood formation improve quality of life under stressful environment in outer space. The serious problem would be their size. Bonsai is one of the Japanese traditional arts. We can study secondly xylem formation, wood formation, under exotic gravitational environment using Bonsai. "CosmoBon" is the small tree Bonsai for our space experiment. It has been recognized that the reaction wood in CosmoBon is formed similar to natural trees. Our goal is to examine feasibility to grow various species of trees in space as bioresource for space agriculture.

  2. Education for Life

    Directory of Open Access Journals (Sweden)

    Michael A Simpson

    1985-09-01

    Full Text Available I’ll do something rather dangerous today, and something very unusual for a major national expert in education. I’ll tell the truth about education. It’s not a pretty story, because it’s a story of murder. Soul murder; the persistent diminution of the natural spirit of inquiry; the solemn clipping of wings; nurturing bonsai brains, preparing not for growth and creation throughout life, but sedation for the long littleness of life. John Kenneth Galbrath once said: I f you can’t always comfort the afflicted — sometimes its useful to afflict the comfortable.

  3. Examination of seed characters of Vachellia farnesiana (L. Wight & Arn. as potentially applicable species in Serbia under climate change conditions

    Directory of Open Access Journals (Sweden)

    Grbić Mihailo

    2014-01-01

    Full Text Available Seeds of sweet acacia (Vachellia farnesiana (L. Wight & Arn. were mechanically scarified and treated with concentrated sulfuric acid in order to determine the permeability degree of the seed coat. The obtained results suggest a stronger form of seed coat dormancy that prevents potential invasiveness after introduction. The species is recommended for limited cultivation in outdoor conditions and unlimited use in interior spaces as full size or bonsai trees. [Projekat Ministarstva nauke Republike Srbije, br. 43007: Istraživanje klimatskih promena i njihovog uticaja na životnu sredinu: praćenje uticaja, adaptacija i ublažavanje

  4. A new species of Pseudorobillarda, an endophyte from Thuja occidentalis in Canada, and a key to the species.

    Science.gov (United States)

    Vujanovic, Vladimir; St-Arnaud, Marc

    2003-01-01

    Pseudorobillarda monica sp. nov. is described and illustrated. The endophyte was isolated from living leaves and bark of twigs of a Thuja occidentalis bonsai (>90 years old) at the Montréal Botanical Garden and ornamental trees in Montréal urban plantations. This pycnidial fungus is typical of the genus in morphology but clearly differs from other species in Pseudorobillarda by the distinct size of the conidiomata and the shape and size of conidia and paraphyses. Its taxonomic placement is discussed and a key to the species of Pseudorobillarda is provided.

  5. Wound-induced endogenous jasmonates stunt plant growth by inhibiting mitosis.

    Science.gov (United States)

    Zhang, Yi; Turner, John G

    2008-01-01

    When plants are repeatedly injured their growth is stunted and the size of organs such as leaves is greatly reduced. The basis of this effect is not well-understood however, even though it reduces yield of crops injured by herbivory, and produces dramatic effects exemplified in ornamental bonsai plants. We have investigated the genetic and physiological basis of this "bonsai effect" by repeatedly wounding leaves of the model plant Arabidopsis. This treatment stunted growth by 50% and increased the endogenous content of jasmonate (JA), a growth inhibitor, by seven-fold. Significantly, repeated wounding did not stunt the growth of the leaves of mutants unable to synthesise JA, or unable to respond to JA including coi1, jai3, myc2, but not jar1. The stunted growth did not result from reduced cell size, but resulted instead from reduced cell number, and was associated with reduced expression of CycB1;2. Wounding caused systemic disappearance of constitutively expressed JAZ1::GUS. Wounding also activates plant immunity. We show that a gene, 12-oxo-phytodienoate reductase, which catalyses a step in JA biosynthesis, and which we confirm is not required for defence, is however required for wound-induced stunting. Our data suggest that intermediates in the JA biosynthetic pathway activate defence, but a primary function of wound-induced JA is to stunt growth through the suppression of mitosis.

  6. Performance analysis of parallel gravitational N-body codes on large GPU clusters

    International Nuclear Information System (INIS)

    Huang, Si-Yi; Spurzem, Rainer; Berczik, Peter

    2016-01-01

    We compare the performance of two very different parallel gravitational N-body codes for astrophysical simulations on large Graphics Processing Unit (GPU) clusters, both of which are pioneers in their own fields as well as on certain mutual scales - NBODY6++ and Bonsai. We carry out benchmarks of the two codes by analyzing their performance, accuracy and efficiency through the modeling of structure decomposition and timing measurements. We find that both codes are heavily optimized to leverage the computational potential of GPUs as their performance has approached half of the maximum single precision performance of the underlying GPU cards. With such performance we predict that a speed-up of 200 – 300 can be achieved when up to 1k processors and GPUs are employed simultaneously. We discuss the quantitative information about comparisons of the two codes, finding that in the same cases Bonsai adopts larger time steps as well as larger relative energy errors than NBODY6++, typically ranging from 10 – 50 times larger, depending on the chosen parameters of the codes. Although the two codes are built for different astrophysical applications, in specified conditions they may overlap in performance at certain physical scales, thus allowing the user to choose either one by fine-tuning parameters accordingly. (paper)

  7. Street drug use among emergency patients in a Public Hospital in Turkey.

    Science.gov (United States)

    Caliskan, F T; Toker, I; Toktas, R; Temizyurek, Z; Unek, O; Zirek, B; Karcioglu, O

    2018-01-01

    Country-specific numbers of street drug (SD) users are well documented. However, little data exists regarding these patients' clinical presentations and outcomes in the emergency department (ED). Therefore, management of these patients in the emergency setting is still a subject of debate. The aim of this study is to determine the symptoms and signs of SD users presenting to the ED, and to report the substances, treatments, and outcomes. In this single-center study, symptoms, clinical findings, diagnoses, and outcomes of patients who reported to have used SDs or were diagnosed as SD users were investigated within a 1-year study period. Chi-square and Mann-Whitney U tests were performed to compare independent variables. Mean age of the 425 study patients was 25 ± 9 years (range: 12-64 years), and 6.1% (n = 26) of the patients were females. SDs used before presentation to the ED were mostly synthetic cannabinoids and "ecstasy." Overall prevalence of SD user admissions in ED was 0.24%. The most common presenting complaint was weakness/faintness in 21.1% (n = 90). Depressed level of consciousness was the most common physical sign (33.3%, n = 142). Incidences of altered mental status were significantly higher among ecstasy and/or bonsai users (n = 14, 27.5%; P = 0.027 and n = 46, 64.8%; P bonsai users-had depressed level of consciousness and required resuscitation.

  8. Performance analysis of parallel gravitational N-body codes on large GPU clusters

    Science.gov (United States)

    Huang, Si-Yi; Spurzem, Rainer; Berczik, Peter

    2016-01-01

    We compare the performance of two very different parallel gravitational N-body codes for astrophysical simulations on large Graphics Processing Unit (GPU) clusters, both of which are pioneers in their own fields as well as on certain mutual scales - NBODY6++ and Bonsai. We carry out benchmarks of the two codes by analyzing their performance, accuracy and efficiency through the modeling of structure decomposition and timing measurements. We find that both codes are heavily optimized to leverage the computational potential of GPUs as their performance has approached half of the maximum single precision performance of the underlying GPU cards. With such performance we predict that a speed-up of 200 - 300 can be achieved when up to 1k processors and GPUs are employed simultaneously. We discuss the quantitative information about comparisons of the two codes, finding that in the same cases Bonsai adopts larger time steps as well as larger relative energy errors than NBODY6++, typically ranging from 10 - 50 times larger, depending on the chosen parameters of the codes. Although the two codes are built for different astrophysical applications, in specified conditions they may overlap in performance at certain physical scales, thus allowing the user to choose either one by fine-tuning parameters accordingly.

  9. Gibberellin-Regulation and Genetic Variations in Leaf Elongation for Tall Fescue in Association with Differential Gene Expression Controlling Cell Expansion.

    Science.gov (United States)

    Xu, Qian; Krishnan, Sanalkumar; Merewitz, Emily; Xu, Jichen; Huang, Bingru

    2016-07-26

    Leaf elongation rate (LER) is an important factor controlling plant growth and productivity. The objective of this study was to determine whether genetic variation in LER for a fast-growing ('K-31'), and a dwarf cultivar ('Bonsai') of tall fescue (Festuca arundinacea) and gibberellic acid (GA) regulation of LER were associated with differential expression of cell-expansion genes. Plants were treated with GA3, trinexapac-ethyl (TE) (GA inhibitor), or water (untreated control) in a hydroponic system. LER of 'K-31' was 63% greater than that of 'Bonsai', which corresponded with 32% higher endogenous GA4 content in leaf and greater cell elongation and production rates under the untreated control condition. Exogenous application of GA3 significantly enhanced LER while TE treatment inhibited leaf elongation due to GA3-stimulation or TE-inhibition of cell elongation and production rate in leaves for both cultivars. Real-time quantitative polymerase chain reaction analysis revealed that three α-expansins, one β-expansin, and three xyloglucan endotransglycosylase (XET) genes were associated with GA-stimulation of leaf elongation, of which, the differential expression of EXPA4 and EXPA7 was related to the genotypic variation in LER of two cultivars. Those differentially-expressed expansin and XET genes could play major roles in genetic variation and GA-regulated leaf elongation in tall fescue.

  10. Wound-induced endogenous jasmonates stunt plant growth by inhibiting mitosis.

    Directory of Open Access Journals (Sweden)

    Yi Zhang

    Full Text Available When plants are repeatedly injured their growth is stunted and the size of organs such as leaves is greatly reduced. The basis of this effect is not well-understood however, even though it reduces yield of crops injured by herbivory, and produces dramatic effects exemplified in ornamental bonsai plants. We have investigated the genetic and physiological basis of this "bonsai effect" by repeatedly wounding leaves of the model plant Arabidopsis. This treatment stunted growth by 50% and increased the endogenous content of jasmonate (JA, a growth inhibitor, by seven-fold. Significantly, repeated wounding did not stunt the growth of the leaves of mutants unable to synthesise JA, or unable to respond to JA including coi1, jai3, myc2, but not jar1. The stunted growth did not result from reduced cell size, but resulted instead from reduced cell number, and was associated with reduced expression of CycB1;2. Wounding caused systemic disappearance of constitutively expressed JAZ1::GUS. Wounding also activates plant immunity. We show that a gene, 12-oxo-phytodienoate reductase, which catalyses a step in JA biosynthesis, and which we confirm is not required for defence, is however required for wound-induced stunting. Our data suggest that intermediates in the JA biosynthetic pathway activate defence, but a primary function of wound-induced JA is to stunt growth through the suppression of mitosis.

