Standard Technical Specifications, Babcock and Wilcox plants

International Nuclear Information System (INIS)

1992-09-01

This NUREG contains improved Standard Technical Specifications (STS) for Babcock and Wilcox (B ampersand W) Plants and documents the positions of the Nuclear Regulatory Commission based on the B ampersand W Owners Group's proposed STS. This document is the result of extensive technical meetings and discussions among the NRC staff, the Nuclear Steam Supply System (NSSS) Owners Groups, the NSSS vendors, and the Nuclear Management and Resources Council (NUMARC). The improved STS were developed based on the criteria in the interim Commission Policy Statement on Technical Specification Improvements for Nuclear Power Reactors, dated February 6, 1987. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes. Volume 1 contains the Specifications for all chapters and sections of the improved STS. This document Volume 2, contains the Bases for Chapters 2.0 and 3.0, and Sections 3.1--3.3 of the improved STS. Volume 3 contains the Bases for Sections 3.4--3.10 of the improved STS

Use of plant-specific PRA in an EOP scope audit

International Nuclear Information System (INIS)

O'Brien, J.J.

1991-01-01

Traditionally, decisions on which accident scenarios to proceduralize as emergency operating procedures (EOPs) have been based on existing design basis analyses, engineering judgment, and probabilistic risk assessments (PRAs) on generic plants. This approach has important strengths and limits. The major limitation of generic PRAs is their inability to account for plant-specific features. Use of plant-specific PRA to determine the impact of proceduralizing, or not proceduralizing, responses to scenarios considers plant-specific features. This helps to eliminate unnecessary EOPs, thus allowing resources to be concentrated on scenarios that are more important for a particular plant. In preparation for a US Nuclear Regulatory Commission audit, a plant-specific PRA was used to assess and quantify the plant's previous decision not to implement six reference emergency response guidelines (ERGs) as procedures. The original justification for nonimplementation of the ERGs was based on engineering judgment. The PRA provided a quantitative justification for implementation/nonimplementation of each guidelines. This analysis accounted for plant-specific design features not common to all reference plants

Standard technical specifications: General Electric plants, BWR/4. Volume 1, Revision 1: Specifications

International Nuclear Information System (INIS)

1995-04-01

This report documents the results of the combined effort of the NRC and the industry to produce improved Standard Technical Specifications (STS), Revision 1 for General Electric BWR/4 Plants. The changes reflected in Revision 1 resulted from the experience gained from license amendment applications to convert to these improved STS or to adopt partial improvements to existing technical specifications. This NUREG is the result of extensive public technical meetings and discussions between the Nuclear Regulatory Commission (NRC) staff and various nuclear power plant licensees, Nuclear Steam Supply System (NSSS) Owners Groups, NSSS vendors, and the Nuclear Energy Institute (NEI). The improved STS were developed based on the criteria in the Final Commission Policy Statement on Technical Specifications Improvements for Nuclear Power Reactors, dated July 22, 1993. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes. Volume 1 contains the Specifications for all chapters and sections of the improved STS. Volume 2 contains the Bases for Chapters 2.0 and 3.0, and Sections 3.1--3.3 of the improved STS. Volume 3 contains the Bases for Sections 3.4--3.10 of the improved STS

Preliminary design of the Carrisa Plains solar central receiver power plant. Volume II. Plant specifications

Energy Technology Data Exchange (ETDEWEB)

Price, R. E.

1983-12-31

The specifications and design criteria for all plant systems and subsystems used in developing the preliminary design of Carrisa Plains 30-MWe Solar Plant are contained in this volume. The specifications have been organized according to plant systems and levels. The levels are arranged in tiers. Starting at the top tier and proceeding down, the specification levels are the plant, system, subsystem, components, and fabrication. A tab number, listed in the index, has been assigned each document to facilitate document location.

Proteomic Analysis of Rhizoctonia solani Identifies Infection-specific, Redox Associated Proteins and Insight into Adaptation to Different Plant Hosts*

Science.gov (United States)

Anderson, Jonathan P.; Hane, James K.; Stoll, Thomas; Pain, Nicholas; Hastie, Marcus L.; Kaur, Parwinder; Hoogland, Christine; Gorman, Jeffrey J.; Singh, Karam B.

2016-01-01

Rhizoctonia solani is an important root infecting pathogen of a range of food staples worldwide including wheat, rice, maize, soybean, potato and others. Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues, however, little is known about how R. solani causes disease. This study capitalizes on recent genomic studies by applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Many of the proteins found in the culture filtrate had predicted functions relating to modification of the plant cell wall, a major activity required for pathogenesis on the plant host, including a number found only under infection conditions. Other infection related proteins included a high proportion of proteins with redox associated functions and many novel proteins without functional classification. The majority of infection only proteins tested were confirmed to show transcript up-regulation during infection including a thaumatin which increased susceptibility to R. solani when expressed in Nicotiana benthamiana. In addition, analysis of expression during infection of different plant hosts highlighted how the infection strategy of this broad host range pathogen can be adapted to the particular host being encountered. Data are available via ProteomeXchange with identifier PXD002806. PMID:26811357

DNA barcoding as a means for identifying medicinal plants of Pakistan

International Nuclear Information System (INIS)

Schori, M.; Showalter, A.M.

2011-01-01

DNA barcoding involves the generation of DNA sequencing data from particular genetic regions in an organism and the use of these sequence data to identify or 'barcode' that organism and distinguish it from other species. Here, DNA barcoding is being used to identify several medicinal plants found in Pakistan and distinguished them from other similar species. Several challenges to the successful implementation of plant DNA barcoding are presented and discussed. Despite these challenges, DNA barcoding has the potential to uniquely identify medicinal plants and provide quality control and standardization of the plant material supplied to the pharmaceutical industry. (author)

Cell-specific expression of plant nutrient transporter genes in orchid mycorrhizae.

Science.gov (United States)

Fochi, Valeria; Falla, Nicole; Girlanda, Mariangela; Perotto, Silvia; Balestrini, Raffaella

2017-10-01

Orchid mycorrhizal protocorms and roots are heterogeneous structures composed of different plant cell-types, where cells colonized by intracellular fungal coils (the pelotons) are close to non-colonized plant cells. Moreover, the fungal coils undergo rapid turnover inside the colonized cells, so that plant cells containing coils at different developmental stages can be observed in the same tissue section. Here, we have investigated by laser microdissection (LMD) the localization of specific plant gene transcripts in different cell-type populations collected from mycorrhizal protocorms and roots of the Mediterranean orchid Serapias vomeracea colonized by Tulasnella calospora. RNAs extracted from the different cell-type populations have been used to study plant gene expression, focusing on genes potentially involved in N uptake and transport and previously identified as up-regulated in symbiotic protocorms. Results clearly showed that some plant N transporters are differentially expressed in cells containing fungal coils at different developmental stages, as well as in non-colonized cells, and allowed the identification of new functional markers associated to coil-containing cells. Copyright © 2017 Elsevier B.V. All rights reserved.

Risk-based technical specifications: Development and application of an approach to the generation of a plant specific real-time risk model

International Nuclear Information System (INIS)

Puglia, B.; Gallagher, D.; Amico, P.; Atefi, B.

1992-10-01

This report describes a process developed to convert an existing PRA into a model amenable to real time, risk-based technical specification calculations. In earlier studies (culminating in NUREG/CR-5742), several risk-based approaches to technical specification were evaluated. A real-time approach using a plant specific PRA capable of modeling plant configurations as they change was identified as the most comprehensive approach to control plant risk. A master fault tree logic model representative of-all of the core damage sequences was developed. Portions of the system fault trees were modularized and supercomponents comprised of component failures with similar effects were developed to reduce the size of the model and, quantification times. Modifications to the master fault tree logic were made to properly model the effect of maintenance and recovery actions. Fault trees representing several actuation systems not modeled in detail in the existing PRA were added to the master fault tree logic. This process was applied to the Surry NUREG-1150 Level 1 PRA. The master logic mode was confirmed. The model was then used to evaluate frequency associated with several plant configurations using the IRRAS code. For all cases analyzed computational time was less than three minutes. This document Volume 2, contains appendices A, B, and C. These provide, respectively: Surry Technical Specifications Model Database, Surry Technical Specifications Model, and a list of supercomponents used in the Surry Technical Specifications Model

Repressor-mediated tissue-specific gene expression in plants

Science.gov (United States)

Meagher, Richard B [Athens, GA; Balish, Rebecca S [Oxford, OH; Tehryung, Kim [Athens, GA; McKinney, Elizabeth C [Athens, GA

2009-02-17

Plant tissue specific gene expression by way of repressor-operator complexes, has enabled outcomes including, without limitation, male sterility and engineered plants having root-specific gene expression of relevant proteins to clean environmental pollutants from soil and water. A mercury hyperaccumulation strategy requires that mercuric ion reductase coding sequence is strongly expressed. The actin promoter vector, A2pot, engineered to contain bacterial lac operator sequences, directed strong expression in all plant vegetative organs and tissues. In contrast, the expression from the A2pot construct was restricted primarily to root tissues when a modified bacterial repressor (LacIn) was coexpressed from the light-regulated rubisco small subunit promoter in above-ground tissues. Also provided are analogous repressor operator complexes for selective expression in other plant tissues, for example, to produce male sterile plants.

Step-wise and lineage-specific diversification of plant RNA polymerase genes and origin of the largest plant-specific subunits.

Science.gov (United States)

Wang, Yaqiong; Ma, Hong

2015-09-01

Proteins often function as complexes, yet little is known about the evolution of dissimilar subunits of complexes. DNA-directed RNA polymerases (RNAPs) are multisubunit complexes, with distinct eukaryotic types for different classes of transcripts. In addition to Pol I-III, common in eukaryotes, plants have Pol IV and V for epigenetic regulation. Some RNAP subunits are specific to one type, whereas other subunits are shared by multiple types. We have conducted extensive phylogenetic and sequence analyses, and have placed RNAP gene duplication events in land plant history, thereby reconstructing the subunit compositions of the novel RNAPs during land plant evolution. We found that Pol IV/V have experienced step-wise duplication and diversification of various subunits, with increasingly distinctive subunit compositions. Also, lineage-specific duplications have further increased RNAP complexity with distinct copies in different plant families and varying divergence for subunits of different RNAPs. Further, the largest subunits of Pol IV/V probably originated from a gene fusion in the ancestral land plants. We propose a framework of plant RNAP evolution, providing an excellent model for protein complex evolution. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Standard Technical Specifications, General Electric Plants, BWR/6

International Nuclear Information System (INIS)

1992-09-01

This NUREG contains improved Standard Technical Specifications (STS) for General Electric Plants, BWR/4, and documents the positions of the Nuclear Regulatory Commission based on the BWR Owners Group's proposed STS. This document is the result of extensive technical meetings and discussions among the NRC staff, the Nuclear Steam Supply System (NSSS) Owners Groups, the NSSS vendors, and the Nuclear Management and Resources Council (NUMARC). The improved STS were developed based on the criteria in the interim Commission Policy Statement on Technical Specification Improvements for Nuclear Power Reactors, dated February 6, 1987. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes. Volume 1 contains the Specifications for all chapters and sections of the improved STS. Volume 2 contains the Bases for Chapters 2.0 and 3.0, and Sections 3.1--3.3 of the improved STS. Volume 3, contains the Bases for Sections 3.4--3.10 of the improved STS

Standard Technical Specifications, General Electric plants, BWR/4

International Nuclear Information System (INIS)

1992-09-01

This NUREG contains improved Standard Technical Specifications (STS) for General Electric Plants, BWR/6, and documents the positions of the Nuclear Regulatory Commission based on the B ampersand W Owners Group's proposed STS. This document is the result of extensive technical meetings and discussions among the NRC staff, the Nuclear Steam Supply System (NSSS) Owners Groups, the NSSS vendors, and the Nuclear Management and Resources Council (NUMARC). The improved STS were developed based on the criteria in the interim Commission Policy Statement on Technical Specification Improvements for Nuclear Power Reactors, dated February 6, 1987. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes. Volume 1 contains the Specifications for all chapters and sections of the improved STS. Volume 2 contains the Bases for Chapters 2.0 and 3.0, and Sections 3.1--3.3 of the improved STS. This document Volume 3, contains the Bases for Sections 3.4--3.10 of the improved STS

Standard Technical Specifications, General Electric plants, BWR/6

International Nuclear Information System (INIS)

1992-09-01

This NUREG contains improved Standard Technical Specifications (STS) for General Electric Plants, BWR/6, and documents the positions of the Nuclear Regulatory Commission based on the B ampersand W Owners Group's proposed STS. This document is the result of extensive technical meetings and discussions among the NRC staff, the Nuclear Steam Supply System (NSSS) Owners Groups, the NSSS vendors, and the Nuclear Management and Resources Council (NUMARC). The improved STS were developed based on the criteria in the interim Commission Policy Statement on Technical Specification Improvements for Nuclear Power Reactors, dated February 6, 1987. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes. Volume 1 contains the Specifications for all chapters and sections of the improved STS. This document Volume 2, contains the Bases for Chapters 2.0 and 3.0, and Sections 3.1--3.3 of the improved STS. Volume 3 contains the Bases for Sections 3.4--3.10 of the improved STS

Standard Technical Specifications, General Electric Plants, BWR/6

International Nuclear Information System (INIS)

1992-09-01

This NUREG contains improved Standard Technical Specifications (STS) for General Electric Plants, BWR/6, and documents the positions of the Nuclear Regulatory Commission based on the B ampersand W Owners Group's proposed STS. This document is the result of extensive technical meetings and discussions among the NRC staff, the Nuclear Steam Supply System (NSSS) Owners Groups, the NSSS vendors, and the Nuclear Management and Resources Council (NUMARC). The improved STS were developed based on the criteria in the interim Commission Policy Statement on Technical Specification Improvements for Nuclear Power Reactors, dated February 6, 1987. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes. This document Volume 1, contains the Specifications for all chapters and sections of the improved STS. Volume 2 contains the Bases for Chapters 2.0 and 3.0, and Sections 3.1--3.3 of the improved STS. Volume 3 contains the Bases for Sections 3.4--3.10 of the improved STS

Standard Technical Specifications, General Electric plants, BWR/4

International Nuclear Information System (INIS)

1992-09-01

This NUREG contains improved Standard Technical Specifications (STS) for General Electric Plants, BWR/6, and documents the positions of the Nuclear Regulatory Commission based on the BWR Owners Group's proposed STS. This document is the result of extensive technical meetings and discussions among the NRC staff, the Nuclear Steam Supply System (NSSS) Owners Groups, the NSSS vendors, and the Nuclear Management and Resources Council (NUMARC). The improved STS were developed based on the criteria in the interim Commission Policy Statement on Technical Specification Improvements for Nuclear Power Reactors, dated February 6, 1987. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes. This document Volume 1 contains the Specifications for all chapters and sections of the improved STS. Volume 2 contains the Bases for Chapters 2.0 and 3.0, and Sections 3.1--3.3 of the improved STS. Volume 3 contains the Bases for Sections 3.4--3.10 of the improved STS

Identifying and Selecting Plants for the Landscape. Volume 23, Number 5.

Science.gov (United States)

Rodekohr, Sherie; Harris, Clark Richard

This handbook on identifying and selecting landscape plants can be used as a reference in landscaping courses or on an individual basis. The first of two sections, Identifying Plants for the Landscape, contains the following tables: shade tree identification; flowering tree identification; evergreen tree identification; flowering shrub…

Bottomland Hardwood Planting: Example Contract Specifications

National Research Council Canada - National Science Library

Humprey, Monica

2002-01-01

This technical note provides an example of contract specifications that can be used as a template by USACE biologists, engineers, or contracting officers for contracting the planting of bottomland hardwood (BLH) seedlings...

Host Specificity in the Parasitic Plant Cytinus hypocistis

International Nuclear Information System (INIS)

Thorogood, C.J.; Hiscock, S.J.

2007-01-01

Host specificity in the parasitic plant Cytinus hypocistis was quantified at four sites in the Algarve region of Portugal from 2002 to 2007. The parasite was found to be locally host specific, and only two hosts were consistently infected: Halimium halimifolium and Cistus monspeliensis. C. hypocistis did not infect hosts in proportion to their abundance; at three sites, 100% of parasites occurred on H. halimifolium which represented just 42.4%, 3% and 19.7% of potential hosts available, respectively. At the remaining site, where H. halimifolium was absent, 100% of parasites occurred on C. monspeliensis which represented 81.1% of potential hosts available. Other species of potential host were consistently uninfected irrespective of their abundance. Ecological niche divergence of host plants H. halimifolium and C. monspeliensis may isolate host-specific races of C. hypocistis, thereby potentially driving allopatric divergence in this parasitic plant.

Utilization of NPP Krsko plant specific simulator

International Nuclear Information System (INIS)

Fifnja, I.; Pribozic, F.; Krajnc, J.

2002-01-01

NPP Krsko started with licensed operator training using its own plant-specific full scope simulator in April 2000. Today, two years after simulator was completed, the benefits of simulator use are visible in various fields. The simulator was effectively used to conduct licensed operator continuing training and practical examinations. Two-year continuous training program was designed to help maintain and improve operator performance. The simulator was also used to provide just-in-time training prior to plant evolutions. Together with licensed operators the non-licensed operators are also included into simulator training to provide affective team training opportunity and to foster good communication and increase scenario realism. Now, the first group of initial licensed operator training using plant-specific simulator is also almost completed. It is the first time that NPP Krsko training department conducted complete initial training and this will represent the great experience for future training. Besides training, the simulator was also utilized for procedure development and validation, operating standards development, testing of plant modifications and other activities, like emergency preparedness procedures validation and training exercises.(author)

Standard technical specifications: Babcock and Wilcox Plants. Revision 1

International Nuclear Information System (INIS)

1995-04-01

This report documents the results of the combined effort of the NRC and the industry to produce improved Standard Technical Specifications (STS), Revision 1 for Babcock ampersand Wilcox Plants. The changes reflected in Revision 1 resulted from the experience gained from license amendment applications to convert to these improved STS or to adopt partial improvements to existing technical specifications. This NUREG is the result of extensive public technical meetings and discussions between the Nuclear Regulatory Commission (NRC) staff and various nuclear power plant licensees, Nuclear Steam Supply System (NSSS) Owners Groups, NSSS vendors, and the Nuclear Energy Institute (NEI). The improved STS were developed based on the criteria in the Final Commission Policy Statement on Technical Specifications Improvements for Nuclear Power Reactors, dated July 22, 1993. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes. Volume 1 contains the Specifications for all chapters and sections of the improved STS. Volume 2 contains the Bases for Chapters 2.0 and 3.0, and Sections 3.1--3.3 of the improved STS. Volume 3 contains the Bases for Sections 3.4--3.9 of the improved STS

Use of plant specific PSA to evaluate incidents at nuclear power plants

International Nuclear Information System (INIS)

1991-06-01

One of the possible applications of the plant specific probabilistic safety assessment (PSA) is its use in the analysis of operational events at the plant. The methodological development in that area was initiated recently in the framework of the IAEA's Incident Reporting System where determination of the safety significance of the event is essential for optimizing feedback of operating experience. This report provides details of the methodology and procedures to be used in event analysis. The report also contains three case studies which have been performed and summarizes lessons learned from those case studies. The results (event probabilities) obtained using plant specific PSA and the results of the analysis of the same events in the framework of the Accident Sequence Precursor (ASP) programmes (generic models) were compared and commented on. 6 refs, figs and tabs

Nuclear utility education and training becoming too plant specific?

International Nuclear Information System (INIS)

Wicks, F.

1986-01-01

As the Supervisor of a university nuclear reactor and operations curriculum, the author has also been offering education and training programs for nuclear utility technical support and operations personnel. Similar results have been reported by other universities offering similar programs. These programs also provide very important benefits to university nuclear engineering departments in terms of much needed revenues during this time of declining student enrollment and also by the information flow from the nuclear utility participants to the university personnel, which can yield both improved courses and identify research opportunities. University programs serve an important complementary function to plant-specific programs and should be continued and supported

Plant specific PTS analysis of Kori Unit 1

Energy Technology Data Exchange (ETDEWEB)

Sung-Yull, Hong; Changheui, Jang; Ill-Seok, Jeong [Korea Eletric Power Research Inst., Daejon (Korea, Republic of); Tae-Eun, Jin [Korea Power Engineering Company, Yonging (Korea, Republic of)

1997-09-01

Currently, a nuclear PLIM (Plant Lifetime Management) program is underway in Korea to extend the operation life of Kori-1 which was originally licensed for 30 years. For the life extension of nuclear power plants, the residual lives of major components should be evaluated for the extended operation period. According to the residual life evaluation of reactor pressure vessel, which was classified as one of the major components crucial to life extension, it was found by screening analysis that reference PTS temperature would exceed screening criteria before the target extended operation years. In order to deal with this problem, a plant-specific PTS analysis for Kori-1 RPV has been initiated. In this paper, the relationship between PTS analysis and Kori-1 PLIM program is briefly described. The plant-specific PTS analysis covers system transient analysis, downcomer mixing analysis, and probabilistic fracture mechanics analysis to check the integrity or RPV during various PTS transients. The step-by-step procedure of the analysis will be described in detail. Finally, various issues regarding RPV materials and its integrity will be briefly mentioned, and their implications on Kori-1 PTS analysis will be discussed. Despite of the screening analysis result concern, it is now expected that Kori-1 PTS issues can be handled through the plant-specific PTS analysis. (author). 14 refs, 4 figs, 2 tabs.

Guidelines for preparing specifications for nuclear power plants (NCIG-04): Final report

International Nuclear Information System (INIS)

1988-04-01

This document provides guidance for preparing technical requirements used in procurement and installation specifications. It is a compilation of recommend practices for writing specifications to preserve the best guidance coming out of recent years experience from construction of nuclear plants. It is intended to: Establish good practices for the content of specifications used for nuclear power plants; Be applicable to a wide range of specifications used for initial construction of plants and modifications to existing plants, including equipment replacement; and Provide guidance to specification preparers and reviewers

Specification and verification of the RTOS for plant protection systems

International Nuclear Information System (INIS)

Kim, Jin Hyun; Ahn, Young Ah; Lee, Su-Young; Choi, Jin Young; Lee, Na Young

2004-01-01

PLC is a computer system for instrumentation and control (I and C) systems such as control of machinery on factory assembly lines. control of machinery on factory assembly lines and Nucleare power plants. In nuclear power industry, systems is classified into 3 classes- Non-safety, safety-related and safety-critical up to integrity on system's using purpose. If PLC is used for controlling reactor in nuclear power plant, it should be identified as safety-critical. PLC has several I and C logics in software, including real-time operating system (RTOS). Hence, RTOS must be also proved that it is safe and reliable by various way and methods. In this paper, we apply formal methods to a development of RTOS for PLC in safety-critical level; Statecharts for specification and model checking for verification. In this paper, we give the results of applying formal methods to RTOS. (author)

Site-specific proteolytic degradation of IgG monoclonal antibodies expressed in tobacco plants.

Science.gov (United States)

Hehle, Verena K; Lombardi, Raffaele; van Dolleweerd, Craig J; Paul, Mathew J; Di Micco, Patrizio; Morea, Veronica; Benvenuto, Eugenio; Donini, Marcello; Ma, Julian K-C

2015-02-01

Plants are promising hosts for the production of monoclonal antibodies (mAbs). However, proteolytic degradation of antibodies produced both in stable transgenic plants and using transient expression systems is still a major issue for efficient high-yield recombinant protein accumulation. In this work, we have performed a detailed study of the degradation profiles of two human IgG1 mAbs produced in plants: an anti-HIV mAb 2G12 and a tumour-targeting mAb H10. Even though they use different light chains (κ and λ, respectively), the fragmentation pattern of both antibodies was similar. The majority of Ig fragments result from proteolytic degradation, but there are only a limited number of plant proteolytic cleavage events in the immunoglobulin light and heavy chains. All of the cleavage sites identified were in the proximity of interdomain regions and occurred at each interdomain site, with the exception of the VL /CL interface in mAb H10 λ light chain. Cleavage site sequences were analysed, and residue patterns characteristic of proteolytic enzymes substrates were identified. The results of this work help to define common degradation events in plant-produced mAbs and raise the possibility of predicting antibody degradation patterns 'a priori' and designing novel stabilization strategies by site-specific mutagenesis. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Specification of the 2nd cryogenic plant for RAON

Science.gov (United States)

Yoon, S.; Ki, T.; Lee, K. W.; Kim, Y.; Jo, H. C.; Kim, D. G.

2017-12-01

RAON is a rare isotope beam facility being built at Daejeon, South Korea. The RAON consists of three linear accelerators, SCL1 (1st SuperConducting LINAC), SCL2, and SCL3. Each LINAC has its own cryogenic plant. The cryogenic plant for SCL2 will provide the cooling for cryomodules, low temperature SC magnets, high temperature SC magnets, and a cryogenic distribution system. This paper describes the specification of the plant including cooling capacity, steady state and transient operation modes, and cooling strategies. In order to reduce CAPEX with the specification, two suppliers will consider no liquid nitrogen pre-cooling, one integrated cold box, and one back-up HP compressor. The detail design of the plant will be started at the end of this year.

An affinity pull-down approach to identify the plant cyclic nucleotide interactome

KAUST Repository

Donaldson, Lara Elizabeth; Meier, Stuart Kurt

2013-01-01

Cyclic nucleotides (CNs) are intracellular second messengers that play an important role in mediating physiological responses to environmental and developmental signals, in species ranging from bacteria to humans. In response to these signals, CNs are synthesized by nucleotidyl cyclases and then act by binding to and altering the activity of downstream target proteins known as cyclic nucleotide-binding proteins (CNBPs). A number of CNBPs have been identified across kingdoms including transcription factors, protein kinases, phosphodiesterases, and channels, all of which harbor conserved CN-binding domains. In plants however, few CNBPs have been identified as homology searches fail to return plant sequences with significant matches to known CNBPs. Recently, affinity pull-down techniques have been successfully used to identify CNBPs in animals and have provided new insights into CN signaling. The application of these techniques to plants has not yet been extensively explored and offers an alternative approach toward the unbiased discovery of novel CNBP candidates in plants. Here, an affinity pull-down technique for the identification of the plant CN interactome is presented. In summary, the method involves an extraction of plant proteins which is incubated with a CN-bait, followed by a series of increasingly stringent elutions that eliminates proteins in a sequential manner according to their affinity to the bait. The eluted and bait-bound proteins are separated by one-dimensional gel electrophoresis, excised, and digested with trypsin after which the resultant peptides are identified by mass spectrometry - techniques that are commonplace in proteomics experiments. The discovery of plant CNBPs promises to provide valuable insight into the mechanism of CN signal transduction in plants. © Springer Science+Business Media New York 2013.

An affinity pull-down approach to identify the plant cyclic nucleotide interactome

KAUST Repository

Donaldson, Lara Elizabeth

2013-09-03

Cyclic nucleotides (CNs) are intracellular second messengers that play an important role in mediating physiological responses to environmental and developmental signals, in species ranging from bacteria to humans. In response to these signals, CNs are synthesized by nucleotidyl cyclases and then act by binding to and altering the activity of downstream target proteins known as cyclic nucleotide-binding proteins (CNBPs). A number of CNBPs have been identified across kingdoms including transcription factors, protein kinases, phosphodiesterases, and channels, all of which harbor conserved CN-binding domains. In plants however, few CNBPs have been identified as homology searches fail to return plant sequences with significant matches to known CNBPs. Recently, affinity pull-down techniques have been successfully used to identify CNBPs in animals and have provided new insights into CN signaling. The application of these techniques to plants has not yet been extensively explored and offers an alternative approach toward the unbiased discovery of novel CNBP candidates in plants. Here, an affinity pull-down technique for the identification of the plant CN interactome is presented. In summary, the method involves an extraction of plant proteins which is incubated with a CN-bait, followed by a series of increasingly stringent elutions that eliminates proteins in a sequential manner according to their affinity to the bait. The eluted and bait-bound proteins are separated by one-dimensional gel electrophoresis, excised, and digested with trypsin after which the resultant peptides are identified by mass spectrometry - techniques that are commonplace in proteomics experiments. The discovery of plant CNBPs promises to provide valuable insight into the mechanism of CN signal transduction in plants. © Springer Science+Business Media New York 2013.

DUF581 is plant specific FCS-like zinc finger involved in protein-protein interaction.

Directory of Open Access Journals (Sweden)

Muhammed Jamsheer K

Full Text Available Zinc fingers are a ubiquitous class of protein domain with considerable variation in structure and function. Zf-FCS is a highly diverged group of C2-C2 zinc finger which is present in animals, prokaryotes and viruses, but not in plants. In this study we identified that a plant specific domain of unknown function, DUF581 is a zf-FCS type zinc finger. Based on HMM-HMM comparison and signature motif similarity we named this domain as FCS-Like Zinc finger (FLZ domain. A genome wide survey identified that FLZ domain containing genes are bryophytic in origin and this gene family is expanded in spermatophytes. Expression analysis of selected FLZ gene family members of A. thaliana identified an overlapping expression pattern suggesting a possible redundancy in their function. Unlike the zf-FCS domain, the FLZ domain found to be highly conserved in sequence and structure. Using a combination of bioinformatic and protein-protein interaction tools, we identified that FLZ domain is involved in protein-protein interaction.

Trans-specific gene silencing of acetyl-CoA carboxylase in a root-parasitic plant.

Science.gov (United States)

Bandaranayake, Pradeepa C G; Yoder, John I

2013-05-01

Parasitic species of the family Orobanchaceae are devastating agricultural pests in many parts of the world. The control of weedy Orobanchaceae spp. is challenging, particularly due to the highly coordinated life cycles of the parasite and host plants. Although host genetic resistance often provides the foundation of plant pathogen management, few genes that confer resistance to root parasites have been identified and incorporated into crop species. Members of the family Orobanchaceae acquire water, nutrients, macromolecules, and oligonucleotides from host plants through haustoria that connect parasite and host plant roots. We are evaluating a resistance strategy based on using interfering RNA (RNAi) that is made in the host but inhibitory in the parasite as a parasite-derived oligonucleotide toxin. Sequences from the cytosolic acetyl-CoA carboxylase (ACCase) gene from Triphysaria versicolor were cloned in hairpin conformation and introduced into Medicago truncatula roots by Agrobacterium rhizogenes transformation. Transgenic roots were recovered for four of five ACCase constructions and infected with T. versicolor against parasitic weeds. In all cases, Triphysaria root viability was reduced up to 80% when parasitizing a host root bearing the hairpin ACCase. Triphysaria root growth was recovered by exogenous application of malonate. Reverse-transcriptase polymerase chain reaction (RT-PCR) showed that ACCase transcript levels were dramatically decreased in Triphysaria spp. parasitizing transgenic Medicago roots. Northern blot analysis identified a 21-nucleotide, ACCase-specific RNA in transgenic M. truncatula and in T. versicolor attached to them. One hairpin ACCase construction was lethal to Medicago spp. unless grown in media supplemented with malonate. Quantitative RT-PCR showed that the Medicago ACCase was inhibited by the Triphysaria ACCase RNAi. This work shows that ACCase is an effective target for inactivation in parasitic plants by trans-specific gene

Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton.

Science.gov (United States)

Su, Junji; Li, Libei; Zhang, Chi; Wang, Caixiang; Gu, Lijiao; Wang, Hantao; Wei, Hengling; Liu, Qibao; Huang, Long; Yu, Shuxun

2018-06-01

Thirty significant associations between 22 SNPs and five plant architecture component traits in Chinese upland cotton were identified via GWAS. Four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits. A candidate gene, Gh_D03G0922, might be responsible for plant height in upland cotton. A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting. To determine the genetic basis of cotton plant architecture, a genome-wide association study (GWAS) was performed using a panel composed of 355 accessions and 93,250 single nucleotide polymorphisms (SNPs) identified using the specific-locus amplified fragment sequencing method. Thirty significant associations between 22 SNPs and five plant architecture component traits were identified via GWAS. Most importantly, four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits, and these SNPs were harbored in one linkage disequilibrium block. Furthermore, 21 candidate genes for plant architecture were predicted in a 0.95-Mb region including the four peak SNPs. One of these genes (Gh_D03G0922) was near the significant SNP D03_31584163 (8.40 kb), and its Arabidopsis homologs contain MADS-box domains that might be involved in plant growth and development. qRT-PCR showed that the expression of Gh_D03G0922 was upregulated in the apical buds and young leaves of the short and compact cotton varieties, and virus-induced gene silencing (VIGS) proved that the silenced plants exhibited increased PH. These results indicate that Gh_D03G0922 is likely the candidate gene for PH in cotton. The genetic variations and candidate genes identified in this study lay a foundation

Plant specific severe accident management - the implementation phase

International Nuclear Information System (INIS)

Prior, R.

1999-01-01

Many plants are in the process of developing on-site guidance for technical staff to respond to a severe accident situation severe accident management guidance (SAMG). Once the guidance is developed, the SAMG must be implemented at the plant site, and this involves addressing a number of additional aspects. In this paper, approaches to this implementation phase are reviewed, including review and verification of plant specific SAMG, organizational aspects and integration with the emergency plan, training of SAMG users, validation and self-assessment and SAMG maintenance. Examples draw on experience from assisting numerous plants to implement symptom based severe accident management guidelines based on the Westinghouse Owners Group approach, in Westinghouse, non-Westinghouse and VVER plant types. It is hoped that it will be of use to those plant operators about to perform these activities.(author)

Modification-specific proteomics in plant biology

DEFF Research Database (Denmark)

Ytterberg, A Jimmy; Jensen, Ole N

2010-01-01

and proteomics. In general, methods for PTM characterization are developed to study yeast and mammalian biology and later adopted to investigate plants. Our point of view is that it is advantageous to enrich for PTMs on the peptide level as part of a quantitative proteomics strategy to not only identify the PTM...

SNF1-related protein kinases 2 are negatively regulated by a plant-specific calcium sensor.

Science.gov (United States)

Bucholc, Maria; Ciesielski, Arkadiusz; Goch, Grażyna; Anielska-Mazur, Anna; Kulik, Anna; Krzywińska, Ewa; Dobrowolska, Grażyna

2011-02-04

SNF1-related protein kinases 2 (SnRK2s) are plant-specific enzymes involved in environmental stress signaling and abscisic acid-regulated plant development. Here, we report that SnRK2s interact with and are regulated by a plant-specific calcium-binding protein. We screened a Nicotiana plumbaginifolia Matchmaker cDNA library for proteins interacting with Nicotiana tabacum osmotic stress-activated protein kinase (NtOSAK), a member of the SnRK2 family. A putative EF-hand calcium-binding protein was identified as a molecular partner of NtOSAK. To determine whether the identified protein interacts only with NtOSAK or with other SnRK2s as well, we studied the interaction of an Arabidopsis thaliana orthologue of the calcium-binding protein with selected Arabidopsis SnRK2s using a two-hybrid system. All kinases studied interacted with the protein. The interactions were confirmed by bimolecular fluorescence complementation assay, indicating that the binding occurs in planta, exclusively in the cytoplasm. Calcium binding properties of the protein were analyzed by fluorescence spectroscopy using Tb(3+) as a spectroscopic probe. The calcium binding constant, determined by the protein fluorescence titration, was 2.5 ± 0.9 × 10(5) M(-1). The CD spectrum indicated that the secondary structure of the protein changes significantly in the presence of calcium, suggesting its possible function as a calcium sensor in plant cells. In vitro studies revealed that the activity of SnRK2 kinases analyzed is inhibited in a calcium-dependent manner by the identified calcium sensor, which we named SCS (SnRK2-interacting calcium sensor). Our results suggest that SCS is involved in response to abscisic acid during seed germination most probably by negative regulation of SnRK2s activity.

Chemical and radiochemical specifications - PWR power plants

International Nuclear Information System (INIS)

Stutzmann, A.

1997-01-01

Published by EDF this document gives the chemical specifications of the PWR (Pressurized Water Reactor) nuclear power plants. Among the chemical parameters, some have to be respected for the safety. These parameters are listed in the STE (Technical Specifications of Exploitation). The values to respect, the analysis frequencies and the time states of possible drops are noticed in this document with the motion STE under the concerned parameter. (A.L.B.)

A powerful tool for plant specific simulations

International Nuclear Information System (INIS)

Boucau, J.; Ofstun, R.

1988-01-01

Following the Three Mile Island (TMI) accident, special emphasis has been placed by the Utilities and Safety Authorities on the training of plant operators and engineers to make them more familiar with the dynamic behavior of the plant in post-accident conditions. With a view to providing transient response under realistic operating conditions, concerns were raised over: the use of conservative safety analysis models for analyzing operational and accident transients; the ability to dynamically simulate the expected operator actions, and the need to simulate the plant during long term cooling recovery. To meet these requirements, an interactive, user friendly, cost efficient dynamic model capable of simulating two-phase conditions is needed. In response to these post-TMI concerns, Westinghouse has developed, the Transient Real-Time Engineering Analysis Tool (TREAT) which is a general purpose interactive thermal-hydraulic network code for thermal-hydraulic transient analysis. The applications of TREAT are numerous and range from engineering studies to plant operator training using the newly developed TREAT SIMULATOR. The purpose of this paper is to describe the TREAT program and potential applications. Special emphasis will be drawn at a plant specific training application performed for a French 4-loop plant

Identifying Beneficial Qualities of Trichoderma parareesei for Plants

Science.gov (United States)

Rubio, M. Belén; Quijada, Narciso M.; Pérez, Esclaudys; Domínguez, Sara; Hermosa, Rosa

2014-01-01

Trichoderma parareesei and Trichoderma reesei (teleomorph Hypocrea jecorina) produce cellulases and xylanases of industrial interest. Here, the anamorphic strain T6 (formerly T. reesei) has been identified as T. parareesei, showing biocontrol potential against fungal and oomycete phytopathogens and enhanced hyphal growth in the presence of tomato exudates or plant cell wall polymers in in vitro assays. A Trichoderma microarray was used to examine the transcriptomic changes in T6 at 20 h of interaction with tomato plants. Out of a total 34,138 Trichoderma probe sets deposited on the microarray, 250 showed a significant change of at least 2-fold in expression in the presence of tomato plants, with most of them being downregulated. T. parareesei T6 exerted beneficial effects on tomato plants in terms of seedling lateral root development, and in adult plants it improved defense against Botrytis cinerea and growth promotion under salt stress. Time course expression patterns (0 to 6 days) observed for defense-related genes suggest that T6 was able to prime defense responses in the tomato plants against biotic and abiotic stresses. Such responses undulated, with a maximum upregulation of the jasmonic acid (JA)/ethylene (ET)-related LOX1 and EIN2 genes and the salt tolerance SOS1 gene at 24 h and that of the salicylic acid (SA)-related PR-1 gene at 48 h after T6 inoculation. Our study demonstrates that the T. parareesei T6-tomato interaction is beneficial to both partners. PMID:24413597

Pinellas Plant FY1990 site specific implementation plan

International Nuclear Information System (INIS)

Klein, R.D.

1990-02-01

This Site Specific Implementation Plan describes the Corrective Action, Environmental Restoration, and Waste Management activities to be performed at the Pinellas Plant in FY1990 (October 1, 1989 to September 30, 1989). These FY1990 activities are described in the Pinellas Plant FY1991--95 Five-Year Plan. The information used to prepare this plan reflects the best estimate of the project scope, schedules, regulatory, and funding requirements at the time of plan preparation. The Environmental Restoration/Waste Management Five-Year Plan is a dynamic document and will be modified each year; the Site Specific Implementation Plan will, in turn, be modified each year to reflect new findings, information, and knowledge of the various projects. 4 figs., 11 tabs

Specificity of DNA import into isolated mitochondria from plants and mammals

Directory of Open Access Journals (Sweden)

Koulintchenko M. V.

2014-01-01

Full Text Available Aim. Investigation of different features of DNA import into plant and human mitochondria, for a better understanding of mitochondrial genetics and generation of biotechnological tools. Methods. DNA up-take experiments with isolated plant mitochondria, using as substrates various sequences associated or not with the specific terminal inverted repeats (TIRs present at each end of the plant mitochondrial linear plasmids. Results. It was established that the DNA import efficiency has a non-linear dependence on DNA size. It was shown that import into plant mitochondria of DNA molecules of «medium» sizes, i. e. between 4 and 7 kb, barely has any sequence specificity: neither TIRs from the 11.6 kb Brassica plasmid, nor TIRs from the Zea mays S-plasmids influenced DNA import into Solanum tuberosum mitochondria. Conclusions. The data obtained support the hypothesis about species-specific import mechanism operating under the mitochondrial linear plasmids transfer into plant mitochondria.

Safety of Nuclear Power Plants: Design. Specific Safety Requirements

International Nuclear Information System (INIS)

2012-01-01

On the basis of the principles included in the Fundamental Safety Principles, IAEA Safety Standards Series No. SF-1, this Safety Requirements publication establishes requirements applicable to the design of nuclear power plants. It covers the design phase and provides input for the safe operation of the power plant. It elaborates on the safety objective, safety principles and concepts that provide the basis for deriving the safety requirements that must be met for the design of a nuclear power plant. Contents: 1. Introduction; 2. Applying the safety principles and concepts; 3. Management of safety in design; 4. Principal technical requirements; 5. General plant design; 6. Design of specific plant systems.

"Chitin-specific" peroxidases in plants.

Science.gov (United States)

Maksimov, I V; Cherepanova, E A; Khairullin, R M

2003-01-01

The activity of various plant peroxidases and the ability of their individual isoforms to bind chitin was studied. Some increase in peroxidase activity was observed in crude extracts in the presence of chitin. Activated peroxidases of some species fell in the fraction not sorbed on chitin and those of other species can bind chitin. Only anionic isoperoxidases from oat (Avena sativa), rice (Oryza sativa), horseradish (Armoracia rusticana), garden radish (Raphanus sativus var. radicula), peanut (Arachis hypogaea), and tobacco (Nicotiana tabacum Link et Otto) were sorbed on chitin. Both anionic and cationic isoforms from pea (Pisum sativum), galega(Galega orientalis), cucumber (Cucumis sativus), and zucchini (Cucurbita pepo L.) were sorbed on chitin. Peroxidase activation under the influence of chitin was correlated to the processes that occur during hypersensitive reaction and lignification of sites, in which pathogenic fungus penetrates into a plant. The role of chitin-specific isoperoxidases in inhibition of fungal growth and connection of this phenomenon with structural characteristics of isoperoxidases are also discussed.

Comparison and lessons learned from plant specific PSA of German NPP

International Nuclear Information System (INIS)

Balfanz, Hans-Peter; Berg, H.P.

2000-01-01

PSA are launched in frame of Periodic Safety Reviews (PSR) in Germany. The aims are to identify overall safety level and relative weak points. Some backfitting measures have been realized for older plants to remove relative weak points and to bring these plants to the state of the art. In this field PSA is well accepted today and is seen as a valuable tool supplementing the deterministic analysis. Main application of PSA within PSR is planned to become mandatory as part of the revision of the German Atomic Energy Act. According to the German PSA Guideline plant specific PSA level 1+ were performed for all 19 In comparison with international practice German PSA are very detailed. Otherwise they do not handle all external events, non-power states and accident management measures as discussed before. The New PSA guideline will cover these aspects and therefore analysts have to take them into account in further PSA. Moreover gathering of plant specific data is needed. The development in this field is driven by the utilities (for instance in frame of their so-called ZEDB project). Public discussion about quantitative risk of industrial hazards is quite limited in Germany and PSA results have only few impacts to this respect. Independent from this PSA for NPP is understood as a diverse tool in supporting the deterministic licensing and supervision process. Risk based decision making as well as informed regulation are just only of the beginning. State of PSA of NPP in Germany, comparison of PSA result of different NPP, German PSA guideline and state of discussion of further development and recommendation of further development of PSA of NPP are discussed in this paper in more detail. (S.Y.)

Comparison and lessons learned from plant specific PSA of German NPP

Energy Technology Data Exchange (ETDEWEB)

Balfanz, Hans-Peter [TUEV Nord, Hamburg (Germany); Berg, H.P.

2000-07-01

PSA are launched in frame of Periodic Safety Reviews (PSR) in Germany. The aims are to identify overall safety level and relative weak points. Some backfitting measures have been realized for older plants to remove relative weak points and to bring these plants to the state of the art. In this field PSA is well accepted today and is seen as a valuable tool supplementing the deterministic analysis. Main application of PSA within PSR is planned to become mandatory as part of the revision of the German Atomic Energy Act. According to the German PSA Guideline plant specific PSA level 1+ were performed for all 19 In comparison with international practice German PSA are very detailed. Otherwise they do not handle all external events, non-power states and accident management measures as discussed before. The New PSA guideline will cover these aspects and therefore analysts have to take them into account in further PSA. Moreover gathering of plant specific data is needed. The development in this field is driven by the utilities (for instance in frame of their so-called ZEDB project). Public discussion about quantitative risk of industrial hazards is quite limited in Germany and PSA results have only few impacts to this respect. Independent from this PSA for NPP is understood as a diverse tool in supporting the deterministic licensing and supervision process. Risk based decision making as well as informed regulation are just only of the beginning. State of PSA of NPP in Germany, comparison of PSA result of different NPP, German PSA guideline and state of discussion of further development and recommendation of further development of PSA of NPP are discussed in this paper in more detail. (S.Y.)

PSA-based optimization of technical specifications for the Borssele nuclear power plant

International Nuclear Information System (INIS)

Seebregts, A.J.; Schoonakker, H.A.

1996-01-01

The Borssele Nuclear Power Plant (NPP) is a Siemens/KWU 472 MWe Pressurized Water Reactor which has been in operation since 1973. In 1989, a Probabilistic Safety Assessment (PSA) program was initiated to complement deterministic safety studies and operational experience in forming a plant safety concept. In 1993, the PSA-MER model was completed and used to determine the effects a package of proposed modifications would have on plant safety and risks to the environment. This model was used to start retrospective risks profile and allowed outage times (AOTs) analyses, which both concerned the calculation of the change in total core damage frequency (TCDF) given a change in configuration. The main problems identified and reported in this paper are: (i) How to calculate the change in TCDF (ΔTCDF)? (section 3); and (ii) How to set practical decision criteria and how to use the PSA as extension to Technical Specifications (TS) AOTs? (section 4). Finally, a pilot study was conducted in order to optimize surveillance test intervals (STIs) which are also part of the TS (section 5). (orig.)

Adapting a reactor safety assessment system for specific plants

International Nuclear Information System (INIS)

Ballard, T.L.; Cordes, G.A.

1991-01-01

The Reactor Safety Assessment System (RSAS) is an expert system being developed by the Idaho National Engineering Laboratory, the University of Maryland (UofM) and US Nuclear Regulatory Commission (NRC) for use in the NRC Operations center. RSAS is designed to help the Reactor Safety Team monitor and project core status during an emergency at a licensed nuclear power plant. Analysis uses a hierarchical plant model based on equipment availability and automatically input parametric plant information. There are 3 families of designs of pressurized water reactors and 75 plants using modified versions of the basic design. In order to make an RSAS model for each power plant, a generic model for a given plant type is used with differences being specified by plant specific files. Graphical displays of this knowledge are flexible enough to handle any plant configuration. A variety of tools have been implemented to make it easy to modify a design to fit a given plant while minimizing chance for error. 3 refs., 4 figs

Identifying plant traits: a key aspect for suitable species selection in ecological restoration of semiarid slopes

Science.gov (United States)

Bochet, Esther; García-Fayos, Patricio

2017-04-01

In the context of ecological restoration, one of the greatest challenges for practitioners and scientists is to select suitable species for revegetation purposes. In semiarid environments where restoration projects often fail, little attention has been paid so far to the contribution of plant traits to species success. The objective of this study was to (1) identify plant traits associated with species success on four roadside situations along an erosion-productivity gradient, and (2) to provide an ecological framework for selecting suitable species on the basis of their morphological and functional traits, applied to semiarid environments. We analyzed the association of 10 different plant traits with species success of 296 species surveyed on the four roadside situations in a semiarid region (Valencia, Spain). Plant traits included general plant traits (longevity, woodiness) and more specific root-, seed- and leaf-related traits (root type, sprouting ability, seed mucilage, seed mass, seed susceptibility to removal, specific leaf area and leaf dry matter content). All of them were selected according to the prevailing limiting ecogeomorphological processes acting along the erosion-productivity gradient. We observed strong shifts along the erosion-productivity gradient in the traits associated to species success. At the harshest end of the gradient, the most intensely eroded and driest one, species success was mainly associated to seed resistance to removal by runoff and to resistance to drought. At the opposite end of the gradient, the most productive one, species success was associated to a competitive-ruderal plant strategy (herbaceous successful species with high specific leaf area and low leaf dry matter content). Our study provides an ecologically-based approach for selecting suitable native species on the basis or their morphological and functional traits and supports a differential trait-based selection of species as regards roadslope type and aspect. In

Technical specifications review of nuclear power plants: a risk-informed evaluation

International Nuclear Information System (INIS)

Saldanha, Pedro Luiz da Cruz; Sousa, Anna Leticia; Frutuoso e Melo, Paulo Fernando Ferreira; Duarte, Juliana Pacheco

2012-01-01

The use of risk information by a regulatory body as part of an integrated decision making process addresses the way in which risk information is being used as part of an integrated process in making decisions about safety issues at nuclear plants – commonly referred to as risk-informed decision making. The risk-informed approach aims to integrate in a systematic manner quantitative and qualitative, deterministic and probabilistic safety considerations to obtain a balanced decision. Probabilistic Safety Assessment (PSA) is a methodology that can be applied to provide a structured analysis process to evaluate the frequency and consequences of accidents scenarios in nuclear power plants. Technical Specifications (TS) are specifications regarding the characteristics of nuclear power plants (variables, systems or components) of overriding importance to nuclear safety and radiation protection, which is an integral part of plant operation authorization. Limiting Conditions of Operation (LCO) are the minimum levels of performance or capacity or operating system components required for the safe operation of nuclear plants, as defined in technical specifications. The Maintenance Rule (MR) is a requirement established by the U. S. Nuclear Regulatory Commission (NRC) to check the effectiveness of maintenance carried out in nuclear plants, and plant configuration control. The control of plant configuration is necessary to verify the impact of the maintenance of a safety device out of service on plant safety. The Electric Power Research Institute (EPRI) has assessed the role of probabilistic safety analysis in the regulation of nuclear power plants with the following objectives: a) to provide utilities with an approach for developing and implementing nuclear power station risk-managed technical specification programs; and b) to complement and supplement existing successful configuration risk management applications such as MR. This paper focuses on the evaluation of EPRI

The impact of technical specification surveillance requirements and allowable outage times on plant availability

International Nuclear Information System (INIS)

Webster, S.A.; Finnicum, D.J.

1985-01-01

Surveillances required to be conducted by a plant's Technical Specifications have resulted in plant shutdowns and lost availability. This paper looks at shutdowns which have occurred due to required surveillance testing and insufficient repair time allowed by Technical Specifications. A loss of plant availability of almost 3% per plant year was found for U.S. pressurized water reactors during the five year period, 1979 to 1984. This figure excludes major problems which required plant shutdown whether or not mandated by the Technical Specifications. In addition to their affect on availability, such shutdowns can add to the challenges to plant safety systems and can affect plant aging by increasing the thermal cycles on plant components

Chemical and radiochemical specifications - PWR power plants; Specifications chimiques et radiochimiques - Centrales REP

Energy Technology Data Exchange (ETDEWEB)

Stutzmann, A [Electricite de France (EDF), 93 - Saint-Denis (France)

1997-07-01

Published by EDF this document gives the chemical specifications of the PWR (Pressurized Water Reactor) nuclear power plants. Among the chemical parameters, some have to be respected for the safety. These parameters are listed in the STE (Technical Specifications of Exploitation). The values to respect, the analysis frequencies and the time states of possible drops are noticed in this document with the motion STE under the concerned parameter. (A.L.B.)

Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities

DEFF Research Database (Denmark)

Radic-Sarikas, Branka; Tsafou, Kalliopi P; Emdal, Kristina B.

2017-01-01

Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any...... associated adverse side effects through reduced dosing, which is particularly important in childhood tumors. Using a parallel phenotypic combinatorial screening approach of cells derived from three pediatric tumor types, we identified Ewing sarcoma-specific interactions of a diverse set of targeted agents...... including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong...

Radiological Effluent Technical Specifications (RETS) implementation, Kewaunee Nuclear Power Plant

International Nuclear Information System (INIS)

Serrano, W.; Akers, D.W.

1985-06-01

A review of the Radiological Effluent Technical Specifications (RETS) for the Kewaunee Nuclear Power Plant was performed. The principal review guidelines used were NUREG-0133, ''Preparation of Radiological Effluent Technical Specifications for Nuclear Power Plants,'' and Draft 7'' of NUREG-0472, Revision 3, ''Radiological Effluent Technical Specifications for Pressurized Water Reactors.'' Draft submittals were discussed with the Licensee by the NRC staff until all items requiring changes to the Technical Specifications were resolved. The Licensee then submitted final proposed RETS to the NRC which were evaluated and found to be in compliance with the NRC review guidelines. The proposed Offsite Dose Calculation Manual and the Radiological Environmental Monitoring Manual were reviewed and generally found to be in compliance with the NRC review guidelines

Flooding PSA with Plant Specific Operating Experiences of Korean PWRs

International Nuclear Information System (INIS)

Choi, Sun Yeong; Yang, Joon Yull

2006-01-01

The purpose of this paper is to update the flooding PSA with Korean plant specific operating experience data and the appropriate estimation method for the flooding frequency to improve the PSA quality. The existing flooding PSA used the NPE (Nuclear Power Experience) database up to 1985 for the flooding frequency. They are all USA plant operating experiences. So an upgraded flooding frequency with Korean specific plant operation experience is required. We also propose a method of only using the PWR (Pressurized Water Reactor) data for the flooding frequency estimation in the case of the flooding area in the primary building even though the existing flooding PSA used both PWR and BWR (Boiled Water Reactor) data for all kinds of plant areas. We evaluate the CDF (Core Damage Frequency) with the modified flooding frequency and compare the results with that of the existing flooding PSA method

Application of Chemical Genomics to Plant-Bacteria Communication: A High-Throughput System to Identify Novel Molecules Modulating the Induction of Bacterial Virulence Genes by Plant Signals.

Science.gov (United States)

Vandelle, Elodie; Puttilli, Maria Rita; Chini, Andrea; Devescovi, Giulia; Venturi, Vittorio; Polverari, Annalisa

2017-01-01

The life cycle of bacterial phytopathogens consists of a benign epiphytic phase, during which the bacteria grow in the soil or on the plant surface, and a virulent endophytic phase involving the penetration of host defenses and the colonization of plant tissues. Innovative strategies are urgently required to integrate copper treatments that control the epiphytic phase with complementary tools that control the virulent endophytic phase, thus reducing the quantity of chemicals applied to economically and ecologically acceptable levels. Such strategies include targeted treatments that weaken bacterial pathogens, particularly those inhibiting early infection steps rather than tackling established infections. This chapter describes a reporter gene-based chemical genomic high-throughput screen for the induction of bacterial virulence by plant molecules. Specifically, we describe a chemical genomic screening method to identify agonist and antagonist molecules for the induction of targeted bacterial virulence genes by plant extracts, focusing on the experimental controls required to avoid false positives and thus ensuring the results are reliable and reproducible.

Using a periclinal chimera to unravel layer-specific gene expression in plants.

Science.gov (United States)

Filippis, Ioannis; Lopez-Cobollo, Rosa; Abbott, James; Butcher, Sarah; Bishop, Gerard J

2013-09-01

Plant organs are made from multiple cell types, and defining the expression level of a gene in any one cell or group of cells from a complex mixture is difficult. Dicotyledonous plants normally have three distinct layers of cells, L1, L2 and L3. Layer L1 is the single layer of cells making up the epidermis, layer L2 the single cell sub-epidermal layer and layer L3 constitutes the rest of the internal cells. Here we show how it is possible to harvest an organ and characterise the level of layer-specific expression by using a periclinal chimera that has its L1 layer from Solanum pennellii and its L2 and L3 layers from Solanum lycopersicum. This is possible by measuring the level of the frequency of species-specific transcripts. RNA-seq analysis enabled the genome-wide assessment of whether a gene is expressed in the L1 or L2/L3 layers. From 13 277 genes that are expressed in both the chimera and the parental lines and with at least one polymorphism between the parental alleles, we identified 382 genes that are preferentially expressed in L1 in contrast to 1159 genes in L2/L3. Gene ontology analysis shows that many genes preferentially expressed in L1 are involved in cutin and wax biosynthesis, whereas numerous genes that are preferentially expressed in L2/L3 tissue are associated with chloroplastic processes. These data indicate the use of such chimeras and provide detailed information on the level of layer-specific expression of genes. © 2013 East Malling Research The Plant Journal © 2013 John Wiley & Sons Ltd.

HPLC-UV Analysis Coupled with Chemometry to Identify Phenolic Biomarkers from Medicinal Plants, used as Ingredients in Two Food Supplement Formulas

Directory of Open Access Journals (Sweden)

Raluca Maria Pop

2013-11-01

Full Text Available . High performance liquid chromatography (HPLC with UV detection is nowadays the reference method to identify and quantify the biomarkers of quality and authenticity of plants and food supplements. Seven medicinal plants were collected from wild flora: Taraxacum officinalis (1, Cynara scolimus (2, Silybum marianum (3, Hypericum perforatum (4,  Chelidonium majus (5, Lycopodium clavatum (6 and  Hippophae rhamnoides (7  leaves and fruits.  Two products (A and B were obtained by mixing individual plant powders. Therefore product A was obtained by mixing dandelion, artichoke and milk thistle, 1:1:1 while product B by mixing St John’s wort, Celandine and Wolf’s claw, 1:1:1. The methanolic extracts of individual plants as well as three different extracts of products A and B (using acidulated water, neutral water and acidulated methanol were analyzed using HPLC-UV for their phenolics’ fingerprint and composition. The qualitative (untargeted analysis and quantitative (targeted analysis results were further compared using Principal Component Analysis (PCA in order to identify their specific biomarkers. Thus, quantitative evaluation of individual phenolics in case of individual plants and products A and B extracts, showed specific and significant differences of composition. Both products A and B contained elagic acid as major compound. For product A, good biomarkers were trans-cinnamic, chlorogenic, caffeic and p-coumaric acids, as well silymarin and silibine originating from milk thistle. For product B, good biomarkers were quercetin and kaempherol, gallic and protocatecuic acids, this product being rich in flavonoids. In conclusion, HPLC-UV coupled with PCA analysis proved to be a rapid and useful way to identify the main biomarkers of plants’ authentication, as well of final products’ quality and safety.

PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups

Directory of Open Access Journals (Sweden)

Huang Hsien-Da

2008-11-01

Full Text Available Abstract Background The elucidation of transcriptional regulation in plant genes is important area of research for plant scientists, following the mapping of various plant genomes, such as A. thaliana, O. sativa and Z. mays. A variety of bioinformatic servers or databases of plant promoters have been established, although most have been focused only on annotating transcription factor binding sites in a single gene and have neglected some important regulatory elements (tandem repeats and CpG/CpNpG islands in promoter regions. Additionally, the combinatorial interaction of transcription factors (TFs is important in regulating the gene group that is associated with the same expression pattern. Therefore, a tool for detecting the co-regulation of transcription factors in a group of gene promoters is required. Results This study develops a database-assisted system, PlantPAN (Plant Promoter Analysis Navigator, for recognizing combinatorial cis-regulatory elements with a distance constraint in sets of plant genes. The system collects the plant transcription factor binding profiles from PLACE, TRANSFAC (public release 7.0, AGRIS, and JASPER databases and allows users to input a group of gene IDs or promoter sequences, enabling the co-occurrence of combinatorial transcription factor binding sites (TFBSs within a defined distance (20 bp to 200 bp to be identified. Furthermore, the new resource enables other regulatory features in a plant promoter, such as CpG/CpNpG islands and tandem repeats, to be displayed. The regulatory elements in the conserved regions of the promoters across homologous genes are detected and presented. Conclusion In addition to providing a user-friendly input/output interface, PlantPAN has numerous advantages in the analysis of a plant promoter. Several case studies have established the effectiveness of PlantPAN. This novel analytical resource is now freely available at http://PlantPAN.mbc.nctu.edu.tw.

Use of model plant hosts to identify Pseudomonas aeruginosa virulence factors

Science.gov (United States)

Rahme, Laurence G.; Tan, Man-Wah; Le, Long; Wong, Sandy M.; Tompkins, Ronald G.; Calderwood, Stephen B.; Ausubel, Frederick M.

1997-01-01

We used plants as an in vivo pathogenesis model for the identification of virulence factors of the human opportunistic pathogen Pseudomonas aeruginosa. Nine of nine TnphoA mutant derivatives of P. aeruginosa strain UCBPP-PA14 that were identified in a plant leaf assay for less pathogenic mutants also exhibited significantly reduced pathogenicity in a burned mouse pathogenicity model, suggesting that P. aeruginosa utilizes common strategies to infect both hosts. Seven of these nine mutants contain TnphoA insertions in previously unknown genes. These results demonstrate that an alternative nonvertebrate host of a human bacterial pathogen can be used in an in vivo high throughput screen to identify novel bacterial virulence factors involved in mammalian pathogenesis. PMID:9371831

Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species.

Science.gov (United States)

Chen, Shilin; Yao, Hui; Han, Jianping; Liu, Chang; Song, Jingyuan; Shi, Linchun; Zhu, Yingjie; Ma, Xinye; Gao, Ting; Pang, Xiaohui; Luo, Kun; Li, Ying; Li, Xiwen; Jia, Xiaocheng; Lin, Yulin; Leon, Christine

2010-01-07

The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL+matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over. Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level. The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.

Standard technical specifications General Electric plants, BWR/6. Volume 1, Revision 1

International Nuclear Information System (INIS)

1995-04-01

This report documents the results of the combined effort of the NRC and the industry to produce improved Standard Technical Specifications (STS), Revision 1 for General Electric BWR/6 Plants. The changes reflected in Revision 1 resulted from the experience gained from license amendment applications to convert to these improved STS or to adopt partial improvements to existing technical specifications. This NUREG is the result of extensive public technical meetings and discussions between the Nuclear Regulatory Commission (NRC) staff and various nuclear power plant licensees, Nuclear Steam Supply System (NSSS) Owners Groups, NSSS vendors, and the Nuclear Energy Institute (NEI). The improved STS were developed based on the criteria in the Final Commission Policy Statement on Technical Specifications Improvements for Nuclear Power Reactors, dated July 22, 1993. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes. Volume 1 contains the Specifications for all chapters and sections of the improved STS. Volume 2 contains the Bases for Chapters 2.0 and 3.0, and Sections 3.1--3.3 of the improved STS. Volume 3 contains the Bases for Sections 3.4--3.10 of the improved STS

Evaluation of Risk Metrics for KHNP Reference Plants Using the Latest Plant Specific Data

International Nuclear Information System (INIS)

Jeon, Ho Jun; Hwang, Seok Won; Ghi, Moon Goo

2010-01-01

As Risk-Informed Applications (RIAs) are actively implemented in the nuclear industry, an issue associated with the technical adequacy of the Probabilistic Safety Assessment (PSA) arises in its data sources. The American Society of Mechanical Engineers (ASME) PRA standard suggests the use of component failure data that represent the as-built and as-operated plant conditions. Furthermore, the peer reviews for the KHNP reference plants stated that the component failure data should be updated to reflect the latest plant specific data available. For ensuring the technical adequacy in PSA data elements, we try to update component failure data to reflect the as-operated plant conditions, and a trend analysis of the failure data is implemented. In addition, by applying the updated failure data to the PSA models of the KHNP reference plants, the risk metrics of Core Damage Frequency (CDF) and Large Early Release Frequency (LERF) are evaluated

Harnessing Biomedical Natural Language Processing Tools to Identify Medicinal Plant Knowledge from Historical Texts.

Science.gov (United States)

Sharma, Vivekanand; Law, Wayne; Balick, Michael J; Sarkar, Indra Neil

2017-01-01

The growing amount of data describing historical medicinal uses of plants from digitization efforts provides the opportunity to develop systematic approaches for identifying potential plant-based therapies. However, the task of cataloguing plant use information from natural language text is a challenging task for ethnobotanists. To date, there have been only limited adoption of informatics approaches used for supporting the identification of ethnobotanical information associated with medicinal uses. This study explored the feasibility of using biomedical terminologies and natural language processing approaches for extracting relevant plant-associated therapeutic use information from historical biodiversity literature collection available from the Biodiversity Heritage Library. The results from this preliminary study suggest that there is potential utility of informatics methods to identify medicinal plant knowledge from digitized resources as well as highlight opportunities for improvement.

Process specifications and standards for the 1970 thorium campaign in the Purex Plant

International Nuclear Information System (INIS)

Van der Cook, R.E.; Ritter, G.L.

1970-01-01

The process specifications and standards for thorium processing operations in the Purex Plant are presented. These specifications represent currently known limits within which plant processing conditions must be maintained to meet defined product requirements safely and with minimum effect on equipment service life. These specifications cover the general areas of feed, essential materials, and chemical hazards

Improved technical specifications and related improvements to safety in commercial Nuclear power plants

International Nuclear Information System (INIS)

Hoffman, D.R.; Demitrack, T.; Schiele, R.; Jones, J.C.

2004-01-01

Many of the commercial nuclear power plants in the United States (US) have been converting a portion of the plant operating license known as the Technical Specifications (TS) in accordance with a document published by the US Nuclear Regulatory Commission (NRC). The TS prescribe commercial nuclear power plant operating requirements. There are several types of nuclear power plants in the US, based on the technology of different vendors, and there is an NRC document that supports each of the five different vendor designs. The NRC documents are known as the Improved Standard Technical Specifications (ISTS) and are contained in a separate document (NUREG series) for each one of the designs. EXCEL Services Corporation (hereinafter EXCEL) has played a major role in the development of the ISTS and in the development, licensing, and implementation of the plant specific Improved Technical Specifications (ITS) (which is based on the ISTS) for the commercial nuclear power plants in the US that have elected to make this conversion. There are currently 103 operating commercial nuclear power plants in the US and 68 of them have successfully completed the conversion to the ITS and are now operating in accordance with their plant specific ITS. The ISTS is focused mainly on safety by ensuring the commercial nuclear reactors can safely shut down and mitigate the consequences of any postulated transient and accident. It accomplishes this function by including requirements directly associated with safety in a document structured systematically and taking into account some key human factors and technical initiatives. This paper discusses the ISTS including its format, content, and detail, the history of the ISTS, the ITS development, licensing, and implementation process, the safety improvements resulting from a plant conversion to ITS, and the importance of the ITS Project to the industry. (Author)

Improved technical specifications and related improvements to safety in commercial Nuclear power plants

Energy Technology Data Exchange (ETDEWEB)

Hoffman, D.R.; Demitrack, T.; Schiele, R.; Jones, J.C. [EXCEL Services Corporation, 11921 Rockville Pike, Suite 100, Rockville, MD 20852 (United States)]. e-mail: donaldh@excelservices.com

2004-07-01

Many of the commercial nuclear power plants in the United States (US) have been converting a portion of the plant operating license known as the Technical Specifications (TS) in accordance with a document published by the US Nuclear Regulatory Commission (NRC). The TS prescribe commercial nuclear power plant operating requirements. There are several types of nuclear power plants in the US, based on the technology of different vendors, and there is an NRC document that supports each of the five different vendor designs. The NRC documents are known as the Improved Standard Technical Specifications (ISTS) and are contained in a separate document (NUREG series) for each one of the designs. EXCEL Services Corporation (hereinafter EXCEL) has played a major role in the development of the ISTS and in the development, licensing, and implementation of the plant specific Improved Technical Specifications (ITS) (which is based on the ISTS) for the commercial nuclear power plants in the US that have elected to make this conversion. There are currently 103 operating commercial nuclear power plants in the US and 68 of them have successfully completed the conversion to the ITS and are now operating in accordance with their plant specific ITS. The ISTS is focused mainly on safety by ensuring the commercial nuclear reactors can safely shut down and mitigate the consequences of any postulated transient and accident. It accomplishes this function by including requirements directly associated with safety in a document structured systematically and taking into account some key human factors and technical initiatives. This paper discusses the ISTS including its format, content, and detail, the history of the ISTS, the ITS development, licensing, and implementation process, the safety improvements resulting from a plant conversion to ITS, and the importance of the ITS Project to the industry. (Author)

Preparation of plant-specific NDA reference material

International Nuclear Information System (INIS)

Abedin-Zadeh, R.; Beetle, T.; Kuhn, E.; Terrey, D.; Turel, S.; Busca, G.; Guardini, S.

1983-01-01

The importance of having suitable and well characterized non-destructive assay (NDA) reference materials for the verification activities of the safeguards control authorities is stressed. The Euratom Inspectorate and the IAEA have initiated an extensive programme for the procurement and preparation of Joint Euratom/IAEA safeguards NDA reference materials with the active participation of the Ispra Establishment of the Euratom Joint Research Centre. The different type and nature of materials, condition of measurements, and plant characteristics and provisions had to be taken into account for plant-specific NDA reference materials. The preparation of each reference material was planned case by case and specific criteria such as limitations in different facilities, measurement capabilities, conditions, product availability and population variability are being ascertained. A procurement scheme was prepared describing step-by-step procedures detailing responsibilities, measurement conditions, destructive analysis schemes, desired characteristics and methods of data evaluation. This paper describes the principles and procedures carried out for the preparation of a reference MOX pin, low enriched uranium reference rods, low enriched uranium reference drums, reference MTR assemblies, and THTR reference pebbles. The scheme for each characterization technique is presented. (author)

A comparative genomics screen identifies a Sinorhizobium meliloti 1021 sodM-like gene strongly expressed within host plant nodules

Directory of Open Access Journals (Sweden)

Queiroux Clothilde

2012-05-01

Full Text Available Abstract Background We have used the genomic data in the Integrated Microbial Genomes system of the Department of Energy’s Joint Genome Institute to make predictions about rhizobial open reading frames that play a role in nodulation of host plants. The genomic data was screened by searching for ORFs conserved in α-proteobacterial rhizobia, but not conserved in closely-related non-nitrogen-fixing α-proteobacteria. Results Using this approach, we identified many genes known to be involved in nodulation or nitrogen fixation, as well as several new candidate genes. We knocked out selected new genes and assayed for the presence of nodulation phenotypes and/or nodule-specific expression. One of these genes, SMc00911, is strongly expressed by bacterial cells within host plant nodules, but is expressed minimally by free-living bacterial cells. A strain carrying an insertion mutation in SMc00911 is not defective in the symbiosis with host plants, but in contrast to expectations, this mutant strain is able to out-compete the S. meliloti 1021 wild type strain for nodule occupancy in co-inoculation experiments. The SMc00911 ORF is predicted to encode a “SodM-like” (superoxide dismutase-like protein containing a rhodanese sulfurtransferase domain at the N-terminus and a chromate-resistance superfamily domain at the C-terminus. Several other ORFs (SMb20360, SMc01562, SMc01266, SMc03964, and the SMc01424-22 operon identified in the screen are expressed at a moderate level by bacteria within nodules, but not by free-living bacteria. Conclusions Based on the analysis of ORFs identified in this study, we conclude that this comparative genomics approach can identify rhizobial genes involved in the nitrogen-fixing symbiosis with host plants, although none of the newly identified genes were found to be essential for this process.

Perspectives on plant vulnerabilities ampersand other plant and containment improvements

International Nuclear Information System (INIS)

LaChance, J.; Kolaczkowski, A.; Kahn, J.

1996-01-01

The primary goal of the Individual Plant Examination (IPE) Program was for licensees to identify plant-unique vulnerabilities and actions to address these vulnerabilities. A review of these vulnerabilities and plant improvements that were identified in the IPEs was performed as part of the IPE Insights Program sponsored by the U.S. Nuclear Regulatory Commission (NRC). The purpose of this effort was to characterize the identified vulnerabilities and the impact of suggested plant improvements. No specific definition for open-quotes vulnerabilityclose quotes was provided in NRC Generic Letter 88-20 or in the subsequent NRC IPE submittal guidance documented in NUREG-1335. Thus licensees were left to use their own definitions. Only 20% of the plants explicitly stated that they had vulnerabilities. However, most licensees identified other plant improvements to address issues not explicitly classified as vulnerabilities, but pertaining to areas in which overall plant safety could potentially be increased. The various definitions of open-quotes vulnerabilityclose quotes used by the licensees, explicitly identified vulnerabilities, proposed plant improvements to address these vulnerabilities, and other plant improvements are summarized and discussed

Specific recognition of fungal pathogens by plants

International Nuclear Information System (INIS)

Knogge, W.; Gierlich, A.; Max-Planck-Institute for Plant Breeding,; Van't Slot, K.A.E.; Papavoine, T.

2001-01-01

Full text: Induction of plant defence reactions and, hence, genotype-specific disease resistance results from the interaction of highly specific plant resistance (R) genes with matching pathogen avirulence (Avr) genes (gene-for-gene interactions). More than thirty R genes acting against different types of pathogens (viruses, bacteria, fungi, oomycetes, nematodes) have been isolated from various plants species. However, with few exceptions it remains to be shown how their products recognise the complementary Avr gene products. To date, Avr genes and their products have been characterised from only three fungal species. These include the NIP1 gene from Rhynchosporium secalis, the causal agent of barley leaf scald. It encodes a small, secreted protein, NIP1, that triggers defence reactions exclusively in barley cultivars expressing the R gene Rrs1. NIP1 also non-specifically stimulates the H + -ATPase activity in barley plasma membranes, suggesting that the host recognition system targets a putative fungal virulence factor. Virulent fungal strains lack the gene or carry an allele encoding a non-functional product. Four NIP1 iso-forms have been characterised; NIP1-I and NIP1-II although both elicitor-active display different levels of activity, whereas the isoforms NIP1-III and NIP1-IV are inactive. After establishing a heterologous expression system, the single amino acids specifying NIP1-III and NIP1-IV were integrated into the NIP1-I sequence and yielded the inactive mutant proteins NIP1-III* and NIP1-IV*. The elicitor-inactive isoforms were also unable to stimulate the H + -ATPase, suggesting that both functions of NIP1 are mediated by a single plant receptor. The 3D structure of NIP1-I has been elucidated by 1 H- and 15 N-NMR spectroscopy. Binding studies using 125 I-NIP1-I revealed a single class of high-affinity binding sites on membranes from both Rrs1- and rrs1-cultivars, suggesting that NIP1-binding is not sufficient for defence triggering and that an

Highly Specific Detection of Five Exotic Quarantine Plant Viruses using RT-PCR

Directory of Open Access Journals (Sweden)

Hoseong Choi

2013-03-01

Full Text Available To detect five plant viruses (Beet black scorch virus, Beet necrotic yellow vein virus, Eggplant mottled dwarf virus, Pelargonium zonate spot virus, and Rice yellow mottle virus for quarantine purposes, we designed 15 RT-PCR primer sets. Primer design was based on the nucleotide sequence of the coat protein gene, which is highly conserved within species. All but one primer set successfully amplified the targets, and gradient PCRs indicated that the optimal temperature for the 14 useful primer sets was 51.9°C. Some primer sets worked well regardless of annealing temperature while others required a very specific annealing temperature. A primer specificity test using plant total RNAs and cDNAs of other plant virus-infected samples demonstrated that the designed primer sets were highly specific and generated reproducible results. The newly developed RT-PCR primer sets would be useful for quarantine inspections aimed at preventing the entry of exotic plant viruses into Korea.

Probing Xylan-Specific Raman Bands for Label-Free Imaging Xylan in Plant Cell Wall

Energy Technology Data Exchange (ETDEWEB)

Zeng, Yining; Yarbrough, John M.; Mittal, Ashutosh; Tucker, Melvin P.; Vinzant, Todd; Himmel, Michael E.

2015-06-15

Xylan constitutes a significant portion of biomass (e.g. 22% in corn stover used in this study). Xylan is also an important source of carbohydrates, besides cellulose, for renewable and sustainable energy applications. Currently used method for the localization of xylan in biomass is to use fluorescence confocal microscope to image the fluorescent dye labeled monoclonal antibody that specifically binds to xylan. With the rapid adoption of the Raman-based label-free chemical imaging techniques in biology, identifying Raman bands that are unique to xylan would be critical for the implementation of the above label-free techniques for in situ xylan imaging. Unlike lignin and cellulose that have long be assigned fingerprint Raman bands, specific Raman bands for xylan remain unclear. The major challenge is the cellulose in plant cell wall, which has chemical units highly similar to that of xylan. Here we report using xylanase to specifically remove xylan from feedstock. Under various degree of xylan removal, with minimum impact to other major cell wall components, i.e. lignin and cellulose, we have identified Raman bands that could be further tested for chemical imaging of xylan in biomass in situ.

Repeated evolution of fungal cultivar specificity in independently evolved ant-plant-fungus symbioses.

Science.gov (United States)

Blatrix, Rumsaïs; Debaud, Sarah; Salas-Lopez, Alex; Born, Céline; Benoit, Laure; McKey, Doyle B; Attéké, Christiane; Djiéto-Lordon, Champlain

2013-01-01

Some tropical plant species possess hollow structures (domatia) occupied by ants that protect the plant and in some cases also provide it with nutrients. Most plant-ants tend patches of chaetothyrialean fungi within domatia. In a few systems it has been shown that the ants manure the fungal patches and use them as a food source, indicating agricultural practices. However, the identity of these fungi has been investigated only in a few samples. To examine the specificity and constancy of ant-plant-fungus interactions we characterised the content of fungal patches in an extensive sampling of three ant-plant symbioses (Petalomyrmex phylax/Leonardoxa africana subsp. africana, Aphomomyrmex afer/Leonardoxa africana subsp. letouzeyi and Tetraponera aethiops/Barteria fistulosa) by sequencing the Internal Transcribed Spacers of ribosomal DNA. For each system the content of fungal patches was constant over individuals and populations. Each symbiosis was associated with a specific, dominant, primary fungal taxon, and to a lesser extent, with one or two specific secondary taxa, all of the order Chaetothyriales. A single fungal patch sometimes contained both a primary and a secondary taxon. In one system, two founding queens were found with the primary fungal taxon only, one that was shown in a previous study to be consumed preferentially. Because the different ant-plant symbioses studied have evolved independently, the high specificity and constancy we observed in the composition of the fungal patches have evolved repeatedly. Specificity and constancy also characterize other cases of agriculture by insects.

Technical specifications on the welding in fuel reprocessing plants

Energy Technology Data Exchange (ETDEWEB)

Karino, Motonobu; Uryu, Mitsuru; Matsui, N.; Nakazawa, Fumio; Imanishi, Makoto; Koizumi; Kazuhiko; Sugawara, Junichi; Tanaka, Hideo

1999-04-01

The past specifications SGN of the welding in JNC was reexamined for the reprocessing plants in order to further promote the quality control. The specification first concerns the quality of raw materials, items of the quality tests, material management, and qualification standards of the welders. It extends over details of the welding techniques, welding design, welding testings, inspection and the judgment standards. (H. Baba)

Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities.

Science.gov (United States)

Radic-Sarikas, Branka; Tsafou, Kalliopi P; Emdal, Kristina B; Papamarkou, Theodore; Huber, Kilian V M; Mutz, Cornelia; Toretsky, Jeffrey A; Bennett, Keiryn L; Olsen, Jesper V; Brunak, Søren; Kovar, Heinrich; Superti-Furga, Giulio

2017-01-01

Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any associated adverse side effects through reduced dosing, which is particularly important in childhood tumors. Using a parallel phenotypic combinatorial screening approach of cells derived from three pediatric tumor types, we identified Ewing sarcoma-specific interactions of a diverse set of targeted agents including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong synergistic propensity in Ewing sarcoma, revealing its targets in critical Ewing sarcoma signaling routes. Using a multilevel experimental approach including quantitative phosphoproteomics, we analyzed the molecular rationale behind the disease-specific synergistic effect of simultaneous application of PKC412 and IGF1R inhibitors. The mechanism of the drug synergy between these inhibitors is different from the sum of the mechanisms of the single agents. The combination effectively inhibited pathway crosstalk and averted feedback loop repression, in EWS-FLI1-dependent manner. Mol Cancer Ther; 16(1); 88-101. ©2016 AACR. ©2016 American Association for Cancer Research.

Automation of technical specification monitoring for nuclear power plants

International Nuclear Information System (INIS)

Lin, J.C.; Abbott, E.C.; Hubbard, F.R.

1986-01-01

The complexity of today's nuclear power plants combined with an equally detailed regulatory process makes it necessary for the plant staff to have access to an automated system capable of monitoring the status of limiting conditions for operation (LCO). Pickard, Lowe and Garrick, Inc. (PLG), has developed the first of such a system, called Limiting Conditions for Operation Monitor (LIMCOM). LIMCOM provides members of the operating staff with an up-to-date comparison of currently operable equipment and plant operating conditions with what is required in the technical specifications. LIMCOM also provides an effective method of screening tagout requests by evaluating their impact on the LCOs. Finally, LIMCOM provides an accurate method of tracking and scheduling routine surveillance. (author)

vProtein: identifying optimal amino acid complements from plant-based foods.

Directory of Open Access Journals (Sweden)

Peter J Woolf

Full Text Available BACKGROUND: Indispensible amino acids (IAAs are used by the body in different proportions. Most animal-based foods provide these IAAs in roughly the needed proportions, but many plant-based foods provide different proportions of IAAs. To explore how these plant-based foods can be better used in human nutrition, we have created the computational tool vProtein to identify optimal food complements to satisfy human protein needs. METHODS: vProtein uses 1251 plant-based foods listed in the United States Department of Agriculture standard release 22 database to determine the quantity of each food or pair of foods required to satisfy human IAA needs as determined by the 2005 daily recommended intake. The quantity of food in a pair is found using a linear programming approach that minimizes total calories, total excess IAAs, or the total weight of the combination. RESULTS: For single foods, vProtein identifies foods with particularly balanced IAA patterns such as wheat germ, quinoa, and cauliflower. vProtein also identifies foods with particularly unbalanced IAA patterns such as macadamia nuts, degermed corn products, and wakame seaweed. Although less useful alone, some unbalanced foods provide unusually good complements, such as Brazil nuts to legumes. Interestingly, vProtein finds no statistically significant bias toward grain/legume pairings for protein complementation. These analyses suggest that pairings of plant-based foods should be based on the individual foods themselves instead of based on broader food group-food group pairings. Overall, the most efficient pairings include sweet corn/tomatoes, apple/coconut, and sweet corn/cherry. The top pairings also highlight the utility of less common protein sources such as the seaweeds laver and spirulina, pumpkin leaves, and lambsquarters. From a public health perspective, many of the food pairings represent novel, low cost food sources to combat malnutrition. Full analysis results are available online

Safety of Nuclear Power Plants: Design. Specific Safety Requirements (Spanish Edition)

International Nuclear Information System (INIS)

2012-01-01

This publication is a revision of Safety Requirements No. NS-R-1, Safety of Nuclear Power Plants: Design. It establishes requirements applicable to the design of nuclear power plants and elaborates on the safety objective, safety principles and concepts that provide the basis for deriving the safety requirements that must be met for the design of a nuclear power plant. It will be useful for organizations involved in the design, manufacture, construction, modification, maintenance, operation and decommissioning of nuclear power plants, as well as for regulatory bodies. Contents: 1. Introduction; 2. Applying the safety principles and concepts; 3. Management of safety in design; 4. Principal technical requirements; 5. General plant design; 6. Design of specific plant systems.

Safety of Nuclear Power Plants: Design. Specific Safety Requirements (Russian Edition)

International Nuclear Information System (INIS)

2012-01-01

This publication is a revision of Safety Requirements No. NS-R-1, Safety of Nuclear Power Plants: Design. It establishes requirements applicable to the design of nuclear power plants and elaborates on the safety objective, safety principles and concepts that provide the basis for deriving the safety requirements that must be met for the design of a nuclear power plant. It will be useful for organizations involved in the design, manufacture, construction, modification, maintenance, operation and decommissioning of nuclear power plants, as well as for regulatory bodies. Contents: 1. Introduction; 2. Applying the safety principles and concepts; 3. Management of safety in design; 4. Principal technical requirements; 5. General plant design; 6. Design of specific plant systems.

Use of neural networks to identify transient operating conditions in nuclear power plants

International Nuclear Information System (INIS)

Uhrig, R.E.; Guo, Z.

1989-01-01

A technique using neural networks as a means of diagnosing specific abnormal conditions or problems in nuclear power plants is investigated and found to be feasible. The technique is based on the fact that each physical state of the plant can be represented by a unique pattern of instrument readings, which can be related to the condition of the plant. Neural networks are used to relate this pattern to the fault or problem. 3 refs., 2 figs., 4 tabs

Repeated evolution of fungal cultivar specificity in independently evolved ant-plant-fungus symbioses.