  11. RNAi-independent de novo DNA methylation revealed in Arabidopsis mutants of chromatin remodeling gene DDM1.

    Science.gov (United States)

    Sasaki, Taku; Kobayashi, Akie; Saze, Hidetoshi; Kakutani, Tetsuji

    2012-06-01

    Methylation of histone H3 lysine 9 (H3K9me) and small RNAs are associated with constitutively silent chromatin in diverse eukaryotes including plants. In plants, silent transposons are also marked by cytosine methylation, especially at non-CpG sites. Transposon-specific non-CpG methylation in plants is controlled by small RNAs and H3K9me. Although it is often assumed that small RNA directs H3K9me, interaction between small RNA and H3K9me has not been directly demonstrated in plants. We have previously shown that a mutation in the chromatin remodeling gene DDM1 (DECREASE IN DNA METHYLATION 1) induces a global decrease but a local increase of cytosine methylation and accumulation of small RNA at a locus called BONSAI. Here we show that de novo BONSAI methylation does not depend on RNAi but does depend on H3K9me. In mutants of H3K9 methyltransferase gene KRYPTONITE or the H3K9me-dependent DNA methyltransferase gene CHROMOMETHYALSE3, the ddm1-induced de novo cytosine methylation was abolished for all three contexts (CpG, CpHpG and CpHpH). Furthermore, RNAi mutants showed strong developmental defects when combined with the ddm1 mutation. Our results revealed unexpected interactions of epigenetic modifications that may be conserved among diverse eukaryotes. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

  12. Reproducibility of the Synthesis of Iron Oxide Nanoparticles Produced by Laser Pyrolysis

    Science.gov (United States)

    Alexandrescu, R.; Bouzas, V.; Costo, R.; Dumitrache, F.; García, M. A.; Morales, M. P.; Morjan, I.; Serna, C. J.; Veintemillas-Verdaguer, S.

    2010-10-01

    During the development of the BONSAI Project, the need for high quantities of iron oxide nanoparticles with some specific characteristics intensified the problem of the reproducibility in the nanoparticle production. Given the fact that the reaction yield for the production of the smallest and more homogeneous nanoparticles (BONFEX4) was very low (in the range of 1g/day), the process had to be repeated several times. These repetitions involved the use of three different CO2 lasers (two of monomodal gaussian beams TEMoo mode with spot sizes of 4 and 3.5 mm and one multimodal of 4 mm spot size). Keeping constant the rest of the experiment parameters (including the laser density) we obtained similar powders in nature as revealed by X-ray diffraction, and similar particle size distributions, but with different magnetic properties. When the same laser was used the reproducibility of the magnetic properties increased significantly.

  13. Simulation of disc-bulge-halo galaxies using parallel GPU based codes

    Science.gov (United States)

    Veles, O.; Berczik, P.; Just, A.

    2016-02-01

    We compare the performance of the very popular Tree-GPU code BONSAI with the older Particle-(Multi)Mesh code SUPERBOX. Both code we run on a same hardware using the GPU acceleration for the force calculation. SUPERBOX is a particle-mesh code with high resolution sub-grid and a higher order NGP (nearest grid point) force-calculation scheme. In our research, we are aiming to demonstrate that the new parallel version of SUPERBOX is capable to do the high resolution simulations of the interaction of the system of disc-bulge-halo composed galaxy. We describe the improvement of performance and scalability of SUPERBOX particularly for the Kepler cluster (NVIDIA K20 GPU). A comparison was made with the very popular and publicly available Tree-GPU code BONSAI†.

  14. Negative regulation of DNA methylation in plants.

    Science.gov (United States)

    Saze, Hidetoshi; Sasaki, Taku; Kakutani, Tetsuji

    2008-01-01

    Cytosine methylation of repeats and genes is important for coordination of genome stability and proper gene function. In plants, DNA methylation is regulated by DNA methyltransferases, chromatin remodeling factors and RNAi machinery. Ectopic DNA hypermethylation at genes causes transcriptional repression and silencing, and the methylation patterns often become heritable over generations. DNA methylation is antagonized by the DNA demethylation enzymes. Recently, we identified a novel jmjC-domain containing gene IBM1 (increase in bonsai methylation1) that also negatively regulates DNA methylation in Arabidopsis. The ibm1 plants show a variety of developmental phenotypes. IBM1 prevents ectopic accumulation of DNA methylation at the BNS genic region, likely through removal of heterochromatic H3K9 methylation mark. DNA and histone demethylation pathways are important for genome-wide patterning of DNA methylation and for epigenetic regulation of plant development.

  15. Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana.

    Science.gov (United States)

    Saze, Hidetoshi; Shiraishi, Akiko; Miura, Asuka; Kakutani, Tetsuji

    2008-01-25

    Differential cytosine methylation of repeats and genes is important for coordination of genome stability and proper gene expression. Through genetic screen of mutants showing ectopic cytosine methylation in a genic region, we identified a jmjC-domain gene, IBM1 (increase in bonsai methylation 1), in Arabidopsis thaliana. In addition to the ectopic cytosine methylation, the ibm1 mutations induced a variety of developmental phenotypes, which depend on methylation of histone H3 at lysine 9. Paradoxically, the developmental phenotypes of the ibm1 were enhanced by the mutation in the chromatin-remodeling gene DDM1 (decrease in DNA methylation 1), which is necessary for keeping methylation and silencing of repeated heterochromatin loci. Our results demonstrate the importance of chromatin remodeling and histone modifications in the differential epigenetic control of repeats and genes.

  16. Implications for kinetochore-microtubule attachment from the structure of an engineered Ndc80 complex.

    Science.gov (United States)

    Ciferri, Claudio; Pasqualato, Sebastiano; Screpanti, Emanuela; Varetti, Gianluca; Santaguida, Stefano; Dos Reis, Gabriel; Maiolica, Alessio; Polka, Jessica; De Luca, Jennifer G; De Wulf, Peter; Salek, Mogjiborahman; Rappsilber, Juri; Moores, Carolyn A; Salmon, Edward D; Musacchio, Andrea

    2008-05-02

    Kinetochores are proteinaceous assemblies that mediate the interaction of chromosomes with the mitotic spindle. The 180 kDa Ndc80 complex is a direct point of contact between kinetochores and microtubules. Its four subunits contain coiled coils and form an elongated rod structure with functional globular domains at either end. We crystallized an engineered "bonsai" Ndc80 complex containing a shortened rod domain but retaining the globular domains required for kinetochore localization and microtubule binding. The structure reveals a microtubule-binding interface containing a pair of tightly interacting calponin-homology (CH) domains with a previously unknown arrangement. The interaction with microtubules is cooperative and predominantly electrostatic. It involves positive charges in the CH domains and in the N-terminal tail of the Ndc80 subunit and negative charges in tubulin C-terminal tails and is regulated by the Aurora B kinase. We discuss our results with reference to current models of kinetochore-microtubule attachment and centromere organization.

  17. A Machine Learning Approach to Reducing the Work of Experts in Article Selection from Database: A Case Study for Regulatory Relations of S. cerevisiae Genes in MEDLINE.

    Science.gov (United States)

    Usuzaka; Sim; Tanaka; Matsuno; Miyano

    1998-01-01

    We consider the problem of selecting the articles of experts' interest from a literature database with the assistance of a machine learning system. For this purpose, we propose the rough reading strategy which combines the experts' knowledge with the machine learning system. For the articles converted through the rough reading strategy, we employ the learning system BONSAI and apply it for discovering rules which may reduce the work of experts in selecting the articles. Furthermore, we devise an algorithm which iterates the above procedure until almost all records of experts' interest are selected. Experimental results by using the articles from Cell show that almost all records of experts' interest are selected while reducing the works of experts drastically.

  18. Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin.

    Science.gov (United States)

    Saze, Hidetoshi; Kitayama, Junko; Takashima, Kazuya; Miura, Saori; Harukawa, Yoshiko; Ito, Tasuku; Kakutani, Tetsuji

    2013-01-01

    Genomes of higher eukaryotes contain many transposable elements, which often localize within the transcribed regions of active genes. Although intragenic transposable elements can be silenced to form heterochromatin, the impact of intragenic heterochromatin on transcription and RNA processing remains largely unexplored. Here we show using a flowering plant, Arabidopsis, that full-length transcript formation over intragenic heterochromatin depends on a protein named IBM2 (Increase in Bonsai Methylation 2), which has a Bromo-Adjacent Homology domain and an RNA recognition motif. Mutation of ibm2 triggers premature termination of transcripts with 3' RNA processing around intragenic heterochromatin at loci including the H3K9 demethylase gene IBM1. The need for IBM2 is circumvented in variant alleles that lack the heterochromatic domain. Our results reveal a mechanism that masks deleterious effects of intragenic heterochromatin, providing evolutionary sources for genetic and epigenetic variations.

  19. Activation of the γ-tubulin complex by the Mto1/2 complex.

    Science.gov (United States)

    Lynch, Eric M; Groocock, Lynda M; Borek, Weronika E; Sawin, Kenneth E

    2014-04-14

    The multisubunit γ-tubulin complex (γ-TuC) is critical for microtubule nucleation in eukaryotic cells, but it remains unclear how the γ-TuC becomes active specifically at microtubule-organizing centers (MTOCs) and not more broadly throughout the cytoplasm. In the fission yeast Schizosaccharomyces pombe, the proteins Mto1 and Mto2 form the Mto1/2 complex, which interacts with the γ-TuC and recruits it to several different types of cytoplasmic MTOC sites. Here, we show that the Mto1/2 complex activates γ-TuC-dependent microtubule nucleation independently of localizing the γ-TuC. This was achieved through the construction of a "minimal" version of Mto1/2, Mto1/2[bonsai], that does not localize to any MTOC sites. By direct imaging of individual Mto1/2[bonsai] complexes nucleating single microtubules in vivo, we further determine the number and stoichiometry of Mto1, Mto2, and γ-TuC subunits Alp4 (GCP2) and Alp6 (GCP3) within active nucleation complexes. These results are consistent with active nucleation complexes containing ∼13 copies each of Mto1 and Mto2 per active complex and likely equimolar amounts of γ-tubulin. Additional experiments suggest that Mto1/2 multimers act to multimerize the fission yeast γ-tubulin small complex and that multimerization of Mto2 in particular may underlie assembly of active microtubule nucleation complexes. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  20. Kinetochore-microtubule attachment throughout mitosis potentiated by the elongated stalk of the kinetochore kinesin CENP-E.

    Science.gov (United States)

    Vitre, Benjamin; Gudimchuk, Nikita; Borda, Ranier; Kim, Yumi; Heuser, John E; Cleveland, Don W; Grishchuk, Ekaterina L

    2014-08-01

    Centromere protein E (CENP-E) is a highly elongated kinesin that transports pole-proximal chromosomes during congression in prometaphase. During metaphase, it facilitates kinetochore-microtubule end-on attachment required to achieve and maintain chromosome alignment. In vitro CENP-E can walk processively along microtubule tracks and follow both growing and shrinking microtubule plus ends. Neither the CENP-E-dependent transport along microtubules nor its tip-tracking activity requires the unusually long coiled-coil stalk of CENP-E. The biological role for the CENP-E stalk has now been identified through creation of "Bonsai" CENP-E with significantly shortened stalk but wild-type motor and tail domains. We demonstrate that Bonsai CENP-E fails to bind microtubules in vitro unless a cargo is contemporaneously bound via its C-terminal tail. In contrast, both full-length and truncated CENP-E that has no stalk and tail exhibit robust motility with and without cargo binding, highlighting the importance of CENP-E stalk for its activity. Correspondingly, kinetochore attachment to microtubule ends is shown to be disrupted in cells whose CENP-E has a shortened stalk, thereby producing chromosome misalignment in metaphase and lagging chromosomes during anaphase. Together these findings establish an unexpected role of CENP-E elongated stalk in ensuring stability of kinetochore-microtubule attachments during chromosome congression and segregation. © 2014 Vitre, Gudimchuk, et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  1. MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes.

    Science.gov (United States)

    Pericard, Pierre; Dufresne, Yoann; Couderc, Loïc; Blanquart, Samuel; Touzet, Hélène

    2018-02-15

    Advances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution. We designed MATAM, a software dedicated to the fast and accurate targeted assembly of short reads sequenced from a genomic marker of interest. The method implements a stepwise process based on construction and analysis of a read overlap graph. It is applied to the assembly of 16S rRNA markers and is validated on simulated, synthetic and genuine metagenomes. We show that MATAM outperforms other available methods in terms of low error rates and recovered fractions and is suitable to provide improved assemblies for precise taxonomic assignments. https://github.com/bonsai-team/matam. pierre.pericard@gmail.com or helene.touzet@univ-lille1.fr. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  2. Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns.

    Science.gov (United States)

    Lei, Mingguang; La, Honggui; Lu, Kun; Wang, Pengcheng; Miki, Daisuke; Ren, Zhizhong; Duan, Cheng-Guo; Wang, Xingang; Tang, Kai; Zeng, Liang; Yang, Lan; Zhang, Heng; Nie, Wenfeng; Liu, Pan; Zhou, Jianping; Liu, Renyi; Zhong, Yingli; Liu, Dong; Zhu, Jian-Kang

    2014-01-07

    DNA methylation is important for the silencing of transposons and other repetitive elements in many higher eukaryotes. However, plant and mammalian genomes have evolved to contain repetitive elements near or inside their genes. How these genes are kept from being silenced by DNA methylation is not well understood. A forward genetics screen led to the identification of the putative chromatin regulator Enhanced Downy Mildew 2 (EDM2) as a cellular antisilencing factor and regulator of genome DNA methylation patterns. EDM2 contains a composite Plant Homeo Domain that recognizes both active and repressive histone methylation marks at the intronic repeat elements in genes such as the Histone 3 lysine 9 demethylase gene Increase in BONSAI Methylation 1 (IBM1) and is necessary for maintaining the expression of these genes by promoting mRNA distal polyadenylation. Because of its role in maintaining IBM1 expression, EDM2 is required for preventing CHG methylation in the bodies of thousands of genes. Our results thus increase the understanding of antisilencing, genome methylation patterns, and regulation of alternative RNA processing by intronic heterochromatin.

  3. Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome.

    Science.gov (United States)

    Inagaki, Soichi; Miura-Kamio, Asuka; Nakamura, Yasukazu; Lu, Falong; Cui, Xia; Cao, Xiaofeng; Kimura, Hiroshi; Saze, Hidetoshi; Kakutani, Tetsuji

    2010-10-20

    In diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Although selective H3K9me is critical for maintaining genome integrity, mechanisms to exclude H3K9me from active genes remain largely unexplored. Here, we show in Arabidopsis that the exclusion depends on a histone demethylase gene, IBM1 (increase in BONSAI methylation). Loss-of-function ibm1 mutation results in ectopic H3K9me and non-CG methylation in thousands of genes. The ibm1-induced genic H3K9me depends on both histone methylase KYP/SUVH4 and DNA methylase CMT3, suggesting interdependence of two epigenetic marks--H3K9me and non-CG methylation. Notably, IBM1 enhances loss of H3K9me in transcriptionally de-repressed sequences. Furthermore, disruption of transcription in genes induces ectopic non-CG methylation, which mimics the loss of IBM1 function. We propose that active chromatin is stabilized by an autocatalytic loop of transcription and H3K9 demethylation. This process counteracts a similarly autocatalytic accumulation of silent epigenetic marks, H3K9me and non-CG methylation.

  4. SHOOT GROWTH1 maintains Arabidopsis epigenomes by regulating IBM1.

    Science.gov (United States)

    Coustham, Vincent; Vlad, Daniela; Deremetz, Aurélie; Gy, Isabelle; Cubillos, Francisco A; Kerdaffrec, Envel; Loudet, Olivier; Bouché, Nicolas

    2014-01-01

    Maintaining correct DNA and histone methylation patterns is essential for the development of all eukaryotes. In Arabidopsis, we identified SHOOT GROWTH1 (SG1), a novel protein involved in the control of gene methylation. SG1 contains both a Bromo-Adjacent Homology (BAH) domain found in several chromatin regulators and an RNA-Recognition Motif (RRM). The sg1 mutations are associated with drastic pleiotropic phenotypes. The mutants degenerate after few generations and are similar to mutants of the histone demethylase INCREASE IN BONSAI METHYLATION1 (IBM1). A methylome analysis of sg1 mutants revealed a large number of gene bodies hypermethylated in the cytosine CHG context, associated with an increase in di-methylation of lysine 9 on histone H3 tail (H3K9me2), an epigenetic mark normally found in silenced transposons. The sg1 phenotype is suppressed by mutations in genes encoding the DNA methyltransferase CHROMOMETHYLASE3 (CMT3) or the histone methyltransferase KRYPTONITE (KYP), indicating that SG1 functions antagonistically to CMT3 or KYP. We further show that the IBM1 transcript is not correctly processed in sg1, and that the functional IBM1 transcript complements sg1. Altogether, our results suggest a function for SG1 in the maintenance of genome integrity by regulating IBM1.

  5. Atypical diabetic ketoacidosis: case report.

    Science.gov (United States)

    Demirci, Hüseyin; Coşar, Ramazan; Çiftçi, Özcan; Sarı, Işılay Kalan

    2015-01-01

    Diabetic ketoacidosis (DKA) is a potentially life-threatening complication of diabetes mellitus and can lead to death if untreated. It is a complex metabolic state characterised by hyperglycaemia, acidosis and ketonuria. Bonsai is one of the herbal incense products that contains synthetic cannabinoid and can be easily accessible via the internet in many countries. It cannot be detected in blood and urine studies using conventional methods. Synthetic cannabinoid abuse is associated with severe side effects, including tachycardia, high blood pressure, acidosis, excess sedation and coma. A 17-year-old male patient was brought to the emergency department with sudden onset of dyspnoea. Laboratory investigations revealed hyperglycaemia, acidosis and ketonuria. He was admitted to the intensive care unit with a diagnosis of diabetic ketoacidosis. He was not considered a typical case of diabetic ketoacidosis because of the tendency to hypokalaemia, persistent tachycardia and bronchoscopic findings. We learned from his friends that he had used cannabis for a week and used bonzai on the day that he was brought to the emergency service. Diabetic ketoacidosis with prolonged acidosis and tendency to hypokalaemia are investigated for the consumption of synthetic cannabinoids.

  6. Epigenetic Regulation of Intronic Transgenes in Arabidopsis.

    Science.gov (United States)

    Osabe, Kenji; Harukawa, Yoshiko; Miura, Saori; Saze, Hidetoshi

    2017-03-24

    Defense mechanisms of plant genomes can epigenetically inactivate repetitive sequences and exogenous transgenes. Loss of mutant phenotypes in intronic T-DNA insertion lines by interaction with another T-DNA locus, termed T-DNA suppression, has been observed in Arabidopsis thaliana, although the molecular basis of establishment and maintenance of T-DNA suppression is poorly understood. Here we show that maintenance of T-DNA suppression requires heterochromatinisation of T-DNA sequences and the nuclear proteins, INCREASED IN BONSAI METHYLATION 2 (IBM2) and ENHANCED DOWNY MILDEW 2 (EDM2), which prevent ectopic 3' end processing of mRNA in atypically long introns containing T-DNA sequences. Initiation of T-DNA suppression is mediated by the canonical RdDM pathway after hybridisation of two T-DNA strains, accompanied by DNA hypermethylation of T-DNA sequences in the F1 generation. Our results reveal the presence of a genome surveillance mechanism through genome hybridisation that masks repetitive DNAs intruding into transcription units.

  7. High-Yield Synthesis of Janus Dendritic Mesoporous Silica@Resorcinol-Formaldehyde Nanoparticles: A Competing Growth Mechanism.

    Science.gov (United States)

    Qu, Lili; Hu, Huicheng; Yu, Jiaqi; Yu, Xiaoya; Liu, Jian; Xu, Yong; Zhang, Qiao

    2017-05-30

    Recently, Janus nanostructures that possess two or more different surface functions have attracted enormous attention because of their unique structures and promising applications in diverse fields. In this work, we present that Janus structured dendritic mesoporous silica@resorcinol-formaldehyde (DMS@RF) nanoparticles can be prepared through a simple one-pot colloidal method. The Janus DMS@RF nanoparticle shows a bonsai-like morphology which consists of a dendritic mesoporous silica part and a spherical RF part. After a systematic study on the growth process, we proposed a competing growth mechanism that accounts for the formation of Janus nanostructures. It is believed that suitable polymerization rate of silica and RF resin is critical. Based on the competing growth mechanism, eccentric and concentric core-shell nanostructures have been successfully prepared by tuning the polymerization rates of silica and RF, respectively. Metal-contained ternary Janus nanoparticles that might be used for catalysis have also been prepared. This research may pave the way for the practical applications of delicate nanomaterials with desired structures and properties.

  8. IBM1, a JmjC domain-containing histone demethylase, is involved in the regulation of RNA-directed DNA methylation through the epigenetic control of RDR2 and DCL3 expression in Arabidopsis.