Directory of Open Access Journals (Sweden)

Rumsaïs Blatrix

Full Text Available Some tropical plant species possess hollow structures (domatia occupied by ants that protect the plant and in some cases also provide it with nutrients. Most plant-ants tend patches of chaetothyrialean fungi within domatia. In a few systems it has been shown that the ants manure the fungal patches and use them as a food source, indicating agricultural practices. However, the identity of these fungi has been investigated only in a few samples. To examine the specificity and constancy of ant-plant-fungus interactions we characterised the content of fungal patches in an extensive sampling of three ant-plant symbioses (Petalomyrmex phylax/Leonardoxa africana subsp. africana, Aphomomyrmex afer/Leonardoxa africana subsp. letouzeyi and Tetraponera aethiops/Barteria fistulosa by sequencing the Internal Transcribed Spacers of ribosomal DNA. For each system the content of fungal patches was constant over individuals and populations. Each symbiosis was associated with a specific, dominant, primary fungal taxon, and to a lesser extent, with one or two specific secondary taxa, all of the order Chaetothyriales. A single fungal patch sometimes contained both a primary and a secondary taxon. In one system, two founding queens were found with the primary fungal taxon only, one that was shown in a previous study to be consumed preferentially. Because the different ant-plant symbioses studied have evolved independently, the high specificity and constancy we observed in the composition of the fungal patches have evolved repeatedly. Specificity and constancy also characterize other cases of agriculture by insects.

Transgenic plants with altered senescence characteristics

Science.gov (United States)

Amasino, Richard M.; Gan, Susheng; Noh, Yoo-Sun

2002-03-19

The identification of senescence-specific promoters from plants is described. Using information from the first senescence-specific promoter, SAG12 from Arabidopsis, other homologous promoters from another plant have been identified. Such promoters may be used to delay senescence in commercially important plants.

Safety of Nuclear Power Plants: Design. Specific Safety Requirements (Chinese Ed.)

International Nuclear Information System (INIS)

2012-01-01

On the basis of the principles included in the Fundamental Safety Principles, IAEA Safety Standards Series No. SF-1, this Safety Requirements publication establishes requirements applicable to the design of nuclear power plants. It covers the design phase and provides input for the safe operation of the power plant. It elaborates on the safety objective, safety principles and concepts that provide the basis for deriving the safety requirements that must be met for the design of a nuclear power plant. Contents: 1. Introduction; 2. Applying the safety principles and concepts; 3. Management of safety in design; 4. Principal technical requirements; 5. General plant design; 6. Design of specific plant systems.

Safety of Nuclear Power Plants: Design. Specific Safety Requirements (French Ed.)

International Nuclear Information System (INIS)

2012-01-01

On the basis of the principles included in the Fundamental Safety Principles, IAEA Safety Standards Series No. SF-1, this Safety Requirements publication establishes requirements applicable to the design of nuclear power plants. It covers the design phase and provides input for the safe operation of the power plant. It elaborates on the safety objective, safety principles and concepts that provide the basis for deriving the safety requirements that must be met for the design of a nuclear power plant. Contents: 1. Introduction; 2. Applying the safety principles and concepts; 3. Management of safety in design; 4. Principal technical requirements; 5. General plant design; 6. Design of specific plant systems.

Safety of Nuclear Power Plants: Design. Specific Safety Requirements (Arabic Ed.)

International Nuclear Information System (INIS)

2012-01-01

On the basis of the principles included in the Fundamental Safety Principles, IAEA Safety Standards Series No. SF-1, this Safety Requirements publication establishes requirements applicable to the design of nuclear power plants. It covers the design phase and provides input for the safe operation of the power plant. It elaborates on the safety objective, safety principles and concepts that provide the basis for deriving the safety requirements that must be met for the design of a nuclear power plant. Contents: 1. Introduction; 2. Applying the safety principles and concepts; 3. Management of safety in design; 4. Principal technical requirements; 5. General plant design; 6. Design of specific plant systems.

Combining multivariate analysis and monosaccharide composition modeling to identify plant cell wall variations by Fourier Transform Near Infrared spectroscopy

Directory of Open Access Journals (Sweden)

Smith-Moritz Andreia M

2011-08-01

Full Text Available Abstract We outline a high throughput procedure that improves outlier detection in cell wall screens using FT-NIR spectroscopy of plant leaves. The improvement relies on generating a calibration set from a subset of a mutant population by taking advantage of the Mahalanobis distance outlier scheme to construct a monosaccharide range predictive model using PLS regression. This model was then used to identify specific monosaccharide outliers from the mutant population.

Combining endangered plants and animals as surrogates to identify priority conservation areas in Yunnan, China

Science.gov (United States)

Yang, Feiling; Hu, Jinming; Wu, Ruidong

2016-08-01

Suitable surrogates are critical for identifying optimal priority conservation areas (PCAs) to protect regional biodiversity. This study explored the efficiency of using endangered plants and animals as surrogates for identifying PCAs at the county level in Yunnan, southwest China. We ran the Dobson algorithm under three surrogate scenarios at 75% and 100% conservation levels and identified four types of PCAs. Assessment of the protection efficiencies of the four types of PCAs showed that endangered plants had higher surrogacy values than endangered animals but that the two were not substitutable; coupled endangered plants and animals as surrogates yielded a higher surrogacy value than endangered plants or animals as surrogates; the plant-animal priority areas (PAPAs) was the optimal among the four types of PCAs for conserving both endangered plants and animals in Yunnan. PAPAs could well represent overall species diversity distribution patterns and overlap with critical biogeographical regions in Yunnan. Fourteen priority units in PAPAs should be urgently considered as optimizing Yunnan’s protected area system. The spatial pattern of PAPAs at the 100% conservation level could be conceptualized into three connected conservation belts, providing a valuable reference for optimizing the layout of the in situ protected area system in Yunnan.

Proteome Analysis of the Plant Pathogenic Fungus Monilinia laxa Showing Host Specificity

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Olja Bregar

2012-01-01

Full Text Available Brown rot fungus Monilinia laxa (Aderh. & Ruhl. Honey is an important plant pathogen in stone and pome fruits in Europe. We applied a proteomic approach in a study of M. laxa isolates obtained from apples and apricots in order to show the host specifity of the isolates and to analyse differentially expressed proteins in terms of host specifity, fungal pathogenicity and identification of candidate proteins for diagnostic marker development. Extracted mycelium proteins were separated by 2-D electrophoresis (2-DE and visualized by Coomassie staining in a non-linear pH range of 3–11 and Mr of 14–116 kDa. We set up a 2-DE reference map of M. laxa, resolving up to 800 protein spots, and used it for image analysis. The average technical coefficient of variance (13 % demonstrated a high reproducibility of protein extraction and 2-D polyacrylamide gel electrophoresis (2-DE PAGE, and the average biological coefficient of variance (23 % enabled differential proteomic analysis of the isolates. Multivariate statistical analysis (principal component analysis discriminated isolates from two different hosts, providing new data that support the existence of a M. laxa specialized form f. sp. mali, which infects only apples. A total of 50 differentially expressed proteins were further analyzed by LC-MS/MS, yielding 41 positive identifications. The identified mycelial proteins were functionally classified into 6 groups: amino acid and protein metabolism, energy production, carbohydrate metabolism, stress response, fatty acid metabolism and other proteins. Some proteins expressed only in apple isolates have been described as virulence factors in other fungi. The acetolactate synthase was almost 11-fold more abundant in apple-specific isolates than in apricot isolates and it might be implicated in M. laxa host specificity. Ten proteins identified only in apple isolates are potential candidates for the development of M. laxa host-specific diagnostic markers.

Preparation of radiological effluent technical specifications for nuclear power plants. a guidance manual for users of standard technical specifications

International Nuclear Information System (INIS)

Boegli, J.S.; Bellamy, R.R.; Britz, W.L.; Waterfield, R.L.

1978-10-01

The purpose of this manual is to describe methods found acceptable to the staff of the U.S. Nuclear Regulatory Commission (NRC) for the calculation of certain key values required in the preparation of proposed radiological effluent Technical Specifications using the Standard Technical Specifications for light-water-cooled nuclear power plants. This manual also provides guidance to applicants for operating licenses for nuclear power plants in the preparation of proposed radiological effluent Technical Specifications or in preparing requests for changes to existing radiological effluent Technical Specifications for operating licenses. The manual additionally describes current staff positions on the methodology for estimating radiation exposure due to the release of radioactive materials in effluents and on the administrative control of radioactive waste treatment systems

Gravimetric phenotyping of whole plant transpiration responses to atmospheric vapour pressure deficit identifies genotypic variation in water use efficiency.

Science.gov (United States)

Ryan, Annette C; Dodd, Ian C; Rothwell, Shane A; Jones, Ros; Tardieu, Francois; Draye, Xavier; Davies, William J

2016-10-01

There is increasing interest in rapidly identifying genotypes with improved water use efficiency, exemplified by the development of whole plant phenotyping platforms that automatically measure plant growth and water use. Transpirational responses to atmospheric vapour pressure deficit (VPD) and whole plant water use efficiency (WUE, defined as the accumulation of above ground biomass per unit of water used) were measured in 100 maize (Zea mays L.) genotypes. Using a glasshouse based phenotyping platform with naturally varying VPD (1.5-3.8kPa), a 2-fold variation in WUE was identified in well-watered plants. Regression analysis of transpiration versus VPD under these conditions, and subsequent whole plant gas exchange at imposed VPDs (0.8-3.4kPa) showed identical responses in specific genotypes. Genotype response of transpiration versus VPD fell into two categories: 1) a linear increase in transpiration rate with VPD with low (high WUE) or high (low WUE) transpiration rate at all VPDs, 2) a non-linear response with a pronounced change point at low VPD (high WUE) or high VPD (low WUE). In the latter group, high WUE genotypes required a significantly lower VPD before transpiration was restricted, and had a significantly lower rate of transpiration in response to VPD after this point, when compared to low WUE genotypes. Change point values were significantly positively correlated with stomatal sensitivity to VPD. A change point in stomatal response to VPD may explain why some genotypes show contradictory WUE rankings according to whether they are measured under glasshouse or field conditions. Furthermore, this novel use of a high throughput phenotyping platform successfully reproduced the gas exchange responses of individuals measured in whole plant chambers, accelerating the identification of plants with high WUE. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Transcriptomic Analysis Using Olive Varieties and Breeding Progenies Identifies Candidate Genes Involved in Plant Architecture.

Science.gov (United States)

González-Plaza, Juan J; Ortiz-Martín, Inmaculada; Muñoz-Mérida, Antonio; García-López, Carmen; Sánchez-Sevilla, José F; Luque, Francisco; Trelles, Oswaldo; Bejarano, Eduardo R; De La Rosa, Raúl; Valpuesta, Victoriano; Beuzón, Carmen R

2016-01-01

Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Little is known about how plant architecture is genetically determined in olive, were most of the existing varieties are traditional with an architecture poorly suited for modern growing and harvesting systems. In the present study, we have carried out microarray analysis of meristematic tissue to compare expression profiles of olive varieties displaying differences in architecture, as well as seedlings from their cross pooled on the basis of their sharing architecture-related phenotypes. The microarray used, previously developed by our group has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. Varieties with distinct architecture phenotypes and individuals from segregating progenies displaying opposite architecture features were used to link phenotype to expression. Here, we identify 2252 differentially expressed genes (DEGs) associated to differences in plant architecture. Microarray results were validated by quantitative RT-PCR carried out on genes with functional annotation likely related to plant architecture. Twelve of these genes were further analyzed in individual seedlings of the corresponding pool. We also examined Arabidopsis mutants in putative orthologs of these targeted candidate genes, finding altered architecture for most of them. This supports a functional conservation between species and potential biological relevance of the candidate genes identified. This study is the first to identify genes associated to plant architecture in olive, and the results obtained could be of great help in future programs aimed at selecting phenotypes adapted to modern cultivation practices in this species.

Pilot program to identify valve failures which impact the safety and operation of light water nuclear power plants

International Nuclear Information System (INIS)

Tsacoyeanes, J.C.; Raju, P.P.

1980-04-01

The pilot program described has been initiated under the Department of Energy Light Water Reactor Safety Research and Development Program and has the following specific objectives: to identify the principal types and causes of failures in valves, valve operators and their controls and associated hardware, which lead to, or could lead to plant trip; and to suggest possible remedies for the prevention of these failures and recommend future research and development programs which could lead to minimizing these valve failures or mitigating their effect on plant operation. The data surveyed cover incidents reported over the six-year period, beginning 1973 through the end of 1978. Three sources of information on valve failures have been consulted: failure data centers, participating organizations in the nuclear power industry, and technical documents

DCD – a novel plant specific domain in proteins involved in development and programmed cell death

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Doerks Tobias

2005-07-01

Full Text Available Abstract Background Recognition of microbial pathogens by plants triggers the hypersensitive reaction, a common form of programmed cell death in plants. These dying cells generate signals that activate the plant immune system and alarm the neighboring cells as well as the whole plant to activate defense responses to limit the spread of the pathogen. The molecular mechanisms behind the hypersensitive reaction are largely unknown except for the recognition process of pathogens. We delineate the NRP-gene in soybean, which is specifically induced during this programmed cell death and contains a novel protein domain, which is commonly found in different plant proteins. Results The sequence analysis of the protein, encoded by the NRP-gene from soybean, led to the identification of a novel domain, which we named DCD, because it is found in plant proteins involved in development and cell death. The domain is shared by several proteins in the Arabidopsis and the rice genomes, which otherwise show a different protein architecture. Biological studies indicate a role of these proteins in phytohormone response, embryo development and programmed cell by pathogens or ozone. Conclusion It is tempting to speculate, that the DCD domain mediates signaling in plant development and programmed cell death and could thus be used to identify interacting proteins to gain further molecular insights into these processes.

Plant Family-Specific Impacts of Petroleum Pollution on Biodiversity and Leaf Chlorophyll Content in the Amazon Rainforest of Ecuador.

Science.gov (United States)

Arellano, Paul; Tansey, Kevin; Balzter, Heiko; Tellkamp, Markus

2017-01-01

In recent decades petroleum pollution in the tropical rainforest has caused significant environmental damage in vast areas of the Amazon region. At present the extent of this damage is not entirely clear. Little is known about the specific impacts of petroleum pollution on tropical vegetation. In a field expedition to the Ecuadorian Amazon over 1100 leaf samples were collected from tropical trees in polluted and unpolluted sites. Plant families were identified for 739 of the leaf samples and compared between sites. Plant biodiversity indices show a reduction of the plant biodiversity when the site was affected by petroleum pollution. In addition, reflectance and transmittance were measured with a field spectroradiometer for every leaf sample and leaf chlorophyll content was estimated using reflectance model inversion with the radiative tranfer model PROSPECT. Four of the 15 plant families that are most representative of the ecoregion (Melastomataceae, Fabaceae, Rubiaceae and Euphorbiaceae) had significantly lower leaf chlorophyll content in the polluted areas compared to the unpolluted areas. This suggests that these families are more sensitive to petroleum pollution. The polluted site is dominated by Melastomataceae and Rubiaceae, suggesting that these plant families are particularly competitive in the presence of pollution. This study provides evidence of a decrease of plant diversity and richness caused by petroleum pollution and of a plant family-specific response of leaf chlorophyll content to petroleum pollution in the Ecuadorian Amazon using information from field spectroscopy and radiative transfer modelling.

Plant Family-Specific Impacts of Petroleum Pollution on Biodiversity and Leaf Chlorophyll Content in the Amazon Rainforest of Ecuador.

Directory of Open Access Journals (Sweden)

Paul Arellano

Full Text Available In recent decades petroleum pollution in the tropical rainforest has caused significant environmental damage in vast areas of the Amazon region. At present the extent of this damage is not entirely clear. Little is known about the specific impacts of petroleum pollution on tropical vegetation. In a field expedition to the Ecuadorian Amazon over 1100 leaf samples were collected from tropical trees in polluted and unpolluted sites. Plant families were identified for 739 of the leaf samples and compared between sites. Plant biodiversity indices show a reduction of the plant biodiversity when the site was affected by petroleum pollution. In addition, reflectance and transmittance were measured with a field spectroradiometer for every leaf sample and leaf chlorophyll content was estimated using reflectance model inversion with the radiative tranfer model PROSPECT. Four of the 15 plant families that are most representative of the ecoregion (Melastomataceae, Fabaceae, Rubiaceae and Euphorbiaceae had significantly lower leaf chlorophyll content in the polluted areas compared to the unpolluted areas. This suggests that these families are more sensitive to petroleum pollution. The polluted site is dominated by Melastomataceae and Rubiaceae, suggesting that these plant families are particularly competitive in the presence of pollution. This study provides evidence of a decrease of plant diversity and richness caused by petroleum pollution and of a plant family-specific response of leaf chlorophyll content to petroleum pollution in the Ecuadorian Amazon using information from field spectroscopy and radiative transfer modelling.

Predicting incursion of plant invaders into Kruger National Park, South Africa: the interplay of general drivers and species-specific factors.

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Vojtěch Jarošík

Full Text Available BACKGROUND: Overcoming boundaries is crucial for incursion of alien plant species and their successful naturalization and invasion within protected areas. Previous work showed that in Kruger National Park, South Africa, this process can be quantified and that factors determining the incursion of invasive species can be identified and predicted confidently. Here we explore the similarity between determinants of incursions identified by the general model based on a multispecies assemblage, and those identified by species-specific models. We analyzed the presence and absence of six invasive plant species in 1.0×1.5 km segments along the border of the park as a function of environmental characteristics from outside and inside the KNP boundary, using two data-mining techniques: classification trees and random forests. PRINCIPAL FINDINGS: The occurrence of Ageratum houstonianum, Chromolaena odorata, Xanthium strumarium, Argemone ochroleuca, Opuntia stricta and Lantana camara can be reliably predicted based on landscape characteristics identified by the general multispecies model, namely water runoff from surrounding watersheds and road density in a 10 km radius. The presence of main rivers and species-specific combinations of vegetation types are reliable predictors from inside the park. CONCLUSIONS: The predictors from the outside and inside of the park are complementary, and are approximately equally reliable for explaining the presence/absence of current invaders; those from the inside are, however, more reliable for predicting future invasions. Landscape characteristics determined as crucial predictors from outside the KNP serve as guidelines for management to enact proactive interventions to manipulate landscape features near the KNP to prevent further incursions. Predictors from the inside the KNP can be used reliably to identify high-risk areas to improve the cost-effectiveness of management, to locate invasive plants and target them for

Predicting Incursion of Plant Invaders into Kruger National Park, South Africa: The Interplay of General Drivers and Species-Specific Factors

Science.gov (United States)

Jarošík, Vojtěch; Pyšek, Petr; Foxcroft, Llewellyn C.; Richardson, David M.; Rouget, Mathieu; MacFadyen, Sandra

2011-01-01

Background Overcoming boundaries is crucial for incursion of alien plant species and their successful naturalization and invasion within protected areas. Previous work showed that in Kruger National Park, South Africa, this process can be quantified and that factors determining the incursion of invasive species can be identified and predicted confidently. Here we explore the similarity between determinants of incursions identified by the general model based on a multispecies assemblage, and those identified by species-specific models. We analyzed the presence and absence of six invasive plant species in 1.0×1.5 km segments along the border of the park as a function of environmental characteristics from outside and inside the KNP boundary, using two data-mining techniques: classification trees and random forests. Principal Findings The occurrence of Ageratum houstonianum, Chromolaena odorata, Xanthium strumarium, Argemone ochroleuca, Opuntia stricta and Lantana camara can be reliably predicted based on landscape characteristics identified by the general multispecies model, namely water runoff from surrounding watersheds and road density in a 10 km radius. The presence of main rivers and species-specific combinations of vegetation types are reliable predictors from inside the park. Conclusions The predictors from the outside and inside of the park are complementary, and are approximately equally reliable for explaining the presence/absence of current invaders; those from the inside are, however, more reliable for predicting future invasions. Landscape characteristics determined as crucial predictors from outside the KNP serve as guidelines for management to enact proactive interventions to manipulate landscape features near the KNP to prevent further incursions. Predictors from the inside the KNP can be used reliably to identify high-risk areas to improve the cost-effectiveness of management, to locate invasive plants and target them for eradication. PMID:22194893

Standard Technical Specifications, General Electric plants, BWR/4

International Nuclear Information System (INIS)

1992-09-01

This NUREG contains improved Standard Technical Specifications (STS) for General Electric Plants, BWR/4, and documents the positions of the Nuclear Regulatory Commission based on the BWR Owners Group's proposed STS. This document is the result of extensive technical meetings and discussions among the NRC staff, the Nuclear Steam Supply System (NSSS) Owners Groups, the NSSS vendors, and the Nuclear Management and Resources Council (NUMARC). The improved STS were developed based on the criteria in the interim Commission Policy Statement on Technical Specification Improvements for Nuclear Power Reactors, dated February 6, 1987. The improved STS will be used as the basis for individual nuclear power specifications. This report contains three volumes. This document, Volume 2, contains the Bases for Chapters 2.0 and 3.0, and Sections 3.1--3.3 of the improved STS

Formosa Plastics Corporation: Plant-Wide Assessment of Texas Plant Identifies Opportunities for Improving Process Efficiency and Reducing Energy Costs

Energy Technology Data Exchange (ETDEWEB)

None

2005-01-01

At Formosa Plastics Corporation's plant in Point Comfort, Texas, a plant-wide assessment team analyzed process energy requirements, reviewed new technologies for applicability, and found ways to improve the plant's energy efficiency. The assessment team identified the energy requirements of each process and compared actual energy consumption with theoretical process requirements. The team estimated that total annual energy savings would be about 115,000 MBtu for natural gas and nearly 14 million kWh for electricity if the plant makes several improvements, which include upgrading the gas compressor impeller, improving the vent blower system, and recovering steam condensate for reuse. Total annual cost savings could be $1.5 million. The U.S. Department of Energy's Industrial Technologies Program cosponsored this assessment.

Race-Specific Adult-Plant Resistance in Winter Wheat to Stripe Rust and Characterization of Pathogen Virulence Patterns.

Science.gov (United States)

Milus, Eugene A; Moon, David E; Lee, Kevin D; Mason, R Esten

2015-08-01

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of wheat in the Great Plains and southeastern United States. Growing resistant cultivars is the preferred means for managing stripe rust, but new virulence in the pathogen population overcomes some of the resistance. The objectives of this study were to characterize the stripe rust resistance in contemporary soft and hard red winter wheat cultivars, to characterize the virulence of P. striiformis f. sp. tritici isolates based on the resistances found in the cultivars, and to determine wheat breeders' perceptions on the importance and methods for achieving stripe rust resistance. Seedlings of cultivars were susceptible to recent isolates, indicating they lacked effective all-stage resistance. However, adult-plants were resistant or susceptible depending on the isolate, indicating they had race-specific adult-plant resistance. Using isolates collected from 1990 to 2013, six major virulence patterns were identified on adult plants of twelve cultivars that were selected as adult-plant differentials. Race-specific adult-plant resistance appears to be the only effective type of resistance protecting wheat from stripe rust in eastern United States. Among wheat breeders, the importance of incorporating stripe rust resistance into cultivars ranged from high to low depending on the frequency of epidemics in their region, and most sources of stripe rust resistance were either unknown or already overcome by virulence in the pathogen population. Breeders with a high priority for stripe rust resistance made most of their selections based on adult-plant reactions in the field, whereas breeders with a low priority for resistance based selections on molecular markers for major all-stage resistance genes.

Plant specification of a generic human-error data through a two-stage Bayesian approach

International Nuclear Information System (INIS)

Heising, C.D.; Patterson, E.I.

1984-01-01

Expert judgement concerning human performance in nuclear power plants is quantitatively coupled with actuarial data on such performance in order to derive plant-specific human-error rate probability distributions. The coupling procedure consists of a two-stage application of Bayes' theorem to information which is grouped by type. The first information type contains expert judgement concerning human performance at nuclear power plants in general. Data collected on human performance at a group of similar plants forms the second information type. The third information type consists of data on human performance in a specific plant which has the same characteristics as the group members. The first and second information types are coupled in the first application of Bayes' theorem to derive a probability distribution for population performance. This distribution is then combined with the third information type in a second application of Bayes' theorem to determine a plant-specific human-error rate probability distribution. The two stage Bayesian procedure thus provides a means to quantitatively couple sparse data with expert judgement in order to obtain a human performance probability distribution based upon available information. Example calculations for a group of like reactors are also given. (author)

Deep sequencing identifies ethnicity-specific bacterial signatures in the oral microbiome.

Directory of Open Access Journals (Sweden)

Matthew R Mason

Full Text Available Oral infections have a strong ethnic predilection; suggesting that ethnicity is a critical determinant of oral microbial colonization. Dental plaque and saliva samples from 192 subjects belonging to four major ethnicities in the United States were analyzed using terminal restriction fragment length polymorphism (t-RFLP and 16S pyrosequencing. Ethnicity-specific clustering of microbial communities was apparent in saliva and subgingival biofilms, and a machine-learning classifier was capable of identifying an individual's ethnicity from subgingival microbial signatures. The classifier identified African Americans with a 100% sensitivity and 74% specificity and Caucasians with a 50% sensitivity and 91% specificity. The data demonstrates a significant association between ethnic affiliation and the composition of the oral microbiome; to the extent that these microbial signatures appear to be capable of discriminating between ethnicities.

Chromatographic fingerprinting as a strategy to identify regulated plants in illegal herbal supplements.

Science.gov (United States)

Custers, D; Van Praag, N; Courselle, P; Apers, S; Deconinck, E

2017-03-01

Erectile dysfunction (ED) is a sexual disorder characterized by the inability to achieve or maintain a sufficiently rigid erection. Despite the availability of non-invasive oral treatment options, many patients turn to herbal alternatives. Furthermore, herbal supplements are increasingly gaining popularity in industrialized countries and, as a consequence, quality control is a highly important issue. Unfortunately, this is not a simple task since plants are often crushed and mixed with other plants, which complicates their identification by usage of classical approaches such as microscopy. The aim of this study was to explore the potential use of chromatographic fingerprinting to identify plants present in herbal preparations intended for the treatment of ED. To achieve this goal, a HPLC-PDA and a HPLC-MS method were developed, using a full factorial experimental design in order to acquire characteristic fingerprints of three plants which are potentially beneficial for treating ED: Epimedium spp., Pausinystalia yohimbe and Tribulus terrestris. The full factorial design demonstrated that for all three plant references a C8 column (250mm×4.6mm; 5µm particle size) is best suited; methanol and an ammonium formate buffer (pH 3) were found to be the best constituents for the mobile phase. The suitability of this strategy was demonstrated by analysing several self-made triturations in three different botanical matrices, which mimic the influential effects that could be expected when analysing herbal supplements. To conclude, this study demonstrates that chromatographic fingerprinting could provide a useful means to identify plants in a complex herbal mixture. Copyright © 2016 Elsevier B.V. All rights reserved.

Interactions among predators and plant specificity protect herbivores from top predators.

Science.gov (United States)

Bosc, Christopher; Pauw, Anton; Roets, Francois; Hui, Cang

2018-05-04

The worldwide loss of top predators from natural and agricultural systems has heightened the need to understand how important they are in controlling herbivore abundance. The effect of top predators on herbivore species is likely to depend on 1) the importance of the consumption of intermediate predators by top predators (intra-guild predation; IGP), but also on 2) plant specificity by herbivores, because specialists may defend themselves better (enemy-free space; EFS). Insectivorous birds, as top predators, are generally known to effectively control herbivorous insects, despite also consuming intermediate predators such as spiders, but how this effect varies among herbivore species in relation to the cascading effects of IGP and EFS is not known. To explore this, we excluded birds from natural fynbos vegetation in South Africa using large netted cages and recorded changes in abundance relative to control plots for 199 plant-dwelling intermediate predator and 341 herbivore morpho-species that varied in their estimated plant specificity. We found a strong negative effect of birds on the total abundance of all intermediate predators, with especially clear effects on spiders (strong IGP). In contrast with previous studies, which document a negative effect of birds on herbivores, we found an overall neutral effect of birds on herbivore abundance, but the effect varied among species: some species were negatively affected by birds, suggesting that they were mainly consumed by birds, whereas others, likely released from spiders by IGP, were positively affected. Some species were also effectively neutrally affected by birds. These tended to be more specialized to plants compared to the other species, which may imply that some plant specialists benefited from protection provided by EFS from both birds and spiders. These results suggest that the response of herbivore species to top predators may depend on cascading effects of interactions among predators and on their degree

Molecular Evolution of the Substrate Specificity of Chloroplastic Aldolases/Rubisco Lysine Methyltransferases in Plants.

Science.gov (United States)

Ma, Sheng; Martin-Laffon, Jacqueline; Mininno, Morgane; Gigarel, Océane; Brugière, Sabine; Bastien, Olivier; Tardif, Marianne; Ravanel, Stéphane; Alban, Claude

2016-04-04

Rubisco and fructose-1,6-bisphosphate aldolases (FBAs) are involved in CO2 fixation in chloroplasts. Both enzymes are trimethylated at a specific lysine residue by the chloroplastic protein methyltransferase LSMT. Genes coding LSMT are present in all plant genomes but the methylation status of the substrates varies in a species-specific manner. For example, chloroplastic FBAs are naturally trimethylated in both Pisum sativum and Arabidopsis thaliana, whereas the Rubisco large subunit is trimethylated only in the former species. The in vivo methylation status of aldolases and Rubisco matches the catalytic properties of AtLSMT and PsLSMT, which are able to trimethylate FBAs or FBAs and Rubisco, respectively. Here, we created chimera and site-directed mutants of monofunctional AtLSMT and bifunctional PsLSMT to identify the molecular determinants responsible for substrate specificity. Our results indicate that the His-Ala/Pro-Trp triad located in the central part of LSMT enzymes is the key motif to confer the capacity to trimethylate Rubisco. Two of the critical residues are located on a surface loop outside the methyltransferase catalytic site. We observed a strict correlation between the presence of the triad motif and the in vivo methylation status of Rubisco. The distribution of the motif into a phylogenetic tree further suggests that the ancestral function of LSMT was FBA trimethylation. In a recent event during higher plant evolution, this function evolved in ancestors of Fabaceae, Cucurbitaceae, and Rosaceae to include Rubisco as an additional substrate to the archetypal enzyme. Our study provides insight into mechanisms by which SET-domain protein methyltransferases evolve new substrate specificity. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

Criticality prevention specifications thorium--uranium-233 separations in the Purex Plant

International Nuclear Information System (INIS)

Matheison, W.E.; Oberg, G.C.; Ritter, G.L.

1970-01-01

The specifications in this document define the limits or restrictions required to maintain an acceptably low probability of the occurrence of a nuclear chain reaction in the Purex Plant while processing irradiated thoria targets. These criticality prevention specifications do not stipulate the system, procedures, or mechanisms to permit operation within the limits or restrictions

The effect of uncertainties in nuclear reactor plant-specific failure data on core damage frequency

International Nuclear Information System (INIS)

Martz, H.F.

1995-05-01

It is sometimes the case in PRA applications that reported plant-specific failure data are, in fact, only estimates which are uncertain. Even for detailed plant-specific data, the reported exposure time or number of demands is often only an estimate of the actual exposure time or number of demands. Likewise the reported number of failure events or incidents is sometimes also uncertain because incident or malfunction reports may be ambiguous. In this report we determine the corresponding uncertainty in core damage frequency which can b attributed to such uncertainties in plant-specific data using a simple but typical nuclear power reactor example

Risk-based analysis methods applied to nuclear power plant technical specifications

International Nuclear Information System (INIS)

Wagner, D.P.; Minton, L.A.; Gaertner, J.P.

1989-01-01

A computer-aided methodology and practical applications of risk-based evaluation of technical specifications are described. The methodology, developed for use by the utility industry, is a part of the overall process of improving nuclear power plant technical specifications. The SOCRATES computer program uses the results of a probabilistic risk assessment or a system-level risk analysis to calculate changes in risk due to changes in the surveillance test interval and/or the allowed outage time stated in the technical specification. The computer program can accommodate various testing strategies (such as staggered or simultaneous testing) to allow modeling of component testing as it is carried out at the plant. The methods and computer program are an integral part of a larger decision process aimed at determining benefits from technical specification changes. These benefits can include cost savings to the utilities by reducing forced shutdowns and decreasing labor requirements for test and maintenance activities, with no adverse impacts on risk. The methodology and the SOCRATES computer program have been used extensively toe valuate several actual technical specifications in case studies demonstrating the methods. Summaries of these applications demonstrate the types of results achieved and the usefulness of the risk-based evaluation in improving the technical specifications

Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

Directory of Open Access Journals (Sweden)

Kiwako S Araki

Full Text Available In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals. We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers. We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms

Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

Science.gov (United States)

Araki, Kiwako S; Kubo, Takuya; Kudoh, Hiroshi

2017-01-01

In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed) and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals). We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers). We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP) loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms, particularly for

Identifying protein phosphorylation sites with kinase substrate specificity on human viruses.

Directory of Open Access Journals (Sweden)

Neil Arvin Bretaña

Full Text Available Viruses infect humans and progress inside the body leading to various diseases and complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication and inhibition of normal host-cell functions. Due to its biological importance, there is a desire to identify the protein phosphorylation sites on human viruses. However, the use of mass spectrometry-based experiments is proven to be expensive and labor-intensive. Furthermore, previous studies which have identified phosphorylation sites in human viruses do not include the investigation of the responsible kinases. Thus, we are motivated to propose a new method to identify protein phosphorylation sites with its kinase substrate specificity on human viruses. The experimentally verified phosphorylation data were extracted from virPTM--a database containing 301 experimentally verified phosphorylation data on 104 human kinase-phosphorylated virus proteins. In an attempt to investigate kinase substrate specificities in viral protein phosphorylation sites, maximal dependence decomposition (MDD is employed to cluster a large set of phosphorylation data into subgroups containing significantly conserved motifs. The experimental human phosphorylation sites are collected from Phospho.ELM, grouped according to its kinase annotation, and compared with the virus MDD clusters. This investigation identifies human kinases such as CK2, PKB, CDK, and MAPK as potential kinases for catalyzing virus protein substrates as confirmed by published literature. Profile hidden Markov model is then applied to learn a predictive model for each subgroup. A five-fold cross validation evaluation on the MDD-clustered HMMs yields an average accuracy of 84.93% for Serine, and 78.05% for Threonine. Furthermore, an independent testing data collected from UniProtKB and Phospho.ELM is used to make a comparison of predictive performance on three popular kinase-specific

Identifying protein phosphorylation sites with kinase substrate specificity on human viruses.

Science.gov (United States)

Bretaña, Neil Arvin; Lu, Cheng-Tsung; Chiang, Chiu-Yun; Su, Min-Gang; Huang, Kai-Yao; Lee, Tzong-Yi; Weng, Shun-Long

2012-01-01

Viruses infect humans and progress inside the body leading to various diseases and complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication and inhibition of normal host-cell functions. Due to its biological importance, there is a desire to identify the protein phosphorylation sites on human viruses. However, the use of mass spectrometry-based experiments is proven to be expensive and labor-intensive. Furthermore, previous studies which have identified phosphorylation sites in human viruses do not include the investigation of the responsible kinases. Thus, we are motivated to propose a new method to identify protein phosphorylation sites with its kinase substrate specificity on human viruses. The experimentally verified phosphorylation data were extracted from virPTM--a database containing 301 experimentally verified phosphorylation data on 104 human kinase-phosphorylated virus proteins. In an attempt to investigate kinase substrate specificities in viral protein phosphorylation sites, maximal dependence decomposition (MDD) is employed to cluster a large set of phosphorylation data into subgroups containing significantly conserved motifs. The experimental human phosphorylation sites are collected from Phospho.ELM, grouped according to its kinase annotation, and compared with the virus MDD clusters. This investigation identifies human kinases such as CK2, PKB, CDK, and MAPK as potential kinases for catalyzing virus protein substrates as confirmed by published literature. Profile hidden Markov model is then applied to learn a predictive model for each subgroup. A five-fold cross validation evaluation on the MDD-clustered HMMs yields an average accuracy of 84.93% for Serine, and 78.05% for Threonine. Furthermore, an independent testing data collected from UniProtKB and Phospho.ELM is used to make a comparison of predictive performance on three popular kinase-specific phosphorylation site

Methodology and application of surrogate plant PRA analysis to the Rancho Seco Power Plant: Final report

International Nuclear Information System (INIS)

Gore, B.F.; Huenefeld, J.C.

1987-07-01

This report presents the development and the first application of generic probabilistic risk assessment (PRA) information for identifying systems and components important to public risk at nuclear power plants lacking plant-specific PRAs. A methodology is presented for using the results of PRAs for similar (surrogate) plants, along with plant-specific information about the plant of interest and the surrogate plants, to infer important failure modes for systems of the plant of interest. This methodology, and the rationale on which it is based, is presented in the context of its application to the Rancho Seco plant. The Rancho Seco plant has been analyzed using PRA information from two surrogate plants. This analysis has been used to guide development of considerable plant-specific information about Rancho Seco systems and components important to minimizing public risk, which is also presented herein

40 CFR 62.15110 - Who must complete the plant-specific training course?

Science.gov (United States)

2010-07-01

...-specific training course? All employees with responsibilities that affect how a municipal waste combustion... 40 Protection of Environment 8 2010-07-01 2010-07-01 false Who must complete the plant-specific training course? 62.15110 Section 62.15110 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY...

40 CFR 60.1655 - Who must complete the plant-specific training course?

Science.gov (United States)

2010-07-01

...-specific training course? All employees with responsibilities that affect how a municipal waste combustion... 40 Protection of Environment 6 2010-07-01 2010-07-01 false Who must complete the plant-specific training course? 60.1655 Section 60.1655 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY...

The compact Selaginella genome identifies changes in gene content associated with the evolution of vascular plants

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor V.; Banks, Jo Ann; Nishiyama, Tomoaki; Hasebe, Mitsuyasu; Bowman, John L.; Gribskov, Michael; dePamphilis, Claude; Albert, Victor A.; Aono, Naoki; Aoyama, Tsuyoshi; Ambrose, Barbara A.; Ashton, Neil W.; Axtell, Michael J.; Barker, Elizabeth; Barker, Michael S.; Bennetzen, Jeffrey L.; Bonawitz, Nicholas D.; Chapple, Clint; Cheng, Chaoyang; Correa, Luiz Gustavo Guedes; Dacre, Michael; DeBarry, Jeremy; Dreyer, Ingo; Elias, Marek; Engstrom, Eric M.; Estelle, Mark; Feng, Liang; Finet, Cedric; Floyd, Sandra K.; Frommer, Wolf B.; Fujita, Tomomichi; Gramzow, Lydia; Gutensohn, Michael; Harholt, Jesper; Hattori, Mitsuru; Heyl, Alexander; Hirai, Tadayoshi; Hiwatashi, Yuji; Ishikawa, Masaki; Iwata, Mineko; Karol, Kenneth G.; Koehler, Barbara; Kolukisaoglu, Uener; Kubo, Minoru; Kurata, Tetsuya; Lalonde, Sylvie; Li, Kejie; Li, Ying; Litt, Amy; Lyons, Eric; Manning, Gerard; Maruyama, Takeshi; Michael, Todd P.; Mikami, Koji; Miyazaki, Saori; Morinaga, Shin-ichi; Murata, Takashi; Mueller-Roeber, Bernd; Nelson, David R.; Obara, Mari; Oguri, Yasuko; Olmstead, Richard G.; Onodera, Naoko; Petersen, Bent Larsen; Pils, Birgit; Prigge, Michael; Rensing, Stefan A.; Riano-Pachon, Diego Mauricio; Roberts, Alison W.; Sato, Yoshikatsu; Scheller, Henrik Vibe; Schulz, Burkhard; Schulz, Christian; Shakirov, Eugene V.; Shibagaki, Nakako; Shinohara, Naoki; Shippen, Dorothy E.; Sorensen, Iben; Sotooka, Ryo; Sugimoto, Nagisa; Sugita, Mamoru; Sumikawa, Naomi; Tanurdzic, Milos; Theilsen, Gunter; Ulvskov, Peter; Wakazuki, Sachiko; Weng, Jing-Ke; Willats, William W.G.T.; Wipf, Daniel; Wolf, Paul G.; Yang, Lixing; Zimmer, Andreas D.; Zhu, Qihui; Mitros, Therese; Hellsten, Uffe; Loque, Dominique; Otillar, Robert; Salamov, Asaf; Schmutz, Jeremy; Shapiro, Harris; Lindquist, Erika; Lucas, Susan; Rokhsar, Daniel

2011-04-28

We report the genome sequence of the nonseed vascular plant, Selaginella moellendorffii, and by comparative genomics identify genes that likely played important roles in the early evolution of vascular plants and their subsequent evolution

Site-Specific Seismic Site Response Model for the Waste Treatment Plant, Hanford, Washington

Energy Technology Data Exchange (ETDEWEB)

Rohay, Alan C.; Reidel, Steve P.

2005-02-24

This interim report documents the collection of site-specific geologic and geophysical data characterizing the Waste Treatment Plant site and the modeling of the site-specific structure response to earthquake ground motions.

Standard technical specifications combustion engineering plants: Bases (Sections 2.0--3.3). Volume 2, Revision 1

International Nuclear Information System (INIS)

1995-04-01

This report documents the results of the combined effort of the NRC and the industry to produce improved Standard Technical Specifications (STS), Revision 1 for General Electric BWR/6 Plants. The changes reflected in Revision 1 resulted from the experience gained from license amendment applications to convert to these improved STS or to adopt partial improvements to existing technical specifications. This NUREG is the result of extensive public technical meetings and discussions between the Nuclear Regulatory Commission (NRC) staff and various nuclear power plant licensees, Nuclear Steam Supply System (NSSS) Owners Groups, NSSS vendors, and the Nuclear Energy Institute (NEI). The improved STS were developed based on the criteria in the Final Commission Policy Statement on Technical Specifications Improvements for Nuclear Power Reactors, dated July 22, 1993. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes

Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities

DEFF Research Database (Denmark)

Radic-Sarikas, Branka; Tsafou, Kalliopi P; Emdal, Kristina B.

2017-01-01

Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any...... including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong...

Multi-omics approach identifies molecular mechanisms of plant-fungus mycorrhizal interaction

Directory of Open Access Journals (Sweden)

Peter E Larsen

2016-01-01

Full Text Available In mycorrhizal symbiosis, plant roots form close, mutually beneficial interactions with soil fungi. Before this mycorrhizal interaction can be established however, plant roots must be capable of detecting potential beneficial fungal partners and initiating the gene expression patterns necessary to begin symbiosis. To predict a plant root – mycorrhizal fungi sensor systems, we analyzed in vitro experiments of Populus tremuloides (aspen tree and Laccaria bicolor (mycorrhizal fungi interaction and leveraged over 200 previously published transcriptomic experimental data sets, 159 experimentally validated plant transcription factor binding motifs, and more than 120-thousand experimentally validated protein-protein interactions to generate models of pre-mycorrhizal sensor systems in aspen root. These sensor mechanisms link extracellular signaling molecules with gene regulation through a network comprised of membrane receptors, signal cascade proteins, transcription factors, and transcription factor biding DNA motifs. Modeling predicted four pre-mycorrhizal sensor complexes in aspen that interact with fifteen transcription factors to regulate the expression of 1184 genes in response to extracellular signals synthesized by Laccaria. Predicted extracellular signaling molecules include common signaling molecules such as phenylpropanoids, salicylate, and, jasmonic acid. This multi-omic computational modeling approach for predicting the complex sensory networks yielded specific, testable biological hypotheses for mycorrhizal interaction signaling compounds, sensor complexes, and mechanisms of gene regulation.

Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada.

Science.gov (United States)

Braukmann, Thomas W A; Kuzmina, Maria L; Sills, Jesse; Zakharov, Evgeny V; Hebert, Paul D N

2017-01-01

Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geographic or taxonomic contexts, but the present investigation expands analysis to consider the performance of these gene regions in discriminating the species in local floras at sites across Canada. To test identification success, we employed a DNA barcode reference library with sequence records for 96% of the 5108 vascular plant species known from Canada, but coverage varied from 94% for rbcL to 60% for ITS2 and 39% for matK. Using plant lists from 27 national parks and one scientific reserve, we tested the efficacy of DNA barcodes in identifying the plants in simulated species assemblages from six biogeographic regions of Canada using BLAST and mothur. Mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) were strong predictors of barcode performance for different plant families and genera, and both metrics supported ITS2 as possessing the highest genetic diversity. All three genes performed strongly in assigning the taxa present in local floras to the correct genus with values ranging from 91% for rbcL to 97% for ITS2 and 98% for matK. However, matK delivered the highest species discrimination (~81%) followed by ITS2 (~72%) and rbcL (~44%). Despite the low number of plant taxa in the Canadian Arctic, DNA barcodes had the least success in discriminating species from this biogeographic region with resolution ranging from 36% with rbcL to 69% with matK. Species resolution was higher in the other settings, peaking in the Woodland region at 52% for rbcL and 87% for matK. Our results indicate that DNA barcoding is very effective in identifying Canadian plants to a genus, and that it performs well in discriminating species in regions where floristic diversity is

Identifying plant cell-surface receptors: combining 'classical' techniques with novel methods.

Science.gov (United States)

Uebler, Susanne; Dresselhaus, Thomas

2014-04-01

Cell-cell communication during development and reproduction in plants depends largely on a few phytohormones and many diverse classes of polymorphic secreted peptides. The peptide ligands are bound at the cell surface of target cells by their membranous interaction partners representing, in most cases, either receptor-like kinases or ion channels. Although knowledge of both the extracellular ligand and its corresponding receptor(s) is necessary to describe the downstream signalling pathway(s), to date only a few ligand-receptor pairs have been identified. Several methods, such as affinity purification and yeast two-hybrid screens, have been used very successfully to elucidate interactions between soluble proteins, but most of these methods cannot be applied to membranous proteins. Experimental obstacles such as low concentration and poor solubility of membrane receptors, as well as instable transient interactions, often hamper the use of these 'classical' approaches. However, over the last few years, a lot of progress has been made to overcome these problems by combining classical techniques with new methodologies. In the present article, we review the most promising recent methods in identifying cell-surface receptor interactions, with an emphasis on success stories outside the field of plant research.

Identify alternative splicing events based on position-specific evolutionary conservation.

Directory of Open Access Journals (Sweden)

Liang Chen

Full Text Available The evolution of eukaryotes is accompanied by the increased complexity of alternative splicing which greatly expands genome information. One of the greatest challenges in the post-genome era is a complete revelation of human transcriptome with consideration of alternative splicing. Here, we introduce a comparative genomics approach to systemically identify alternative splicing events based on the differential evolutionary conservation between exons and introns and the high-quality annotation of the ENCODE regions. Specifically, we focus on exons that are included in some transcripts but are completely spliced out for others and we call them conditional exons. First, we characterize distinguishing features among conditional exons, constitutive exons and introns. One of the most important features is the position-specific conservation score. There are dramatic differences in conservation scores between conditional exons and constitutive exons. More importantly, the differences are position-specific. For flanking intronic regions, the differences between conditional exons and constitutive exons are also position-specific. Using the Random Forests algorithm, we can classify conditional exons with high specificities (97% for the identification of conditional exons from intron regions and 95% for the classification of known exons and fair sensitivities (64% and 32% respectively. We applied the method to the human genome and identified 39,640 introns that actually contain conditional exons and classified 8,813 conditional exons from the current RefSeq exon list. Among those, 31,673 introns containing conditional exons and 5,294 conditional exons classified from known exons cannot be inferred from RefSeq, UCSC or Ensembl annotations. Some of these de novo predictions were experimentally verified.

Species-specific identification from incomplete sampling: applying DNA barcodes to monitoring invasive solanum plants.

Science.gov (United States)

Zhang, Wei; Fan, Xiaohong; Zhu, Shuifang; Zhao, Hong; Fu, Lianzhong

2013-01-01

Comprehensive sampling is crucial to DNA barcoding, but it is rarely performed because materials are usually unavailable. In practice, only a few rather than all species of a genus are required to be identified. Thus identification of a given species using a limited sample is of great importance in current application of DNA barcodes. Here, we selected 70 individuals representing 48 species from each major lineage of Solanum, one of the most species-rich genera of seed plants, to explore whether DNA barcodes can provide reliable specific-species discrimination in the context of incomplete sampling. Chloroplast genes ndhF and trnS-trnG and the nuclear gene waxy, the commonly used markers in Solanum phylogeny, were selected as the supplementary barcodes. The tree-building and modified barcode gap methods were employed to assess species resolution. The results showed that four Solanum species of quarantine concern could be successfully identified through the two-step barcoding sampling strategy. In addition, discrepancies between nuclear and cpDNA barcodes in some samples demonstrated the ability to discriminate hybrid species, and highlights the necessity of using barcode regions with different modes of inheritance. We conclude that efficient phylogenetic markers are good candidates as the supplementary barcodes in a given taxonomic group. Critically, we hypothesized that a specific-species could be identified from a phylogenetic framework using incomplete sampling-through this, DNA barcoding will greatly benefit the current fields of its application.

Feasibility assessment of a risk-based approach to technical specifications

International Nuclear Information System (INIS)

Atefi, B.; Gallagher, D.W.

1991-05-01

To assess the potential use of risk and reliability techniques for improving the effectiveness of the technical specifications to control plant operational risk, the Technical Specifications Branch of the Nuclear Regulatory Commission initiated an effort to identify and evaluate alternative risk-based approaches that could bring greater risk perspective to these requirements. In the first phase four alternative approaches were identified and their characteristics were analyzed. Among these, the risk-based approach to technical specifications is the most promising approach for controlling plant operational risk using technical specifications. The second phase of the study concentrated on detailed characteristics of the real time risk-based approach. It is concluded that a real time risk-based approach to technical specifications has the potential to improve both plant safety and availability. 33 figs., 5 figs., 6 tabs

Activity and specificity of TRV-mediated gene editing in plants

KAUST Repository

Ali, Zahir

2015-06-03

© 2015 Taylor and Francis Group, LLC. Plant trait engineering requires efficient targeted genome-editing technologies. Clustered regularly interspaced palindromic repeats (CRISPRs)/ CRISPR associated (Cas) type II system is used for targeted genome-editing applications across eukaryotic species including plants. Delivery of genome engineering reagents and recovery of mutants remain challenging tasks for in planta applications. Recently, we reported the development of Tobacco rattle virus (TRV)-mediated genome editing in Nicotiana benthamiana. TRV infects the growing points and possesses small genome size; which facilitate cloning, multiplexing, and agroinfections. Here, we report on the persistent activity and specificity of the TRV-mediated CRISPR/Cas9 system for targeted modification of the Nicotiana benthamiana genome. Our data reveal the persistence of the TRVmediated Cas9 activity for up to 30 d post-agroinefection. Further, our data indicate that TRV-mediated genome editing exhibited no off-target activities at potential off-targets indicating the precision of the system for plant genome engineering. Taken together, our data establish the feasibility and exciting possibilities of using virus-mediated CRISPR/Cas9 for targeted engineering of plant genomes.

Hypocretin neuron-specific transcriptome profiling identifies the sleep modulator Kcnh4a.

Science.gov (United States)

Yelin-Bekerman, Laura; Elbaz, Idan; Diber, Alex; Dahary, Dvir; Gibbs-Bar, Liron; Alon, Shahar; Lerer-Goldshtein, Tali; Appelbaum, Lior

2015-10-01

Sleep has been conserved throughout evolution; however, the molecular and neuronal mechanisms of sleep are largely unknown. The hypothalamic hypocretin/orexin (Hcrt) neurons regulate sleep\\wake states, feeding, stress, and reward. To elucidate the mechanism that enables these various functions and to identify sleep regulators, we combined fluorescence cell sorting and RNA-seq in hcrt:EGFP zebrafish. Dozens of Hcrt-neuron-specific transcripts were identified and comprehensive high-resolution imaging revealed gene-specific localization in all or subsets of Hcrt neurons. Clusters of Hcrt-neuron-specific genes are predicted to be regulated by shared transcription factors. These findings show that Hcrt neurons are heterogeneous and that integrative molecular mechanisms orchestrate their diverse functions. The voltage-gated potassium channel Kcnh4a, which is expressed in all Hcrt neurons, was silenced by the CRISPR-mediated gene inactivation system. The mutant kcnh4a (kcnh4a(-/-)) larvae showed reduced sleep time and consolidation, specifically during the night, suggesting that Kcnh4a regulates sleep.

Analysis of 16S rRNA and mxaF genes revealing insights into Methylobacterium niche-specific plant association

Science.gov (United States)

Dourado, Manuella Nóbrega; Andreote, Fernando Dini; Dini-Andreote, Francisco; Conti, Raphael; Araújo, Janete Magali; Araújo, Welington Luiz

2012-01-01

The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM) bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA) and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase) ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant. PMID:22481887

Analysis of 16S rRNA and mxaF genes reveling insights into Methylobacterium niche-specific plant association

Directory of Open Access Journals (Sweden)

Manuella Nóbrega Dourado

2012-01-01

Full Text Available The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant.

Analysis of 16S rRNA and mxaF genes revealing insights into Methylobacterium niche-specific plant association.

Science.gov (United States)

Dourado, Manuella Nóbrega; Andreote, Fernando Dini; Dini-Andreote, Francisco; Conti, Raphael; Araújo, Janete Magali; Araújo, Welington Luiz

2012-01-01

The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM) bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA) and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase) ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant.

Failure cause and failure rate evaluation on pumps of BWR plants in PSA. Hypothesis testing for typical or plant specific failure rate of pumps

International Nuclear Information System (INIS)

Sanada, Takahiro; Nakamura, Makoto

2009-01-01

In support of domestic nuclear industry effort to gather and analyze failure data of components concerning nuclear power plants, Nuclear Information Archives (NUCIA) are published for useful information to help PSA. This report focuses on NUCIA pertaining to pumps in domestic nuclear power plants, and provides the reliable estimation on failure rate of pumps resulting from failure cause analysis and hypothesis testing of classified and plant specific failure rate of pumps for improving quality in PSA. The classified and plant specific failure rate of pumps are estimated by analyzing individual domestic nuclear power plant's data of 26 Boiling Water Reactors (BWRs) concerning functionally structurally classified pump failures reported from beginning of commercial operation to March 31, 2007. (author)

Custom-Designed Molecular Scissors for Site-Specific Manipulation of the Plant and Mammalian Genomes

Science.gov (United States)

Kandavelou, Karthikeyan; Chandrasegaran, Srinivasan

Zinc finger nucleases (ZFNs) are custom-designed molecular scissors, engineered to cut at specific DNA sequences. ZFNs combine the zinc finger proteins (ZFPs) with the nonspecific cleavage domain of the FokI restriction enzyme. The DNA-binding specificity of ZFNs can be easily altered experimentally. This easy manipulation of the ZFN recognition specificity enables one to deliver a targeted double-strand break (DSB) to a genome. The targeted DSB stimulates local gene targeting by several orders of magnitude at that specific cut site via homologous recombination (HR). Thus, ZFNs have become an important experimental tool to make site-specific and permanent alterations to genomes of not only plants and mammals but also of many other organisms. Engineering of custom ZFNs involves many steps. The first step is to identify a ZFN site at or near the chosen chromosomal target within the genome to which ZFNs will bind and cut. The second step is to design and/or select various ZFP combinations that will bind to the chosen target site with high specificity and affinity. The DNA coding sequence for the designed ZFPs are then assembled by polymerase chain reaction (PCR) using oligonucleotides. The third step is to fuse the ZFP constructs to the FokI cleavage domain. The ZFNs are then expressed as proteins by using the rabbit reticulocyte in vitro transcription/translation system and the protein products assayed for their DNA cleavage specificity.

Membrane topology and identification of key residues of EaDAcT, a plant MBOAT with unusual substrate specificity.

Science.gov (United States)

Tran, Tam N T; Shelton, Jennifer; Brown, Susan; Durrett, Timothy P

2017-10-01

Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) catalyzes the transfer of an acetyl group from acetyl-CoA to the sn-3 position of diacylglycerol to form 3-acetyl-1,2-diacyl-sn-glycerol (acetyl-TAG). EaDAcT belongs to a small, plant-specific subfamily of the membrane bound O-acyltransferases (MBOAT) that acylate different lipid substrates. Sucrose gradient density centrifugation revealed that EaDAcT colocalizes to the same fractions as an endoplasmic reticulum (ER)-specific marker. By mapping the membrane topology of EaDAcT, we obtained an experimentally determined topology model for a plant MBOAT. The EaDAcT model contains four transmembrane domains (TMDs), with both the N- and C-termini orientated toward the lumen of the ER. In addition, there is a large cytoplasmic loop between the first and second TMDs, with the MBOAT signature region of the protein embedded in the third TMD close to the interface between the membrane and the cytoplasm. During topology mapping, we discovered two cysteine residues (C187 and C293) located on opposite sides of the membrane that are important for enzyme activity. In order to identify additional amino acid residues important for acetyltransferase activity, we isolated and characterized acetyltransferases from other acetyl-TAG-producing plants. Among them, the acetyltransferase from Euonymus fortunei possessed the highest activity in vivo and in vitro. Mutagenesis of conserved amino acids revealed that S253, H257, D258 and V263 are essential for EaDAcT activity. Alteration of residues unique to the acetyltransferases did not alter the unique acyl donor specificity of EaDAcT, suggesting that multiple amino acids are important for substrate recognition. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Tumor specific cytotoxicity of arctigenin isolated from herbal plant Arctium lappa L.

Science.gov (United States)

Susanti, Siti; Iwasaki, Hironori; Itokazu, Yukiyoshi; Nago, Mariko; Taira, Naoyuki; Saitoh, Seikoh; Oku, Hirosuke

2012-10-01

The effectiveness of cancer chemotherapy is often limited by the toxicity to other tissues in the body. Therefore, the identification of non-toxic chemotherapeutics from herbal medicines remains to be an attractive goal to advance cancer treatments. This study evaluated the cytotoxicity profiles of 364 herbal plant extracts, using various cancer and normal cell lines. The screening found occurrence of A549 (human lung adenocarcinoma) specific cytotoxicity in nine species of herbal plants, especially in the extract of Arctium lappa L. Moreover, purification of the selective cytotoxicity in the extract of Arctium lappa L. resulted in the identification of arctigenin as tumor specific agent that showed cytotoxicity to lung cancer (A549), liver cancer (HepG2) and stomach cancer (KATO III) cells, while no cytotoxicity to several normal cell lines. Arctigenin specifically inhibited the proliferation of cancer cells, which might consequently lead to the induction of apoptosis. In conclusion, this study found that arctigenin was one of cancer specific phytochemicals, and in part responsible for the tumor selective cytotoxicity of the herbal medicine.

SMM-system: A mining tool to identify specific markers in Salmonella enterica.

Science.gov (United States)

Yu, Shuijing; Liu, Weibing; Shi, Chunlei; Wang, Dapeng; Dan, Xianlong; Li, Xiao; Shi, Xianming

2011-03-01

This report presents SMM-system, a software package that implements various personalized pre- and post-BLASTN tasks for mining specific markers of microbial pathogens. The main functionalities of SMM-system are summarized as follows: (i) converting multi-FASTA file, (ii) cutting interesting genomic sequence, (iii) automatic high-throughput BLASTN searches, and (iv) screening target sequences. The utility of SMM-system was demonstrated by using it to identify 214 Salmonella enterica-specific protein-coding sequences (CDSs). Eighteen primer pairs were designed based on eighteen S. enterica-specific CDSs, respectively. Seven of these primer pairs were validated with PCR assay, which showed 100% inclusivity for the 101 S. enterica genomes and 100% exclusivity of 30 non-S. enterica genomes. Three specific primer pairs were chosen to develop a multiplex PCR assay, which generated specific amplicons with a size of 180bp (SC1286), 238bp (SC1598) and 405bp (SC4361), respectively. This study demonstrates that SMM-system is a high-throughput specific marker generation tool that can be used to identify genus-, species-, serogroup- and even serovar-specific DNA sequences of microbial pathogens, which has a potential to be applied in food industries, diagnostics and taxonomic studies. SMM-system is freely available and can be downloaded from http://foodsafety.sjtu.edu.cn/SMM-system.html. Copyright © 2011 Elsevier B.V. All rights reserved.

Meta-scale mountain grassland observatories uncover commonalities as well as specific interactions among plant and non-rhizosphere soil bacterial communities.

Science.gov (United States)

Yashiro, Erika; Pinto-Figueroa, Eric; Buri, Aline; Spangenberg, Jorge E; Adatte, Thierry; Niculita-Hirzel, Helene; Guisan, Antoine; van der Meer, Jan Roelof

2018-04-10

Interactions between plants and bacteria in the non-rhizosphere soil are rarely assessed, because they are less direct and easily masked by confounding environmental factors. By studying plant vegetation alliances and soil bacterial community co-patterning in grassland soils in 100 sites across a heterogeneous mountain landscape in the western Swiss Alps, we obtained sufficient statistical power to disentangle common co-occurrences and weaker specific interactions. Plant alliances and soil bacterial communities tended to be synchronized in community turnover across the landscape, largely driven by common underlying environmental factors, such as soil pH or elevation. Certain alliances occurring in distinct, local, environmental conditions were characterized by co-occurring specialist plant and bacterial species, such as the Nardus stricta and Thermogemmatisporaceae. In contrast, some generalist taxa, like Anthoxanthum odoratum and 19 Acidobacteria species, spanned across multiple vegetation alliances. Meta-scale analyses of soil bacterial community composition and vegetation surveys, complemented with local edaphic measurements, can thus prove useful to identify the various types of plant-bacteria interactions and the environments in which they occur.

Geomorphologic specificities of selected sites for nuclear power plants in Czechoslovakia

International Nuclear Information System (INIS)

Kalvoda, J.; Demek, J.

1991-01-01

The contribution of geomorphology to the complex evaluation of properties of sites for the construction and operation of nuclear facilities is demonstrated. The unique manifestation of the present geodynamics at the Jaslovske Bohunice nuclear power plant locality and the spatial correlations of annals of the specific morphotectonic development of georeliefs of that nuclear power plant with the location of the epicentral earthquake zones are shown. The results of the geomorphological survey in the surroundings of the Temelin nuclear power plant construction site are described and a drawing is reproduced showing how the georelief of this locality divides into areas with different categories of occurrence of morpho-structural formations. For the Tetov locality, where the construction of a nuclear power plant is planned, the changes in the course of the Labe (Elbe) river which occurred in the Pleistocene are of importance in the assessment of the intensity of geodynamic processes. The geomorphological and geotectonic complexity of the planned Blahutovice nuclear power plant construction site is demonstrated. A drawing shows the morphotectonic situation in the surroundings of that construction site. (Z.S.). 4 figs

Endemic plants harbour specific Trichoderma communities with an exceptional potential for biocontrol of phytopathogens.

Science.gov (United States)

Zachow, Christin; Berg, Christian; Müller, Henry; Monk, Jana; Berg, Gabriele

2016-10-10

Trichoderma strains exhibit enormous potential for applications in biotechnology, in particular as biocontrol agents against pathogens. However, little is known about the diversity of plant-associated Trichoderma communities at a global scale and their antagonistic spectrum. In order to gather information about structure and function, we compared Trichoderma biomes of endemic (Aeonium, Diospyros, Hebe, Rhododendron) and cosmopolitan plants (Zea mays) in a global study encompassing the area Northwest Africa to New Zealand via the European Alps and Madagascar. At the quantitative level we found no differences between cosmopolitan and endemic plants. Statistically significant differences were detected at the qualitative level: Trichoderma populations of endemic plants were highly specific and diverse with hot spots appearing in Madagascar and New Zealand. By contrast, maize plants from all sites shared the majority of Trichoderma species (65.5%). Interestingly, the high above ground biodiversity in ecosystems containing endemic plants was confirmed by a high below ground Trichoderma diversity. Despite the differences, we found a global Trichoderma core community shared by all analysed plants, which was dominated by T. koningii and T. koningiopsis. Amplicon-based network analyses revealed a high similarity between maize Trichoderma grown world-wide and distinct populations of endemic plants. Furthermore, Trichoderma strains from endemic plants showed a higher antagonistic activity against fungal pathogens compared to maize-associated strains. Our results showed that endemic plants are associated with a specific Trichoderma microbiome which possesses a high antagonistic activity indicating that it has potential to be used for biocontrol purposes. Copyright © 2016 Elsevier B.V. All rights reserved.

EDF's approach to determine specifications for nuclear power plant bulk chemicals

International Nuclear Information System (INIS)

Basile, Alix; Dijoux, Michel; Le-Calvar, Marc; Gressier, Frederic; Mole, Didier

2012-09-01

Chemical impurities in the primary, secondary and auxiliary nuclear power plants circuits generate risks of corrosion of the fuel cladding, steel and nickel based alloys. The PMUC (Products and Materials Used in plants) organization established by EDF intends to limit this risk by specifying maximum levels of impurities in products and materials used for the operation and maintenance of Nuclear Power Plants (NPPs). Bulk chemicals specifications, applied on primary and secondary circuit chemicals and hydrogen and nitrogen gases, are particularly important to prevent chemical species to be involved in the corrosion of the NPPs materials. The application of EDF specifications should lead to reasonably exclude any risk of degradation of the first and second containment barriers and auxiliary circuits Important to Safety (IPS) by limiting the concentrations of chlorides, fluorides, sulfates... The risk of metal embrittlement by elements with low melting point (mercury, lead...) is also included. For the primary circuit, the specifications intend to exclude the risk of activation of impurities introduced by the bulk chemicals. For the first containment barrier, to reduce the risk of deposits like zeolites, PMUC products specifications set limit values for calcium, magnesium, aluminum and silica. EDF's approach for establishing specifications for bulk chemicals is taking also into account the capacity of industrial production, as well as costs, limitations of analytical control methods (detection limits) and environmental releases issues. This paper aims to explain EDF's approach relative to specifications of impurities in bulk chemicals. Also presented are the various parameters taken into account to determine the maximum pollution levels in the chemicals, the theoretical hypothesis to set the specifications and the calculation method used to verify that the specifications are suitable. (authors)

Standard technical specifications: Combustion engineering plants. Volume 3, Revision 1: Bases (Sections 3.4--3.9)

International Nuclear Information System (INIS)

1995-04-01

This report documents the results of the combined effort of the NRC and the industry to produce improved Standard Technical Specifications (STS), Revision 1 for Combustion Engineering Plants. The changes reflected in Revision 1 resulted from the experience gained from license amendment applications to convert to these improved STS or to adopt partial improvements to existing technical specifications. This NUREG is the result of extensive public technical meetings and discussions between the Nuclear Regulatory Commission (NRC) staff and various nuclear power plant licensees, Nuclear Steam Supply System (NSSS) Owners Groups, NSSS vendors, and the Nuclear Energy Institute (NEI). The improved STS were developed based on the criteria in the Final Commission Policy Statement on Technical Specifications Improvements for Nuclear Power Reactors, dated July 22, 1993. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes. Volume 1 contains the Specifications for all chapters and sections of the improved STS. Volume 2 contains the Bases for Chapters 2.0 and 3.0, and Sections 3.1--3.3 of the improved STS Volume 3 contains the Bases for Sections 3.4--3.9 of the improved STS

Digital I and C system pre-tests using plant specific simulators

International Nuclear Information System (INIS)

Holl, B.; Probst, H.; Wischert, W.

2006-01-01

The paper focuses on strategic aspects of the implementation of modern digital instrumentation and control system (I and C) in nuclear power plant (NPP) training simulators and points out the way to identify the most appropriate implementation method of the digital I and C system in the simulator development environment which fulfils the requirement imposed by the nuclear power plants. This regards mainly training aspects, simulator as a test bed for design verification and validation (V and V), and software maintenance aspects with respect to future evolutions of the digital I and C system. (author)

Plant-based foods containing cell wall polysaccharides rich in specific active monosaccharides protect against myocardial injury in rat myocardial infarction models.

Science.gov (United States)

Lim, Sun Ha; Kim, Yaesil; Yun, Ki Na; Kim, Jin Young; Jang, Jung-Hee; Han, Mee-Jung; Lee, Jongwon

2016-12-08

Many cohort studies have shown that consumption of diets containing a higher composition of foods derived from plants reduces mortality from coronary heart disease (CHD). Here, we examined the active components of a plant-based diet and the underlying mechanisms that reduce the risk of CHD using three rat models and a quantitative proteomics approach. In a short-term myocardial infarction (MI) model, intake of wheat extract (WE), the representative cardioprotectant identified by screening approximately 4,000 samples, reduced myocardial injury by inhibiting apoptosis, enhancing ATP production, and maintaining protein homeostasis. In long-term post-MI models, this myocardial protection resulted in ameliorating adverse left-ventricular remodelling, which is a predictor of heart failure. Among the wheat components, arabinose and xylose were identified as active components responsible for the observed efficacy of WE, which was administered via ingestion and tail-vein injections. Finally, the food components of plant-based diets that contained cell wall polysaccharides rich in arabinose, xylose, and possibly fucose were found to confer protection against myocardial injury. These results show for the first time that specific monosaccharides found in the cell wall polysaccharides in plant-based diets can act as active ingredients that reduce CHD by inhibiting postocclusion steps, including MI and heart failure.

Using a plant health system framework to assess plant clinic performance in Uganda

DEFF Research Database (Denmark)

Danielsen, Solveig; Matsiko, Frank B.

2016-01-01

and expand, new analytical frameworks and tools are needed to identify factors influencing performance of services and systems in specific contexts, and to guide interventions. In this paper we apply a plant health system framework to assess plant clinic performance, using Uganda as a case study...... factors, influenced by basic operational and financial concerns, inter-institutional relations and public sector policies. Overall, there was a fairly close match between the plant health system attributes and plant clinic performance, suggesting that the framework can help explain system functioning....... A comparative study of plant clinics was carried out between July 2010 and September 2011 in the 12 districts where plant clinics were operating at that time. The framework enabled us to organise multiple issues and identify key features that affected the plant clinics. Clinic performance was, among other...

Effect of plant species on the specific activity of 65Zn and 54Mn

International Nuclear Information System (INIS)

Muraoka, T.; Neptune, A.M.L.

1983-01-01

The effect of five plant species on the specific activity of 65 Zn and 54 Mn is studied. Soybean (Glycine max (L.) Merril), bean (Phaseolus vulgaris, L.), rice (Oryza sativa, L.), wheat (Triticum aestivum, L.) and tomato (Lycopersium esculentum Mill) were grown in PV and TE soils labelled with 65 Zn and 54 Mn. The plants were harvested 30 days after seeding and specific activities of zinco and manganese were determined in the above ground part and in the roots. (M.A.C.) [pt

Comparison of methods applicable to evaluation of nuclear power plant technical specifications

International Nuclear Information System (INIS)

Cho, N.Z.; Bozoki, G.E.; Youngblood, R.W.

1986-01-01

This study compares three probabilistic methods based on the static fault tree analysis, time-dependent unavailability analysis, and Markov analysis, which can be used to evaluate technical specifications in nuclear power plants. They are tested on a sample problem which was devised to closely represent the important and essential characteristics that should be addressed in determination and evaluation of the technical specifications

Genome-wide mapping of virulence in brown planthopper identifies loci that break down host plant resistance.

Science.gov (United States)

Jing, Shengli; Zhang, Lei; Ma, Yinhua; Liu, Bingfang; Zhao, Yan; Yu, Hangjin; Zhou, Xi; Qin, Rui; Zhu, Lili; He, Guangcun

2014-01-01

Insects and plants have coexisted for over 350 million years and their interactions have affected ecosystems and agricultural practices worldwide. Variation in herbivorous insects' virulence to circumvent host resistance has been extensively documented. However, despite decades of investigation, the genetic foundations of virulence are currently unknown. The brown planthopper (Nilaparvata lugens) is the most destructive rice (Oryza sativa) pest in the world. The identification of the resistance gene Bph1 and its introduction in commercial rice varieties prompted the emergence of a new virulent brown planthopper biotype that was able to break the resistance conferred by Bph1. In this study, we aimed to construct a high density linkage map for the brown planthopper and identify the loci responsible for its virulence in order to determine their genetic architecture. Based on genotyping data for hundreds of molecular markers in three mapping populations, we constructed the most comprehensive linkage map available for this species, covering 96.6% of its genome. Fifteen chromosomes were anchored with 124 gene-specific markers. Using genome-wide scanning and interval mapping, the Qhp7 locus that governs preference for Bph1 plants was mapped to a 0.1 cM region of chromosome 7. In addition, two major QTLs that govern the rate of insect growth on resistant rice plants were identified on chromosomes 5 (Qgr5) and 14 (Qgr14). This is the first study to successfully locate virulence in the genome of this important agricultural insect by marker-based genetic mapping. Our results show that the virulence which overcomes the resistance conferred by Bph1 is controlled by a few major genes and that the components of virulence originate from independent genetic characters. The isolation of these loci will enable the elucidation of the molecular mechanisms underpinning the rice-brown planthopper interaction and facilitate the development of durable approaches for controlling this most

Genome-wide mapping of virulence in brown planthopper identifies loci that break down host plant resistance.

Directory of Open Access Journals (Sweden)

Shengli Jing

Full Text Available Insects and plants have coexisted for over 350 million years and their interactions have affected ecosystems and agricultural practices worldwide. Variation in herbivorous insects' virulence to circumvent host resistance has been extensively documented. However, despite decades of investigation, the genetic foundations of virulence are currently unknown. The brown planthopper (Nilaparvata lugens is the most destructive rice (Oryza sativa pest in the world. The identification of the resistance gene Bph1 and its introduction in commercial rice varieties prompted the emergence of a new virulent brown planthopper biotype that was able to break the resistance conferred by Bph1. In this study, we aimed to construct a high density linkage map for the brown planthopper and identify the loci responsible for its virulence in order to determine their genetic architecture. Based on genotyping data for hundreds of molecular markers in three mapping populations, we constructed the most comprehensive linkage map available for this species, covering 96.6% of its genome. Fifteen chromosomes were anchored with 124 gene-specific markers. Using genome-wide scanning and interval mapping, the Qhp7 locus that governs preference for Bph1 plants was mapped to a 0.1 cM region of chromosome 7. In addition, two major QTLs that govern the rate of insect growth on resistant rice plants were identified on chromosomes 5 (Qgr5 and 14 (Qgr14. This is the first study to successfully locate virulence in the genome of this important agricultural insect by marker-based genetic mapping. Our results show that the virulence which overcomes the resistance conferred by Bph1 is controlled by a few major genes and that the components of virulence originate from independent genetic characters. The isolation of these loci will enable the elucidation of the molecular mechanisms underpinning the rice-brown planthopper interaction and facilitate the development of durable approaches for

Development of specific data of plant for a safety probabilistic analysis

International Nuclear Information System (INIS)

Gonzalez C, M.; Nelson E, P.

2004-01-01

In this work the development of specific data of plant is described for the Safety Probabilistic Analysis (APS) of the Laguna Verde Central. The description of those used methods concentrate on the obtention of rates of failure of the equipment and frequencies of initiator events modeled in the APS, making mention to other types of data that also appeal to specific sources of the plant. The method to obtain the rates of failure of the equipment takes advantage the information of failures of components and unavailability of systems obtained entreaty in execution with the Maintenance Rule (1OCFR50.65). The method to develop the frequencies of initiators take in account the registered operational experience as reportable events. In both cases the own experience is combined with published generic data using Bayesian realized techniques. Details are provided about the gathering of information, the confirmations of consistency and adjustment necessities, presenting examples of the obtained results. (Author)

77 FR 12002 - Mount Baker-Snoqualmie National Forest Site-Specific Invasive Plant Treatment Project and Forest...

Science.gov (United States)

2012-02-28

... Invasive Plant Treatment Project and Forest Plan Amendment Number 28 AGENCY: Forest Service, USDA. ACTION... Forest. The current Forest-wide treatment approach pre-dates the Pacific Northwest Region Invasive Plant... interdisciplinary analysis: (1) Whether or not to authorize site- specific invasive plant treatments using...

Reproductive organ and vascular specific promoter of the rice plasma membrane Ca2+ATPase mediates environmental stress responses in plants.

Science.gov (United States)

Huda, Kazi Md Kamrul; Banu, Mst Sufara Akhter; Pathi, Krishna Mohan; Tuteja, Narendra

2013-01-01

Plasma membrane Ca(2+)ATPase is a transport protein in the plasma membrane of cells and helps in removal of calcium (Ca(2+)) from the cell, hence regulating Ca(2+) level within cells. Though plant Ca(2+)ATPases have been shown to be involved in plant stress responses but their promoter regions have not been well studied. The 1478 bp promoter sequence of rice plasma membrane Ca(2+)ATPase contains cis-acting elements responsive to stresses and plant hormones. To identify the functional region, serial deletions of the promoter were fused with the GUS sequence and four constructs were obtained. These were differentially activated under NaCl, PEG cold, methyl viologen, abscisic acid and methyl jasmonate treatments. We demonstrated that the rice plasma membrane Ca(2+)ATPase promoter is responsible for vascular-specific and multiple stress-inducible gene expression. Only full-length promoter showed specific GUS expression under stress conditions in floral parts. High GUS activity was observed in roots with all the promoter constructs. The -1478 to -886 bp flanking region responded well upon treatment with salt and drought. Only the full-length promoter presented cold-induced GUS expression in leaves, while in shoots slight expression was observed for -1210 and -886 bp flanking region. The -1210 bp deletion significantly responded to exogenous methyl viologen and abscisic acid induction. The -1210 and -886 bp flanking region resulted in increased GUS activity in leaves under methyl jasmonate treatments, whereas in shoots the -886 bp and -519 bp deletion gave higher expression. Salicylic acid failed to induce GUS activities in leaves for all the constructs. The rice plasma membrane Ca(2+)ATPase promoter is a reproductive organ-specific as well as vascular-specific. This promoter contains drought, salt, cold, methyl viologen, abscisic acid and methyl jasmonate related cis-elements, which regulated gene expression. Overall, the tissue-specificity and inducible nature of this

Reproductive organ and vascular specific promoter of the rice plasma membrane Ca2+ATPase mediates environmental stress responses in plants.

Directory of Open Access Journals (Sweden)

Kazi Md Kamrul Huda

Full Text Available Plasma membrane Ca(2+ATPase is a transport protein in the plasma membrane of cells and helps in removal of calcium (Ca(2+ from the cell, hence regulating Ca(2+ level within cells. Though plant Ca(2+ATPases have been shown to be involved in plant stress responses but their promoter regions have not been well studied.The 1478 bp promoter sequence of rice plasma membrane Ca(2+ATPase contains cis-acting elements responsive to stresses and plant hormones. To identify the functional region, serial deletions of the promoter were fused with the GUS sequence and four constructs were obtained. These were differentially activated under NaCl, PEG cold, methyl viologen, abscisic acid and methyl jasmonate treatments. We demonstrated that the rice plasma membrane Ca(2+ATPase promoter is responsible for vascular-specific and multiple stress-inducible gene expression. Only full-length promoter showed specific GUS expression under stress conditions in floral parts. High GUS activity was observed in roots with all the promoter constructs. The -1478 to -886 bp flanking region responded well upon treatment with salt and drought. Only the full-length promoter presented cold-induced GUS expression in leaves, while in shoots slight expression was observed for -1210 and -886 bp flanking region. The -1210 bp deletion significantly responded to exogenous methyl viologen and abscisic acid induction. The -1210 and -886 bp flanking region resulted in increased GUS activity in leaves under methyl jasmonate treatments, whereas in shoots the -886 bp and -519 bp deletion gave higher expression. Salicylic acid failed to induce GUS activities in leaves for all the constructs.The rice plasma membrane Ca(2+ATPase promoter is a reproductive organ-specific as well as vascular-specific. This promoter contains drought, salt, cold, methyl viologen, abscisic acid and methyl jasmonate related cis-elements, which regulated gene expression. Overall, the tissue-specificity and inducible

Weed control by direct injection of plant protection products according to specific situations

Directory of Open Access Journals (Sweden)

Krebs, Mathias

2016-02-01

Full Text Available Precision Farming in agriculture allows a site-specific management of the crop. The aim of plant protection is to apply plant protection products (PPP according to the site specific requirements on the field. Within the context of a research program to promote innovation, a sprayer with direct injection of plant protection products was developed. The direct injection offers site specific spraying of different individual PPP in a single pass. The sprayer prototype is equipped with a special spray boom combining three nozzle lines. In order to prevent delay times, the nozzle lines are preloaded before spraying. First results for weed control from test stand measurements and field trials showed that the injection pumps work with high accuracy. The prototype can be used without delay times site specific with up to three different herbicides. Field trials for site-specific weed control in winter wheat demonstrate the applicability of the system under practical conditions. By treatment of subareas herbicides and therefore costs could be saved. A reduction in yield compared with the conventionally treated field areas could not be ascertained. Also an efficacy reduction through washout of active ingredient from target surfaces due to simultaneous use of all three nozzle lines with up to 1050 l/ha application rate could not be detected. At high water spray rates, the efficacy effect occurs delayed. Overall, the newly developed direct injection system proved fieldabillity during the first tests. So weed control can be carried out situation-responsive, which can save herbicides and environmental impacts are reduced.

Plant critical concept

International Nuclear Information System (INIS)

O'Regan, P.J.

1996-01-01

The objective of the effort summarized in this paper is to support O and M cost reduction efforts by focusing resources on components and processes critical to plant performance. This effort will identify where resources on nonplant critical components and processes can be reduced or eliminated. This method will use a functional assessment as the basis for component-specific evaluations and ranking. This effort consists of two stages conducted in series. The first stage is to deterministically identify that set of plant components that are relevant from a plant performance perspective (i.e., safety, economics, reliability). The second stage probabilistically ranks that set of plant components from an importance perspective, where importance pertains to the particular application and is probabilistically weighted. The results of a pilot study identified that only a relatively small set of components are truly critical from an integrated plant performance perspective. These results are consistent with work being conducted at other nuclear power plants, as well as other commercial facilities. Initial implementation of this effort is estimated to reduce O and M costs on the order of $1 million per year. Subsequent applications are anticipated to increase that savings to $4--$5 million per year

Evaluation of Antigen-Conjugated Fluorescent Beads to Identify Antigen-Specific B Cells

Directory of Open Access Journals (Sweden)

Isabel Correa

2018-03-01

Full Text Available Selection of single antigen-specific B cells to identify their expressed antibodies is of considerable interest for evaluating human immune responses. Here, we present a method to identify single antibody-expressing cells using antigen-conjugated fluorescent beads. To establish this, we selected Folate Receptor alpha (FRα as a model antigen and a mouse B cell line, expressing both the soluble and the membrane-bound forms of a human/mouse chimeric antibody (MOv18 IgG1 specific for FRα, as test antibody-expressing cells. Beads were conjugated to FRα using streptavidin/avidin-biotin bridges and used to select single cells expressing the membrane-bound form of anti-FRα. Bead-bound cells were single cell-sorted and processed for single cell RNA retrotranscription and PCR to isolate antibody heavy and light chain variable regions. Variable regions were then cloned and expressed as human IgG1/k antibodies. Like the original clone, engineered antibodies from single cells recognized native FRα. To evaluate whether antigen-coated beads could identify specific antibody-expressing cells in mixed immune cell populations, human peripheral blood mononuclear cells (PBMCs were spiked with test antibody-expressing cells. Antigen-specific cells could comprise up to 75% of cells selected with antigen-conjugated beads when the frequency of the antigen-positive cells was 1:100 or higher. In PBMC pools, beads conjugated to recombinant antigens FRα and HER2 bound antigen-specific anti-FRα MOv18 and anti-HER2 Trastuzumab antibody-expressing cells, respectively. From melanoma patient-derived B cells selected with melanoma cell line-derived protein-coated fluorescent beads, we generated a monoclonal antibody that recognized melanoma antigen-coated beads. This approach may be further developed to facilitate analysis of B cells and their antibody profiles at the single cell level and to help unravel humoral immune repertoires.

Evaluation of Antigen-Conjugated Fluorescent Beads to Identify Antigen-Specific B Cells.

Science.gov (United States)

Correa, Isabel; Ilieva, Kristina M; Crescioli, Silvia; Lombardi, Sara; Figini, Mariangela; Cheung, Anthony; Spicer, James F; Tutt, Andrew N J; Nestle, Frank O; Karagiannis, Panagiotis; Lacy, Katie E; Karagiannis, Sophia N

2018-01-01

Selection of single antigen-specific B cells to identify their expressed antibodies is of considerable interest for evaluating human immune responses. Here, we present a method to identify single antibody-expressing cells using antigen-conjugated fluorescent beads. To establish this, we selected Folate Receptor alpha (FRα) as a model antigen and a mouse B cell line, expressing both the soluble and the membrane-bound forms of a human/mouse chimeric antibody (MOv18 IgG1) specific for FRα, as test antibody-expressing cells. Beads were conjugated to FRα using streptavidin/avidin-biotin bridges and used to select single cells expressing the membrane-bound form of anti-FRα. Bead-bound cells were single cell-sorted and processed for single cell RNA retrotranscription and PCR to isolate antibody heavy and light chain variable regions. Variable regions were then cloned and expressed as human IgG1/k antibodies. Like the original clone, engineered antibodies from single cells recognized native FRα. To evaluate whether antigen-coated beads could identify specific antibody-expressing cells in mixed immune cell populations, human peripheral blood mononuclear cells (PBMCs) were spiked with test antibody-expressing cells. Antigen-specific cells could comprise up to 75% of cells selected with antigen-conjugated beads when the frequency of the antigen-positive cells was 1:100 or higher. In PBMC pools, beads conjugated to recombinant antigens FRα and HER2 bound antigen-specific anti-FRα MOv18 and anti-HER2 Trastuzumab antibody-expressing cells, respectively. From melanoma patient-derived B cells selected with melanoma cell line-derived protein-coated fluorescent beads, we generated a monoclonal antibody that recognized melanoma antigen-coated beads. This approach may be further developed to facilitate analysis of B cells and their antibody profiles at the single cell level and to help unravel humoral immune repertoires.