    Science.gov (United States)

    Fan, Di; Dai, Yan; Wang, Xuncheng; Wang, Zhenjie; He, Hang; Yang, Hongchun; Cao, Ying; Deng, Xing Wang; Ma, Ligeng

    2012-10-01

    Small RNA-directed DNA methylation (RdDM) is an important epigenetic pathway in Arabidopsis that controls the expression of multiple genes and several developmental processes. RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3) are necessary factors in 24-nt small interfering RNA (siRNA) biogenesis, which is part of the RdDM pathway. Here, we found that Increase in BONSAI Methylation 1 (IBM1), a conserved JmjC family histone demethylase, is directly associated with RDR2 and DCL3 chromatin. The mutation of IBM1 induced the hypermethylation of H3K9 and DNA non-CG sites within RDR2 and DCL3, which repressed their expression. A genome-wide analysis suggested that the reduction in RDR2 and DCL3 expression affected siRNA biogenesis in a locus-specific manner and disrupted RdDM-directed gene repression. Together, our results suggest that IBM1 regulates gene expression through two distinct pathways: direct association to protect genes from silencing by preventing the coupling of histone and DNA methylation, and indirect silencing of gene expression through RdDM-directed repression.

  9. Phenazepam abuse in the UK: an emerging problem causing serious adverse health problems, including death.

    Science.gov (United States)

    Corkery, John Martin; Schifano, Fabrizio; Ghodse, Abdol Hamid

    2012-05-01

    Phenazepam (fenazepam; 7-bromo-5-(2-chlorophenyl)-1,3-dihydro-2H-1,4-benzodiazepin-2-one; PNZ, 'Bonsai') is a benzodiazepine developed in the former Soviet Union during the 1970s to treat neurological disorders, epilepsy, and alcohol withdrawal syndrome. Its recreational use appears to have increased over recent years. Because of the lack of accessible data on this substance, it is important that information is made available to health professionals. A literature search was conducted in relevant databases (Medline, Toxbase, PsychInfo, etc.), grey literature (using Google Scholar) and Internet sites to identify key data on phenazepam, including epidemiology such as availability, price, supply sources, confiscations, and health-related problems. Information from these sources indicates the potential for serious adverse health consequences for this drug when taken recreationally and that its use is spreading in the USA and Europe. Although first use was reported in the UK in October 2009, major concerns in the UK arose in summer 2010 when individuals across Britain were admitted to hospital following overdose. Nine UK fatalities were reported in which phenazepam was detected in post mortem toxicology but not implicated in death. The first UK death directly involving phenazepam was notified in July and the second in November 2011. This paper summarises the key information about phenazepam abuse and health problems of which health professionals, especially those in Emergency Departments, should be aware and presents new information in respect of fatalities caused by the drug. Copyright © 2012 John Wiley & Sons, Ltd.

  10. New mouse model of skeletal muscle atrophy using spiral wire immobilization.

    Science.gov (United States)

    Onda, Akiko; Kono, Hajime; Jiao, Qibin; Akimoto, Takayuki; Miyamoto, Toshikazu; Sawada, Yasuhiro; Suzuki, Katsuhiko; Kusakari, Yoichiro; Minamisawa, Susumu; Fukubayashi, Toru

    2016-10-01

    Disuse-induced skeletal muscle atrophy is a serious concern; however, there is not an effective mouse model to elucidate the molecular mechanisms. We developed a noninvasive atrophy model in mice. After the ankle joints of mice were bandaged into a bilateral plantar flexed position, either bilateral or unilateral hindlimbs were immobilized by wrapping in bonsai steel wire. After 3, 5, or 10 days of immobilization of the hip, knee, and ankle, the weight of the soleus and plantaris muscles decreased significantly in both bilateral and unilateral immobilization. MAFbx/atrogin-1 and MuRF1 mRNA was found to have significantly increased in both muscles, consistent with disuse-induced atrophy. Notably, the procedure did not result in either edema or necrosis in the fixed hindlimbs. This method allows repeated, direct access to the immobilized muscle, making it a useful procedure for concurrent application and assessment of various therapeutic interventions. Muscle Nerve 54: 788-791, 2016. © 2016 Wiley Periodicals, Inc.

  11. Kinetochore–microtubule attachment throughout mitosis potentiated by the elongated stalk of the kinetochore kinesin CENP-E

    Science.gov (United States)

    Vitre, Benjamin; Gudimchuk, Nikita; Borda, Ranier; Kim, Yumi; Heuser, John E.; Cleveland, Don W.; Grishchuk, Ekaterina L.

    2014-01-01

    Centromere protein E (CENP-E) is a highly elongated kinesin that transports pole-proximal chromosomes during congression in prometaphase. During metaphase, it facilitates kinetochore–microtubule end-on attachment required to achieve and maintain chromosome alignment. In vitro CENP-E can walk processively along microtubule tracks and follow both growing and shrinking microtubule plus ends. Neither the CENP-E–dependent transport along microtubules nor its tip-tracking activity requires the unusually long coiled-coil stalk of CENP-E. The biological role for the CENP-E stalk has now been identified through creation of “Bonsai” CENP-E with significantly shortened stalk but wild-type motor and tail domains. We demonstrate that Bonsai CENP-E fails to bind microtubules in vitro unless a cargo is contemporaneously bound via its C-terminal tail. In contrast, both full-length and truncated CENP-E that has no stalk and tail exhibit robust motility with and without cargo binding, highlighting the importance of CENP-E stalk for its activity. Correspondingly, kinetochore attachment to microtubule ends is shown to be disrupted in cells whose CENP-E has a shortened stalk, thereby producing chromosome misalignment in metaphase and lagging chromosomes during anaphase. Together these findings establish an unexpected role of CENP-E elongated stalk in ensuring stability of kinetochore–microtubule attachments during chromosome congression and segregation. PMID:24920822

  12. Open source clustering software.

    Science.gov (United States)

    de Hoon, M J L; Imoto, S; Nolan, J; Miyano, S

    2004-06-12

    We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C. The C Clustering Library and the corresponding Python C extension module Pycluster were released under the Python License, while the Perl module Algorithm::Cluster was released under the Artistic License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well as the corresponding command-line program, were released under the same license as the original Cluster code. The complete source code is available at http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster. Alternatively, Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available as part of the Biopython distribution.

  13. An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites.

    Science.gov (United States)

    Miura, Asuka; Nakamura, Miyuki; Inagaki, Soichi; Kobayashi, Akie; Saze, Hidetoshi; Kakutani, Tetsuji

    2009-04-22

    Differential cytosine methylation of genes and transposons is important for maintaining integrity of plant genomes. In Arabidopsis, transposons are heavily methylated at both CG and non-CG sites, whereas the non-CG methylation is rarely found in active genes. Our previous genetic analysis suggested that a jmjC domain-containing protein IBM1 (increase in BONSAI methylation 1) prevents ectopic deposition of non-CG methylation, and this process is necessary for normal Arabidopsis development. Here, we directly determined the genomic targets of IBM1 through high-resolution genome-wide analysis of DNA methylation. The ibm1 mutation induced extensive hyper-methylation in thousands of genes. Transposons were unaffected. Notably, long transcribed genes were most severely affected. Methylation of genes is limited to CG sites in wild type, but CHG sites were also methylated in the ibm1 mutant. The ibm1-induced hyper-methylation did not depend on previously characterized components of the RNAi-based DNA methylation machinery. Our results suggest novel transcription-coupled mechanisms to direct genic methylation not only at CG but also at CHG sites. IBM1 prevents the CHG methylation in genes, but not in transposons.

  14. Sporadic ret-rearranged papillary carcinoma of the thyroid: a subset of slow growing, less aggressive thyroid neoplasms?

    Science.gov (United States)

    Soares, P; Fonseca, E; Wynford-Thomas, D; Sobrinho-Simões, M

    1998-05-01

    Despite the large amount of information accumulated on the role played by ret activation in the oncogenesis of papillary thyroid carcinoma (PTC), the biological and clinical significance of such activation 'in vivo' remains controversial. The aim of this study was to address some of the existing controversies by comparing two groups of unselected PTCs, one with and the other without ret rearrangement, with regard to several clinicopathological and biological features. Thirty-three PTCs were selected at random. ret rearrangement was found in eight cases (24.2 per cent) using Southern blot analysis. The mean age of the patients with tumours displaying ret rearrangement (28 +/- 3.1 years) was significantly lower than that of the patients harbouring cases that did not present rearrangement (45 +/- 2.9 years). The large majority of the tumours with ret rearrangement displayed a papillary or mixed follicular-papillary pattern and very low proliferative activity. ret rearrangement correlated significantly with decreased cytoplasmic expression of E-cadherin. No significant differences were found regarding the gender of the patients, tumour size, multicentricity, extrathyroidal growth, vascular invasion, lymphocytic infiltration, lymph node involvement or the expression of E-cadherin (membrane), c-erb-B2, c-met, Bcl-2, and vimentin. It is proposed that sporadic PTCs harbouring a ret rearrangement occur frequently as slow growing, papillary, or predominantly papillary tumours that do not usually progress towards less differentiated neoplasms representing what might be described as a Bonsai phenotype.

  15. Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1.

    Science.gov (United States)

    Saze, Hidetoshi; Kakutani, Tetsuji

    2007-08-08

    Epigenetically silent transposons and repeats constitute a substantial proportion of eukaryotic genomes, but their impact on cellular gene function remains largely unexplored. In Arabidopsis, transposons are silenced by DNA methylation, and this methylation is often abolished by mutations in a chromatin-remodeling gene DDM1 (DECREASE IN DNA METHYLATION 1). The ddm1 mutation induces various types of developmental abnormalities through de-repression of transposons and repeats. Here, we report a novel mechanism for a ddm1-induced syndrome, called bonsai (bns). We identified the gene responsible for the bns phenotypes by genetic linkage analysis and subsequent transcriptional analysis. The bns phenotypes are due to silencing of a putative Anaphase-Promoting Complex (APC) 13 gene. The BNS gene silencing was associated with DNA hypermethylation, which is in contrast to the ddm1-induced hypomethylation in the other genomic regions. This paradoxical BNS hypermethylation was reproducibly induced during self-pollination of the ddm1 mutant, and it was mediated by a long interspersed nuclear element (LINE) retrotransposon flanking the BNS gene. We discuss possible molecular mechanisms and the evolutionary implications of transposon-mediated epigenetic changes in the BNS locus.

  16. DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns.

    Science.gov (United States)

    Rigal, Mélanie; Kevei, Zoltán; Pélissier, Thierry; Mathieu, Olivier

    2012-06-29

    The stability of epigenetic patterns is critical for genome integrity and gene expression. This highly coordinated process involves interrelated positive and negative regulators that impact distinct epigenetic marks, including DNA methylation and dimethylation at histone H3 lysine 9 (H3K9me2). In Arabidopsis, mutations in the DNA methyltransferase MET1, which maintains CG methylation, result in aberrant patterns of other epigenetic marks, including ectopic non-CG methylation and the relocation of H3K9me2 from heterochromatin into gene-rich chromosome regions. Here, we show that the expression of the H3K9 demethylase IBM1 (increase in BONSAI methylation 1) requires DNA methylation. Surprisingly, the regulatory methylated region is contained in an unusually large intron that is conserved in IBM1 orthologues. The re-establishment of IBM1 expression in met1 mutants restored the wild-type H3K9me2 nuclear patterns, non-CG DNA methylation and transcriptional patterns at selected loci, which included DNA demethylase genes. These results provide a mechanistic explanation for long-standing puzzling observations in met1 mutants and reveal yet another layer of control in the interplay between DNA methylation and histone modification, which stabilizes DNA methylation patterns at genes.

  17. Utilizing evolutionary information and gene expression data for estimating gene networks with bayesian network models.

    Science.gov (United States)

    Tamada, Yoshinori; Bannai, Hideo; Imoto, Seiya; Katayama, Toshiaki; Kanehisa, Minoru; Miyano, Satoru

    2005-12-01

    Since microarray gene expression data do not contain sufficient information for estimating accurate gene networks, other biological information has been considered to improve the estimated networks. Recent studies have revealed that highly conserved proteins that exhibit similar expression patterns in different organisms, have almost the same function in each organism. Such conserved proteins are also known to play similar roles in terms of the regulation of genes. Therefore, this evolutionary information can be used to refine regulatory relationships among genes, which are estimated from gene expression data. We propose a statistical method for estimating gene networks from gene expression data by utilizing evolutionarily conserved relationships between genes. Our method simultaneously estimates two gene networks of two distinct organisms, with a Bayesian network model utilizing the evolutionary information so that gene expression data of one organism helps to estimate the gene network of the other. We show the effectiveness of the method through the analysis on Saccharomyces cerevisiae and Homo sapiens cell cycle gene expression data. Our method was successful in estimating gene networks that capture many known relationships as well as several unknown relationships which are likely to be novel. Supplementary information is available at http://bonsai.ims.u-tokyo.ac.jp/~tamada/bayesnet/.

  18. Inferring dynamic gene networks under varying conditions for transcriptomic network comparison.

    Science.gov (United States)

    Shimamura, Teppei; Imoto, Seiya; Yamaguchi, Rui; Nagasaki, Masao; Miyano, Satoru

    2010-04-15

    Elucidating the differences between cellular responses to various biological conditions or external stimuli is an important challenge in systems biology. Many approaches have been developed to reverse engineer a cellular system, called gene network, from time series microarray data in order to understand a transcriptomic response under a condition of interest. Comparative topological analysis has also been applied based on the gene networks inferred independently from each of the multiple time series datasets under varying conditions to find critical differences between these networks. However, these comparisons often lead to misleading results, because each network contains considerable noise due to the limited length of the time series. We propose an integrated approach for inferring multiple gene networks from time series expression data under varying conditions. To the best of our knowledge, our approach is the first reverse-engineering method that is intended for transcriptomic network comparison between varying conditions. Furthermore, we propose a state-of-the-art parameter estimation method, relevance-weighted recursive elastic net, for providing higher precision and recall than existing reverse-engineering methods. We analyze experimental data of MCF-7 human breast cancer cells stimulated by epidermal growth factor or heregulin with several doses and provide novel biological hypotheses through network comparison. The software NETCOMP is available at http://bonsai.ims.u-tokyo.ac.jp/ approximately shima/NETCOMP/.

  19. [Air negative ion concentration in different modes of courtyard forests in southern mountainous areas of Jinan, Shandong Province of East China].

    Science.gov (United States)

    Wang, Xiao-Lei; Li, Chuan-Rong; Xu, Jing-Wei; Hu, Ding-Meng; Zhao, Zhen-Lei; Zhang, Liu-dong

    2013-02-01

    Taking five typical courtyard forests and a non-forest courtyard in southern mountains areas of Jinan as test objects, a synchronous observation was conducted on the air negative ion concentration and related meteorological factors in March-December, 2010. The air negative ion concentration in the test courtyards showed an obvious seasonal variation, being in the order of summer > autumn > spring > winter. The diurnal variation of the air negative ion concentration presented a double peak curve, with the maximum in 10:00 - 11:00 and 16:00 - 17:00 and the minimum around 12:00. The daily air quality was the best at 10:00 and 16:00, and better in afternoon than in the morning. Summer time and garden sketch mode had the best air quality in a year. The mean annual air negative ion and the coefficient of air ion (CI) of the test courtyards were in the order of garden sketch > economic fruit forest > natural afforested forest > flowers and bonsai > farm tourist > non-forest, with the air negative ion concentration being 813, 745, 695, 688, 649, and 570 ions.cm-3, and the CI being 1.22, 1.11, 0.85, 0.84, 0.83, and 0.69, respectively. It could be concluded that garden sketch was the ideal courtyard forest mode. The air negative ion concentration was significantly positively correlated with air temperature and relative humidity, but irrelevant to light intensity.

  20. Latrunculin B-induced plant dwarfism: Plant cell elongation is F-actin-dependent.

    Science.gov (United States)

    Baluska, F; Jasik, J; Edelmann, H G; Salajová, T; Volkmann, D

    2001-03-01

    Marine macrolides latrunculins are highly specific toxins which effectively depolymerize actin filaments (generally F-actin) in all eukaryotic cells. We show that latrunculin B is effective on diverse cell types in higher plants and describe the use of this drug in probing F-actin-dependent growth and in plant development-related processes. In contrast to other eukaryotic organisms, cell divisions occurs in plant cells devoid of all actin filaments. However, the alignment of the division planes is often distorted. In addition to cell division, postembryonic development and morphogenesis also continue in the absence of F-actin. These experimental data suggest that F-actin is of little importance in the morphogenesis of higher plants, and that plants can develop more or less normally without F-actin. In contrast, F-actin turns out to be essential for cell elongation. When latrunculin B was added during germination, morphologically normal Arabidopsis and rye seedlings developed but, as a result of the absence of cell elongation, these were stunted, resembling either genetic dwarfs or environmental bonsai plants. In conclusion, F-actin is essential for the plant cell elongation, while this F-actin-dependent cell elongation is not an essential feature of plant-specific developmental programs.

  1. The application of total vertical projections for the unbiased estimation of the length of blood vessels and other structures by magnetic resonance imaging.

    Science.gov (United States)

    Roberts, N; Howard, C V; Cruz-Orive, L M; Edwards, R H

    1991-01-01

    A new stereological method has recently been developed to estimate the total length of a bounded curve in 3D from a sample of projections about a vertical axis. Unlike other methods based on serial section reconstructions, the new method is unbiased (i.e., it has zero systematic error). A basic requirement, not difficult to fulfill in many cases, is that the masking of one structure by another is not appreciable. The application of the new method to real curvilinear structures using a clinical magnetic resonance (MR) imager is illustrated. The first structure measured was a twisted water-filled glass tube of known length. The accuracy of the method was assessed: With six vertical projections, the tube length was measured to within 2% of the true value. The second example was a living bonsai tree, and the third was a clinical application of MR angiography. The possibility of applying the method to other scientific disciplines, for example, the monitoring of plant root growth, is discussed.

  2. XMAP215 polymerase activity is built by combining multiple tubulin-binding TOG domains and a basic lattice-binding region.

    Science.gov (United States)

    Widlund, Per O; Stear, Jeffrey H; Pozniakovsky, Andrei; Zanic, Marija; Reber, Simone; Brouhard, Gary J; Hyman, Anthony A; Howard, Jonathon

    2011-02-15

    XMAP215/Dis1 family proteins positively regulate microtubule growth. Repeats at their N termini, called TOG domains, are important for this function. While TOG domains directly bind tubulin dimers, it is unclear how this interaction translates to polymerase activity. Understanding the functional roles of TOG domains is further complicated by the fact that the number of these domains present in the proteins of different species varies. Here, we take advantage of a recent crystal structure of the third TOG domain from Caenorhabditis elegans, Zyg9, and mutate key residues in each TOG domain of XMAP215 that are predicted to be important for interaction with the tubulin heterodimer. We determined the contributions of the individual TOG domains to microtubule growth. We show that the TOG domains are absolutely required to bind free tubulin and that the domains differentially contribute to XMAP215's overall affinity for free tubulin. The mutants' overall affinity for free tubulin correlates well with polymerase activity. Furthermore, we demonstrate that an additional basic region is important for targeting to the microtubule lattice and is critical for XMAP215 to function at physiological concentrations. Using this information, we have engineered a "bonsai" protein, with two TOG domains and a basic region, that has almost full polymerase activity.

  3. SHOOT GROWTH1 maintains Arabidopsis epigenomes by regulating IBM1.

    Directory of Open Access Journals (Sweden)

    Vincent Coustham

    Full Text Available Maintaining correct DNA and histone methylation patterns is essential for the development of all eukaryotes. In Arabidopsis, we identified SHOOT GROWTH1 (SG1, a novel protein involved in the control of gene methylation. SG1 contains both a Bromo-Adjacent Homology (BAH domain found in several chromatin regulators and an RNA-Recognition Motif (RRM. The sg1 mutations are associated with drastic pleiotropic phenotypes. The mutants degenerate after few generations and are similar to mutants of the histone demethylase INCREASE IN BONSAI METHYLATION1 (IBM1. A methylome analysis of sg1 mutants revealed a large number of gene bodies hypermethylated in the cytosine CHG context, associated with an increase in di-methylation of lysine 9 on histone H3 tail (H3K9me2, an epigenetic mark normally found in silenced transposons. The sg1 phenotype is suppressed by mutations in genes encoding the DNA methyltransferase CHROMOMETHYLASE3 (CMT3 or the histone methyltransferase KRYPTONITE (KYP, indicating that SG1 functions antagonistically to CMT3 or KYP. We further show that the IBM1 transcript is not correctly processed in sg1, and that the functional IBM1 transcript complements sg1. Altogether, our results suggest a function for SG1 in the maintenance of genome integrity by regulating IBM1.

  4. Bionomics and Formation of “Bonsai” Colonies With Long-Term Rearing of Coptotermes formosanus (Isoptera: Rhinotermitidae).

    Science.gov (United States)

    Osbrink, W L A; Cornelius, M L; Showler, A T

    2016-04-01

    This laboratory study reports the ability of Formosan subterranean termite, Coptotermes formosanus Shiraki, colonies to survive for at least 9 yr while restricted to a sweater box. Colonies survived by limiting queen size and worker numbers, allowing these bonsai colonies to thrive. Queen physogastry appeared to plateau with 9-yr-old queens not larger than 6-yr-old queens, but nearly triple the size of 2-yr-old queens. Nine-year-old colony worker numbers were not greater than 6-yr-old colonies, but worker numbers were greater than in 2-yr-old colonies. Such colony survival under conditions of restricted resources provides a mechanism for re-infestation of areas following extensive area-wide control efforts. “Bonsai” colonies are relevant to the ability of marginalized colonies to avoid detection and then expand and invade into areas once the large, mature colonies are eliminated, and their potential to produce alates to start new C. formosanus colonies in areas which have been subjected to colony elimination programs impacts termite management strategies.