Evaluation of Antigen-Conjugated Fluorescent Beads to Identify Antigen-Specific B Cells

Science.gov (United States)

Correa, Isabel; Ilieva, Kristina M.; Crescioli, Silvia; Lombardi, Sara; Figini, Mariangela; Cheung, Anthony; Spicer, James F.; Tutt, Andrew N. J.; Nestle, Frank O.; Karagiannis, Panagiotis; Lacy, Katie E.; Karagiannis, Sophia N.

2018-01-01

Selection of single antigen-specific B cells to identify their expressed antibodies is of considerable interest for evaluating human immune responses. Here, we present a method to identify single antibody-expressing cells using antigen-conjugated fluorescent beads. To establish this, we selected Folate Receptor alpha (FRα) as a model antigen and a mouse B cell line, expressing both the soluble and the membrane-bound forms of a human/mouse chimeric antibody (MOv18 IgG1) specific for FRα, as test antibody-expressing cells. Beads were conjugated to FRα using streptavidin/avidin-biotin bridges and used to select single cells expressing the membrane-bound form of anti-FRα. Bead-bound cells were single cell-sorted and processed for single cell RNA retrotranscription and PCR to isolate antibody heavy and light chain variable regions. Variable regions were then cloned and expressed as human IgG1/k antibodies. Like the original clone, engineered antibodies from single cells recognized native FRα. To evaluate whether antigen-coated beads could identify specific antibody-expressing cells in mixed immune cell populations, human peripheral blood mononuclear cells (PBMCs) were spiked with test antibody-expressing cells. Antigen-specific cells could comprise up to 75% of cells selected with antigen-conjugated beads when the frequency of the antigen-positive cells was 1:100 or higher. In PBMC pools, beads conjugated to recombinant antigens FRα and HER2 bound antigen-specific anti-FRα MOv18 and anti-HER2 Trastuzumab antibody-expressing cells, respectively. From melanoma patient-derived B cells selected with melanoma cell line-derived protein-coated fluorescent beads, we generated a monoclonal antibody that recognized melanoma antigen-coated beads. This approach may be further developed to facilitate analysis of B cells and their antibody profiles at the single cell level and to help unravel humoral immune repertoires. PMID:29628923

40 CFR 60.1170 - What plant-specific training must I provide?

Science.gov (United States)

2010-07-01

...) December 6, 2001. (3) The date before an employee assumes responsibilities that affect operation of the... 40 Protection of Environment 6 2010-07-01 2010-07-01 false What plant-specific training must I provide? 60.1170 Section 60.1170 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR...

An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom.

Science.gov (United States)

Vujaklija, Ivan; Bielen, Ana; Paradžik, Tina; Biđin, Siniša; Goldstein, Pavle; Vujaklija, Dušica

2016-02-18

The massive accumulation of protein sequences arising from the rapid development of high-throughput sequencing, coupled with automatic annotation, results in high levels of incorrect annotations. In this study, we describe an approach to decrease annotation errors of protein families characterized by low overall sequence similarity. The GDSL lipolytic family comprises proteins with multifunctional properties and high potential for pharmaceutical and industrial applications. The number of proteins assigned to this family has increased rapidly over the last few years. In particular, the natural abundance of GDSL enzymes reported recently in plants indicates that they could be a good source of novel GDSL enzymes. We noticed that a significant proportion of annotated sequences lack specific GDSL motif(s) or catalytic residue(s). Here, we applied motif-based sequence analyses to identify enzymes possessing conserved GDSL motifs in selected proteomes across the plant kingdom. Motif-based HMM scanning (Viterbi decoding-VD and posterior decoding-PD) and the here described PD/VD protocol were successfully applied on 12 selected plant proteomes to identify sequences with GDSL motifs. A significant number of identified GDSL sequences were novel. Moreover, our scanning approach successfully detected protein sequences lacking at least one of the essential motifs (171/820) annotated by Pfam profile search (PfamA) as GDSL. Based on these analyses we provide a curated list of GDSL enzymes from the selected plants. CLANS clustering and phylogenetic analysis helped us to gain a better insight into the evolutionary relationship of all identified GDSL sequences. Three novel GDSL subfamilies as well as unreported variations in GDSL motifs were discovered in this study. In addition, analyses of selected proteomes showed a remarkable expansion of GDSL enzymes in the lycophyte, Selaginella moellendorffii. Finally, we provide a general motif-HMM scanner which is easily accessible through

Development of Nuclear Plant Specific Analysis Simulators with ATLAS

International Nuclear Information System (INIS)

Jakubowski, Z.; Draeger, P.; Horche, W.; Pointner, W.

2006-01-01

The simulation software ATLAS, based on the best-estimate code ATHLET, has been developed by the GRS for a range of applications in the field of nuclear plant safety analysis. Through application of versatile simulation tools and graphical interfaces the user should be able to analyse with ATLAS all essential accident scenarios. Detailed analysis simulators for several German and Russian NPPs are being constructed on the basis of ATLAS. An overview of the ATLAS is presented in the paper, describing its configuration, functions performed by main components and relationships among them. A significant part of any power plant simulator are the balance-of-plant (BOP) models, not only because all the plant transients and non-LOCA accidents can be initiated by operation of BOP systems, but also because the response of the plant to transients or accidents is strongly influenced by the automatic operation of BOP systems. Modelling aspects of BOP systems are shown in detail, also the interface between the process model and BOP systems. Special emphasis has been put on the BOP model builder based on the methodology developed in the GRS. The BOP modeler called GCSM-Generator is an object oriented tool which runs on the online expert system G2. It is equipped with utilities to edit the BOP models, to verification them and to generate a GCSM code, specific for the ATLAS. The communication system of ATLAS presents graphically the results of the simulation and allows interactively influencing the execution of the simulation process (malfunctions, manual control). Displays for communications with simulated processes and presentation of calculations results are also presented. In the framework of the verification of simulation models different tools are used e.g. the PC-codes MATHCAD for the calculation and documentation, ATLET-Input-Graphic for control of geometry data and the expert system G2 for development of BOP-Models. The validation procedure and selected analyses results

Identifying and utilizing resistance to Puccinia striiformis in wheat

International Nuclear Information System (INIS)

Line, R.F.; Allan, R.E.; Konzak, C.F.

1976-01-01

Resistance to Puccinia striiformis in wheat cultivars, breeding lines, and induced mutants, was studied on plants exposed to natural rust inoculum at field sites and on plants inoculated with specific races and grown under controlled temperatures. Based on infection types and disease intensity at various stages of plant growth throughout the duration of rust establishment, the following resistance-types (R-types) were identified: R-type 1, plants resistant or susceptible at all stages of growth and at both low and high temperatures throughout duration of rust establishment; R-type 2, plants initially resistant in the seedling stage but eventually become susceptible, plants resistant at later stages in the field; R-type 3, variable resistance in the seedling stage, high resistance in later growth stages; R-type 4, plants resistant in the eedling stage, but susceptible in late stages of growth; R-type 5, plants susceptible, but the pathogen is slow to sporulate and consequently, rust increases slower in the field; R-type 6, plants susceptible at low temperatures and resistant at high temperatures at all stages of growth; R-type 7, plants very susceptible at both low and high temperatures in the seedling stage and at low temperatures in later stages; when temperatures are high, plants become more resistant in later stages; R-type 8, plants susceptible at all stages, when rust intensity is low and when not under stress, but become more resistant when intensity is high or under moderate stress in the field. Combinations of the above types were also observed. Techniques for identifying resistance to stripe rust, race specificity of the resistance-types, relationship of plant growth habit and head characteristics to disease intensity, historical significance of various types of resistance in the United States, and methods of using the resistance-types are also discussed. (author)

An integrated translation of design data of a nuclear power plant from a specification-driven plant design system to neutral model data

International Nuclear Information System (INIS)

Mun, Duhwan; Yang, Jeongsam

2010-01-01

How to efficiently integrate and manage lifecycle data of a nuclear power plant has gradually become an important object of study. Because plants usually have a very long period of operation and maintenance, the plant design data need to be presented in a computer-interpretable form and to be independent of any commercial systems. The conversion of plant design data from various design systems into neutral model data is therefore an important technology for the effective operation and maintenance of plants. In this study, a neutral model for the efficient integration of plant design data is chosen from among the currently available options and extended in order to cover the information model requirements of nuclear power plants in Korea. After the mapping of the neutral model and the data model of a specification-driven plant design system, a plant data translator is also implemented in accordance with the schema mapping results.

An integrated translation of design data of a nuclear power plant from a specification-driven plant design system to neutral model data

Energy Technology Data Exchange (ETDEWEB)

Mun, Duhwan, E-mail: dhmun@moeri.re.k [Marine Safety and Pollution Response Research Department, Maritime and Ocean Engineering Research Institute, KORDI, 171 Jang-dong, Yuseong-gu, Daejeon 305-343 (Korea, Republic of); Yang, Jeongsam, E-mail: jyang@ajou.ac.k [Division of Industrial and Information Systems Engineering, Ajou University, San 5, Wonchun-dong, Yeongtong-gu, Suwon 443-749 (Korea, Republic of)

2010-03-15

How to efficiently integrate and manage lifecycle data of a nuclear power plant has gradually become an important object of study. Because plants usually have a very long period of operation and maintenance, the plant design data need to be presented in a computer-interpretable form and to be independent of any commercial systems. The conversion of plant design data from various design systems into neutral model data is therefore an important technology for the effective operation and maintenance of plants. In this study, a neutral model for the efficient integration of plant design data is chosen from among the currently available options and extended in order to cover the information model requirements of nuclear power plants in Korea. After the mapping of the neutral model and the data model of a specification-driven plant design system, a plant data translator is also implemented in accordance with the schema mapping results.

Calibration of a Plant Uptake Model with Plant- and Site-Specific. Data for Uptake of Chlorinated Organic Compounds into Radish

DEFF Research Database (Denmark)

Trapp, Stefan

2015-01-01

The uptake of organic pollutants by plants is an important process for the exposure of humans to toxic chemicals. The objective of this study was to calibrate the parameters of a common plant uptake model by comparison to experimental results from literature. Radish was grown in contaminated soil...... with default data and site-specific data were similar. Deposition from air was the major uptake mechanism into shoots. Transport from soil with resuspended particles was only relevant for the contaminated plot. The calculation results (in dry weight) were most sensitive to changes of the water content of plant...

Standard technical specifications: Babcock and Wilcox plants. Volume 3, Revision 1: Bases (Sections 3.4--3.9)

International Nuclear Information System (INIS)

1995-04-01

This report documents the results of the combined effort of the NRC and the industry to produce improved Standard Technical Specifications (STS), Revision 1 for Babcock and Wilcox Plants. The changes reflected in Revision 1 resulted from the experience gained from license amendment applications to convert to these improved STS or to adopt partial improvements to existing technical specifications. This NUREG is the result of extensive public technical meetings and discussions between the Nuclear Regulatory Commission (NRC) staff and various nuclear power plant licensees, Nuclear Steam Supply System (NSSS) Owners Groups, NSSS vendors, and the Nuclear Energy Institute (NEI). The improved STS were developed based on the criteria in the Final Commission Policy Statement on Technical Specifications Improvements for Nuclear Power Reactors, dated July 22, 1993. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes. Volume 1 contains the Specifications for all chapters and sections of the improved STS. Volume 2 contains the Bases for Chapters 2.0 and 3.0, and Sections 3.1--3.3 of the improved STS. Volume 3 contains the Bases for Sections 3.4--3.9 of the improved STS

Plants of the fynbos biome harbour host species-specific bacterial communities.

Science.gov (United States)

Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

2016-08-01

The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Individual plant examination and future PRA applications

International Nuclear Information System (INIS)

Monty, B.S.; Sursock, J.P.; Thierry, R.J.

1992-01-01

PRA is being used in many areas of plant operation as has been demonstrated in previous studies. With the U.S. NRC's emphasis on the use of risk to identify plant vulnerabilities and the development of plant specific PRA models for all plants, it is expected that the use of PRA will be expanded. Key areas where this is expected to occur include the development of risk-based Technical Specifications, risk management, and risk-centered maintenance programs. This paper focuses on the Individual Plant Examination requirement and the possible uses of risk-based methods in controlling plant operation to enhance plant safety and availability, and how the IPE requirement will potentially further this area of development. (orig./DG)

Use of plant specific information in life management

International Nuclear Information System (INIS)

Simola, K.; Talja, H.

2002-01-01

In plant life management decisions are made on prevention and mitigation measures of ageing phenomena. In these processes, information from several sources has to be combined, and the decisions are based on data and analyses including lots of uncertainties. In order to make good decisions, the uncertainties and limitations related to both analyses and the raw data should be recognised. A schematic presentation of the information used in the decision making with an emphasis on data needs and analyses for the technical life assessment of a component is given. On the way from the raw data to the final decision on ageing management there are several steps where engineering judgement is used or more sophisticated analyses are made. In this paper we present a view upon the decision making process in managing the ageing of components, systems and structures. Further, we propose practices to improve the transparency of ageing analyses and means to improve the availability and usability of plant specific information for ageing management purposes. The availability of plant specific information and easy access to these records are vital for the efficient ageing management. Often, the data collection and record keeping has not been organised in an efficient way and the use of experience data is very laborious. As illustrated, a lot of plant specific information is needed in ageing assessment. It is also very important to ensure that the information is up-to-date, e.g. possible modifications are taken into account in lifetime predictions. As an example of improvement in the data collection practices we shortly summarise the pipeline analysis and monitoring system that VTT is developing together with TVO. The system is meant to contain all up-to-date information necessary to analyse and monitor piping systems of an operating plant. The core of the system contains five databases. Piping database contains information like geometry, material, loading, detected cracks etc. All

Consequences of intra-specific metabolic diversity in plants for soil organisms : a baseline approach for evaluating ecological effects of genetic modifications

NARCIS (Netherlands)

Kabouw, P.

2012-01-01

Plant intra-specific variation, i.e. variation within a plant species, is known to affect organisms that are directly associated to plants. These effects may be due to for example differences in nutritional quality or defensive metabolites. Plant intra-specific variation can also affect

Compositions and methods for xylem-specific expression in plant cells

Energy Technology Data Exchange (ETDEWEB)

Han, Kyung-Hwan; Ko, Jae-Heung

2017-12-19

The invention provides promoter sequences that regulate specific expression of operably linked sequences in developing xylem cells and/or in developing xylem tissue. The developing xylem-specific sequences are exemplified by the DX5, DX8, DX11, and DX15 promoters, portions thereof, and homologs thereof. The invention further provides expression vectors, cells, tissues and plants that contain the invention's sequences. The compositions of the invention and methods of using them are useful in, for example, improving the quantity (biomass) and/or the quality (wood density, lignin content, sugar content etc.) of expressed biomass feedstock products that may be used for bioenergy, biorefinary, and generating wood products such as pulp, paper, and solid wood.

Screening of potential medicinal plants from District Sawat specific for controlling women diseases

International Nuclear Information System (INIS)

Sarwat, A.; Shinwari, Z.K.; Ahmad, N.

2012-01-01

Ethnobotany provides a scientific rationale to identify medicinally important plant species, especially for finding new drugs that play vital role in the treatment of different diseases. This ethnobotanical survey of Swat, Khyber Pakhtunkhwa (KP) was carried out to identify medicinally important plant species that are traditionally used to treat gynecological disorders and infectious diseases, and to study their antimicrobial potential against pathogens that cause infections in females. The antimicrobial activities were investigated using the well diffusion method against four different bacterial strains and one fungal strain. Results showed that out of 12 plants studied, seven plants exhibited inhibitory effects against Candida albicans, Staphylococcus aureus, Klebsiella pneumoniae and Escherichia coli. Woodfordia fruticosa, Quercus dilatata, Erythrina variegata, Ficus religiosa and Berberis lycium showed high antifungal activity against C. albicans with minimum inhibitory concentration (MIC) values of 2.5, 1.25, 0.625, 1.25, 0.3125 mg/ml and minimum bactericidal concentration (MBC) values of 5, 2.5, 1.25, 2.5, 0.625 mg/ml, respectively. Both Woodfordia fruticosa and Quercus dilatata showed antimicrobial potential against E. coli and K. pneumoniae with similar MIC values of 2.5 mg/ml and MBC values of 5 mg/ml. Plants exhibiting inhibitory potential against S. aureus were Woodfordia fruticosa, Quercus dilatata, Azadirachta indica and Curcuma longa and all of them possessed similar MIC values of 5 mg/ml and MBC values of 2.5 mg/ml, respectively. None of the plants showed antimicrobial activity against Pseudomonas aeruginosa. Proximate analysis showed that in comparative assessment of the various species, Zanthoxylum alatum had the highest fat and energy values. (author)

Plant specific risk informed decision making -a vision for Indian PHWR

International Nuclear Information System (INIS)

Guptan, Rajee; Mohan, Nalini; Ghadge, S.G.; Bajaj, S.S.

2006-01-01

The objective of Nuclear Power Plant (NPP) safety is to ensure and demonstrate that the risk from NPP to public and plant personnel is acceptably low. As a supplement to the deterministic approach, use of probabilistic techniques has been gaining grounds. Probabilistic Safety Assessment (PSA) is a popular international practice to calculate plant risk to the public, environment and plant personnel, in the event of an accident taking place in the plant. The risk posed by Nuclear Reactors to the Public at large is a very important issue in the public acceptance of a Nuclear Power Programme in any country. Risk Definition, generally accepted at present as the measure of possibility for an accidental event and severity of its effects to occur, simultaneously comprises both the probability (frequency) of potential damage occurrence and extent of this damage. NPCIL' s vision is to provide safe, reliable and cost effective energy to the nation by ensuring safe operation of the plants, limiting radiation exposure to plant personnel and public within prescribed limits. To achieve this vision our mission is to enhance the technical competency, resources and the awareness towards improved safety culture specific to Probabilistic Safety Assessment for applying PSA Studies to Risk Informed Decision making. This mission translates into the goal of completion of full scope PSA, with the co-operation and synergetic efforts of the Head quarters and Operating Station experts. NPCIL will then be self sufficient in applying Probabilistic Studies in Risk Informed Decision making to minimize risk and back fitting design changes to optimize the existing design and operating practices, thus providing for safe, reliable and cost effective energy to the nation. (author)

Specificity of salt marsh diazotrophs for vegetation zones and plant hosts

Directory of Open Access Journals (Sweden)

Debra Aline Davis

2012-03-01

Full Text Available Salt marshes located on the east coast of temperate North America are highly productive, typically nitrogen-limited, and support diverse assemblages of nitrogen fixing (diazotrophic bacteria. The distributions of these diazotrophs are strongly influenced by plant host and abiotic environmental parameters. Crab Haul Creek Basin, North Inlet, SC, USA is a tidally dominated marsh that displays discrete plant zones distributed along an elevation gradient from the tidal creek bank to the terrestrial forest. These zones are defined by gradients of abiotic environmental variables, particularly salinity and sulfide. DGGE fingerprinting and phylogenetic analyses of recovered sequences demonstrated that the distributions of some diazotrophs indicate plant host specificity and that diazotroph assemblages across the marsh gradient are heavily influenced by edaphic conditions. Broadly distributed diazotrophs capable of maintaining populations in all environmental conditions across the gradient are also present in these assemblages. Parsimony test results confirm that diazotroph assemblages in different plant zones are significantly (p<0.01 different across the marsh landscape. Results also indicated that diazotroph assemblages associated with different plant hosts growing in the same area of the marsh were structurally similar confirming the influence of edaphic parameters on these assemblages. Principal Component Analysis of DGGE gel banding patterns confirmed these results. This article reviews and analyzes data from North Inlet Estuary, addressing diazotroph assemblage structure and the influence of plant host and environmental conditions. New data demonstrate the heterogeneity of salt marsh rhizosphere microenvironments, and corroborate previous findings from different plant hosts growing at several locations within this estuary. These data support the hypothesis that the biogeography of microorganisms is non-random and is partially driven by

Optimisation of technical specifications using probabilistic methods

International Nuclear Information System (INIS)

Ericsson, G.; Knochenhauer, M.; Hultqvist, G.

1986-01-01

During the last few years the development of methods for modifying and optimising nuclear power plant Technical Specifications (TS) for plant operations has received increased attention. Probalistic methods in general, and the plant and system models of probabilistic safety assessment (PSA) in particular, seem to provide the most forceful tools for optimisation. This paper first gives some general comments on optimisation, identifying important parameters and then gives a description of recent Swedish experiences from the use of nuclear power plant PSA models and results for TS optimisation

Nanobody-Directed Specific Degradation of Proteins by the 26S-Proteasome in Plants

OpenAIRE

Baudisch, Bianca; Pfort, Ingrid; Sorge, Eberhard; Conrad, Udo

2018-01-01

Here, we present data showing the directed degradation of target proteins recognized by a specific nanobody in transgenic plants. Green fluorescent protein was depleted by a chimeric nanobody fused to a distinct F-box domain, which enables protein degradation via the ubiquitin proteasome pathway. This technique could thus be used to knock out other proteins of interest in planta using specific, high-affinity binding proteins.

Nanobody-Directed Specific Degradation of Proteins by the 26S-Proteasome in Plants.

Science.gov (United States)

Baudisch, Bianca; Pfort, Ingrid; Sorge, Eberhard; Conrad, Udo

2018-01-01

Here, we present data showing the directed degradation of target proteins recognized by a specific nanobody in transgenic plants. Green fluorescent protein was depleted by a chimeric nanobody fused to a distinct F-box domain, which enables protein degradation via the ubiquitin proteasome pathway. This technique could thus be used to knock out other proteins of interest in planta using specific, high-affinity binding proteins.

A decision support system for identifying abnormal operating procedures in a nuclear power plant

International Nuclear Information System (INIS)

Hsieh, Min-Han; Hwang, Sheue-Ling; Liu, Kang-Hong; Liang, Sheau-Farn Max; Chuang, Chang-Fu

2012-01-01

Highlights: ► A decision support system has been constructed and verified. ► The operator's decision-making time was decreased by about 25%. ► The accuracy was increased by about 18%. ► The system prevents overlooking important information. ► Fewer erroneous solutions were implemented, and the mental workload was reduced. - Abstract: In order to prevent safety hazards that can result from inappropriate decisions made by the operators of a nuclear power plant (NPP), this study was undertaken to develop a decision support system to reduce the complexity of the decision-making process by aiding operators’ cognitive activities, integrating unusual symptoms, and identifying the most suitable abnormal operating procedure (AOP) for operators. The study was conducted from the perspective of human factors engineering in order to compare the process that operators originally used to select an AOP with a process that included a support system for AOP identification. The results of the study indicated that the existence of a support system reduces errors by quickly suggesting likely AOPs. With such a support system in place, there were clear improvements in human performance, i.e., decision-making time decreased by about 25%, and the accuracy of the operators’ decisions, judged by the successful resolution of specific problems, increased by about 18%. In addition, there were fewer erroneous solutions implemented, and the mental workload was reduced. Hence, the decision support system is proposed as a training tool in identifying AOPs in the main control room (MCR).

The development of specific reliability database for a Korean Nuclear Power Plant

International Nuclear Information System (INIS)

Park, S.K.; Park, B.L.; Kim, M.R.; Jeong, B.H.; Kwon, J.J.

2001-01-01

The object of this study is to develop reliability database for PSA application such as failure rate for safety related components, test and maintenance unavailability and common cause failure factors except for initiating event frequencies during the period of 10 years from 1990 to 1999. In this study we developed plant-specific reliability database for PSA (Probabilistic Safety Assessment) application and compared it with generic reliability database developed in the US such as EPRI-URD, IEEE-500, NUCLARR etc, in the component type basis. We have found that there are some general differences in the component failure rate and test and maintenance unavailability. We described the characteristics of differences for some important component types. We also analyzed the reasons for the differences in the aspect of maintenance terms such as maintenance policy and maintenance practice. We found that maintenance terms are important factors for the numbers of plant-specific reliability database. (author)

Saporin-conjugated tetramers identify efficacious anti-HIV CD8+ T-cell specificities

DEFF Research Database (Denmark)

Leitman, Ellen M.; Palmer, Christine D.; Buus, Søren

2017-01-01

Antigen-specific T-cells are highly variable, spanning potent antiviral efficacy and damaging auto-reactivity. In virus infections, identifying the most efficacious responses is critical to vaccine design. However, current methods depend on indirect measures or on ex vivo expanded CTL clones. We...

Tamarisk coalition - native riparian plant materials program

Science.gov (United States)

Stacy Kolegas

2012-01-01

The Tamarisk Coalition (TC), a nonprofit organization dedicated to riparian restoration in the western United States, has created a Native Plant Materials Program to address the identified need for native riparian plant species for use in revegetation efforts on the Colorado Plateau. The specific components of the Native Plant Materials Program include: 1) provide seed...

Genetics and molecular mapping of genes for race-specific all-stage resistance and non-race-specific high-temperature adult-plant resistance to stripe rust in spring wheat cultivar Alpowa.

Science.gov (United States)

Lin, F; Chen, X M

2007-05-01

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most widespread and destructive wheat diseases worldwide. Growing resistant cultivars is the preferred control of the disease. The spring wheat cultivar 'Alpowa' has both race-specific, all-stage resistance and non-race-specific, high-temperature adult-plant (HTAP) resistances to stripe rust. To identify genes for the stripe rust resistances, Alpowa was crossed with 'Avocet Susceptible' (AVS). Seedlings of the parents, and F(1), F(2) and F(3) progeny were tested with races PST-1 and PST-21 of P. striiformis f. sp. tritici under controlled greenhouse conditions. Alpowa has a single partially dominant gene, designated as YrAlp, conferring all-stage resistance. Resistance gene analog polymorphism (RGAP) and simple sequence repeat (SSR) techniques were used to identify molecular markers linked to YrAlp. A linkage group of five RGAP markers and two SSR markers was constructed for YrAlp using 136 F(3) lines. Amplification of a set of nulli-tetrasomic Chinese Spring lines with RGAP markers Xwgp47 and Xwgp48 and the two SSR markers indicated that YrAlp is located on the short arm of chromosome 1B. To map quantitative trait loci (QTLs) for the non-race-specific HTAP resistance, the parents and 136 F(3) lines were tested at two sites near Pullman and one site near Mount Vernon, Washington, under naturally infected conditions. A major HTAP QTL was consistently detected across environments and was located on chromosome 7BL. Because of its chromosomal location and the non-race-specific nature of the HTAP resistance, this gene is different from previously described genes for adult-plant resistance, and is therefore designated Yr39. The gene contributed to 64.2% of the total variation of relative area under disease progress curve (AUDPC) data and 59.1% of the total variation of infection type data recorded at the heading-flowering stages. Two RGAP markers, Xwgp36 and Xwgp45 with the highest R (2) values

Standard Technical Specifications General Electric plants, BWR/4:Bases (Sections 3.4-3.10). Volume 3, Revision 1

International Nuclear Information System (INIS)

1995-04-01

This report documents the results of the combined effort of the NRC and the industry to produce improved Standard Technical Specifications (STS), Revision 1 for General Electric BWR/4 Plants. The changes reflected in Revision 1 resulted from the experience gained from license amendment applications to convert to these improved STS or to adopt partial improvements to existing technical specifications. This NUREG is the result of extensive public technical meetings and discussions between the Nuclear Regulatory Commission (NRC) staff and various nuclear power plant licensees, Nuclear Steam Supply System (NSSS) Owners Groups, NSSS vendors, and the Nuclear Energy Institute (NEI). The improved STS were developed based on the criteria in the Final Commission Policy Statement on Technical Specifications Improvements for Nuclear Power Reactors, dated July 22, 1993. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes. Volume 1 contains the specifications for all chapters and sections of the improved STS. Volume 2 contains he Bases for Chapters 2.0 and 3.0, and Sections 3.1-3.3 of the improved STS. This document, Volume 3, contains the Bases for Sections 3.4-3.10 of the improved STS

Standard Technical Specifications General Electric plants, BWR/4: Bases (Sections 2.0-3.3). Volume 2, Revision 1

International Nuclear Information System (INIS)

1995-04-01

This report documents the results of the combined effort of the NRC and the industry produce improved Standard Technical Specifications (STS), Revision 1 for General Electric BWR/4 Plants. The changes reflected in Revision 1 resulted from the experience gained from license amendment applications to convert to these improved ST or to adopt partial improvements to existing technical specifications. This NUREG is the result of extensive public technical meetings and discussions between the Nuclear Regulatory Commission (NRC) staff and various nuclear power plant licensees, Nuclear Steam Supply System (NSSS) Owners Groups, NSSS vendors, and the Nuclear Energy Institute (NEI). The improved STS were developed based on the criteria in the Final Commission Policy Statement on Technical Specifications Improvements for Nuclear Power Reactors, dated July 22, 1993. The improved STS will be used as the basis for individual nuclear power plant licensees to develop improved plant-specific technical specifications. This report contains three volumes. Volume I contains the Specifications for all chapters and sections of the improved STS. This document, Volume 2, contains the Bases for Chapters 2.0 and 3.0, and Sections 3.1-3.3 of the improved STS. Volume 3 contains the Bases for Sections 3.4-3.10 of the improved STS

Family-specific vs. universal PCR primers for the study of mitochondrial DNA in plants

Directory of Open Access Journals (Sweden)

Aleksić Jelena M.

2016-01-01

Full Text Available Mitochondrial genomes (mtDNAs or mitogenomes of seed plants are characterized by a notoriously unstable organization on account of which available so-called universal or consensus primers may fail to fulfil their foreseen function - amplification of various mtDNA regions in a broad range of plant taxa. Thus, the primers developed for groups assumed to have similar organization of their mitogenomes, such as families, may facilitate a broader usage of more variable non-coding portions of these genomes in group members. Using in silico PCR method and six available complete mitogenomes of Fabaceae, it has been demonstrated that only three out of 36 published universal primer and three Medicago sativa-specific primer pairs that amplify various mtDNA regions are suitable for six representatives of the Fabaceae family upon minor modifications, and develop 21 Fabaceae-specific primer pairs for amplification of all 14 cis-splicing introns in genes of NADH subunits (nad genes which represent the most commonly used non-coding mtDNA regions in various studies in plants. Using the same method and six available complete mitogenomes of representatives of related families Cucurbitaceae, Euphorbiaceae and Rosaceae and a model plant, Arabidopsis thaliana, it has further been demonstrated that applicability of newly developed primer pairs for amplification of nad introns in more or less related taxa was dependent not only on species evolutionary distances but also on their genome sizes. A reported set of 24 primer pairs is a valuable resource which may facilitate a broader usage of mtDNA variability in future studies at both intra- and inter-specific levels in Fabaceae, which is the third largest family of flowering plants rarely studied at the mtDNA level, and in other more or less related taxa. [Projekat Ministarstva nauke Republike Srbije, br. 173005

STEPS: source term estimation based on plant status phase 0 - the technical specifications of the containment module

International Nuclear Information System (INIS)

Vamanu, D.V.

1998-01-01

location of radioactive leaks (sources) in a representative variety of LWRs, the most probable routes that leaks would follow from containments to the environment (pathways), the depletion, including safety-engineered reduction mechanisms mitigating releases (release phenomenology and control modeling) and the evaluation of the radioactivity effectively escaping from plant confinements (off-site risk potential). The main thrust and scientific challenge in developing the specifications rested on the effort to identify, critically review, adapt and articulate into a 'do-able' structure a disconcerting variety of models and constitutive equations for the complex phenomenology of radioactive releases to reactor containments, and its dynamics featuring natural and safety-engineered depletion, on the way to the environment. The emerging CONTAINMENT models and codes, developed in two versions, essentially rely on an inter twinned box-structuring of the release and paths, coupled mass-balance equations and hierarchical inputs addressing different possible levels of knowledge on the plant status during the accident. Subject to international review by the STEPS Contracting Parties, the Technical Specifications of the CONTAINMENT module and the feasibility demonstration codes developed in Bucharest were recognized (Zurich, July 1997; Helsinki, January 1998; Zurich, April 1998) as a valid platform, instrumental collection of models, algorithms and user-interfaces for the foreseen code development. (author)

Infrared spectroscopy of pollen identifies plant species and genus as well as environmental conditions.

Directory of Open Access Journals (Sweden)

Boris Zimmermann

Full Text Available BACKGROUND: It is imperative to have reliable and timely methodologies for analysis and monitoring of seed plants in order to determine climate-related plant processes. Moreover, impact of environment on plant fitness is predominantly based on studies of female functions, while the contribution of male gametophytes is mostly ignored due to missing data on pollen quality. We explored the use of infrared spectroscopy of pollen for an inexpensive and rapid characterization of plants. METHODOLOGY: The study was based on measurement of pollen samples by two Fourier transform infrared techniques: single reflectance attenuated total reflectance and transmission measurement of sample pellets. The experimental set, with a total of 813 samples, included five pollination seasons and 300 different plant species belonging to all principal spermatophyte clades (conifers, monocotyledons, eudicots, and magnoliids. RESULTS: The spectroscopic-based methodology enables detection of phylogenetic variations, including the separation of confamiliar and congeneric species. Furthermore, the methodology enables measurement of phenotypic plasticity by the detection of inter-annual variations within the populations. The spectral differences related to environment and taxonomy are interpreted biochemically, specifically variations of pollen lipids, proteins, carbohydrates, and sporopollenins. The study shows large variations of absolute content of nutrients for congenital species pollinating in the same environmental conditions. Moreover, clear correlation between carbohydrate-to-protein ratio and pollination strategy has been detected. Infrared spectral database with respect to biochemical variation among the range of species, climate and biogeography will significantly improve comprehension of plant-environment interactions, including impact of global climate change on plant communities.

Technical specification improvement through safety margin considerations

International Nuclear Information System (INIS)

Howard, R.C.; Jansen, R.L.

1986-01-01

Westinghouse has developed an approach for utilizing safety analysis margin considerations to improve plant operability through technical specification revision. This approach relies on the identification and use of parameter interrelations and sensitivities to identify acceptable operating envelopes. This paper summarizes technical specification activities to date and presents the use of safety margin considerations as another viable method to obtain technical specification improvement

Transcriptional Profiling Identifies Location-Specific and Breed-Specific Differentially Expressed Genes in Embryonic Myogenesis in Anas Platyrhynchos.

Directory of Open Access Journals (Sweden)

Rong-Ping Zhang

Full Text Available Skeletal muscle growth and development are highly orchestrated processes involving significant changes in gene expressions. Differences in the location-specific and breed-specific genes and pathways involved have important implications for meat productions and meat quality. Here, RNA-Seq was performed to identify differences in the muscle deposition between two muscle locations and two duck breeds for functional genomics studies. To achieve those goals, skeletal muscle samples were collected from the leg muscle (LM and the pectoral muscle (PM of two genetically different duck breeds, Heiwu duck (H and Peking duck (P, at embryonic 15 days. Functional genomics studies were performed in two experiments: Experiment 1 directly compared the location-specific genes between PM and LM, and Experiment 2 compared the two breeds (H and P at the same developmental stage (embryonic 15 days. Almost 13 million clean reads were generated using Illumina technology (Novogene, Beijing, China on each library, and more than 70% of the reads mapped to the Peking duck (Anas platyrhynchos genome. A total of 168 genes were differentially expressed between the two locations analyzed in Experiment 1, whereas only 8 genes were differentially expressed when comparing the same location between two breeds in Experiment 2. Gene Ontology (GO and the Kyoto Encyclopedia of Genes and Genomes pathways (KEGG were used to functionally annotate DEGs (differentially expression genes. The DEGs identified in Experiment 1 were mainly involved in focal adhesion, the PI3K-Akt signaling pathway and ECM-receptor interaction pathways (corrected P-value<0.05. In Experiment 2, the DEGs were associated with only the ribosome signaling pathway (corrected P-value<0.05. In addition, quantitative real-time PCR was used to confirm 15 of the differentially expressed genes originally detected by RNA-Seq. A comparative transcript analysis of the leg and pectoral muscles of two duck breeds not only

A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants.

Directory of Open Access Journals (Sweden)

Dong Wang

2006-11-01

Full Text Available Many biological processes are controlled by intricate networks of transcriptional regulators. With the development of microarray technology, transcriptional changes can be examined at the whole-genome level. However, such analysis often lacks information on the hierarchical relationship between components of a given system. Systemic acquired resistance (SAR is an inducible plant defense response involving a cascade of transcriptional events induced by salicylic acid through the transcription cofactor NPR1. To identify additional regulatory nodes in the SAR network, we performed microarray analysis on Arabidopsis plants expressing the NPR1-GR (glucocorticoid receptor fusion protein. Since nuclear translocation of NPR1-GR requires dexamethasone, we were able to control NPR1-dependent transcription and identify direct transcriptional targets of NPR1. We show that NPR1 directly upregulates the expression of eight WRKY transcription factor genes. This large family of 74 transcription factors has been implicated in various defense responses, but no specific WRKY factor has been placed in the SAR network. Identification of NPR1-regulated WRKY factors allowed us to perform in-depth genetic analysis on a small number of WRKY factors and test well-defined phenotypes of single and double mutants associated with NPR1. Among these WRKY factors we found both positive and negative regulators of SAR. This genomics-directed approach unambiguously positioned five WRKY factors in the complex transcriptional regulatory network of SAR. Our work not only discovered new transcription regulatory components in the signaling network of SAR but also demonstrated that functional studies of large gene families have to take into consideration sequence similarity as well as the expression patterns of the candidates.

Identifying and quantifying energy savings on fired plant using low cost modelling techniques

International Nuclear Information System (INIS)

Tucker, Robert; Ward, John

2012-01-01

Research highlights: → Furnace models based on the zone method for radiation calculation are described. → Validated steady-state and transient models have been developed. → We show how these simple models can identify the best options for saving energy. → High emissivity coatings predicted to give performance enhancement on a fired heater. → Optimal heat recovery strategies on a steel reheating furnace are predicted. -- Abstract: Combustion in fired heaters, boilers and furnaces often accounts for the major energy consumption on industrial processes. Small improvements in efficiency can result in large reductions in energy consumption, CO 2 emissions, and operating costs. This paper will describe some useful low cost modelling techniques based on the zone method to help identify energy saving opportunities on high temperature fuel-fired process plant. The zone method has for many decades, been successfully applied to small batch furnaces through to large steel-reheating furnaces, glass tanks, boilers and fired heaters on petrochemical plant. Zone models can simulate both steady-state furnace operation and more complex transient operation typical of a production environment. These models can be used to predict thermal efficiency and performance, and more importantly, to assist in identifying and predicting energy saving opportunities from such measures as: ·Improving air/fuel ratio and temperature controls. ·Improved insulation. ·Use of oxygen or oxygen enrichment. ·Air preheating via flue gas heat recovery. ·Modification to furnace geometry and hearth loading. There is also increasing interest in the application of refractory coatings for increasing surface radiation in fired plant. All of the techniques can yield savings ranging from a few percent upwards and can deliver rapid financial payback, but their evaluation often requires robust and reliable models in order to increase confidence in making financial investment decisions. This paper gives

Biochemical characterization of the tomato phosphatidylinositol-specific phospholipase C (PI-PLC) family and its role in plant immunity

NARCIS (Netherlands)

Abd-El-Haliem, Ahmed; Vossen, J.H.; Zeijl, van Arjan; Dezhsetan, Sara; Testerink, Christa; Seidl, M.F.; Beck, Martina; Strutt, James; Robatzek, Silke; Joosten, M.H.A.J.

2016-01-01

Plants possess effective mechanisms to quickly respond to biotic and abiotic stresses. The rapid activation of phosphatidylinositol-specific phospholipase C (PLC) enzymes occurs early after the stimulation of plant immune-receptors. Genomes of different plant species encode multiple PLC homologs

The polyphenol oxidase gene family in land plants: Lineage-specific duplication and expansion

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Tran Lan T

2012-08-01

Full Text Available Abstract Background Plant polyphenol oxidases (PPOs are enzymes that typically use molecular oxygen to oxidize ortho-diphenols to ortho-quinones. These commonly cause browning reactions following tissue damage, and may be important in plant defense. Some PPOs function as hydroxylases or in cross-linking reactions, but in most plants their physiological roles are not known. To better understand the importance of PPOs in the plant kingdom, we surveyed PPO gene families in 25 sequenced genomes from chlorophytes, bryophytes, lycophytes, and flowering plants. The PPO genes were then analyzed in silico for gene structure, phylogenetic relationships, and targeting signals. Results Many previously uncharacterized PPO genes were uncovered. The moss, Physcomitrella patens, contained 13 PPO genes and Selaginella moellendorffii (spike moss and Glycine max (soybean each had 11 genes. Populus trichocarpa (poplar contained a highly diversified gene family with 11 PPO genes, but several flowering plants had only a single PPO gene. By contrast, no PPO-like sequences were identified in several chlorophyte (green algae genomes or Arabidopsis (A. lyrata and A. thaliana. We found that many PPOs contained one or two introns often near the 3’ terminus. Furthermore, N-terminal amino acid sequence analysis using ChloroP and TargetP 1.1 predicted that several putative PPOs are synthesized via the secretory pathway, a unique finding as most PPOs are predicted to be chloroplast proteins. Phylogenetic reconstruction of these sequences revealed that large PPO gene repertoires in some species are mostly a consequence of independent bursts of gene duplication, while the lineage leading to Arabidopsis must have lost all PPO genes. Conclusion Our survey identified PPOs in gene families of varying sizes in all land plants except in the genus Arabidopsis. While we found variation in intron numbers and positions, overall PPO gene structure is congruent with the phylogenetic

Nanobody-Directed Specific Degradation of Proteins by the 26S-Proteasome in Plants

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Bianca Baudisch

2018-02-01

Full Text Available Here, we present data showing the directed degradation of target proteins recognized by a specific nanobody in transgenic plants. Green fluorescent protein was depleted by a chimeric nanobody fused to a distinct F-box domain, which enables protein degradation via the ubiquitin proteasome pathway. This technique could thus be used to knock out other proteins of interest in planta using specific, high-affinity binding proteins.

Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils

CSIR Research Space (South Africa)

Ramond, JB

2015-02-01

Full Text Available identified in a wide range of natural (e.g. soils, sediments, estuarine, and freshwaters) and man created or impacted habitats (e.g. wastewater treatment plants and agricultural soils). However, little is known on the plant-species association of AOBs...