  5. Topology and structure of an engineered human cohesin complex bound to Pds5B.

    Science.gov (United States)

    Hons, Michael T; Huis In 't Veld, Pim J; Kaesler, Jan; Rombaut, Pascaline; Schleiffer, Alexander; Herzog, Franz; Stark, Holger; Peters, Jan-Michael

    2016-08-23

    The cohesin subunits Smc1, Smc3 and Scc1 form large tripartite rings which mediate sister chromatid cohesion and chromatin structure. These are thought to entrap DNA with the help of the associated proteins SA1/2 and Pds5A/B. Structural information is available for parts of cohesin, but analyses of entire cohesin complexes are limited by their flexibility. Here we generated a more rigid 'bonsai' cohesin by truncating the coiled coils of Smc1 and Smc3 and used single-particle electron microscopy, chemical crosslinking-mass spectrometry and in silico modelling to generate three-dimensional models of cohesin bound to Pds5B. The HEAT-repeat protein Pds5B forms a curved structure around the nucleotide-binding domains of Smc1 and Smc3 and bridges the Smc3-Scc1 and SA1-Scc1 interfaces. These results indicate that Pds5B forms an integral part of the cohesin ring by contacting all other cohesin subunits, a property that may reflect the complex role of Pds5 proteins in controlling cohesin-DNA interactions.

  6. Atypical Diabetic Ketoacidosis: Case Report

    Directory of Open Access Journals (Sweden)

    Hüseyin Demirci

    2015-03-01

    Full Text Available Background: Diabetic ketoacidosis (DKA is a potentially life-threatening complication of diabetes mellitus and can lead to death if untreated. It is a complex metabolic state characterised by hyperglycaemia, acidosis and ketonuria. Bonsai is one of the herbal incense products that contains synthetic cannabinoid and can be easily accessible via the internet in many countries. It cannot be detected in blood and urine studies using conventional methods. Synthetic cannabinoid abuse is associated with severe side effects, including tachycardia, high blood pressure, acidosis, excess sedation and coma. Case Report: A 17-year-old male patient was brought to the emergency department with sudden onset of dyspnoea. Laboratory investigations revealed hyperglycaemia, acidosis and ketonuria. He was admitted to the intensive care unit with a diagnosis of diabetic ketoacidosis. He was not considered a typical case of diabetic ketoacidosis because of the tendency to hypokalaemia, persistent tachycardia and bronchoscopic findings. We learned from his friends that he had used cannabis for a week and used bonzai on the day that he was brought to the emergency service. Conclusion: Diabetic ketoacidosis with prolonged acidosis and tendency to hypokalaemia are investigated for the consumption of synthetic cannabinoids.

  7. The contribution of woody plant materials on the several conditions in a space environment

    Science.gov (United States)

    Tomita-Yokotani, Kaori; Baba, Keiichi; Suzuki, Toshisada; Kimura, Shunta; Sato, Seigo; Katoh, Hiroshi; Abe, Yusuke; Katayama, Takeshi

    Woody plant materials have several utilization elements in our habitation environment on earth. The studies of woody plants under a space-environment in the vegetable kingdom have a high contribution to the study of various and exotic environmental responses, too. Woody plants can produce an excess oxygen, woody materials for the living cabin, and provide a biomass by cultivating crops and other species of creatures. Tree material would become to be a tool in closed bio-ecosystems such as an environment in a space. We named the trees used as material for the experiment related to space environments “CosmoBon”, small tree bonsai. Japanese cherry tree, “Sakura”, is famous and lovely tree in Japan. One species of “Sakura”, “Mamezakura, Prunus incisa”, is not only lovely tree species, but also suitable tree for the model tree of our purpose. The species of Prunus incisa is originally grown in volcano environment. That species of Sakura is originally grown on Mt. Fuji aria, oligotrophic place. We will try to build the best utilization usage of woody plant under the space environment by “Mamezakura” as a model tree. Here, we will show the importance of uniformity of materials when we will use the tree materials in a space environment. We will also discuss that tree has a high possibility of utilization under the space environments by using our several results related to this research.

  8. Unusual side effect of cannabis use: acute abdomen due to duodenal perforation.

    Science.gov (United States)

    Buyukbese Sarsu, Sevgi

    2016-12-01

    The chronic use of synthetic cannabinoids (SCs) which has become an increasingly prevalent problem can rarely cause gastric and duodenal ulcer because of their effects on gastric secretion and emptying. Since peptic ulcer disease (PUD) is a rarely seen entity in patients who consult to the emergency service with complaints of abdominal pain, most of the physicians do not suspect of this clinical diagnosis. Perforation is a mortal complication of PUD, and early diagnosis and emergency surgery are life-saving procedures. A 16-year-old male patient was referred to our emergency service from another center with abdominal distension, complaints of abdominal pain, and bilious vomiting. His medical history revealed that he had been regularly using bonsai for the past 3 years. Plain abdominal radiograms of standing position revealed subdiaphragmatic free air, then we performed laparotomy which disclosed perforation of the first part of the duodenum. Surgical intervention with omental patch and primary closure (Graham patch) was successful. The patient who underwent nasogastric decompression and received antibiotherapy had not experienced any complication during the postoperative follow-up period. Herein, as an unusual manifestation, a patient who developed duodenal perforation following chronic SC use has been reported. In adolescent patients admitted with PUD or its complications to the emergency services, it is important to inquire for the use of addictive substances which are increasingly prevalent in order to determine the etiology.

  9. Reverse genetic characterization of cytosolic acetyl-CoA generation by ATP-citrate lyase in Arabidopsis.

    Science.gov (United States)

    Fatland, Beth L; Nikolau, Basil J; Wurtele, Eve Syrkin

    2005-01-01

    Acetyl-CoA provides organisms with the chemical flexibility to biosynthesize a plethora of natural products that constitute much of the structural and functional diversity in nature. Recent studies have characterized a novel ATP-citrate lyase (ACL) in the cytosol of Arabidopsis thaliana. In this study, we report the use of antisense RNA technology to generate a series of Arabidopsis lines with a range of ACL activity. Plants with even moderately reduced ACL activity have a complex, bonsai phenotype, with miniaturized organs, smaller cells, aberrant plastid morphology, reduced cuticular wax deposition, and hyperaccumulation of starch, anthocyanin, and stress-related mRNAs in vegetative tissue. The degree of this phenotype correlates with the level of reduction in ACL activity. These data indicate that ACL is required for normal growth and development and that no other source of acetyl-CoA can compensate for ACL-derived acetyl-CoA. Exogenous malonate, which feeds into the carboxylation pathway of acetyl-CoA metabolism, chemically complements the morphological and chemical alterations associated with reduced ACL expression, indicating that the observed metabolic alterations are related to the carboxylation pathway of cytosolic acetyl-CoA metabolism. The observations that limiting the expression of the cytosolic enzyme ACL reduces the accumulation of cytosolic acetyl-CoA-derived metabolites and that these deficiencies can be alleviated by exogenous malonate indicate that ACL is a nonredundant source of cytosolic acetyl-CoA.

  10. Soil conditions and plant growth'

    Science.gov (United States)

    Passioura, J. B.

    2002-02-01

    Plants can respond to soil conditions in ways that can not readily be explained in terms of the ability of the roots to take up water and nutrients. Roots may sense difficult conditions in the soil and thence send inhibitory signals to the shoots which harden the plants against the consequences of a deteriorating or restrictive environment, especially if the plants' water supply is at risk. Generally, this behaviour can be interpreted as feedforward responses to the soil becoming too dry or too hard, or to the available soil volume being very small as with bonsai plants, or to roots' becoming infected with pathogens. However, soil that is too soft or in which the roots are forced to grow in very large pores can also induce large conservative responses, the significance of which is unclear. The inhibitory signals may affect stomatal conductance, cell expansion, cell division and the rate of leaf appearance. Their nature is still under debate, and the debate is becoming increasingly complex, which probably signifies that a network of hormonal and other responses is involved in attuning the growth and development of a plant to its environment.

  11. Chemical Constituents from the Branches of Carpinus turczaninowii with Antioxidative Activities

    Energy Technology Data Exchange (ETDEWEB)

    Ko, Ha Na; Kim, Jung Mi; Bu, Hee Jung; Lee, Nam Ho [Jeju National Univ., Jeju (Korea, Republic of)

    2013-08-15

    Eight compounds were identified in ethanol extracts prepared from the branches of C. turczaninowii. The compounds, besides 5 and 6, were isolated for the first time from this woody plant. Pyracrenic acid (4) and quercitrin (8) showed potent DPPH free radical scavenging activities with SC{sub 50} values of 55.2 and 62.4 μM, respectively, where ascorbic acid (SC{sub 50} 43.5 μM) was used as a positive control. Compounds 4, 5, 6 and 8 showed strong activities in ABTS{sup +} radical scavenging assay, with SC{sub 50} values of 34.1, 42.1, 45.8 and 29.6 μM, respectively. These activities are comparable in potency to ascorbic acid (SC{sub 50} 31.6 μM). Based on these results, C. turczaninowii extracts are expected to be useful antioxidative agents, potentially applicable in food or cosmetic industries, based on the results of further studies. Korean hornbeam Carpinus turczaninowii is a deciduous woody plant belonging to the family Betulaceae. This flora is endemic to Korea, and can reach a height of 15 m. In the autumn, the fallen leaves of C. turczaninowii display a beautiful orange-red color and the tree is commonly used for bonsai in Korea. The wood is very hard, dense and fine textured, and has been used for making agricultural tools and furniture. Previous chemical investigation on this plant indicated only the existence of flavonoids such as naringenin and quercetin glycosides from the leaves. We have recently reported the isolation diarylheptanoids possessing anti-inflammatory activities from the ethanol extract of C. turczaninowii.

  12. A statistical framework for genome-wide discovery of biomarker splice variations with GeneChip Human Exon 1.0 ST Arrays.

    Science.gov (United States)

    Yoshida, Ryo; Numata, Kazuyuki; Imoto, Seiya; Nagasaki, Masao; Doi, Atsushi; Ueno, Kazuko; Miyano, Satoru

    2006-01-01

    Alternative splicing is an important regulatory mechanism that generates multiple mRNA transcripts which are transcribed into functionally diverse proteins. According to the current studies, aberrant transcripts due to splicing mutations are known to cause for 15% of genetic diseases. Therefore understanding regulatory mechanism of alternative splicing is essential for identifying potential biomarkers for several types of human diseases. Most recently, advent of GeneChip Human Exon 1.0 ST Array enables us to measure genome-wide expression profiles of over one million exons. With this new microarray platform, analysis of functional gene expressions could be extended to detect not only differentially expressed genes, but also a set of specific-splicing events that are differentially observed between one or more experimental conditions, e.g. tumor or normal control cells. In this study, we address the statistical problems to identify differentially observed splicing variations from exon expression profiles. The proposed method is organized according to the following process: (1) Data preprocessing for removing systematic biases from the probe intensities. (2) Whole transcript analysis with the analysis of variance (ANOVA) to identify a set of loci that cause the alternative splicing-related to a certain disease. We test the proposed statistical approach on exon expression profiles of colorectal carcinoma. The applicability is verified and discussed in relation to the existing biological knowledge. This paper intends to highlight the potential role of statistical analysis of all exon microarray data. Our work is an important first step toward development of more advanced statistical technology. Supplementary information and materials are available from http://bonsai.ims.u-tokyo.ac.jp/~yoshidar/IBSB2006_ExonArray.htm.

  13. RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1.

    Science.gov (United States)

    Wang, Xingang; Duan, Cheng-Guo; Tang, Kai; Wang, Bangshing; Zhang, Huiming; Lei, Mingguang; Lu, Kun; Mangrauthia, Satendra K; Wang, Pengcheng; Zhu, Guohui; Zhao, Yang; Zhu, Jian-Kang

    2013-09-17

    DNA methylation-dependent heterochromatin formation is a conserved mechanism of epigenetic silencing of transposons and other repeat elements in many higher eukaryotes. Genes adjacent to repetitive elements are often also subjected to this epigenetic silencing. Consequently, plants have evolved antisilencing mechanisms such as active DNA demethylation mediated by the REPRESSOR OF SILENCING 1 (ROS1) family of 5-methylcytosine DNA glycosylases to protect these genes from silencing. Some transposons and other repeat elements have found residence in the introns of genes. It is unclear how these intronic repeat elements-containing genes are regulated. We report here the identification of ANTI-SILENCING 1 (ASI1), a bromo-adjacent homology domain and RNA recognition motif-containing protein, from a forward genetic screen for cellular antisilencing factors in Arabidopsis thaliana. ASI1 is required to prevent promoter DNA hypermethylation and transcriptional silencing of some transgenes. Genome-wide DNA methylation analysis reveals that ASI1 has a similar role to that of the histone H3K9 demethylase INCREASE IN BONSAI METHYLATION 1 (IBM1) in preventing CHG methylation in the bodies of thousands of genes. We found that ASI1 is an RNA-binding protein and ensures the proper expression of IBM1 full-length transcript by associating with an intronic heterochromatic repeat element of IBM1. Through mRNA sequencing, we identified many genes containing intronic transposon elements that require ASI1 for proper expression. Our results suggest that ASI1 associates with intronic heterochromatin and binds the gene transcripts to promote their 3' distal polyadenylation. The study thus reveals a unique mechanism by which higher eukaryotes deal with the collateral effect of silencing intronic repeat elements.

  14. Extensive survey of molecules related to wood formation and gravity for space agriculture.

    Science.gov (United States)

    Motohashi, Kyohei; Tomita-Yokotani, Kaori; Baba, Keiichi; Furukawa, Jun; Sato, Seigo; Suzuki, Toshisada; Hashimoto, Hirofumi; Yamashita, Masamichi; Japanese Space Tree Working Group

    Most, if not all, terrestrial subjects are under the influence of gravity. Since the gravitational force is proportional to the mass of subject, gravity is dominant for larger masses. The response of a plant against gravity is not an exception in this respect even it shows rather complicated features. For the angiosperm tree, its shape is determined by the forming tension wood, which induces more tensile stress in the xylem than in the normal wood. The mechanism of tension wood formation and its relevance to gravity have been extensively studied. Gibberellin is known to be responsible for this phenomenon in angiosperm tree, for example, the Japanese cherry tree, Prunus jamasakura. However, full understanding of the mechanisms has not yet been clarified. For an extensive survey of molecules related to tension wood formation, we induced an artificial tension wood formation and examined the tension wood formation by microscopic observations with double-staining. This enables the screening of really functional molecules in the space environment for future space agriculture. We demonstrated that Prunus incise is suitable for this research as a test material based on several reasons. We focused our attention in the region of the branch, i.e., the CosmoTree in CosmoBon, and established an experimental system to analyze the real functional factors of the tension wood. This study might ensure wood formation in a space environment and use woody plants as a material for space development. ("CosmoBon" is the Bonsai small tree for our space experiments. "CosmoTree" is a small branch/tree.)

  15. Suppression of 4-coumarate-CoA ligase in the coniferous gymnosperm Pinus radiata.

    Science.gov (United States)

    Wagner, Armin; Donaldson, Lloyd; Kim, Hoon; Phillips, Lorelle; Flint, Heather; Steward, Diane; Torr, Kirk; Koch, Gerald; Schmitt, Uwe; Ralph, John

    2009-01-01

    Severe suppression of 4-coumarate-coenzyme A ligase (4CL) in the coniferous gymnosperm Pinus radiata substantially affected plant phenotype and resulted in dwarfed plants with a "bonsai tree-like" appearance. Microscopic analyses of stem sections from 2-year-old plants revealed substantial morphological changes in both wood and bark tissues. This included the formation of weakly lignified tracheids that displayed signs of collapse and the development of circumferential bands of axial parenchyma. Acetyl bromide-soluble lignin assays and proton nuclear magnetic resonance studies revealed lignin reductions of 36% to 50% in the most severely affected transgenic plants. Two-dimensional nuclear magnetic resonance and pyrolysis-gas chromatography-mass spectrometry studies indicated that lignin reductions were mainly due to depletion of guaiacyl but not p-hydroxyphenyl lignin. 4CL silencing also caused modifications in the lignin interunit linkage distribution, including elevated beta-aryl ether (beta-O-4 unit) and spirodienone (beta-1) levels, accompanied by lower phenylcoumaran (beta-5), resinol (beta-beta), and dibenzodioxocin (5-5/beta-O-4) levels. A sharp depletion in the level of saturated (dihydroconiferyl alcohol) end groups was also observed. Severe suppression of 4CL also affected carbohydrate metabolism. Most obvious was an up to approximately 2-fold increase in galactose content in wood from transgenic plants due to increased compression wood formation. The molecular, anatomical, and analytical data verified that the isolated 4CL clone is associated with lignin biosynthesis and illustrated that 4CL silencing leads to complex, often surprising, physiological and morphological changes in P. radiata.

  16. Chemical Constituents from the Branches of Carpinus turczaninowii with Antioxidative Activities

    International Nuclear Information System (INIS)

    Ko, Ha Na; Kim, Jung Mi; Bu, Hee Jung; Lee, Nam Ho

    2013-01-01

    Eight compounds were identified in ethanol extracts prepared from the branches of C. turczaninowii. The compounds, besides 5 and 6, were isolated for the first time from this woody plant. Pyracrenic acid (4) and quercitrin (8) showed potent DPPH free radical scavenging activities with SC 50 values of 55.2 and 62.4 μM, respectively, where ascorbic acid (SC 50 43.5 μM) was used as a positive control. Compounds 4, 5, 6 and 8 showed strong activities in ABTS + radical scavenging assay, with SC 50 values of 34.1, 42.1, 45.8 and 29.6 μM, respectively. These activities are comparable in potency to ascorbic acid (SC 50 31.6 μM). Based on these results, C. turczaninowii extracts are expected to be useful antioxidative agents, potentially applicable in food or cosmetic industries, based on the results of further studies. Korean hornbeam Carpinus turczaninowii is a deciduous woody plant belonging to the family Betulaceae. This flora is endemic to Korea, and can reach a height of 15 m. In the autumn, the fallen leaves of C. turczaninowii display a beautiful orange-red color and the tree is commonly used for bonsai in Korea. The wood is very hard, dense and fine textured, and has been used for making agricultural tools and furniture. Previous chemical investigation on this plant indicated only the existence of flavonoids such as naringenin and quercetin glycosides from the leaves. We have recently reported the isolation diarylheptanoids possessing anti-inflammatory activities from the ethanol extract of C. turczaninowii

  17. The dynamics of stellar disks in live dark-matter halos

    Science.gov (United States)

    Fujii, M. S.; Bédorf, J.; Baba, J.; Portegies Zwart, S.

    2018-03-01

    Recent developments in computer hardware and software enable researchers to simulate the self-gravitating evolution of galaxies at a resolution comparable to the actual number of stars. Here we present the results of a series of such simulations. We performed N-body simulations of disk galaxies with between 100 and 500 million particles over a wide range of initial conditions. Our calculations include a live bulge, disk, and dark matter halo, each of which is represented by self-gravitating particles in the N-body code. The simulations are performed using the gravitational N-body tree-code Bonsai running on the Piz Daint supercomputer. We find that the time scale over which the bar forms increases exponentially with decreasing disk-mass fraction and that the bar formation epoch exceeds a Hubble time when the disk-mass fraction is ˜0.35. These results can be explained with the swing-amplification theory. The condition for the formation of m = 2 spirals is consistent with that for the formation of the bar, which is also an m = 2 phenomenon. We further argue that the non-barred grand-design spiral galaxies are transitional, and that they evolve to barred galaxies on a dynamical timescale. We also confirm that the disk-mass fraction and shear rate are important parameters for the morphology of disk galaxies. The former affects the number of spiral arms and the bar formation epoch, and the latter determines the pitch angle of the spiral arms.

  18. Economics of Distance and Online Learning Theory, Practice and Research

    Directory of Open Access Journals (Sweden)

    reviewed by TOJDE

    2009-10-01

    Learning: The Role of Embedded Learning inCreating a Competitive Workforce, Jade Nguyen Strattner and Diana OblingerSECTION SIX: OPEN AND VIRTUAL SCHOOLINGChapter 13: Open Basic Education: Organizational Structures, Costs and Benefits,Palitha EdirisinghaSECTION SEVEN: RESEARCH AND DEVELOPMENTChapter 14: From Baobab to Bonsai: Revisiting Methodological Issues in the Costs andEconomics of Distance Education and Distributed e-Learning, Thomas HülsmannSECTION EIGHT: EPILOGUEChapter 15: Implications for Planning and Management of Distance and On-lineLearning, William Bramble and Santosh Panda

  19. Isolation and characterization of sex chromosome rearrangements generating male muscle dystrophy and female abnormal oogenesis in the silkworm, Bombyx mori.