Methodology for identifying boundaries of systems important to safety in CANDU nuclear power plants

International Nuclear Information System (INIS)

Therrien, S.; Komljenovic, D.; Therrien, P.; Ruest, C.; Prevost, P.; Vaillancourt, R.

2007-01-01

This paper presents a methodology developed to identify the boundaries of the systems important to safety (SIS) at the Gentilly-2 Nuclear Power Plant (NPP), Hydro-Quebec. The SIS boundaries identification considers nuclear safety only. Components that are not identified as important to safety are systematically identified as related to safety. A global assessment process such as WANO/INPO AP-913 'Equipment Reliability Process' will be needed to implement adequate changes in the management rules of those components. The paper depicts results in applying the methodology to the Shutdown Systems 1 and 2 (SDS 1, 2), and to the Emergency Core Cooling System (ECCS). This validation process enabled fine tuning the methodology, performing a better estimate of the effort required to evaluate a system, and identifying components important to safety of these systems. (author)

A novel data mining method to identify assay-specific signatures in functional genomic studies

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Guidarelli Jack W

2006-08-01

Full Text Available Abstract Background: The highly dimensional data produced by functional genomic (FG studies makes it difficult to visualize relationships between gene products and experimental conditions (i.e., assays. Although dimensionality reduction methods such as principal component analysis (PCA have been very useful, their application to identify assay-specific signatures has been limited by the lack of appropriate methodologies. This article proposes a new and powerful PCA-based method for the identification of assay-specific gene signatures in FG studies. Results: The proposed method (PM is unique for several reasons. First, it is the only one, to our knowledge, that uses gene contribution, a product of the loading and expression level, to obtain assay signatures. The PM develops and exploits two types of assay-specific contribution plots, which are new to the application of PCA in the FG area. The first type plots the assay-specific gene contribution against the given order of the genes and reveals variations in distribution between assay-specific gene signatures as well as outliers within assay groups indicating the degree of importance of the most dominant genes. The second type plots the contribution of each gene in ascending or descending order against a constantly increasing index. This type of plots reveals assay-specific gene signatures defined by the inflection points in the curve. In addition, sharp regions within the signature define the genes that contribute the most to the signature. We proposed and used the curvature as an appropriate metric to characterize these sharp regions, thus identifying the subset of genes contributing the most to the signature. Finally, the PM uses the full dataset to determine the final gene signature, thus eliminating the chance of gene exclusion by poor screening in earlier steps. The strengths of the PM are demonstrated using a simulation study, and two studies of real DNA microarray data – a study of

Identifying States along the Hematopoietic Stem Cell Differentiation Hierarchy with Single Cell Specificity via Raman Spectroscopy.

Science.gov (United States)

Ilin, Yelena; Choi, Ji Sun; Harley, Brendan A C; Kraft, Mary L

2015-11-17

A major challenge for expanding specific types of hematopoietic cells ex vivo for the treatment of blood cell pathologies is identifying the combinations of cellular and matrix cues that direct hematopoietic stem cells (HSC) to self-renew or differentiate into cell populations ex vivo. Microscale screening platforms enable minimizing the number of rare HSCs required to screen the effects of numerous cues on HSC fate decisions. These platforms create a strong demand for label-free methods that accurately identify the fate decisions of individual hematopoietic cells at specific locations on the platform. We demonstrate the capacity to identify discrete cells along the HSC differentiation hierarchy via multivariate analysis of Raman spectra. Notably, cell state identification is accurate for individual cells and independent of the biophysical properties of the functionalized polyacrylamide gels upon which these cells are cultured. We report partial least-squares discriminant analysis (PLS-DA) models of single cell Raman spectra enable identifying four dissimilar hematopoietic cell populations across the HSC lineage specification. Successful discrimination was obtained for a population enriched for long-term repopulating HSCs (LT-HSCs) versus their more differentiated progeny, including closely related short-term repopulating HSCs (ST-HSCs) and fully differentiated lymphoid (B cells) and myeloid (granulocytes) cells. The lineage-specific differentiation states of cells from these four subpopulations were accurately identified independent of the stiffness of the underlying biomaterial substrate, indicating subtle spectral variations that discriminated these populations were not masked by features from the culture substrate. This approach enables identifying the lineage-specific differentiation stages of hematopoietic cells on biomaterial substrates of differing composition and may facilitate correlating hematopoietic cell fate decisions with the extrinsic cues that

Medicinal plants of Lorestan

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shahla ahmadi

2010-03-01

Full Text Available Collection and determination of medicinal plants in Lorestan province have been carried out for 6 years in the agriculture and natural resources research of center of Lorestan. The aims of this study were collection and identification the medicinal plans that grow in Loretta province, their distribution, habitat, traditional uses, utilized organ, manner of usage, botany specification, local name, Persian name and scientific name. Material and methods: Medicinal plants were collected from different regions by using field and library study for these goals we prepared a list of recorded medicinal plants from Lorestan, identified the local herbal experts. Results: Finally we collected 151 medicinal plant identified that related to 63 families and 90 genuses. The Lamiaceae, Compositae, Legominosae , Liliaceae, Umbelliferae and . Rosaceae are the greatest family in the Lorestan province. Diction: According to the literature 96 medicinal plans were recorded from Lorestan, but during this study we collected and identified 151 medicinal plants in Lorestan province. Comparing with those that recorded from Bushehr 70 sp.(9, Hormozgan 113 sp.(10, Markazi 144 sp. And Kordestan 144 sp(11. We have more diversity but comparing with Zanjan 163 sp.(13, Hamedan 315 sp.(14 And Qazvin 250 sp.(15 We have less diversity in medicinal plants.

Genome-wide survey and expression analysis of the plant-specific NAC transcription factor family in soybean during development and dehydration stress.

Science.gov (United States)

Le, Dung Tien; Nishiyama, Rie; Watanabe, Yasuko; Mochida, Keiichi; Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo; Tran, Lam-Son Phan

2011-08-01

Plant-specific NAC transcription factors (TFs) play important roles in regulating diverse biological processes, including development, senescence, growth, cell division and responses to environmental stress stimuli. Within the soybean genome, we identified 152 full-length GmNAC TFs, including 11 membrane-bound members. In silico analysis of the GmNACs, together with their Arabidopsis and rice counterparts, revealed similar NAC architecture. Next, we explored the soybean Affymetrix array and Illumina transcriptome sequence data to analyse tissue-specific expression profiles of GmNAC genes. Phylogenetic analysis using stress-related NAC TFs from Arabidopsis and rice as seeding sequences identified 58 of the 152 GmNACs as putative stress-responsive genes, including eight previously reported dehydration-responsive GmNACs. We could design gene-specific primers for quantitative real-time PCR verification of 38 out of 50 newly predicted stress-related genes. Twenty-five and six GmNACs were found to be induced and repressed 2-fold or more, respectively, in soybean roots and/or shoots in response to dehydration. GmNAC085, whose amino acid sequence was 39%; identical to that of well-known SNAC1/ONAC2, was the most induced gene upon dehydration, showing 390-fold and 20-fold induction in shoots and roots, respectively. Our systematic analysis has identified excellent tissue-specific and/or dehydration-responsive candidate GmNAC genes for in-depth characterization and future development of improved drought-tolerant transgenic soybeans.

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

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Dunja Knapp

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

Evaluating the influence of plant-specific physiological parameterizations on the partitioning of land surface energy fluxes

Science.gov (United States)

Sulis, Mauro; Langensiepen, Matthias; Shrestha, Prabhakar; Schickling, Anke; Simmer, Clemens; Kollet, Stefan

2015-04-01

Vegetation has a significant influence on the partitioning of radiative forcing, the spatial and temporal variability of soil water and soil temperature. Therefore plant physiological properties play a key role in mediating and amplifying interactions and feedback mechanisms in the soil-vegetation-atmosphere continuum. Because of the direct impact on latent heat fluxes, these properties may also influence weather generating processes, such as the evolution of the atmospheric boundary layer (ABL). In land surface models, plant physiological properties are usually obtained from literature synthesis by unifying several plant/crop species in predefined vegetation classes. In this work, crop-specific physiological characteristics, retrieved from detailed field measurements, are included in the bio-physical parameterization of the Community Land Model (CLM), which is a component of the Terrestrial Systems Modeling Platform (TerrSysMP). The measured set of parameters for two typical European mid-latitudinal crops (sugar beet and winter wheat) is validated using eddy covariance measurements (sensible heat and latent heat) over multiple years from three measurement sites located in the North Rhine-Westphalia region, Germany. We found clear improvements of CLM simulations, when using the crop-specific physiological characteristics of the plants instead of the generic crop type when compared to the measurements. In particular, the increase of latent heat fluxes in conjunction with decreased sensible heat fluxes as simulated by the two new crop-specific parameter sets leads to an improved quantification of the diurnal energy partitioning. These findings are cross-validated using estimates of gross primary production extracted from net ecosystem exchange measurements. This independent analysis reveals that the better agreement between observed and simulated latent heat using the plant-specific physiological properties largely stems from an improved simulation of the

Improving chemistry performance in CANDU plants

International Nuclear Information System (INIS)

Turner, C.; Guzonas, D.

2010-01-01

There is a strong interplay between coolant chemistry and materials selection in any nuclear power plant system. To achieve the design life of reactor components it is necessary to monitor and control relevant chemistry parameters, such as ionic conductivity, pH, concentrations of dissolved ions and redox species (e.g., hydrogen, hydrazine, oxygen) and the concentrations of suspended corrosion products. Chemistry specifications are set to achieve a balance between the sometimes conflicting requirements to minimize corrosion and radiological dose and to minimize operating and maintenance costs over the lifetime of the plant. For the past decade, Atomic Energy of Canada Limited (AECL) has taken a rigorous and disciplined approach to reviewing and updating all aspects of chemistry control in the CANDU® nuclear power plant (NPP). This approach has included proactively reviewing chemistry operating experience from existing CANDU® and other water-cooled NPPs worldwide to identify and address emerging issues, updating all of our chemistry control documentation to ensure that each chemistry parameter is linked to a specific requirement (e.g., reduce activity transport, monitor for condenser leak) and incorporating the latest results from our Research and Development (R and D) programs to ensure that all chemistry specifications are supported by a sound rationale. The results of this review and update have been incorporated into updated chemistry specifications and, in some cases, modified operating procedures for new and existing plants. In addition, recommendations have been made for design modifications to improve chemistry control in new build plants, especially during periods of shutdown and startup when chemistry control has traditionally been more challenging. Chemistry control in new-build CANDU® plants will rely increasingly on the use of on-line instrumentation interfaced directly to AECL's state-of-the-art chemistry monitoring, diagnostics and analysis

DNA binding by the plant-specific NAC transcription factors in crystal and solution

DEFF Research Database (Denmark)

Welner, Ditte Hededam; Lindemose, Søren; Grossmann, J. Günter

2012-01-01

angle X-ray scattering on complexes with oligonucleotides, mutagenesis and (DNase I and uranyl photo-) footprinting, is combined to form a structural view of DNA-binding, and for the first time provide experimental evidence for the speculated relationship between plant-specific NAC proteins, WRKY...

A Complementary Bioinformatics Approach to Identify Potential Plant Cell Wall Glycosyltransferase-Encoding Genes

DEFF Research Database (Denmark)

Egelund, Jack; Skjøt, Michael; Geshi, Naomi

2004-01-01

Plant cell wall (CW) synthesizing enzymes can be divided into the glycan (i.e. cellulose and callose) synthases, which are multimembrane spanning proteins located at the plasma membrane, and the glycosyltransferases (GTs), which are Golgi localized single membrane spanning proteins, believed....... Although much is known with regard to composition and fine structures of the plant CW, only a handful of CW biosynthetic GT genes-all classified in the CAZy system-have been characterized. In an effort to identify CW GTs that have not yet been classified in the CAZy database, a simple bioinformatics...... approach was adopted. First, the entire Arabidopsis proteome was run through the Transmembrane Hidden Markov Model 2.0 server and proteins containing one or, more rarely, two transmembrane domains within the N-terminal 150 amino acids were collected. Second, these sequences were submitted...

De novo assembly and characterization of the transcriptome of the parasitic weed dodder identifies genes associated with plant parasitism.

Science.gov (United States)

Ranjan, Aashish; Ichihashi, Yasunori; Farhi, Moran; Zumstein, Kristina; Townsley, Brad; David-Schwartz, Rakefet; Sinha, Neelima R

2014-11-01

Parasitic flowering plants are one of the most destructive agricultural pests and have major impact on crop yields throughout the world. Being dependent on finding a host plant for growth, parasitic plants penetrate their host using specialized organs called haustoria. Haustoria establish vascular connections with the host, which enable the parasite to steal nutrients and water. The underlying molecular and developmental basis of parasitism by plants is largely unknown. In order to investigate the process of parasitism, RNAs from different stages (i.e. seed, seedling, vegetative strand, prehaustoria, haustoria, and flower) were used to de novo assemble and annotate the transcriptome of the obligate plant stem parasite dodder (Cuscuta pentagona). The assembled transcriptome was used to dissect transcriptional dynamics during dodder development and parasitism and identified key gene categories involved in the process of plant parasitism. Host plant infection is accompanied by increased expression of parasite genes underlying transport and transporter categories, response to stress and stimuli, as well as genes encoding enzymes involved in cell wall modifications. By contrast, expression of photosynthetic genes is decreased in the dodder infective stages compared with normal stem. In addition, genes relating to biosynthesis, transport, and response of phytohormones, such as auxin, gibberellins, and strigolactone, were differentially expressed in the dodder infective stages compared with stems and seedlings. This analysis sheds light on the transcriptional changes that accompany plant parasitism and will aid in identifying potential gene targets for use in controlling the infestation of crops by parasitic weeds. © 2014 American Society of Plant Biologists. All Rights Reserved.

The female gametophyte: an emerging model for cell type-specific systems biology in plant development

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Marc William Schmid

2015-11-01

Full Text Available Systems biology, a holistic approach describing a system emerging from the interactions of its molecular components, critically depends on accurate qualitative determination and quantitative measurements of these components. Development and improvement of large-scale profiling methods (omics now facilitates comprehensive measurements of many relevant molecules. For multicellular organisms, such as animals, fungi, algae, and plants, the complexity of the system is augmented by the presence of specialized cell types and organs, and a complex interplay within and between them. Cell type-specific analyses are therefore crucial for the understanding of developmental processes and environmental responses. This review first gives an overview of current methods used for large-scale profiling of specific cell types exemplified by recent advances in plant biology. The focus then lies on suitable model systems to study plant development and cell type specification. We introduce the female gametophyte of flowering plants as an ideal model to study fundamental developmental processes. Moreover, the female reproductive lineage is of importance for the emergence of evolutionary novelties such as an unequal parental contribution to the tissue nurturing the embryo or the clonal production of seeds by asexual reproduction (apomixis. Understanding these processes is not only interesting from a developmental or evolutionary perspective, but bears great potential for further crop improvement and the simplification of breeding efforts. We finally highlight novel methods, which are already available or which will likely soon facilitate large-scale profiling of the specific cell types of the female gametophyte in both model and non-model species. We conclude that it may take only few years until an evolutionary systems biology approach toward female gametogenesis may decipher some of its biologically most interesting and economically most valuable processes.

Engineering of plants with improved properties as biofuels feedstocks by vessel-specific complementation of xylan biosynthesis mutants

Directory of Open Access Journals (Sweden)

Petersen Pia Damm

2012-11-01

Full Text Available Abstract Background Cost-efficient generation of second-generation biofuels requires plant biomass that can easily be degraded into sugars and further fermented into fuels. However, lignocellulosic biomass is inherently recalcitrant toward deconstruction technologies due to the abundant lignin and cross-linked hemicelluloses. Furthermore, lignocellulosic biomass has a high content of pentoses, which are more difficult to ferment into fuels than hexoses. Engineered plants with decreased amounts of xylan in their secondary walls have the potential to render plant biomass a more desirable feedstock for biofuel production. Results Xylan is the major non-cellulosic polysaccharide in secondary cell walls, and the xylan deficient irregular xylem (irx mutants irx7, irx8 and irx9 exhibit severe dwarf growth phenotypes. The main reason for the growth phenotype appears to be xylem vessel collapse and the resulting impaired transport of water and nutrients. We developed a xylan-engineering approach to reintroduce xylan biosynthesis specifically into the xylem vessels in the Arabidopsis irx7, irx8 and irx9 mutant backgrounds by driving the expression of the respective glycosyltransferases with the vessel-specific promoters of the VND6 and VND7 transcription factor genes. The growth phenotype, stem breaking strength, and irx morphology was recovered to varying degrees. Some of the plants even exhibited increased stem strength compared to the wild type. We obtained Arabidopsis plants with up to 23% reduction in xylose levels and 18% reduction in lignin content compared to wild-type plants, while exhibiting wild-type growth patterns and morphology, as well as normal xylem vessels. These plants showed a 42% increase in saccharification yield after hot water pretreatment. The VND7 promoter yielded a more complete complementation of the irx phenotype than the VND6 promoter. Conclusions Spatial and temporal deposition of xylan in the secondary cell wall of

Environmental Restoration Site-Specific Plan for the Paducah Gaseous Diffusion Plant, FY 93

International Nuclear Information System (INIS)

1993-01-01

This report provides an overview of the major Environmental Restoration (ER) concerns at Paducah Gaseous Diffusion Plant (PGDP). The identified solid waste management units at PGDP are listed. In the Department of Energy (DOE) Five Year Plan development process, one or more waste management units are addressed in a series of activity data sheets (ADSs) which identify planned scope, schedule, and cost objectives that are representative of the current state of planned technical development for individual or multiple sites

Environmental Restoration Site-Specific Plan for the Portsmouth Gaseous Diffusion Plant, FY 93

International Nuclear Information System (INIS)

1993-01-01

The purpose of this Site-Specific Plan (SSP) is to describe past, present, and future activities undertaken to implement Environmental Restoration and Waste Management goals at the Portsmouth Gaseous Diffusion Plant (PORTS). The SSP is presented in sections emphasizing Environmental Restoration description of activities, resources, and milestones

Plant lessons: exploring ABCB functionality through structural modeling

Directory of Open Access Journals (Sweden)

Aurélien eBailly

2012-01-01

Full Text Available In contrast to mammalian ABCB1 proteins, narrow substrate specificity has been extensively documented for plant orthologs shown to catalyze the transport of the plant hormone, auxin. Using the crystal structures of the multidrug exporters Sav1866 and MmABCB1 as templates, we have developed structural models of plant ABCB proteins with a common architecture. Comparisons of these structures identified kingdom-specific candidate substrate-binding regions within the translocation chamber formed by the transmembrane domains of ABCBs from the model plant Arabidopsis. These results suggest an early evolutionary divergence of plant and mammalian ABCBs. Validation of these models becomes a priority for efforts to elucidate ABCB function and manipulate this class of transporters to enhance plant productivity and quality.

Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

NARCIS (Netherlands)

van Leeuwen, E.M.; Karssen, L.C.; Deelen, J.; Isaacs, A.; Medina-Gomez, C.; Mbarek, H.; Kanterakis, A.; Trompet, S.; Postmus, I.; Verweij, N.; van Enckevort, D.; Huffman, J.E.; White, C.C.; Feitosa, M.F.; Bartz, T.M.; Manichaikul, A.; Joshi, P.K.; Peloso, G.M.; Deelen, P.; Dijk, F.; Willemsen, G.; de Geus, E.J.C.; Milaneschi, Y.; Penninx, B.W.J.H.; Francioli, L.C.; Menelaou, A.; Pulit, S.L.; Rivadeneira, F.; Hofman, A.; Oostra, B.A.; Franco, O.H.; Mateo Leach, I.; Beekman, M.; de Craen, A.J.; Uh, H.W.; Trochet, H.; Hocking, L.J.; Porteous, D.J.; Sattar, N.; Packard, C.J.; Buckley, B.M.; Brody, J.A.; Bis, J.C.; Rotter, J.I.; Mychaleckyj, J.C.; Campbell, H.; Duan, Q.; Lange, L.A.; Wilson, J.F.; Hayward, C.; Polasek, O.; Vitart, V.; Rudan, I.; Wright, A.F.; Rich, S.S.; Psaty, B.M.; Borecki, I.B.; Kearney, P.M.; Stott, D.J.; Cupples, L.A.; Jukema, J.W.; van der Harst, P.; Sijbrands, E.J.; Hottenga, J.J.; Uitterlinden, A.G.; Swertz, M.A.; van Ommen, G.J.B; Bakker, P.I.W.; Slagboom, P.E.; Boomsma, D.I.; Wijmenga, C.; van Duijn, C.M.

2015-01-01

Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (∼35,000 samples) with the population-specific reference panel created

Best practices in identifying, reporting and screening operating experience at nuclear power plants

International Nuclear Information System (INIS)

2008-03-01

IAEA Safety Standards Series No. SF-1 entitled Fundamental Safety Principles: Safety Fundamentals states the need for operating organizations to establish a programme for the collection and analysis of operating experience in nuclear power plants. Such a programme ensures that operating experience is analysed, events important to safety are reviewed in depth, lessons learned are disseminated to the staff of the organization and to relevant national and international organizations, and corrective actions are effectively implemented. This publication has been developed to provide advice and assistance to nuclear installations, and related institutions including contractors and support organizations to strengthen and enhance their own feedback process through the implementation of best practices in identifying, reporting and screening processes and to assess the effectiveness of the above areas. To support a proactive safety management approach the nuclear installations are enhancing the operating experience feedback (OEF) processes. For this purpose, the nuclear industry is striving to collect more information on occurrences that are useful to address the early signs of declining performance and improve operational safety performance. In this environment a strong reporting culture that motivates people to identify and report issues is an important attribute. As a consequence, the number and diversity of issues identified increases, and there is a need to set thresholds of screening for further treatment. Thus, the establishment of an effective identification, reporting and screening process is very beneficial to streamline the efforts, and ensure that major incidents and latent weaknesses are being addressed and that operating experience is treated according to its significance. This leads to improved safety and production. This publication was written to complement the publication IAEA Services Series No. 10 - PROSPER Guidelines - Guidelines for Peer Review and for

Standard technical specifications, Westinghouse Plants: Bases (Sections 3.4--3.9). Volume 3, Revision 1

International Nuclear Information System (INIS)

1995-04-01

This NUREG contains the improved Standard Technical Specifications (STS) for Westinghouse plants. Revision 1 incorporates the cumulative changes to Revision 0, which was published in September 1992. The changes reflected in Revision 1 resulted from the experience gained from license amendment applications to convert to these improved STS or to adopt partial improvements to existing technical specifications. This NUREG is the result of extensive public technical meetings and discussions between the Nuclear Regulatory Commission (NRC) staff and various nuclear power plant licensees, Nuclear Steam Supply System (NSSS) Owners Groups, specifically the Westinghouse Owners Group (WOG), NSSS vendors, and the Nuclear Energy Institute (NEI). The improved STS were developed based on the criteria in the Final Commission Policy Statement on Technical Specifications Improvements for Nuclear Power Reactors, dated July 22, 1993 (58 FR 39132). Licensees are encouraged to upgrade their technical specifications consistent with those criteria and conforming, to the extent practical and consistent with the licensing basis for the facility, to Revision 1 to the improved STS. The Commission continues to place the highest priority on requests for complete conversions to the improved STS. Licensees adopting portions of the improved STS to existing technical specifications should adopt all related requirements, as applicable, to achieve a high degree of standardization and consistency

Standard technical specifications, Westinghouse Plants: Bases (Sections 2.0--3.3). Volume 2, Revision 1

International Nuclear Information System (INIS)

1995-04-01

This NUREG contains the improved Standard Technical Specifications (STS) for Westinghouse plants. Revision 1 incorporates the cumulative changes to Revision 0, which was published in September 1992. The changes reflected in Revision 1 resulted from the experience gained from license amendment applications to convert to these improved STS or to adopt partial improvements to existing technical specifications. This NUREG is the result of extensive public technical meetings and discussions between the Nuclear Regulatory Commission (NRC) staff and various nuclear power plant licensees, Nuclear Steam Supply System (NSSS) Owners Groups, specifically the Westinghouse Owners Group (WOG), NSSS vendors, and the Nuclear Energy Institute (NEI). The improved STS were developed based on the criteria in the Final Commission Policy Statement on Technical Specifications Improvements for Nuclear Power Reactors, dated July 22, 1993 (58 FR 39132). Licensees are encouraged to upgrade their technical specifications consistent with those criteria and conforming, to the extent practical and consistent with the licensing basis for the facility, to Revision 1 to the improved STS. The Commission continues to place the highest priority on requests for complete conversions to the improved STS. Licensees adopting portions of the improved STS to existing technical specifications should adopt all related requirements, as applicable, to achieve a high degree of standardization and consistency

High-Throughput Screening to Identify Regulators of Meiosis-Specific Gene Expression in Saccharomyces cerevisiae.

Science.gov (United States)

Kassir, Yona

2017-01-01

Meiosis and gamete formation are processes that are essential for sexual reproduction in all eukaryotic organisms. Multiple intracellular and extracellular signals feed into pathways that converge on transcription factors that induce the expression of meiosis-specific genes. Once triggered the meiosis-specific gene expression program proceeds in a cascade that drives progress through the events of meiosis and gamete formation. Meiosis-specific gene expression is tightly controlled by a balance of positive and negative regulatory factors that respond to a plethora of signaling pathways. The budding yeast Saccharomyces cerevisiae has proven to be an outstanding model for the dissection of gametogenesis owing to the sophisticated genetic manipulations that can be performed with the cells. It is possible to use a variety selection and screening methods to identify genes and their functions. High-throughput screening technology has been developed to allow an array of all viable yeast gene deletion mutants to be screened for phenotypes and for regulators of gene expression. This chapter describes a protocol that has been used to screen a library of homozygous diploid yeast deletion strains to identify regulators of the meiosis-specific IME1 gene.

Multiplex PCR for specific and robust detection of Xanthomonas campestris pv. musacearum in pure culture and infected plant material

DEFF Research Database (Denmark)

Adriko, John; Aritua, V.; Mortensen, Carmen Nieves

2012-01-01

The present study developed a pathovar-specific PCR for the detection of Xanthomonas campestris pv. musacearum (Xcm), the cause of banana xanthomonas wilt, by amplification of a 265-bp region of the gene encoding the general secretion pathway protein D (GspD). A distinct DNA fragment......-specific PCR was successfully multiplexed with internal control primers targeting 16S rDNA for application on DNA from bacterial cultures and with primers targeting plant mitochondrial 26S rDNA for application on DNA extracted from plant material. Diagnostic discrimination of healthy and infected plants...

A 10-MWe solar-thermal central-receiver pilot plant: Solar facilities design integration. Plant operating/training manual (RADL-Item 2-36)

Science.gov (United States)

1982-07-01

Plant and system level operating instructions are provided for the Barstow Solar Pilot Plant. Individual status instructions are given that identify plant conditions, process controller responsibilities, process conditions and control accuracies, operating envelopes, and operator cautions appropriate to the operating condition. Transition operating instructions identify the sequence of activities to be carried out to accomplish the indicated transition. Most transitions involve the startup or shutdown of an individual flowpath. Background information is provided on collector field operations, and the heliostat groupings and specific commands used in support receiver startup are defined.

The microbiome of medicinal plants: diversity and importance for plant growth, quality and health.

Science.gov (United States)

Köberl, Martina; Schmidt, Ruth; Ramadan, Elshahat M; Bauer, Rudolf; Berg, Gabriele

2013-12-20

Past medicinal plant research primarily focused on bioactive phytochemicals, however, the focus is currently shifting due to the recognition that a significant number of phytotherapeutic compounds are actually produced by associated microbes or through interaction with their host. Medicinal plants provide an enormous bioresource of potential use in modern medicine and agriculture, yet their microbiome is largely unknown. The objective of this review is (i) to introduce novel insights into the plant microbiome with a focus on medicinal plants, (ii) to provide details about plant- and microbe-derived ingredients of medicinal plants, and (iii) to discuss possibilities for plant growth promotion and plant protection for commercial cultivation of medicinal plants. In addition, we also present a case study performed both to analyse the microbiome of three medicinal plants (Matricaria chamomilla L., Calendula officinalis L., and Solanum distichum Schumach. and Thonn.) cultivated on organically managed Egyptian desert farm and to develop biological control strategies. The soil microbiome of the desert ecosystem was comprised of a high abundance of Gram-positive bacteria of prime importance for pathogen suppression under arid soil conditions. For all three plants, we observed a clearly plant-specific selection of the microbes as well as highly specific diazotrophic communities that overall identify plant species as important drivers in structural and functional diversity. Lastly, native Bacillus spec. div. strains were able to promote plant growth and elevate the plants' flavonoid production. These results underline the numerous links between the plant-associated microbiome and the plant metabolome.

Allele-specific deletions in mouse tumors identify Fbxw7 as germline modifier of tumor susceptibility.

Directory of Open Access Journals (Sweden)

Jesus Perez-Losada

Full Text Available Genome-wide association studies (GWAS have been successful in finding associations between specific genetic variants and cancer susceptibility in human populations. These studies have identified a range of highly statistically significant associations between single nucleotide polymorphisms (SNPs and susceptibility to development of a range of human tumors. However, the effect of each SNP in isolation is very small, and all of the SNPs combined only account for a relatively minor proportion of the total genetic risk (5-10%. There is therefore a major requirement for alternative routes to the discovery of genetic risk factors for cancer. We have previously shown using mouse models that chromosomal regions harboring susceptibility genes identified by linkage analysis frequently exhibit allele-specific genetic alterations in tumors. We demonstrate here that the Fbxw7 gene, a commonly mutated gene in a wide range of mouse and human cancers, shows allele-specific deletions in mouse lymphomas and skin tumors. Lymphomas from three different F1 hybrids show 100% allele-specificity in the patterns of allelic loss. Parental alleles from 129/Sv or Spretus/Gla mice are lost in tumors from F1 hybrids with C57BL/6 animals, due to the presence of a specific non-synonymous coding sequence polymorphism at the N-terminal portion of the gene. A specific genetic test of association between this SNP and lymphoma susceptibility in interspecific backcross mice showed a significant linkage (p = 0.001, but only in animals with a functional p53 gene. These data therefore identify Fbxw7 as a p53-dependent tumor susceptibility gene. Increased p53-dependent tumor susceptibility and allele-specific losses were also seen in a mouse skin model of skin tumor development. We propose that analysis of preferential allelic imbalances in tumors may provide an efficient means of uncovering genetic variants that affect mouse and human tumor susceptibility.

Using sensitivity analysis to identify key factors for the propagation of a plant epidemic.

Science.gov (United States)

Rimbaud, Loup; Bruchou, Claude; Dallot, Sylvie; Pleydell, David R J; Jacquot, Emmanuel; Soubeyrand, Samuel; Thébaud, Gaël

2018-01-01

Identifying the key factors underlying the spread of a disease is an essential but challenging prerequisite to design management strategies. To tackle this issue, we propose an approach based on sensitivity analyses of a spatiotemporal stochastic model simulating the spread of a plant epidemic. This work is motivated by the spread of sharka, caused by plum pox virus , in a real landscape. We first carried out a broad-range sensitivity analysis, ignoring any prior information on six epidemiological parameters, to assess their intrinsic influence on model behaviour. A second analysis benefited from the available knowledge on sharka epidemiology and was thus restricted to more realistic values. The broad-range analysis revealed that the mean duration of the latent period is the most influential parameter of the model, whereas the sharka-specific analysis uncovered the strong impact of the connectivity of the first infected orchard. In addition to demonstrating the interest of sensitivity analyses for a stochastic model, this study highlights the impact of variation ranges of target parameters on the outcome of a sensitivity analysis. With regard to sharka management, our results suggest that sharka surveillance may benefit from paying closer attention to highly connected patches whose infection could trigger serious epidemics.

Use of percentile rank sum method in identifying repetitive high occupational radiation dose jobs in a nuclear power plant

International Nuclear Information System (INIS)

Cho, Y.H.; Ko, H.S.; Kim, S.H.; Kang, C.S.; Moon, J.H.; Kim, K.D.

2004-01-01

The cost-effective reduction of occupational radiation dose (ORD) at a nuclear power plant could not be achieved without going through an extensive analysis of accumulated ORD data of existing plants. Through the data analysis, it is required to identify what are the jobs of repetitive high ORD at the nuclear power plant. In general the point value method commonly used, over-estimates the role of mean and median values to identify the high ORD jobs which can lead to misjudgment. In this study, Percentile Rank Sum Method (PRSM) is proposed to identify repetitive high ORD jobs, which is based on non-parametric statistical theory. As a case study, the method is applied to ORD data of maintenance and repair jobs at Kori units 3 and 4 that are pressurized water reactors with 950 MWe capacity and have been operated since 1986 and 1987, respectively in Korea. The results were verified and validated, and PRSM has been demonstrated to be an efficient method of analyzing the data. (authors)

Selenium Content, Influential Factors Within the Plant and the Transformation of Different Selenium Specification

Directory of Open Access Journals (Sweden)

LIU Yuan-yuan

2014-12-01

Full Text Available The paper collected relevant literatures on selenium and explored the function to plant, selenium content, influential factors and selenium specification and transformation. We believed that there should be more deep researches on function of selenium to plant. Approaches of molecular, genetic engineering and isotope could be employed to breed selenium rich crops and possibilities in practice. More efforts should be spent on the technologies research for improving selenium level in crops under natural soil conditions to sustainably utilize the selenium resources.

Economics of production of biogas from specifically-grown plant material. [New Zealand

Energy Technology Data Exchange (ETDEWEB)

Stewart, D. J.

1977-10-15

The production of biogas from plant materials is technologically very simple, and is the only process currently available (other than direct burning) for conversion of cellulose materials into energy or fuels that is feasible at a farm-scale, or even a home-scale, as well as a large industrial plant scale. For this reason the economics of biogas production can be considered at the farm-scale as well as the industrial scale. An accurate assessment of the economics at the farm-scale is possible, because commercially produced units are now available in New Zealand and in operation. However, although large-scale plants have been proposed and costed in the USA for the conversion of the cellulose component of garbage into biogas, operational data are not yet available, and the costing has not been applied to the use of specifically-grown plant material. Nevertheless, the large-scale plants envisaged use a large number of digesters each of 100,000 gallons capacity and can thus be regarded as a combination of farm-size units, although with some economics in digester size, number of pumps required, etc. For these reasons, this review of the economics of biogas production is based on the operation of commercial 20,000 gallon digesters available in NZ for farm-scale use. Factors governing the economics of farm-scale and industrial-scale production of biogas will be discussed in section 6.

Subcellular Targeting of Methylmercury Lyase Enhances Its Specific Activity for Organic Mercury Detoxification in Plants1

Science.gov (United States)

Bizily, Scott P.; Kim, Tehryung; Kandasamy, Muthugapatti K.; Meagher, Richard B.

2003-01-01

Methylmercury is an environmental pollutant that biomagnifies in the aquatic food chain with severe consequences for humans and other animals. In an effort to remove this toxin in situ, we have been engineering plants that express the bacterial mercury resistance enzymes organomercurial lyase MerB and mercuric ion reductase MerA. In vivo kinetics experiments suggest that the diffusion of hydrophobic organic mercury to MerB limits the rate of the coupled reaction with MerA (Bizily et al., 2000). To optimize reaction kinetics for organic mercury compounds, the merB gene was engineered to target MerB for accumulation in the endoplasmic reticulum and for secretion to the cell wall. Plants expressing the targeted MerB proteins and cytoplasmic MerA are highly resistant to organic mercury and degrade organic mercury at 10 to 70 times higher specific activity than plants with the cytoplasmically distributed wild-type MerB enzyme. MerB protein in endoplasmic reticulum-targeted plants appears to accumulate in large vesicular structures that can be visualized in immunolabeled plant cells. These results suggest that the toxic effects of organic mercury are focused in microenvironments of the secretory pathway, that these hydrophobic compartments provide more favorable reaction conditions for MerB activity, and that moderate increases in targeted MerB expression will lead to significant gains in detoxification. In summary, to maximize phytoremediation efficiency of hydrophobic pollutants in plants, it may be beneficial to target enzymes to specific subcellular environments. PMID:12586871

Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.).

Science.gov (United States)

Pradhan, Seema; Kant, Chandra; Verma, Subodh; Bhatia, Sabhyata

2017-01-01

The CCCH zinc finger is a group of proteins characterised by a typical motif consisting of three cysteine residues and one histidine residue. These proteins have been reported to play important roles in regulation of plant growth, developmental processes and environmental responses. In the present study, genome wide analysis of the CCCH zinc finger gene family was carried out in the available chickpea genome. Various bioinformatics tools were employed to predict 58 CCCH zinc finger genes in chickpea (designated CarC3H1-58), which were analysed for their physio-chemical properties. Phylogenetic analysis classified the proteins into 12 groups in which members of a particular group had similar structural organization. Further, the numbers as well as the types of CCCH motifs present in the CarC3H proteins were compared with those from Arabidopsis and Medicago truncatula. Synteny analysis revealed valuable information regarding the evolution of this gene family. Tandem and segmental duplication events were identified and their Ka/Ks values revealed that the CarC3H gene family in chickpea had undergone purifying selection. Digital, as well as real time qRT-PCR expression analysis was performed which helped in identification of several CarC3H members that expressed preferentially in specific chickpea tissues as well as during abiotic stresses (desiccation, cold, salinity). Moreover, molecular characterization of an important member CarC3H45 was carried out. This study provides comprehensive genomic information about the important CCCH zinc finger gene family in chickpea. The identified tissue specific and abiotic stress specific CCCH genes could be potential candidates for further characterization to delineate their functional roles in development and stress.

Risk based optimization of technical specifications for operation of nuclear power plants

International Nuclear Information System (INIS)

1993-12-01

The objective of the report is to present an overview of the risk and reliability based approaches (using a probabilistic safety assessment (PSA)) for improving nuclear power plant technical specifications (TS). In that case, it will provide an information base to the Member States in seeking PSA based applications to enhance the effectiveness of their technical specifications. To achieve this objective, the report discusses the basic objectives and reasons for seeking TS changes, the methods, data requirements and uses of different types of applications, and an overview of different applications that have been completed, including detailed descriptions of selected applications. Refs, figs and tabs

Development of Nested PCR-Based Specific Markers for Detection of Peach Rosette Mosaic Virus in Plant Quarantine.

Science.gov (United States)

Lee, S; Kim, C S; Shin, Y G; Kim, J H; Kim, Y S; Jheong, W H

2016-03-01

The Peach rosette mosaic virus (PRMV) is a plant pathogen of the genus Nepovirus, and has been designated as a controlled quarantine virus in Korea. In this study, a specific reverse transcription (RT)-PCR marker set, nested PCR marker set, and modified-plasmid positive control were developed to promptly and accurately diagnose PRMV at plant-quarantine sites. The final selected PRMV-specific RT-PCR marker was PRMV-N10/C70 (967 bp), and the nested PCR product of 419 bp was finally amplified. The modified-plasmid positive control, in which the SalI restriction-enzyme region (GTCGAC) was inserted, verified PRMV contamination in a comparison with the control, enabling a more accurate diagnosis. It is expected that the developed method will continuously contribute to the plant-quarantine process in Korea.

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome.

Science.gov (United States)

Johnston, Henry Richard; Hu, Yi-Juan; Gao, Jingjing; O'Connor, Timothy D; Abecasis, Gonçalo R; Wojcik, Genevieve L; Gignoux, Christopher R; Gourraud, Pierre-Antoine; Lizee, Antoine; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Kenny, Eimear E; Bustamante, Carlos; Beaty, Terri H; Mathias, Rasika A; Barnes, Kathleen C; Qin, Zhaohui S

2017-04-21

A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.

Specific PCR detection of Fusarium oxysporum f. sp. raphani: a causal agent of Fusarium wilt on radish plants.

Science.gov (United States)

Kim, H; Hwang, S-M; Lee, J H; Oh, M; Han, J W; Choi, G J

2017-08-01

Fusarium oxysporum, a causal agent of Fusarium wilt, is one of the most important fungal pathogens worldwide, and detection of F. oxysporum DNA at the forma specialis level is crucial for disease diagnosis and control. In this study, two novel F. oxysporum f. sp. raphani (For)-specific primer sets were designed, FOR1-F/FOR1-R and FOR2-F/FOR2-R, to target FOQG_17868 and FOQG_17869 ORFs, respectively, which were selected based on the genome comparison of other formae speciales of F. oxysporum including conglutinans, cubense, lycopersici, melonis, and pisi. The primer sets FOR1-F/FOR1-R and FOR2-F/FOR2-R that amplified a 610- and 425-bp DNA fragment, respectively, were specific to For isolates which was confirmed using a total of 40 F. oxysporum isolates. From infected plants, the FOR2-F/FOR2-R primer set directly detected the DNA fragment of For isolates even when the radish plants were collected in their early stage of disease development. Although the loci targeted by the For-specific primer sets were not likely involved in the pathogenesis, the primer set FOR2-F/FOR2-R is available for the determination of pathogenicity of radish-infecting F. oxysporum isolates. This study is the first report providing novel primer sets to detect F. oxysporum f. sp. raphani. Because plant pathogenic Fusarium oxysporum has been classified into special forms based on its host specificity, identification of F. oxysporum usually requires a pathogenicity assay as well as knowledge of the morphological characteristics. For rapid and reliable diagnosis, this study provides PCR primer sets that specifically detect Fusarium oxysporum f. sp. raphani (For) which is a devastating pathogen of radish plants. Because one of the primer sets directly detected the DNA fragment of For isolates from infected plants, the specific PCR method demonstrated in this study will provide a foundation for integrated disease management practices in commodity crops. © 2017 The Society for Applied Microbiology.

Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB).

Science.gov (United States)

Wang, Nai-Jyuan; Lee, Chi-Ching; Cheng, Chao-Sheng; Lo, Wei-Cheng; Yang, Ya-Fen; Chen, Ming-Nan; Lyu, Ping-Chiang

2012-01-01

Plant non-specific lipid transfer proteins (nsLTPs) are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, participating in plant defence activity against bacterial and fungal pathogens, and enhancing cell wall extension in tobacco. However, the lipid transfer mechanism of nsLTPs is still unclear, and comprehensive information of nsLTPs is difficult to obtain. In this study, we identified 595 nsLTPs from 121 different species and constructed an nsLTPs database--nsLTPDB--which comprises the sequence information, structures, relevant literatures, and biological data of all plant nsLTPs http://nsltpdb.life.nthu.edu.tw/. Meanwhile, bioinformatics and statistics methods were implemented to develop a classification method for nsLTPs based on the patterns of the eight highly-conserved cysteine residues, and to suggest strict Prosite-styled patterns for Type I and Type II nsLTPs. The pattern of Type I is C X2 V X5-7 C [V, L, I] × Y [L, A, V] X8-13 CC × G X12 D × [Q, K, R] X2 CXC X16-21 P X2 C X13-15C, and that of Type II is C X4 L X2 C X9-11 P [S, T] X2 CC X5 Q X2-4 C[L, F]C X2 [A, L, I] × [D, N] P X10-12 [K, R] X4-5 C X3-4 P X0-2 C. Moreover, we referred the Prosite-styled patterns to the experimental mutagenesis data that previously established by our group, and found that the residues with higher conservation played an important role in the structural stability or lipid binding ability of nsLTPs. Taken together, this research has suggested potential residues that might be essential to modulate the structural and functional properties of plant nsLTPs. Finally, we proposed some biologically important sites of the nsLTPs, which are described by using a new Prosite-styled pattern that we defined.

Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB

Directory of Open Access Journals (Sweden)

Wang Nai-Jyuan

2012-01-01

Full Text Available Abstract Background Plant non-specific lipid transfer proteins (nsLTPs are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, participating in plant defence activity against bacterial and fungal pathogens, and enhancing cell wall extension in tobacco. However, the lipid transfer mechanism of nsLTPs is still unclear, and comprehensive information of nsLTPs is difficult to obtain. Methods In this study, we identified 595 nsLTPs from 121 different species and constructed an nsLTPs database -- nsLTPDB -- which comprises the sequence information, structures, relevant literatures, and biological data of all plant nsLTPs http://nsltpdb.life.nthu.edu.tw/. Results Meanwhile, bioinformatics and statistics methods were implemented to develop a classification method for nsLTPs based on the patterns of the eight highly-conserved cysteine residues, and to suggest strict Prosite-styled patterns for Type I and Type II nsLTPs. The pattern of Type I is C X2 V X5-7 C [V, L, I] × Y [L, A, V] X8-13 CC × G X12 D × [Q, K, R] X2 CXC X16-21 P X2 C X13-15C, and that of Type II is C X4 L X2 C X9-11 P [S, T] X2 CC X5 Q X2-4 C[L, F]C X2 [A, L, I] × [D, N] P X10-12 [K, R] X4-5 C X3-4 P X0-2 C. Moreover, we referred the Prosite-styled patterns to the experimental mutagenesis data that previously established by our group, and found that the residues with higher conservation played an important role in the structural stability or lipid binding ability of nsLTPs. Conclusions Taken together, this research has suggested potential residues that might be essential to modulate the structural and functional properties of plant nsLTPs. Finally, we proposed some biologically important sites of the nsLTPs, which are described by using a new Prosite-styled pattern that we defined.

Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes

Science.gov (United States)

Trinkle-Mulcahy, Laura; Boulon, Séverine; Lam, Yun Wah; Urcia, Roby; Boisvert, François-Michel; Vandermoere, Franck; Morrice, Nick A.; Swift, Sam; Rothbauer, Ulrich; Leonhardt, Heinrich; Lamond, Angus

2008-01-01

The identification of interaction partners in protein complexes is a major goal in cell biology. Here we present a reliable affinity purification strategy to identify specific interactors that combines quantitative SILAC-based mass spectrometry with characterization of common contaminants binding to affinity matrices (bead proteomes). This strategy can be applied to affinity purification of either tagged fusion protein complexes or endogenous protein complexes, illustrated here using the well-characterized SMN complex as a model. GFP is used as the tag of choice because it shows minimal nonspecific binding to mammalian cell proteins, can be quantitatively depleted from cell extracts, and allows the integration of biochemical protein interaction data with in vivo measurements using fluorescence microscopy. Proteins binding nonspecifically to the most commonly used affinity matrices were determined using quantitative mass spectrometry, revealing important differences that affect experimental design. These data provide a specificity filter to distinguish specific protein binding partners in both quantitative and nonquantitative pull-down and immunoprecipitation experiments. PMID:18936248

Towards the identification of flower-specific genes in Citrus spp

Directory of Open Access Journals (Sweden)

Marcelo Carnier Dornelas

2007-01-01

Full Text Available Citrus sinensis is a perennial woody species, for which genetic approaches to the study of reproductive development are not readily amenable. Here, the usefulness of the CitEST Expressed Sequence Tag (EST database is demonstrated as a reliable new resource for identifying novel genes exclusively related to Citrus reproductive biology. We performed the analysis of an EST dataset of the CitEST Project containing 4,330 flower-derived cDNA sequences. Relying on bioinformatics tools, sequences exclusively present in this flower-derived sequence collection were selected and used for the identification of Citrus putative flower-specific genes. Our analysis revealed several Citrus sequences showing significant similarity to conserved genes known to have flower-specific expression and possessing functions related to flower metabolism and/or reproductive development in diverse plant species. Comparison of the Citrus flower-specific sequences with all available plant peptide sequences unraveled 247 unique transcripts not identified elsewhere within the plant kingdom. Additionally, 49 transcripts, for which no biological function could be attributed by means of sequence comparisons, were found to be conserved among plant species. These results allow further gene expression analysis and possibly novel approaches to the understanding of reproductive development in Citrus.

Karrikins Identified in Biochars Indicate Post-Fire Chemical Cues Can Influence Community Diversity and Plant Development.

Directory of Open Access Journals (Sweden)

Jitka Kochanek

Full Text Available Karrikins are smoke-derived compounds that provide strong chemical cues to stimulate seed germination and seedling growth. The recent discovery in Arabidopsis that the karrikin perception system may be present throughout angiosperms implies a fundamental plant function. Here, we identify the most potent karrikin, karrikinolide (KAR1, in biochars and determine its role in species unique plant responses.Biochars were prepared by three distinct commercial-scale pyrolysis technologies using systematically selected source material and their chemical properties, including karrikinolide, were quantified. Dose-response assays determined the effects of biochar on seed germination for two model species that require karrikinolide to break dormancy (Solanum orbiculatum, Brassica tourneforttii and on seedling growth using two species that display plasticity to karrikins, biochar and phytotoxins (Lactuca sativa, Lycopersicon esculentum. Multivariate analysis examined relationships between biochar properties and the plant phenotype.Results showed that karrikin abundant biochars stimulated dormant seed germination and seedling growth via mechanisms analogous to post-fire chemical cues. The individual species response was associated with its sensitivity to karrikinolide and inhibitory compounds within the biochars. These findings are critical for understanding why biochar influences community composition and plant physiology uniquely for different species and reaffirms that future pyrolysis technologies promise by-products that concomitantly sequester carbon and enhance plant growth for ecological and broader plant related applications.

Identifying nuclear power plant transients using the Discrete Binary Artificial Bee Colony (DBABC) algorithm

Energy Technology Data Exchange (ETDEWEB)

Oliveira, Iona M.S. de; Schirru, Roberto, E-mail: ioliveira@con.ufrj.br, E-mail: schirru@lmp.ufrj.br [Coordenacoa dos Programas de Pos-Graduacao em Engenharia (UFRJ/PEN/COPPE), Rio de Janeiro, RJ (Brazil). Programa de Engenharia Nuclear

2011-07-01

The identification of possible transients in a nuclear power plant is a highly relevant problem. This is mainly due to the fact that the operation of a nuclear power plant involves a large number of state variables whose behaviors are extremely dynamic. In risk situations, besides the huge cognitive overload that operators are submitted to, there is also the problem related with the considerable decrease in the effective time for correct decision making. To minimize these problems and help operators to make the corrective actions in due time, this paper presents a new contribution in this area and introduces an experimental transient identification system based exclusively on the abilities of the Discrete Binary Artificial Bee Colony (DBABC) algorithm to find the best centroid positions that correctly identifies a transient in a nuclear power plant. The DBABC is a reworking of the Artificial Bee Colony (ABC) algorithm which presents the advantage of operating in both continuous and discrete search spaces. Through the analysis of experimental results, the effective performance of the proposed DBABC algorithm is shown against some well known best performing algorithms from the literature. (author)

Identifying nuclear power plant transients using the Discrete Binary Artificial Bee Colony (DBABC) algorithm

International Nuclear Information System (INIS)

Oliveira, Iona M.S. de; Schirru, Roberto

2011-01-01

The identification of possible transients in a nuclear power plant is a highly relevant problem. This is mainly due to the fact that the operation of a nuclear power plant involves a large number of state variables whose behaviors are extremely dynamic. In risk situations, besides the huge cognitive overload that operators are submitted to, there is also the problem related with the considerable decrease in the effective time for correct decision making. To minimize these problems and help operators to make the corrective actions in due time, this paper presents a new contribution in this area and introduces an experimental transient identification system based exclusively on the abilities of the Discrete Binary Artificial Bee Colony (DBABC) algorithm to find the best centroid positions that correctly identifies a transient in a nuclear power plant. The DBABC is a reworking of the Artificial Bee Colony (ABC) algorithm which presents the advantage of operating in both continuous and discrete search spaces. Through the analysis of experimental results, the effective performance of the proposed DBABC algorithm is shown against some well known best performing algorithms from the literature. (author)

The microbiome of medicinal plants: diversity and importance for plant growth, quality and health

Directory of Open Access Journals (Sweden)

Martina eKöberl

2013-12-01

Full Text Available Past medicinal plant research primarily focused on bioactive phytochemicals, however the focus is currently shifting due to the recognition that a significant number of phytotherapeutic compounds are actually produced by associated microbes or through interaction with their host. Medicinal plants provide an enormous bioresource of potential use in modern medicine and agriculture, yet their microbiome is largely unknown. The objective of this review is i to introduce novel insights into the plant microbiome with a focus on medicinal plants, ii to provide details about plant- and microbe-derived ingredients of medicinal plants, and iii to discuss possibilities for plant growth promotion and plant protection for commercial cultivation of medicinal plants. In addition, we also present a case study performed both to analyse the microbiome of three medicinal plants (Matricaria chamomilla L., Calendula officinalis L. and Solanum distichum Schumach. and Thonn. cultivated on organically managed Egyptian desert farm and to develop biological control strategies. The soil microbiome of the desert ecosystem was comprised of a high abundance of Gram-positive bacteria of prime importance for pathogen suppression under arid soil conditions. For all three plants, we observed a clearly plant-specific selection of the microbes as well as highly specific diazotrophic communities that overall identify plant species as important drivers in structural and functional diversity. Lastly, native Bacillus spec. div. strains were able to promote plant growth and elevate the plants’ flavonoid production. These results underline the numerous links between the plant-associated microbiome and the plant metabolome.

Ubiquitous water-soluble molecules in aquatic plant exudates determine specific insect attraction.

Science.gov (United States)

Sérandour, Julien; Reynaud, Stéphane; Willison, John; Patouraux, Joëlle; Gaude, Thierry; Ravanel, Patrick; Lempérière, Guy; Raveton, Muriel

2008-10-08

Plants produce semio-chemicals that directly influence insect attraction and/or repulsion. Generally, this attraction is closely associated with herbivory and has been studied mainly under atmospheric conditions. On the other hand, the relationship between aquatic plants and insects has been little studied. To determine whether the roots of aquatic macrophytes release attractive chemical mixtures into the water, we studied the behaviour of mosquito larvae using olfactory experiments with root exudates. After testing the attraction on Culex and Aedes mosquito larvae, we chose to work with Coquillettidia species, which have a complex behaviour in nature and need to be attached to plant roots in order to obtain oxygen. This relationship is non-destructive and can be described as commensal behaviour. Commonly found compounds seemed to be involved in insect attraction since root exudates from different plants were all attractive. Moreover, chemical analysis allowed us to identify a certain number of commonly found, highly water-soluble, low-molecular-weight compounds, several of which (glycerol, uracil, thymine, uridine, thymidine) were able to induce attraction when tested individually but at concentrations substantially higher than those found in nature. However, our principal findings demonstrated that these compounds appeared to act synergistically, since a mixture of these five compounds attracted larvae at natural concentrations (0.7 nM glycerol, insect relationships in aquatic eco-systems.

The Active Jasmonate JA-Ile Regulates a Specific Subset of Plant Jasmonate-Mediated Resistance to Herbivores in Nature

Directory of Open Access Journals (Sweden)

Meredith C. Schuman

2018-06-01

Full Text Available The jasmonate hormones are essential regulators of plant defense against herbivores and include several dozen derivatives of the oxylipin jasmonic acid (JA. Among these, the conjugate jasmonoyl isoleucine (JA-Ile has been shown to interact directly with the jasmonate co-receptor complex to regulate responses to jasmonate signaling. However, functional studies indicate that some aspects of jasmonate-mediated defense are not regulated by JA-Ile. Thus, it is not clear whether JA-Ile is best characterized as the master jasmonate regulator of defense, or if it regulates more specific aspects. We investigated possible functions of JA-Ile in anti-herbivore resistance of the wild tobacco Nicotiana attenuata, a model system for plant-herbivore interactions. We first analyzed the soluble and volatile secondary metabolomes of irJAR4xirJAR6, asLOX3, and WT plants, as well as an RNAi line targeting the jasmonate co-receptor CORONATINE INSENSITIVE 1 (irCOI1, following a standardized herbivory treatment. irJAR4xirJAR6 were the most similar to WT plants, having a ca. 60% overlap in differentially regulated metabolites with either asLOX3 or irCOI1. In contrast, while at least 25 volatiles differed between irCOI1 or asLOX3 and WT plants, there were few or no differences in herbivore-induced volatile emission between irJAR4xirJAR6 and WT plants, in glasshouse- or field-collected samples. We then measured the susceptibility of jasmonate-deficient vs. JA-Ile-deficient plants in nature, in comparison to wild-type (WT controls, and found that JA-Ile-deficient plants (irJAR4xirJAR6 are much better defended even than a mildly jasmonate-deficient line (asLOX3. The differences among lines could be attributed to differences in damage from specific herbivores, which appeared to prefer either one or the other jasmonate-deficient phenotype. We further investigated the elicitation of one herbivore-induced volatile known to be jasmonate-regulated and to mediate resistance to

Transgenic plants over-expressing insect-specific microRNA acquire insecticidal activity against Helicoverpa armigera: an alternative to Bt-toxin technology.

Science.gov (United States)

Agrawal, Aditi; Rajamani, Vijayalakshmi; Reddy, Vanga Siva; Mukherjee, Sunil Kumar; Bhatnagar, Raj K

2015-10-01

The success of Bt transgenics in controlling predation of crops has been tempered by sporadic emergence of resistance in targeted insect larvae. Such emerging threats have prompted the search for novel insecticidal molecules that are specific and could be expressed through plants. We have resorted to small RNA-based technology for an investigative search and focused our attention to an insect-specific miRNA that interferes with the insect molting process resulting in the death of the larvae. In this study, we report the designing of a vector that produces artificial microRNA (amiR), namely amiR-24, which targets the chitinase gene of Helicoverpa armigera. This vector was used as transgene in tobacco. Northern blot and real-time analysis revealed the high level expression of amiR-24 in transgenic tobacco plants. Larvae feeding on the transgenic plants ceased to molt further and eventually died. Our results demonstrate that transgenic tobacco plants can express amiR-24 insectice specific to H. armigera.

Grid connected integrated community energy system. Phase II: final stage 2 report. Outline specifications of cogeneration plant; continued

Energy Technology Data Exchange (ETDEWEB)

1978-03-22

Specifications are presented for the electrical equipment, site preparation, building construction and mechanical systems for a dual-purpose power plant to be located on the University of Minnesota campus. This power plant will supply steam and electrical power to a grid-connected Integrated Community Energy System. (LCL)

Safety of Nuclear Power Plants: Design. Specific Safety Requirements (Russian Edition); Bezopasnost' atomnykh ehlektrostantsij: proektirovanie. Konkretnye trebovaniya bezopasnosti

Energy Technology Data Exchange (ETDEWEB)

NONE

2012-04-15

This publication is a revision of Safety Requirements No. NS-R-1, Safety of Nuclear Power Plants: Design. It establishes requirements applicable to the design of nuclear power plants and elaborates on the safety objective, safety principles and concepts that provide the basis for deriving the safety requirements that must be met for the design of a nuclear power plant. It will be useful for organizations involved in the design, manufacture, construction, modification, maintenance, operation and decommissioning of nuclear power plants, as well as for regulatory bodies. Contents: 1. Introduction; 2. Applying the safety principles and concepts; 3. Management of safety in design; 4. Principal technical requirements; 5. General plant design; 6. Design of specific plant systems.

Identifying the impacts of climate change on key pests and diseases of plant and animal industries

International Nuclear Information System (INIS)

Luck, Jo; Aurambout, Jean-Philippe; Finlay, Kyla; Azuloas, Joe; Constable, Fiona; Rijswijk, Bonny Rowles-Van

2007-01-01

Full text: Full text: Climate change is increasingly recognised as a major threat to natural and agricultural systems. Understanding these threats will enable government and primary industries to better prepare and adapt to climate change. While observations of climate change are well documented, the potential effects on pests, pathogens and their hosts are not clearly understood. To address this, a review of the potential impacts on plant biosecurity was undertaken to determine the effects of climate change on the behaviour and distribution of emergent plant pests and pathogens. The review identified increasing C02 and temperature, decreasing frost events, heavy and unseasonal rains, increased humidity, drought, cyclones and hurricanes, and warmer winter temperatures as influencing the behaviour of plant pests and pathogens. To study the effects of these changes in detail, three key plant biosecurity threats were analysed in case studies; wheat stripe rust, silver leaf whitefly and citrus canker. The predicted distribution of citrus canker was examined with increasing temperature scenarios using the bioclimatic model CLIMEX. The model predicted a southerly shift in the geographic range of the causal organism which would threaten the major southern citrus growing regions in future climates. A similar study on Bluetongue disease of sheep, spread by the Culicoides midge, also predicted a southerly shift in the vector's geographic range. Significant limitations were identified with bioclimatic modelling when examining the effects of climate change on pests and diseases. The model was unable to assess the plant and animal response to increasing temperature in conjunction with the pest. Also the influence of temperature on the life cycle of the organism, pathogenicity of strains, competition with other species, host coverage and the general effect on the biology of the organism could not be assessed. To begin to address this, a dynamic model was constructed using daily

Introduction to the 'CAS' nuclear propulsion plant for ships: specific safety options

International Nuclear Information System (INIS)

Verdeau, J.J.; Baujat, J.

1978-01-01

After a brief review of the development of nuclear propulsion in FRANCE (Land Based Prototype PAT 1964 - Navy nuclear ships - Advanced Nuclear Boiler Prototype CAP 1975 and now the CAS nuclear plant), the specific safety options of CAS are presented: cold, compartmented fuel (plates); reduced flow during LOCA; permanent cooling of fuel during LOCA; pressurized, entirely passive containment; no control rod ejection and possibility of temporary storage of spent fuel on board [fr

Pyrosequencing data reveals tissue-specific expression of lineage-specific transcripts in chickpea

OpenAIRE

Garg, Rohini; Jain, Mukesh

2011-01-01

Chickpea is a very important crop legume plant, which provides a protein-rich supplement to cereal-based diets and has the ability to fix atmospheric nitrogen. Despite its economic importance, the functional genomic resources for chickpea are very limited. Recently, we reported the complete transcriptome of chickpea using next generation sequencing technologies. We analyzed the tissue-specific expression of chickpea transcripts based on RNA-seq data. In addition, we identified two sets of lin...

High specificity but contrasting biodiversity of Sphagnum-associated bacterial and plant communities in bog ecosystems independent of the geographical region.

Science.gov (United States)

Opelt, Katja; Berg, Christian; Schönmann, Susan; Eberl, Leo; Berg, Gabriele

2007-10-01

Mosses represent ecological niches that harbor a hitherto largely uncharacterized microbial diversity. To investigate which factors affect the biodiversity of bryophyte-associated bacteria, we analyzed the bacterial communities associated with two moss species, which exhibit different ecological behaviors and importance in bog ecosystems, Sphagnum magellanicum and Sphagnum fallax, from six temperate and boreal bogs in Germany and Norway. Furthermore, their surrounding plant communities were studied. Molecular analysis of bacterial communities was determined by single-strand conformation polymorphism (SSCP) analysis using eubacterial and genus-specific primers for the dominant genera Burkholderia and Serratia as well as by sequence analysis of a Burkholderia 16S rRNA gene clone library. Plant communities were analyzed by monitoring the abundance and composition of bryophyte and vascular plant species, and by determining ecological indicator values. Interestingly, we found a high degree of host specificity for associated bacterial and plant communities of both Sphagnum species independent of the geographical region. Calculation of diversity indices on the basis of SSCP gels showed that the S. fallax-associated communities displayed a statistically significant higher degree of diversity than those associated with S. magellanicum. In contrast, analyses of plant communities of Sphagnum-specific habitats resulted in a higher diversity of S. magellanicum-specific habitats for all six sites. The higher content of nutrients in the S. fallax-associated ecosystems can explain higher diversity of microorganisms.

Specific interactions between arbuscular mycorrhizal fungi and plant growth-promoting bacteria--as revealed by different combinations

Energy Technology Data Exchange (ETDEWEB)

Jaderlund, Lotta; Arthurson, Veronica; Granhall, Ulf; Jansson, Janet K.

2008-05-15

The interactions between two plant growth promoting rhizobacteria (PGPR), Pseudomonas fluorescens SBW25 and Paenibacillus brasilensis PB177, two arbuscular mycorrhizal (AM) fungi (Glomus mosseae and G. intraradices) and one pathogenic fungus (Microdochium nivale) were investigated on winter wheat (Triticum aestivum cultivar Tarso) in a greenhouse trial. PB177, but not SBW25, had strong inhibitory effects on M. nivale in dual culture plate assays. The results from the greenhouse experiment show very specific interactions; e.g. the two AM fungi react differently when interacting with the same bacteria on plants. G. intraradices (single inoculation or together with SBW25) increased plant dry weight on M. nivale infested plants, suggesting that the pathogenic fungus is counteracted by G. intraradices, but PB177 inhibited this positive effect. This is an example of two completely different reactions between the same AM fungus and two species of bacteria, previously known to enhance plant growth and inhibit pathogens. When searching for plant growth promoting microorganisms it is therefore important to test for the most suitable combination of plant, bacteria and fungi in order to get satisfactory plant growth benefits.

DEVELOPING SITE-SPECIFIC DERIVED CONCENTRATION GUIDELINE LEVELS FOR MULTIPLE MEDIA AT THE CONNECTICUT YANKEE HADDAM NECK PLANT

International Nuclear Information System (INIS)

Taylor, S.W.; Smith, L.C.; Carr, R.K.; Carson, A.; Darois, E.

2003-01-01

As part of the license termination process, site-specific Derived Concentration Guideline Levels for the Haddam Neck Plant site are developed for soil, groundwater, concrete left standing, and concrete demolished that satisfy the radiological criteria for unrestricted use as defined in 10 CFR 20.1402. Background information on the license termination process and characteristics of the Haddam Neck Plant site are presented. The dose models and associated resident farmer and building occupancy scenarios, applicable pathways, and critical groups developed to establish the Derived Concentration Guideline Levels are described. A parameter assignment process is introduced wherein general population values are used to establish behavioral and metabolic parameters representative of an average member of the critical group, while the uncertainty associated with important physical parameters is considered. A key element of the parameter assignment process is the use of sensitivity analysis to identify the dose sensitive physical parameters and to ensure that such parameters are assigned conservative values. Structuring the parameter assignment process, completing the formal sensitivity analyses, and assigning conservative values to the sensitive physical parameters in a consistent way establishes a calculation framework that lead to Derived Concentration Guideline Levels with a uniform level of conservatism across all media and all radionuclides

Stable isotope fingerprinting: a novel method for identifying plant, fungal, or bacterial origins of amino acids

Science.gov (United States)

Thomas Larsen; D. Lee Taylor; Mary Beth Leigh; Diane M. O' Brien

2009-01-01

Amino acids play an important role in ecology as essential nutrients for animals and as currencies in symbiotic associations. Here we present a new approach to tracing the origins of amino acids by identifying unique patterns of carbon isotope signatures generated by amino acid synthesis in plants, fungi, and bacteria ("13C fingerprints...

Structure-function relationship of a plant NCS1 member - Homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from arabidopsis

KAUST Repository

Witz, Sandra

2014-03-12

Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members. 2014 Witz et al.

Site-specific analysis of hybrid geothermal/fossil power plants. Volume One. Roosevelt Hot Springs KGRA

Energy Technology Data Exchange (ETDEWEB)

1977-06-01

The economics of a particular hybrid plant must be evaluated with respect to a specific site. This volume focuses on the Roosevelt Hot Springs KGRA. The temperature, pressure, and flow rate data given suggests the site deserves serious consideration for a hybrid plant. Key siting considerations which must be addressed before an economic judgment can be attempted are presented as follows: the availability, quality, and cost of coal; the availability of water; and the availability of transmission. Seismological and climate factors are presented. (MHR)

Algorithm of actions to identify and reduce risks in the production of milk and plant products

Directory of Open Access Journals (Sweden)

L. E. Glagoleva

2016-01-01

Full Text Available Foods with a new generation of functional and improved consumer properties, corresponds to the modern concepts of nutrition science and consumer needs. functional food production is a major global trend in food science and the subject of innovation. One of the important trends is the use of plant complexes and plant food systems. Using the plant complexes (PC and plant food systems (PFS provides a number of benefits: improved consumer properties of the product, do not need to change the process, it is possible to control directional rheological properties and consistency of the finished products, reduced the number of risk points in the production cycle. This paper describes the development of an algorithm of action to identify and mitigate risks in the production of milk and plant products. Also conducted a risk analysis, identified and assessed the risks in the process of production, installed capacity of available resources to reduce the level of risk. Established and submitted to the critical control points in production processes, as well as the critical limits for each critical control points, and the procedure for corrective action in case of violations of the past. During the study, measured changes in the quantitative and qualitative composition of microflora of semi-finished and Quantity of Mesophilic Aerobic and Facultative Anaerobic Microorganisms (QMAFAnM. To determine QMAFAnM samples were taken: 1 – cheesecakes (control, 2 – cheesecakes with RPS. Microbiological studies analyzed frozen-conjugated semi-finished products was determined within 90 days. It is clear from the data that the cottage cheese with semi-finished products have a lower RPM 11.7%. Analyzing the data, it is possible to conclude that the physico-chemical, organoleptic and microbiological indicators of products was developed to set standards on cheese semi-finished products. multilevel structure that characterizes the quality indicators has been developed and is

Fungal Infection Induces Sex-Specific Transcriptional Changes and Alters Sexual Dimorphism in the Dioecious Plant Silene latifolia.

Directory of Open Access Journals (Sweden)

Niklaus Zemp

2015-10-01

Full Text Available Sexual dimorphism, including differences in morphology, behavior and physiology between females and males, is widespread in animals and plants and is shaped by gene expression differences between the sexes. Such expression differences may also underlie sex-specific responses of hosts to pathogen infections, most notably when pathogens induce partial sex reversal in infected hosts. The genetic changes associated with sex-specific responses to pathogen infections on the one hand, and sexual dimorphism on the other hand, remain poorly understood. The dioecious White Campion (Silene latifolia displays sexual dimorphism in floral traits and infection with the smut fungus Micobrotryum lychnidis-dioicae induces a partial sex reversal in females. We find strong sex-specific responses to pathogen infection and reduced sexual dimorphism in infected S. latifolia. This provides a direct link between pathogen-mediated changes in sex-biased gene expression and altered sexual dimorphism in the host. Expression changes following infection affected mainly genes with male-biased expression in healthy plants. In females, these genes were up-regulated, leading to a masculinization of the transcriptome. In contrast, infection in males was associated with down-regulation of these genes, leading to a demasculinization of the transcriptome. To a lesser extent, genes with female-biased expression in healthy plants were also affected in opposite directions in the two sexes. These genes were overall down-regulated in females and up-regulated in males, causing, respectively, a defeminization in infected females and a feminization of the transcriptome in infected males. Our results reveal strong sex-specific responses to pathogen infection in a dioecious plant and provide a link between pathogen-induced changes in sex-biased gene expression and sexual dimorphism.

Fungal Infection Induces Sex-Specific Transcriptional Changes and Alters Sexual Dimorphism in the Dioecious Plant Silene latifolia.

Science.gov (United States)

Zemp, Niklaus; Tavares, Raquel; Widmer, Alex

2015-10-01

Sexual dimorphism, including differences in morphology, behavior and physiology between females and males, is widespread in animals and plants and is shaped by gene expression differences between the sexes. Such expression differences may also underlie sex-specific responses of hosts to pathogen infections, most notably when pathogens induce partial sex reversal in infected hosts. The genetic changes associated with sex-specific responses to pathogen infections on the one hand, and sexual dimorphism on the other hand, remain poorly understood. The dioecious White Campion (Silene latifolia) displays sexual dimorphism in floral traits and infection with the smut fungus Micobrotryum lychnidis-dioicae induces a partial sex reversal in females. We find strong sex-specific responses to pathogen infection and reduced sexual dimorphism in infected S. latifolia. This provides a direct link between pathogen-mediated changes in sex-biased gene expression and altered sexual dimorphism in the host. Expression changes following infection affected mainly genes with male-biased expression in healthy plants. In females, these genes were up-regulated, leading to a masculinization of the transcriptome. In contrast, infection in males was associated with down-regulation of these genes, leading to a demasculinization of the transcriptome. To a lesser extent, genes with female-biased expression in healthy plants were also affected in opposite directions in the two sexes. These genes were overall down-regulated in females and up-regulated in males, causing, respectively, a defeminization in infected females and a feminization of the transcriptome in infected males. Our results reveal strong sex-specific responses to pathogen infection in a dioecious plant and provide a link between pathogen-induced changes in sex-biased gene expression and sexual dimorphism.

Useful Principles in Plant Excellence Promotion

International Nuclear Information System (INIS)

Kavsek, D.; Bozin, B.

2002-01-01

This presentation offers a discussion of some principles identified from a review of significant industry events that affected the safety or reliability of a large number of nuclear power plants worldwide. Over the years of operation, a number of events have occurred in nuclear power plants that have involved problems in human performance. A review of these and other significant events has identified recurring weaknesses in plant safety culture and policy and procedure weaknesses. Focusing attention on strengthening relevant processes can help plants avoid similar significant events. Events continue to occur because the lessons learned from industry and plant operating experience are ineffectively used. In some cases, industry events have been communicated to the personnel of the plant in question, but without a thorough explanation of the lessons learned and applicability to the plant. The corrective actions identified have sometimes been limited in scope and have not fully addressed generic issues. The review and implementation of corrective actions for in-house events have sometimes been inadequate to prevent recurrences. An effective operating experience program can significantly reduce the potential for recurring events. The value of learning and applying the knowledge gained from operating experience should be an integral part of plant culture and promoted as an expectation. When operating experience is reviewed, generic issues and causal factors should be explored, rather than focusing on the unique problems that led to a specific event. Lessons learned and applicability to the plant must be clearly identified, corrective action taken, and changes thoroughly communicated to the plant personnel. Their understanding of the changes and the reasons for them should then be confirmed. The following principles will be discussed in this presentation: recognizing conditions during evolutions, promoting teamwork, recognizing fundamental knowledge weaknesses

COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC MICROBIAL GENETIC MARKERS IN COW FECAL SAMPLES

Science.gov (United States)

Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host specific markers. Here, we describe the application of a genome fragment enrichment met...

Specific 137Cs and 90Sr accumulation in living soil cover plants of forest cenoses

International Nuclear Information System (INIS)

Ermakova, O.O.; Kuz'mich, O.T.; Kazej, A.P.

2000-01-01

Observations of the radionuclide content in 38 species of living soil cover plants were carried out in Pinetum myrtillosum, pleuroziosum; Quercetum pteridiosum; Betuletum myrtillosum; Glutinoso-Alnetum filipendulosum, Glutinoso-Alnetum. Radiological monitoring for the 137 Cs and 90 Sr content in living cover plants of forest cenosis in Belarus allows 137 Cs and 90 Sr accumulation to be predicted for the plants of lower circles of forest cenosis. a obtained one can notice that the radionuclide accumulation intensity depends on the contamination density of the accumulation soil layer, forest growing conditions, species and first of all on the weather conditions of the year of observation. Unfavourable conditions (drought) lead to an increase in 137 Cs accumulation by a factor of 3-5 depending on the plant species. The maximum values was obtained in ferns which grow under all the controlled forest growing conditions. The species specific character of 137 Cs and 90 Sr accumulation is due to their ecological-physiological peculiarities. The relationship was found between the caesium-137 accumulation and macro element quantity in overground organs of living soil cover plants. (authors)

Ferritin gene organization: differences between plants and animals suggest possible kingdom-specific selective constraints.

Science.gov (United States)

Proudhon, D; Wei, J; Briat, J; Theil, E C

1996-03-01

Ferritin, a protein widespread in nature, concentrates iron approximately 10(11)-10(12)-fold above the solubility within a spherical shell of 24 subunits; it derives in plants and animals from a common ancestor (based on sequence) but displays a cytoplasmic location in animals compared to the plastid in contemporary plants. Ferritin gene regulation in plants and animals is altered by development, hormones, and excess iron; iron signals target DNA in plants but mRNA in animals. Evolution has thus conserved the two end points of ferritin gene expression, the physiological signals and the protein structure, while allowing some divergence of the genetic mechanisms. Comparison of ferritin gene organization in plants and animals, made possible by the cloning of a dicot (soybean) ferritin gene presented here and the recent cloning of two monocot (maize) ferritin genes, shows evolutionary divergence in ferritin gene organization between plants and animals but conservation among plants or among animals; divergence in the genetic mechanism for iron regulation is reflected by the absence in all three plant genes of the IRE, a highly conserved, noncoding sequence in vertebrate animal ferritin mRNA. In plant ferritin genes, the number of introns (n = 7) is higher than in animals (n = 3). Second, no intron positions are conserved when ferritin genes of plants and animals are compared, although all ferritin gene introns are in the coding region; within kingdoms, the intron positions in ferritin genes are conserved. Finally, secondary protein structure has no apparent relationship to intron/exon boundaries in plant ferritin genes, whereas in animal ferritin genes the correspondence is high. The structural differences in introns/exons among phylogenetically related ferritin coding sequences and the high conservation of the gene structure within plant or animal kingdoms of the gene structure within plant or animal kingdoms suggest that kingdom-specific functional constraints may

Species specific and environment induced variation of δ13C and δ15N in alpine plants

Directory of Open Access Journals (Sweden)

Yang eYang

2015-06-01

Full Text Available Stable carbon and nitrogen isotope signals in plant tissues integrate plant-environment interactions over long periods. In this study, we hypothesized that humid alpine life conditions are narrowing the scope for significant deviations from common carbon, water and nitrogen relations as captured by stable isotope signals. We explored the variation in δ13C and δ15N in 32 plant species from tissue type to ecosystem scale across a suite of locations at c. 2500 m elevation in the Swiss Alps. Foliar δ13C and δ15N varied among species by about 3-4 ‰ and 7-8 ‰ respectively. However, there was no overall difference in means of δ13C and δ15N for species sampled in different plant communities or when bulk plant dry matter harvests of different plant communities were compared. δ13C was found to be highly species specific, so that the ranking among species was mostly maintained across 11 habitats. However, δ15N varied significantly from place to place in all species (a range of 2.7 ‰ except in Fabaceae (Trifolium alpinum and Juncaceae (Luzula lutea. There was also a substantial variation among individuals of the same species collected next to each other. No difference was found in foliar δ15N of non-legumes, which were either collected next to or away from the most common legume, T. alpinum. δ15N data place Cyperaceae and Juncaceae, just like Fabaceae, in a low discrimination category, well separated from other families. Soil δ15N was higher than in plants and increased with soil depth. The results indicate a high functional diversity in alpine plants that is similar to that reported for low elevation plants. We conclude that the surprisingly high variation in δ13C and δ15N signals in the studied high elevation plants is largely species specific (genetic and insensitive to obvious environmental cues.

Auxiliary feedwater system risk-based inspection guide for the North Anna nuclear power plants

International Nuclear Information System (INIS)

Nickolaus, J.R.; Moffitt, N.E.; Gore, B.F.; Vo, T.V.

1992-10-01

In a study sponsored by the US Nuclear regulatory Commission (NRC), Pacific Northwest Laboratory has developed and applied a methodology for deriving plant-specific risk-based inspection guidance for the auxiliary feedwater (AFW) system at pressurized water reactors that have not undergone probabilistic risk assessment (PRA). This methodology uses existing PRA results and plant operating experience information. Existing PRA-based inspection guidance information recently developed for the NRC for various plants was used to identify generic component failure modes. This information was then combined with plant-specific and industry-wide component information and failure data to identify failure modes and failure mechanisms for the AFW system at the selected plants. North Anna was selected as a plant for study. The product of this effort is a prioritized listing of AFW failures which have occurred at the plant and at other PWRs. This listing is intended for use by the NRC inspectors in preparation of inspection plans addressing AFW risk important components at the North Anna plant

The knowledge-based framework for a nuclear power plant operator advisor

International Nuclear Information System (INIS)

Miller, D.W.

1989-01-01

An important facet in the design, development, and evaluation of aids for complex systems is the identification of the tasks performed by the operator. Operator aids utilizing artificial intelligence, or more specifically knowledge-based systems, require identification of these tasks in the context of a knowledge-based framework. In this context, the operator responses to the plant behavior are to monitor and comprehend the state of the plant, identify normal and abnormal plant conditions, diagnose abnormal plant conditions, predict plant response to specific control actions, and select the best available control action, implement a feasible control action, monitor system response to the control action, and correct for any inappropriate responses. These tasks have been identified to formulate a knowledge-based framework for an operator advisor under development at Ohio State University that utilizes the generic task methodology proposed by Chandrasekaran. The paper lays the foundation to identify the responses as a knowledge-based set of tasks in accordance with the expected human operator responses during an event. Initial evaluation of the expert system indicates the potential for an operator aid that will improve the operator's ability to respond to both anticipated and unanticipated events

An overview of insights gained and lessons learned from U.S. plant-specific PRA studies

International Nuclear Information System (INIS)

Joksimovich, V.

1985-01-01

Probabilistic Risk Assessment (PRA) has been under development for over twenty years, but it has reached the level of widespread use only in the aftermath of the TMI accident. Over thirty PRAs have now been completed in the U.S. PRAs have been in the mainstream of many licensing decisions because the NRC recognizes that they provide independent and comprehensive plant safety audit. Some difficulties have been experienced leading to interpretive and intercomparison studies. Numerous global and plant-specific insights have been derived. A new application termed risk management is clearly emerging. (orig./HP)

Association of Animal and Plant Protein Intake With All-Cause and Cause-Specific Mortality.

Science.gov (United States)

Song, Mingyang; Fung, Teresa T; Hu, Frank B; Willett, Walter C; Longo, Valter D; Chan, Andrew T; Giovannucci, Edward L

2016-10-01

Defining what represents a macronutritionally balanced diet remains an open question and a high priority in nutrition research. Although the amount of protein may have specific effects, from a broader dietary perspective, the choice of protein sources will inevitably influence other components of diet and may be a critical determinant for the health outcome. To examine the associations of animal and plant protein intake with the risk for mortality. This prospective cohort study of US health care professionals included 131 342 participants from the Nurses' Health Study (1980 to end of follow-up on June 1, 2012) and Health Professionals Follow-up Study (1986 to end of follow-up on January 31, 2012). Animal and plant protein intake was assessed by regularly updated validated food frequency questionnaires. Data were analyzed from June 20, 2014, to January 18, 2016. Hazard ratios (HRs) for all-cause and cause-specific mortality. Of the 131 342 participants, 85 013 were women (64.7%) and 46 329 were men (35.3%) (mean [SD] age, 49 [9] years). The median protein intake, as assessed by percentage of energy, was 14% for animal protein (5th-95th percentile, 9%-22%) and 4% for plant protein (5th-95th percentile, 2%-6%). After adjusting for major lifestyle and dietary risk factors, animal protein intake was not associated with all-cause mortality (HR, 1.02 per 10% energy increment; 95% CI, 0.98-1.05; P for trend = .33) but was associated with higher cardiovascular mortality (HR, 1.08 per 10% energy increment; 95% CI, 1.01-1.16; P for trend = .04). Plant protein was associated with lower all-cause mortality (HR, 0.90 per 3% energy increment; 95% CI, 0.86-0.95; P for trend animal protein of various origins with plant protein was associated with lower mortality. In particular, the HRs for all-cause mortality were 0.66 (95% CI, 0.59-0.75) when 3% of energy from plant protein was substituted for an equivalent amount of protein from processed red meat, 0.88 (95% CI

Insertion of a specific fungal 3'-phosphoadenosine-5'-phosphatase motif into a plant homologue improves halotolerance and drought tolerance of plants.

Science.gov (United States)

Gašparič, Meti Buh; Lenassi, Metka; Gostinčar, Cene; Rotter, Ana; Plemenitaš, Ana; Gunde-Cimerman, Nina; Gruden, Kristina; Zel, Jana

2013-01-01

Soil salinity and drought are among the most serious agricultural and environmental problems of today. Therefore, investigations of plant resistance to abiotic stress have received a lot of attention in recent years. In this study, we identified the complete coding sequence of a 3'-phosphoadenosine-5'-phosphatase protein, ApHal2, from the halotolerant yeast Aureobasidium pullulans. Expression of the ApHAL2 gene in a Saccharomyces cerevisiae hal2 mutant complemented the mutant auxotrophy for methionine, and rescued the growth of the hal2 mutant in media with high NaCl concentrations. A 21-amino-acids-long region of the ApHal2 enzyme was inserted into the Arabidopsis thaliana homologue of Hal2, the SAL1 phosphatase. The inserted sequence included the META motif, which has previously been implicated in increased sodium tolerance of the Hal2 homologue from a related fungal species. Transgenic Arabidopsis plants overexpressing this modified SAL1 (mSAL1) showed improved halotolerance and drought tolerance. In a medium with an elevated salt concentration, mSAL1-expressing plants were twice as likely to have roots in a higher length category in comparison with the wild-type Arabidopsis and with plants overexpressing the native SAL1, and had 5% to 10% larger leaf surface area under moderate and severe salt stress, respectively. Similarly, after moderate drought exposure, the mSAL1-expressing plants showed 14% increased dry weight after revitalisation, with no increase in dry weight of the wild-type plants. With severe drought, plants overexpressing native SAL1 had the worst rehydration success, consistent with the recently proposed role of SAL1 in severe drought. This was not observed for plants expressing mSAL1. Therefore, the presence of this fungal META motif sequence is beneficial under conditions of increased salinity and moderate drought, and shows no drawbacks for plant survival under severe drought. This demonstrates that adaptations of extremotolerant fungi should

Quantitative proteomics links metabolic pathways to specific developmental stages of the plant-pathogenic oomycete Phytophthora capsici.