    Science.gov (United States)

    Fujii, T; Yokoyama, T; Ninagi, O; Kakehashi, K; Obara, Y; Nenoi, M; Ishikawa, T; Mita, K; Shimada, T; Abe, H

    2007-07-01

    In deletion-mapping of W-specific RAPD (W-RAPD) markers and putative female determinant gene (Fem), we used X-ray irradiation to break the translocation-carrying W chromosome (W( Ze )). We succeeded in obtaining a fragment of the W( Ze ) chromosome designated as Ze (W), having 3 of 12 W-RAPD markers (W-Bonsai, W-Yukemuri-S, W-Yukemuri-L). Inheritance of the Ze (W) fragment by males indicates that it does not include the Fem gene. On the basis of these results, we determined the relative positions of W-Yukemuri-S and W-Yukemuri-L, and we narrowed down the region where Fem gene is located. In addition to the Ze (W) fragment, the Z chromosome was also broken into a large fragment (Z(1)) having the +( sch ) (1-21.5) and a small fragment (Z(2)) having the +( od ) (1-49.6). Moreover, a new chromosomal fragment (Ze (W)Z(2)) was generated by a fusion event between the Ze (W) and the Z(2) fragments. We analyzed the genetic behavior of the Z(1) fragment and the Ze (W)Z(2) fragment during male (Z/Z(1) Ze (W)Z(2)) and female (Z(1) Ze (W)Z(2)/W) meiosis using phenotypic markers. It was observed that the Z(1) fragment and the Z or the W chromosomes separate without fail. On the other hand, non-disjunction between the Ze (W)Z(2) fragment and the Z chromosome and also between the Ze (W)Z(2) fragment and the W chromosome occurred. Furthermore, the females (2A: Z/Ze (W)Z(2)/W) and males (2A: Z/Z(1)) resulting from non-disjunction between the Ze (W)Z(2) fragment and the W chromosome had phenotypic defects: namely, females exhibited abnormal oogenesis and males were flapless due to abnormal indirect flight muscle structure. These results suggest that Z(2) region of the Z chromosome contains dose-sensitive gene(s), which are involved in oogenesis and indirect flight muscle development.

  20. Partial deletions of the W chromosome due to reciprocal translocation in the silkworm Bombyx mori.

    Science.gov (United States)

    Abe, H; Seki, M; Ohbayashi, F; Tanaka, N; Yamashita, J; Fujii, T; Yokoyama, T; Takahashi, M; Banno, Y; Sahara, K; Yoshido, A; Ihara, J; Yasukochi, Y; Mita, K; Ajimura, M; Suzuki, M G; Oshiki, T; Shimada, T

    2005-08-01

    In the silkworm, Bombyx mori (female, ZW; male, ZZ), femaleness is determined by the presence of a single W chromosome, irrespective of the number of autosomes or Z chromosomes. The W chromosome is devoid of functional genes, except the putative female-determining gene (Fem). However, there are strains in which chromosomal fragments containing autosomal markers have been translocated on to W. In this study, we analysed the W chromosomal regions of the Zebra-W strain (T(W;3)Ze chromosome) and the Black-egg-W strain (T(W;10)+(w-2) chromosome) at the molecular level. Initially, we undertook a project to identify W-specific RAPD markers, in addition to the three already established W-specific RAPD markers (W-Kabuki, W-Samurai and W-Kamikaze). Following the screening of 3648 arbitrary 10-mer primers, we obtained nine W-specific RAPD marker sequences (W-Bonsai, W-Mikan, W-Musashi, W-Rikishi, W-Sakura, W-Sasuke, W-Yukemuri-L, W-Yukemuri-S and BMC1-Kabuki), almost all of which contained the border regions of retrotransposons, namely portions of nested retrotransposons. We confirmed the presence of eleven out of twelve W-specific RAPD markers in the normal W chromosomes of twenty-five silkworm strains maintained in Japan. These results indicate that the W chromosomes of the strains in Japan are almost identical in type. The Zebra-W strain (T(W;3)Ze chromosome) lacked the W-Samurai and W-Mikan RAPD markers and the Black-egg-W strain (T(W;10)+(w-2) chromosome) lacked the W-Mikan RAPD marker. These results strongly indicate that the regions containing the W-Samurai and W-Mikan RAPD markers or the W-Mikan RAPD marker were deleted in the T(W;3)Ze and T(W;10)+(w-2) chromosomes, respectively, due to reciprocal translocation between the W chromosome and the autosome. This deletion apparently does not affect the expression of Fem; therefore, this deleted region of the W chromosome does not contain the putative Fem gene.

  1. Evidence of local evolution of tomato-infecting begomovirus species in West Africa: characterization of tomato leaf curl Mali virus and tomato yellow leaf crumple virus from Mali.

    Science.gov (United States)

    Zhou, Y-C; Noussourou, M; Kon, T; Rojas, M R; Jiang, H; Chen, L-F; Gamby, K; Foster, R; Gilbertson, R L

    2008-01-01

    Tomato yellow leaf curl (TYLC) and tomato leaf curl (ToLC) diseases are serious constraints to tomato production in Mali and other countries in West Africa. In 2003 and 2004, samples of tomato showing virus-like symptoms were collected during a survey of tomato virus diseases in Mali. Three predominant symptom phenotypes were observed: (1) TYLC/ToLC (stunted upright growth and upcurled leaves with interveinal yellowing and vein purpling), (2) yellow leaf crumple and (3) broccoli or bonsai (severe stunting and distorted growth). Squash blot (SB) hybridization with a general begomovirus probe and/or SB/PCR analyses revealed begomovirus infection in plants with each of these symptom phenotypes and no evidence of phytoplasma infection. Sequence analysis of PCR-amplified begomovirus fragments revealed two putative new begomovirus species associated with the TYLC/ToLC and yellow leaf crumple symptom phenotypes, respectively. Full-length clones of these begomoviruses were obtained using PCR and overlapping primers. When introduced into N. benthamiana and tomato plants, these clones induced upward leaf curling and crumpling (the TYLC/ToLC-associated begomovirus) or downward leaf curl/yellow mottle (yellow leaf crumple-associated begomovirus) symptoms. Thus, these begomoviruses were named tomato leaf curl Mali virus (ToLCMLV) and tomato yellow leaf crumple virus (ToYLCrV). The genome organization of both viruses was similar to those of other monopartite begomoviruses. ToLCMLV and ToYLCrV were most closely related to each other and to tobacco leaf curl Zimbabwe virus (TbLCZV-[ZW]) and tomato curly stunt virus from South Africa (ToCSV-ZA). Thus, these likely represent tomato-infecting begomoviruses that evolved from indigenous begomoviruses on the African continent. Mixed infections of ToLCMLV and ToYLCrV in N. benthamiana and tomato plants resulted in more severe symptoms than in plants infected with either virus alone, suggesting a synergistic interaction. Agroinoculation

  2. Teppeki, selective insecticide about Bombus terrestris.

    Science.gov (United States)

    Fanigliulo, Angela; Filì, Vittorio; Pacella, Rosa; Comes, Soccorsa; Crescenzi, Aniello

    2009-01-01

    At a time when a highly controversial debate about the causes of the widespread deaths of bees is taking place all over Europe, which accused the agriculture and its practices with particular reference to the harmful effects of some insecticides, it seems important to point out as another insecticide, the Teppeki, can be selective about bumble and have a good compatibility with the activity of the apiaries. This insecticide has the active ingredient flonicamid (500 g/kg) belonging to a new chemical class, called pyridinecarboxamides: the product works systemic and is known as having a long lasting efficacy against all important aphid species. Bioagritest test facility of Pignola (PZ, Italy) has conducted in two successive production cycles an experimental trial on a tomato hydroponic cultivation within the Agricola Bonsai farm in Sibari (CS, Italy), whose objective was to measure the selectivity of flonicamid on Bombus terrestris, insects playing an important role in the pollination of certain species grown in greenhouse such as Tomato, Eggplant, Pepper and Cucumber. On the pollinated flower B. terrestris leaves some trace of its visit, a typical dark trademark: on the detection of the marking of flowers was based the testing program conducted by Bioagritest. Two thesis were compared: A, standard) treatment with a foliar insecticide, the neonicotinoide acetamiprid, normally used for control of aphids and whiteflies (unlike other neonicotinoides--imidacloprid and thiametoxam--quite selective about B. terrestris) and B, Teppeki) foliar treatment with Teppeki, to the maximum dose indicated on the label. The experimental design included the use of randomized blocks with 4 repetitions (4 plots/thesis with 100 plants each). In every thesis six B. terrestris hives were placed 2 days before treatment: the respective holes remained closed during the treatment and the 12 following hours. In order to verify the pollination, by the detection of the flower marking, 2 flowers

  3. First report of the land planarian Diversibipalium multilineatum (Makino & Shirasawa, 1983) (Platyhelminthes, Tricladida, Continenticola) in Europe.

    Science.gov (United States)

    Mazza, Giuseppe; Menchetti, Mattia; Sluys, Ronald; Solà, Eduard; Riutort, Marta; Tricarico, Elena; Justine, Jean-Lou; Cavigioli, Luca; Mori, Emiliano

    2016-01-26

    Introduction of alien species may significantly affect soil ecosystems, through predation or disruption of components of native ecosystems (Winsor et al. 2004; Álvarez-Presas et al. 2014; Justine et al. 2014). Land planarians have been reported as alien species in soils throughout the world and, among those, some species are considered to be successful invaders, e.g. Platydemus manokwari de Beauchamp, 1963, Arthurdendyus triangulatus (Dendy, 1894), Bipalium adventitium Hyman, 1943, Bipalium kewense Moseley, 1878 and Dolichoplana striata Moseley, 1877 (Winsor et al. 2004; Álvarez-Presas et al. 2014; Justine et al. 2014, 2015). Soil moisture status seems to be an important element for their successful invasion (Fraser & Boag 1998). In Europe at least 18 species of alien land planarians have been recorded since now and some of them are considered as invasive ones, e.g. P. manokwari (cf. Justine et al. 2014). Although the alien land planarian B. kewense has been reported to occur in many greenhouses in Italy (Bello et al. 1995), no data are available on its establishment and/or impact on natural environments. On 28th September 2014, 20 specimens (~1 individual/m2) of the land planarian Diversibipalium multilineatum (Makino & Shirasawa, 1983) (Fig. 1), native to Japan, were collected under pots, branches and plastic materials in a private garden located in the center of Bologna (Emilia Romagna, Central Italy), near the urban park Giardini Margherita (44°29' N, 11°21' E; WGS84). Thirty plant species (both indigenous and alien), mainly cultivated as bonsai (e.g. Lagerstroemia indica L., Juniperus procumbens (Siebold ex Endl.) Miquel), were present in this shady, wet garden (25 m2). Between March 2014 and June 2015, 70 more specimens of D. multilineatum were collected at the same site, mainly at dusk and dawn after rain. Reproduction by fission and regeneration processes were observed in several of those specimens, which were kept for some time in captivity. A specimen