Science.gov (United States)

Pang, Zhili; Srivastava, Vaibhav; Liu, Xili; Bulone, Vincent

2017-04-01

The oomycete Phytophthora capsici is a plant pathogen responsible for important losses to vegetable production worldwide. Its asexual reproduction plays an important role in the rapid propagation and spread of the disease in the field. A global proteomics study was conducted to compare two key asexual life stages of P. capsici, i.e. the mycelium and cysts, to identify stage-specific biochemical processes. A total of 1200 proteins was identified using qualitative and quantitative proteomics. The transcript abundance of some of the enriched proteins was also analysed by quantitative real-time polymerase chain reaction. Seventy-three proteins exhibited different levels of abundance between the mycelium and cysts. The proteins enriched in the mycelium are mainly associated with glycolysis, the tricarboxylic acid (or citric acid) cycle and the pentose phosphate pathway, providing the energy required for the biosynthesis of cellular building blocks and hyphal growth. In contrast, the proteins that are predominant in cysts are essentially involved in fatty acid degradation, suggesting that the early infection stage of the pathogen relies primarily on fatty acid degradation for energy production. The data provide a better understanding of P. capsici biology and suggest potential metabolic targets at the two different developmental stages for disease control. © 2016 BSPP AND JOHN WILEY & SONS LTD.

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

Science.gov (United States)

Ding, Tao; Melcher, Ulrich

2016-01-01

Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

Directory of Open Access Journals (Sweden)

Tao Ding

Full Text Available Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

CloudNeo: a cloud pipeline for identifying patient-specific tumor neoantigens.

Science.gov (United States)

Bais, Preeti; Namburi, Sandeep; Gatti, Daniel M; Zhang, Xinyu; Chuang, Jeffrey H

2017-10-01

We present CloudNeo, a cloud-based computational workflow for identifying patient-specific tumor neoantigens from next generation sequencing data. Tumor-specific mutant peptides can be detected by the immune system through their interactions with the human leukocyte antigen complex, and neoantigen presence has recently been shown to correlate with anti T-cell immunity and efficacy of checkpoint inhibitor therapy. However computing capabilities to identify neoantigens from genomic sequencing data are a limiting factor for understanding their role. This challenge has grown as cancer datasets become increasingly abundant, making them cumbersome to store and analyze on local servers. Our cloud-based pipeline provides scalable computation capabilities for neoantigen identification while eliminating the need to invest in local infrastructure for data transfer, storage or compute. The pipeline is a Common Workflow Language (CWL) implementation of human leukocyte antigen (HLA) typing using Polysolver or HLAminer combined with custom scripts for mutant peptide identification and NetMHCpan for neoantigen prediction. We have demonstrated the efficacy of these pipelines on Amazon cloud instances through the Seven Bridges Genomics implementation of the NCI Cancer Genomics Cloud, which provides graphical interfaces for running and editing, infrastructure for workflow sharing and version tracking, and access to TCGA data. The CWL implementation is at: https://github.com/TheJacksonLaboratory/CloudNeo. For users who have obtained licenses for all internal software, integrated versions in CWL and on the Seven Bridges Cancer Genomics Cloud platform (https://cgc.sbgenomics.com/, recommended version) can be obtained by contacting the authors. jeff.chuang@jax.org. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Plant-specific responses to zinc contamination in a semi-field lysimeter and on hydroponics

International Nuclear Information System (INIS)

Bernhard, Roland; Verkleij, Jos A.C.; Nelissen, Hans J.M.; Vink, Jos P.M.

2005-01-01

The species Agrostis stolonifera, Brassica napus and Trifolium repens representing different ecological strategies, were selected to study the effect of Zn contamination on Zn tolerance, uptake and accumulation patterns. Parallel tests were carried out with increasing concentrations of Zn in a semi-field lysimeter and hydroponics in the climate chamber. A significant reduction in biomass production or root length and an increase in shoot Zn concentration was observed for all species at increasing external Zn concentrations. However, shoot biomass production, Zn tolerance and Zn accumulation differed significantly among the tested species. The results in both experimental set-ups were quite similar concerning Zn tolerance and accumulation and improved the validity of the findings. The rather specific responses of the different plant species to Zn contamination interfere with the more generic approach used in risk assessment studies. Maximum amounts of Zn in shoot are not likely to cause a risk to herbivores. - Effects of Zn contamination showed different responses in uptake and accumulation patterns of site-specific plant species, which were similar in a semi-field experiment and under controlled conditions

Plant-specific responses to zinc contamination in a semi-field lysimeter and on hydroponics

Energy Technology Data Exchange (ETDEWEB)

Bernhard, Roland [Department of Ecology and Physiology of Plants, Vrije Universiteit, De Boelelaan 1085, NL-1081 HV Amsterdam (Netherlands); Verkleij, Jos A.C. [Department of Ecology and Physiology of Plants, Vrije Universiteit, De Boelelaan 1085, NL-1081 HV Amsterdam (Netherlands)]. E-mail: jos.verkleij@falw.vu.nl; Nelissen, Hans J.M. [Department of Ecology and Physiology of Plants, Vrije Universiteit, De Boelelaan 1085, NL-1081 HV Amsterdam (Netherlands); Vink, Jos P.M. [Department of Chemistry and Ecotoxicology, RIZA, PO Box 17, NL-8200 AA Lelystad (Netherlands)

2005-11-15

The species Agrostis stolonifera, Brassica napus and Trifolium repens representing different ecological strategies, were selected to study the effect of Zn contamination on Zn tolerance, uptake and accumulation patterns. Parallel tests were carried out with increasing concentrations of Zn in a semi-field lysimeter and hydroponics in the climate chamber. A significant reduction in biomass production or root length and an increase in shoot Zn concentration was observed for all species at increasing external Zn concentrations. However, shoot biomass production, Zn tolerance and Zn accumulation differed significantly among the tested species. The results in both experimental set-ups were quite similar concerning Zn tolerance and accumulation and improved the validity of the findings. The rather specific responses of the different plant species to Zn contamination interfere with the more generic approach used in risk assessment studies. Maximum amounts of Zn in shoot are not likely to cause a risk to herbivores. - Effects of Zn contamination showed different responses in uptake and accumulation patterns of site-specific plant species, which were similar in a semi-field experiment and under controlled conditions.

Auxiliary feedwater system risk-based inspection guide for the Ginna Nuclear Power Plant

International Nuclear Information System (INIS)

Pugh, R.; Gore, B.F.; Vo, T.V.; Moffitt, N.E.

1991-09-01

In a study sponsored by the US Nuclear Regulatory Commission (NRC), Pacific Northwest Laboratory has developed and applied a methodology for deriving plant-specific risk-based inspection guidance for the auxiliary feedwater (AFW) system at pressurized water reactors that have not undergone probabilistic risk assessment (PRA). This methodology uses existing PRA results and plant operating experience information. Existing PRA-based inspection guidance information recently developed for the NRC for various plants was used to identify generic component failure modes. This information was then combined with plant-specific and industry-wide component information and failure data to identify failure modes and failure mechanisms for the AFW system at the selected plants. Ginna was selected as the eighth plant for study. The product of this effort is a prioritized listing of AFW failures which have occurred at the plant and at other PWRs. This listing is intended for use by NRC inspectors in the preparation of inspection plans addressing AFW risk-important components at the Ginna plant. 23 refs., 1 fig., 1 tab

Ubiquitous water-soluble molecules in aquatic plant exudates determine specific insect attraction.

Directory of Open Access Journals (Sweden)

Julien Sérandour

Full Text Available Plants produce semio-chemicals that directly influence insect attraction and/or repulsion. Generally, this attraction is closely associated with herbivory and has been studied mainly under atmospheric conditions. On the other hand, the relationship between aquatic plants and insects has been little studied. To determine whether the roots of aquatic macrophytes release attractive chemical mixtures into the water, we studied the behaviour of mosquito larvae using olfactory experiments with root exudates. After testing the attraction on Culex and Aedes mosquito larvae, we chose to work with Coquillettidia species, which have a complex behaviour in nature and need to be attached to plant roots in order to obtain oxygen. This relationship is non-destructive and can be described as commensal behaviour. Commonly found compounds seemed to be involved in insect attraction since root exudates from different plants were all attractive. Moreover, chemical analysis allowed us to identify a certain number of commonly found, highly water-soluble, low-molecular-weight compounds, several of which (glycerol, uracil, thymine, uridine, thymidine were able to induce attraction when tested individually but at concentrations substantially higher than those found in nature. However, our principal findings demonstrated that these compounds appeared to act synergistically, since a mixture of these five compounds attracted larvae at natural concentrations (0.7 nM glycerol, <0.5 nM uracil, 0.6 nM thymine, 2.8 nM uridine, 86 nM thymidine, much lower than those found for each compound tested individually. These results provide strong evidence that a mixture of polyols (glycerol, pyrimidines (uracil, thymine, and nucleosides (uridine, thymidine functions as an efficient attractive signal in nature for Coquillettidia larvae. We therefore show for the first time, that such commonly found compounds may play an important role in plant-insect relationships in aquatic eco-systems.

WMAXC: a weighted maximum clique method for identifying condition-specific sub-network.

Directory of Open Access Journals (Sweden)

Bayarbaatar Amgalan

Full Text Available Sub-networks can expose complex patterns in an entire bio-molecular network by extracting interactions that depend on temporal or condition-specific contexts. When genes interact with each other during cellular processes, they may form differential co-expression patterns with other genes across different cell states. The identification of condition-specific sub-networks is of great importance in investigating how a living cell adapts to environmental changes. In this work, we propose the weighted MAXimum clique (WMAXC method to identify a condition-specific sub-network. WMAXC first proposes scoring functions that jointly measure condition-specific changes to both individual genes and gene-gene co-expressions. It then employs a weaker formula of a general maximum clique problem and relates the maximum scored clique of a weighted graph to the optimization of a quadratic objective function under sparsity constraints. We combine a continuous genetic algorithm and a projection procedure to obtain a single optimal sub-network that maximizes the objective function (scoring function over the standard simplex (sparsity constraints. We applied the WMAXC method to both simulated data and real data sets of ovarian and prostate cancer. Compared with previous methods, WMAXC selected a large fraction of cancer-related genes, which were enriched in cancer-related pathways. The results demonstrated that our method efficiently captured a subset of genes relevant under the investigated condition.

Protein carbonylation in plants

DEFF Research Database (Denmark)

Møller, Ian Max; Havelund, Jesper; Rogowska-Wrzesinska, Adelina

2017-01-01

This chapter provides an overview of the current knowledge on protein carbonylation in plants and its role in plant physiology. It starts with a brief outline of the turnover and production sites of reactive oxygen species (ROS) in plants and the causes of protein carbonylation. This is followed...... by a description of the methods used to study protein carbonylation in plants, which is also very brief as the methods are similar to those used in studies on animals. The chapter also focuses on protein carbonylation in plants in general and in mitochondria and in seeds in particular, as case stories where...... specific carbonylated proteins have been identified. Protein carbonylation appears to accumulate at all stages of seed development and germination investigated to date. In some cases, such as seed aging, it is probably simply an accumulation of oxidative damage. However, in other cases protein...

Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas.

Directory of Open Access Journals (Sweden)

Hong Lu

Full Text Available Xanthomonas is a large genus of plant-associated and plant-pathogenic bacteria. Collectively, members cause diseases on over 392 plant species. Individually, they exhibit marked host- and tissue-specificity. The determinants of this specificity are unknown.To assess potential contributions to host- and tissue-specificity, pathogenesis-associated gene clusters were compared across genomes of eight Xanthomonas strains representing vascular or non-vascular pathogens of rice, brassicas, pepper and tomato, and citrus. The gum cluster for extracellular polysaccharide is conserved except for gumN and sequences downstream. The xcs and xps clusters for type II secretion are conserved, except in the rice pathogens, in which xcs is missing. In the otherwise conserved hrp cluster, sequences flanking the core genes for type III secretion vary with respect to insertion sequence element and putative effector gene content. Variation at the rpf (regulation of pathogenicity factors cluster is more pronounced, though genes with established functional relevance are conserved. A cluster for synthesis of lipopolysaccharide varies highly, suggesting multiple horizontal gene transfers and reassortments, but this variation does not correlate with host- or tissue-specificity. Phylogenetic trees based on amino acid alignments of gum, xps, xcs, hrp, and rpf cluster products generally reflect strain phylogeny. However, amino acid residues at four positions correlate with tissue specificity, revealing hpaA and xpsD as candidate determinants. Examination of genome sequences of xanthomonads Xylella fastidiosa and Stenotrophomonas maltophilia revealed that the hrp, gum, and xcs clusters are recent acquisitions in the Xanthomonas lineage.Our results provide insight into the ancestral Xanthomonas genome and indicate that differentiation with respect to host- and tissue-specificity involved not major modifications or wholesale exchange of clusters, but subtle changes in a small

The plant non-specific phospholipase C gene family. Novel competitors in lipid signalling

Czech Academy of Sciences Publication Activity Database

Pokotylo, Igor; Pejchar, Přemysl; Potocký, Martin; Kocourková, Daniela; Krčková, Zuzana; Ruelland, E.; Kravets, V.; Martinec, Jan

2013-01-01

Roč. 52, č. 1 (2013), s. 62-79 ISSN 0163-7827 R&D Projects: GA ČR(CZ) GAP501/12/1942; GA ČR(CZ) GPP501/12/P950; GA MŠk ME09108; GA AV ČR IAA601110916 Institutional research plan: CEZ:AV0Z50380511 Keywords : Plant nonspecific phospholipase C * Phosphatidylcholine-specific phospholipase C * Diacylglycerol Subject RIV: ED - Physiology Impact factor: 12.963, year: 2013

Identifying and naming plant-pathogenic fungi: past, present, and future.

Science.gov (United States)

Crous, Pedro W; Hawksworth, David L; Wingfield, Michael J

2015-01-01

Scientific names are crucial in communicating knowledge about fungi. In plant pathology, they link information regarding the biology, host range, distribution, and potential risk. Our understanding of fungal biodiversity and fungal systematics has undergone an exponential leap, incorporating genomics, web-based systems, and DNA data for rapid identification to link species to metadata. The impact of our ability to recognize hitherto unknown organisms on plant pathology and trade is enormous and continues to grow. Major challenges for phytomycology are intertwined with the Genera of Fungi project, which adds DNA barcodes to known biodiversity and corrects the application of old, established names via epi- or neotypification. Implementing the one fungus-one name system and linking names to validated type specimens, cultures, and reference sequences will provide the foundation on which the future of plant pathology and the communication of names of plant pathogens will rest.

Clinical importance of non-specific lipid transfer proteins as food allergens

NARCIS (Netherlands)

van Ree, R.

2002-01-01

Non-specific lipid transfer proteins (nsLTPs) have recently been identified as plant food allergens. They are good examples of true food allergens, in the sense that they are capable of sensitizing, i.e. inducing specific IgE, as well as of eliciting severe symptoms. This is in contrast with most

Selective chemical binding enhances cesium tolerance in plants through inhibition of cesium uptake.

Science.gov (United States)

Adams, Eri; Chaban, Vitaly; Khandelia, Himanshu; Shin, Ryoung

2015-03-05

High concentrations of cesium (Cs(+)) inhibit plant growth but the detailed mechanisms of Cs(+) uptake, transport and response in plants are not well known. In order to identify small molecules with a capacity to enhance plant tolerance to Cs(+), chemical library screening was performed using Arabidopsis. Of 10,000 chemicals tested, five compounds were confirmed as Cs(+) tolerance enhancers. Further investigation and quantum mechanical modelling revealed that one of these compounds reduced Cs(+) concentrations in plants and that the imidazole moiety of this compound bound specifically to Cs(+). Analysis of the analogous compounds indicated that the structure of the identified compound is important for the effect to be conferred. Taken together, Cs(+) tolerance enhancer isolated here renders plants tolerant to Cs(+) by inhibiting Cs(+) entry into roots via specific binding to the ion thus, for instance, providing a basis for phytostabilisation of radiocesium-contaminated farmland.

Optimization and improvement of the technical specifications for Santa Maria de Garona and Cofrentes nuclear power plants

International Nuclear Information System (INIS)

Norte Gomez, M.D.; Alcantud, F.; Hoyo, C. del

1993-01-01

Technical Specifications (TS) form one of the basic documents necessary for licensing nuclear power plants and are required by the Government in accordance with Article 26 of the Regulation for Nuclear and Radioactive Facilities. They contain specific plant characteristics and operating limits to provide adequate protection for the safety and health of operators and the general public. For operator actuation, TS include all the surveillance requirements and limiting operating conditions (operation at full power, startup, hot and cold shutdown, and refueling outage) of safety-related systems. They also include the conventional support systems which are necessary to keep the plant in a safe operating conditioner to bring it to safe shutdown in the event of incidents or hypothetical accidents. Because of the large volume of information contained in the TS, the NRC and American utility owners began to simplify and improve the initial standard TS, which has given way to the development of a TS Optimization Program in the USA under the auspices of the NRC. Empresarios Agrupados has been contracted by the BWR Spanish Owners' Group (GPE-BWR) to develop optimized TS for the Santa Maria de Garona and Cofrentes Nuclear Power Plants. The optimized and improved TS are simplified versions of the current ones and facilitate the work of plant operators. They help to prevent risks, and reduce the number of potential transients caused by the large number of tests required by current TS. Plant operational safety is enhanced and higher effective operation is achieved. The GPE-BWR has submitted the first part of the optimized TS with their corresponding Bases to the Spanish Nuclear Council (CSN), for comment and subsequent approval. Once the TS are approved by the Spanish Nuclear Council, the operators of the Santa Maria de Garona and Cofrentes Nuclear Power Plants will be given a training and adaptation course prior to their implementation. (author)

Towards identifying host cell-type specific response patterns to bacterial endosymbiosis

DEFF Research Database (Denmark)

Gavrilovic, Srdjan

The establishment of Symbiotic Nitrogen Fixation (SNF) is a complex process. It requires highly sophisticated signal exchanges between host plant and bacteria in order to fine-tune the molecular mechanisms necessary for optimal performance of the symbiosis, which ultimately determines the evoluti......The establishment of Symbiotic Nitrogen Fixation (SNF) is a complex process. It requires highly sophisticated signal exchanges between host plant and bacteria in order to fine-tune the molecular mechanisms necessary for optimal performance of the symbiosis, which ultimately determines......, and whole plant transformants were regenerated. These will form a basis for isolating transcriptionally active mRNA fractions associated with ribosomes and 21 nt long small RNAs from targeted cell populations....

Butterfly Larval Host Plant use in a Tropical Urban Context: Life History Associations, Herbivory, and Landscape Factors

Science.gov (United States)

Tiple, Ashish D.; Khurad, Arun M.; Dennis, Roger L. H.

2011-01-01

This study examines butterfly larval host plants, herbivory and related life history attributes within Nagpur City, India. The larval host plants of 120 butterfly species are identified and their host specificity, life form, biotope, abundance and perennation recorded; of the 126 larval host plants, most are trees (49), with fewer herbs (43), shrubs (22), climbers (7) and stem parasites (2). They include 89 wild, 23 cultivated, 11 wild/cultivated and 3 exotic plant species; 78 are perennials, 43 annuals and 5 biannuals. Plants belonging to Poaceae and Fabaceae are most widely used by butterfly larvae. In addition to distinctions in host plant family affiliation, a number of significant differences between butterfly families have been identified in host use patterns: for life forms, biotopes, landforms, perennation, host specificity, egg batch size and ant associations. These differences arising from the development of a butterfly resource database have important implications for conserving butterfly species within the city area. Differences in overall butterfly population sizes within the city relate mainly to the number of host plants used, but other influences, including egg batch size and host specificity are identified. Much of the variation in population size is unaccounted for and points to the need to investigate larval host plant life history and strategies as population size is not simply dependent on host plant abundance. PMID:21864159

Is an ecosystem services-based approach developed for setting specific protection goals for plant protection products applicable to other chemicals?

Science.gov (United States)

Maltby, Lorraine; Jackson, Mathew; Whale, Graham; Brown, A Ross; Hamer, Mick; Solga, Andreas; Kabouw, Patrick; Woods, Richard; Marshall, Stuart

2017-02-15

Clearly defined protection goals specifying what to protect, where and when, are required for designing scientifically sound risk assessments and effective risk management of chemicals. Environmental protection goals specified in EU legislation are defined in general terms, resulting in uncertainty in how to achieve them. In 2010, the European Food Safety Authority (EFSA) published a framework to identify more specific protection goals based on ecosystem services potentially affected by plant protection products. But how applicable is this framework to chemicals with different emission scenarios and receptor ecosystems? Four case studies used to address this question were: (i) oil refinery waste water exposure in estuarine environments; (ii) oil dispersant exposure in aquatic environments; (iii) down the drain chemicals exposure in a wide range of ecosystems (terrestrial and aquatic); (iv) persistent organic pollutant exposure in remote (pristine) Arctic environments. A four-step process was followed to identify ecosystems and services potentially impacted by chemical emissions and to define specific protection goals. Case studies demonstrated that, in principle, the ecosystem services concept and the EFSA framework can be applied to derive specific protection goals for a broad range of chemical exposure scenarios. By identifying key habitats and ecosystem services of concern, the approach offers the potential for greater spatial and temporal resolution, together with increased environmental relevance, in chemical risk assessments. With modifications including improved clarity on terminology/definitions and further development/refinement of the key concepts, we believe the principles of the EFSA framework could provide a methodical approach to the identification and prioritization of ecosystems, ecosystem services and the service providing units that are most at risk from chemical exposure. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights

Trojan technical specification verification project

International Nuclear Information System (INIS)

Bates, L.; Rickenback, M.

1991-01-01

The Trojan Technical Specification Verification (TTSV) project at the Trojan plant of Portland General Electric Company was motivated by the recognition that many numbers in the Trojan technical specifications (TTS) potentially lacked the consideration of instrument- and/or process-related errors. The plant setpoints were known to consider such errors, but many of the values associated with the limiting conditions for operation (LCO) did not. In addition, the existing plant instrument error analyses were based on industry values that do not reflect the Trojan plant-specific experience. The purpose of this project is to ensure that the Trojan plant setpoint and LCO values include plant-specific instrument error

Novel HTS strategy identifies TRAIL-sensitizing compounds acting specifically through the caspase-8 apoptotic axis.

Directory of Open Access Journals (Sweden)

Darren Finlay

Full Text Available Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand (TRAIL is potentially a very important therapeutic as it shows selectivity for inducing apoptosis in cancer cells whilst normal cells are refractory. TRAIL binding to its cognate receptors, Death Receptors-4 and -5, leads to recruitment of caspase-8 and classical activation of downstream effector caspases, leading to apoptosis. As with many drugs however, TRAIL's usefulness is limited by resistance, either innate or acquired. We describe here the development of a novel 384-well high-throughput screening (HTS strategy for identifying potential TRAIL-sensitizing agents that act solely in a caspase-8 dependent manner. By utilizing a TRAIL resistant cell line lacking caspase-8 (NB7 compared to the same cells reconstituted with the wild-type protein, or with a catalytically inactive point mutant of caspase-8, we are able to identify compounds that act specifically through the caspase-8 axis, rather than through general toxicity. In addition, false positive hits can easily be "weeded out" in this assay due to their activity in cells lacking caspase-8-inducible activity. Screening of the library of pharmacologically active compounds (LOPAC was performed as both proof-of-concept and to discover potential unknown TRAIL sensitizers whose mechanism is caspase-8 mediated. We identified known TRAIL sensitizers from the library and identified new compounds that appear to sensitize specifically through caspase-8. In sum, we demonstrate proof-of-concept and discovery of novel compounds with a screening strategy optimized for the detection of caspase-8 pathway-specific TRAIL sensitizers. This screen was performed in the 384-well format, but could easily be further miniaturized, allows easy identification of artifactual false positives, and is highly scalable to accommodate diverse libraries.

Site-specific analysis of hybrid geothermal/fossil power plants

Energy Technology Data Exchange (ETDEWEB)

1977-06-01

A preliminary economic analysis of a hybrid geothermal/coal power plant was completed for four geothermal resource areas: Roosevelt Hot Springs, Coso Hot Springs, East Mesa, and Long Valley. A hybrid plant would be economically viable at Roosevelt Hot Springs and somewhat less so at Coso Hot Springs. East Mesa and Long Valley show no economic promise. A well-designed hybrid plant could use geothermal energy for boiler feedwater heating, auxiliary power, auxiliary heating, and cooling water. Construction and operation of a hybrid plant at either Roosevelt Hot Springs or Coso Hot Springs is recommended. A modified version of the Lawrence Berkeley Livermore GEOTHM Program is the major analytical tool used in the analysis. The Intermountain Power Project is the reference all coal-fired plant.

Prototype for an automated technical specification information system

International Nuclear Information System (INIS)

Quinn, E.L.; Mills, R.H.; Groves, J.E.

1985-01-01

The Southern California Edison (SCE) Automated Technical Specification Information System (ATSIS) at the San Onofre nuclear generating station (SONGS) has been developed as a prototype for an on-line information management system. This system provides an appropriate level of update, inquiry, and report generation capabilities to help support plant operators at SONGS in their efforts to anticipate, identify, document, and track certain actions and activities associated with plant technical specifications and associated limiting conditions of operation (LCOs). Substantially increased emphasis is being placed on adherence to nuclear regulatory requirements and commitments contained on the operating licenses of nuclear power plants. Additionally, as each year passes, such requirements are becoming increasingly detailed and complex, making it more and more difficult to track and ensure total compliance with the many and varied requirements. To assist the operations department at SONGs in meeting their regulatory commitments, in January 1985 SCE commenced gathering together the leading technical expertise available in the industry to develop a computerized system to track all technical specification-related equipment for operability and impact on LCOs

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

Science.gov (United States)

Godec, Jernej; Tan, Yan; Liberzon, Arthur; Tamayo, Pablo; Bhattacharya, Sanchita; Butte, Atul J; Mesirov, Jill P; Haining, W Nicholas

2016-01-19

Gene-expression profiling has become a mainstay in immunology, but subtle changes in gene networks related to biological processes are hard to discern when comparing various datasets. For instance, conservation of the transcriptional response to sepsis in mouse models and human disease remains controversial. To improve transcriptional analysis in immunology, we created ImmuneSigDB: a manually annotated compendium of ∼5,000 gene-sets from diverse cell states, experimental manipulations, and genetic perturbations in immunology. Analysis using ImmuneSigDB identified signatures induced in activated myeloid cells and differentiating lymphocytes that were highly conserved between humans and mice. Sepsis triggered conserved patterns of gene expression in humans and mouse models. However, we also identified species-specific biological processes in the sepsis transcriptional response: although both species upregulated phagocytosis-related genes, a mitosis signature was specific to humans. ImmuneSigDB enables granular analysis of transcriptomic data to improve biological understanding of immune processes of the human and mouse immune systems. Copyright © 2016 Elsevier Inc. All rights reserved.

Auxiliary feedwater system risk-based inspection guide for the Palo Verde Nuclear Power Plant

International Nuclear Information System (INIS)

Bumgardner, J.D.; Moffitt, N.E.; Gore, B.F.; Vo, T.V.; Sloan, J.A.

1993-02-01

In a study sponsored by the US Nuclear Regulatory Commission (NRC), Pacific Northwest Laboratory has developed and applied a methodology for deriving plant-specific risk-based inspection guidance for the auxiliary feedwater (AFW) system at pressurized water reactors that have not undergone probabilistic risk assessment (PRA). This methodology uses existing PRA results and plant operating experience information. Existing PRA-based inspection guidance information recently developed for the NRC for various plants was used to identify generic component failure modes. This information was then combined with plant-specific and industry-wide component information and failure data to identify failure modes and failure mechanisms for the AFW system at the selected plants. Palo Verde was selected as one of a series of plants for study. The product of this effort is a prioritized listing of AFW failures which have occurred at the plant and at other PWRs. This listing is intended for use by NRC inspectors in the preparation of inspection plans addressing AFW risk-important components at the Palo Verde plants

Auxiliary feedwater system risk-based inspection guide for the McGuire nuclear power plant

International Nuclear Information System (INIS)

Bumgardner, J.D.; Lloyd, R.C.; Moffitt, N.E.; Gore, B.F.; Vo, T.V.

1994-05-01

In a study sponsored by the US Nuclear Regulatory Commission (NRC), Pacific Northwest Laboratory has developed and applied a methodology for deriving plant-specific risk-based inspection guidance for the auxiliary feedwater (AFW) system at pressurized water reactors that have not undergone probabilistic risk assessment (PRA). This methodology uses existing PRA results and plant operating experience information. Existing PRA-based inspection guidance information recently developed for the NRC for various plants was used to identify generic component failure modes. This information was then combined with plant-specific and industry-wide component information and failure data to identify failure modes and failure mechanisms for the AFW system at the selected plants. McGuire was selected as one of a series of plants for study. The product of this effort is a prioritized listing of AFW failures which have occurred at the plant and at other PWRs. This listing is intended for use by NRC inspectors in the preparation of inspection plans addressing AFW risk-important components at the McGuire plant

Auxiliary feedwater system risk-based inspection guide for the Maine Yankee Nuclear Power Plant

International Nuclear Information System (INIS)

Gore, B.F.; Vo, T.V.; Moffitt, N.E.; Bumgardner, J.D.

1992-10-01

In a study sponsored by the US Nuclear Regulatory Commission (NRC), Pacific Northwest Laboratory has developed and applied a methodology for deriving plant-specific risk-based inspection guidance for the auxiliary feedwater (AFW) system at pressurized water reactors that have not undergone probabilistic risk assessment (PRA). This methodology uses existing PRA results and plant operating experience information. Existing PRA-based inspection guidance information recently developed for the NRC for various plants was used to identify generic component failure modes. The information was then combined with plant-specific and industry-wide component information and failure data to identify failure modes and failure mechanisms for the AFW system at the selected plants. Maine Yankee was selected as one of a series of plants for study. ne product of this effort is a prioritized listing of AFW failures which have occurred at the plant and at other PWRs. This listing is intended for use by NRC inspectors in the preparation of inspection plans addressing AFW risk-important components at the Maine Yankee plant

Auxiliary feedwater system risk-based inspection guide for the Point Beach nuclear power plant

International Nuclear Information System (INIS)

Lloyd, R.C.; Moffitt, N.E.; Gore, B.F.; Vo, T.V.; Vehec, T.A.

1993-02-01

In a study sponsored by the US Nuclear Regulatory Commission (NRC), Pacific Northwest Laboratory has developed and applied a methodology for deriving plant-specific risk-based inspection guidance for the auxiliary feedwater (AFW) system at pressurized water reactors that have not undergone probabilistic risk assessment (PRA). This methodology uses existing PRA results and plant operating experience information. Existing PRA-based inspection guidance information recently developed for the NRC for various plants was used to identify generic component failure modes. This information was then combined with plant-specific and industry-wide component information and failure data to identify failure modes and failure mechanisms for the AFW system at the selected plants. Point Beach was selected as one of a series of plants for study. The product of this effort is a prioritized listing of AFW failures which have occurred at the plant and at other PWRS. This listing is intended for use by NRC inspectors in the preparation of inspection plans addressing AFW risk-important components at the Point Beach plant

Data integration aids understanding of butterfly-host plant networks.

Science.gov (United States)

Muto-Fujita, Ai; Takemoto, Kazuhiro; Kanaya, Shigehiko; Nakazato, Takeru; Tokimatsu, Toshiaki; Matsumoto, Natsushi; Kono, Mayo; Chubachi, Yuko; Ozaki, Katsuhisa; Kotera, Masaaki

2017-03-06

Although host-plant selection is a central topic in ecology, its general underpinnings are poorly understood. Here, we performed a case study focusing on the publicly available data on Japanese butterflies. A combined statistical analysis of plant-herbivore relationships and taxonomy revealed that some butterfly subfamilies in different families feed on the same plant families, and the occurrence of this phenomenon more than just by chance, thus indicating the independent acquisition of adaptive phenotypes to the same hosts. We consequently integrated plant-herbivore and plant-compound relationship data and conducted a statistical analysis to identify compounds unique to host plants of specific butterfly families. Some of the identified plant compounds are known to attract certain butterfly groups while repelling others. The additional incorporation of insect-compound relationship data revealed potential metabolic processes that are related to host plant selection. Our results demonstrate that data integration enables the computational detection of compounds putatively involved in particular interspecies interactions and that further data enrichment and integration of genomic and transcriptomic data facilitates the unveiling of the molecular mechanisms involved in host plant selection.

Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls.

Science.gov (United States)

MacMillan, Colleen P; Birke, Hannah; Chuah, Aaron; Brill, Elizabeth; Tsuji, Yukiko; Ralph, John; Dennis, Elizabeth S; Llewellyn, Danny; Pettolino, Filomena A

2017-07-18

Knowledge of plant secondary cell wall (SCW) regulation and deposition is mainly based on the Arabidopsis model of a 'typical' lignocellulosic SCW. However, SCWs in other plants can vary from this. The SCW of mature cotton seed fibres is highly cellulosic and lacks lignification whereas xylem SCWs are lignocellulosic. We used cotton as a model to study different SCWs and the expression of the genes involved in their formation via RNA deep sequencing and chemical analysis of stem and seed fibre. Transcriptome comparisons from cotton xylem and pith as well as from a developmental series of seed fibres revealed tissue-specific and developmentally regulated expression of several NAC transcription factors some of which are likely to be important as top tier regulators of SCW formation in xylem and/or seed fibre. A so far undescribed hierarchy was identified between the top tier NAC transcription factors SND1-like and NST1/2 in cotton. Key SCW MYB transcription factors, homologs of Arabidopsis MYB46/83, were practically absent in cotton stem xylem. Lack of expression of other lignin-specific MYBs in seed fibre relative to xylem could account for the lack of lignin deposition in seed fibre. Expression of a MYB103 homolog correlated with temporal expression of SCW CesAs and cellulose synthesis in seed fibres. FLAs were highly expressed and may be important structural components of seed fibre SCWs. Finally, we made the unexpected observation that cell walls in the pith of cotton stems contained lignin and had a higher S:G ratio than in xylem, despite that tissue's lacking many of the gene transcripts normally associated with lignin biosynthesis. Our study in cotton confirmed some features of the currently accepted gene regulatory cascade for 'typical' plant SCWs, but also revealed substantial differences, especially with key downstream NACs and MYBs. The lignocellulosic SCW of cotton xylem appears to be achieved differently from that in Arabidopsis. Pith cell walls in

77 FR 29391 - An Approach for Probabilistic Risk Assessment in Risk-Informed Decisions on Plant-Specific...

Science.gov (United States)

2012-05-17

... NUCLEAR REGULATORY COMMISSION [NRC-2012-0110] An Approach for Probabilistic Risk Assessment in Risk-Informed Decisions on Plant-Specific Changes to the Licensing Basis AGENCY: Nuclear Regulatory Commission. ACTION: Draft regulatory guide; request for comment. SUMMARY: The U.S. Nuclear Regulatory...

Improving the action requirements of technical specifications: A risk-comparison of continued operation and plant shutdown

International Nuclear Information System (INIS)

Kim, I.S.; Samanta, P.K.

1994-01-01

When the systems needed to remove decay heat are inoperable or degraded, the risk of shutting down the plant may be comparable to, or even higher than, that of continuing power operation with the equipment inoperable while giving priority to repairs. This concern arises because the plant may not have sufficient capability for removing decay heat during the shutdown. However, Technical Specifications (TSs) often require ''immediate'' shutdown of the plant. In this paper, the authors present risk-based analyses of the various operational policy alternatives available in such situations, with an example application to the standby service water (SSW) system of a BWR. These analyses can be used to define risk-effective requirements for those standby safety systems under discussion

Improving the action requirements of technical specifications: A risk-comparison of continued operation and plant shutdown

Energy Technology Data Exchange (ETDEWEB)

Kim, I.S.; Samanta, P.K. [Brookhaven National Lab., Upton, NY (United States); Mankamo, T.

1995-04-01

When the systems needed to remove decay heat are inoperable or degraded, the risk of shutting down the plant may be comparable to, or even higher than, that of continuing power operation with the equipment inoperable while giving priority to repairs. This concern arises because the plant may not have sufficient capability for removing decay heat during the shutdown. However, Technical Specifications (TSs) often require {open_quotes}immediate{close_quotes} shutdown of the plant. In this paper, we present risk-based analyses of the various operational policy alternatives available in such situations, with an example application to the standby service water (SSW) system of a BWR. These analyses can be used to define risk-effective requirements for those standby safety systems under discussion.

Anti-gout Potential of Malaysian Medicinal Plants.

Science.gov (United States)

Abu Bakar, Fazleen I; Abu Bakar, Mohd F; Rahmat, Asmah; Abdullah, Norazlin; Sabran, Siti F; Endrini, Susi

2018-01-01

Gout is a type of arthritis that causes painful inflammation in one or more joints. In gout, elevation of uric acid in the blood triggers the formation of crystals, causing joint pain. Malaysia is a mega-biodiversity country that is rich in medicinal plants species. Therefore, its flora might offer promising therapies for gout. This article aims to systematically review the anti-gout potential of Malaysian medicinal plants. Articles on gout published from 2000 to 2017 were identified using PubMed, Scopus, ScienceDirect, and Google Scholar with the following keyword search terms: "gout," "medicinal plants," "Malaysia," "epidemiology," " in vitro," and " in vivo ." In this study, 85 plants were identified as possessing anti-gout activity. These plants had higher percentages of xanthine oxidase inhibitory activity (>85%); specifically, the Momordica charantia, Chrysanthemum indicum, Cinnamomum cassia, Kaempferia galanga, Artemisia vulgaris , and Morinda elliptica had the highest values, due to their diverse natural bioactive compounds, which include flavonoids, phenolics, tannin, coumarins, luteolin, and apigenin. This review summarizes the anti-gout potential of Malaysian medicinal plants but the mechanisms, active compounds, pharmacokinetics, bioavailability, and safety of the plants still remain to be elucidated.

Standard technical specifications - Babcock and Wilcox Plants: Bases (Sections 2.0-3.3). Volume 2, Revision 1

International Nuclear Information System (INIS)

1995-04-01

This NUREG contains the improved Standard Technical Specifications (STS) for Babcock and Wilcox (B ampersand W) plants. Revision 1 incorporates the cumulative changes to Revision 0, which was published in September 1992. The changes reflected in Revision 1 resulted from the experience gained from license amendment applications to convert to these improved STS or to adopt partial improvements to existing technical specifications. This NUREG is the result of extensive public technical meetings and discussions between the Nuclear Regulatory Commission (NRC) staff and various nuclear power plant licensees, Nuclear Steam Supply System (NSSS) Owners Groups, specifically the B ampersand W Owners Group (BWOG), NSSS vendors, and the Nuclear Energy Institute (NEI). The improved STS were developed based on the criteria in the Final Commission Policy Statement on Technical Specifications Improvements for Nuclear Power Reactors, dated July 22, 1993 (58 FR 39132). Licensees are encouraged to upgrade their technical specifications consistent with those criteria and conforming, to the extent practical and consistent with the licensing basis for the facility, to Revision 1 to the improved STS. The Commission continues to place the highest priority on requests for complete conversions to the improved STS. Licensees adopting portions of the improved STS to existing technical specifications should adopt all related requirements, as applicable, to achieve a high degree of standardization and consistency

Genotype-specific responses to light stress in eelgrass Zostera marina, a marine foundation plant

DEFF Research Database (Denmark)

Salo, Tiina Elina; Reusch, Thorsten B. H.

2015-01-01

, and their performance during light limitation and 4 wk of recovery was compared to non-shaded controls. In addition to growth and biomass, we investigated storage carbohydrates and quantified the expression of genes involved in carbohydrate metabolism, photosynthesis and control of oxidative stress. Plants showed......Within mono-specific meadows of clonal plants, genotypic diversity may functionally replace species diversity. Little is known about the variability in performance and plasticity of different genotypes towards anthropogenically induced stressors. In this field experiment we compared light......-limitation stress responses and recovery of different eelgrass Zostera marina genotypes to assess the variability in phenotypic plasticity and gene expression between different genotypes. Replicated monoculture plots of 4 genotypes were subjected to a simulated turbidity period of 4 wk using shading screens...

Insights into the substrate specificity of plant peptide deformylase, an essential enzyme with potential for the development of novel biotechnology applications in agriculture.

Science.gov (United States)

Dirk, Lynnette M A; Schmidt, Jack J; Cai, Yiying; Barnes, Jonathan C; Hanger, Katherine M; Nayak, Nihar R; Williams, Mark A; Grossman, Robert B; Houtz, Robert L; Rodgers, David W

2008-08-01

The crystal structure of AtPDF1B [Arabidopsis thaliana PDF (peptide deformylase) 1B; EC 3.5.1.88], a plant specific deformylase, has been determined at a resolution of 2.4 A (1 A=0.1 nm). The overall fold of AtPDF1B is similar to other peptide deformylases that have been reported. Evidence from the crystal structure and gel filtration chromatography indicates that AtPDF1B exists as a symmetric dimer. PDF1B is essential in plants and has a preferred substrate specificity towards the PS II (photosystem II) D1 polypeptide. Comparative analysis of AtPDF1B, AtPDF1A, and the type 1B deformylase from Escherichia coli, identifies a number of differences in substrate binding subsites that might account for variations in sequence preference. A model of the N-terminal five amino acids from the D1 polypeptide bound in the active site of AtPDF1B suggests an influence of Tyr(178) as a structural determinant for polypeptide substrate specificity through hydrogen bonding with Thr(2) in the D1 sequence. Kinetic analyses using a polypeptide mimic of the D1 N-terminus was performed on AtPDF1B mutated at Tyr(178) to alanine, phenylalanine or arginine (equivalent residue in AtPDF1A). The results suggest that, whereas Tyr(178) can influence catalytic activity, other residues contribute to the overall preference for the D1 polypeptide.

Flow cytometric purification of Colletotrichum higginsianum biotrophic hyphae from Arabidopsis leaves for stage-specific transcriptome analysis.

Science.gov (United States)

Takahara, Hiroyuki; Dolf, Andreas; Endl, Elmar; O'Connell, Richard

2009-08-01

Generation of stage-specific cDNA libraries is a powerful approach to identify pathogen genes that are differentially expressed during plant infection. Biotrophic pathogens develop specialized infection structures inside living plant cells, but sampling the transcriptome of these structures is problematic due to the low ratio of fungal to plant RNA, and the lack of efficient methods to isolate them from infected plants. Here we established a method, based on fluorescence-activated cell sorting (FACS), to purify the intracellular biotrophic hyphae of Colletotrichum higginsianum from homogenates of infected Arabidopsis leaves. Specific selection of viable hyphae using a fluorescent vital marker provided intact RNA for cDNA library construction. Pilot-scale sequencing showed that the library was enriched with plant-induced and pathogenicity-related fungal genes, including some encoding small, soluble secreted proteins that represent candidate fungal effectors. The high purity of the hyphae (94%) prevented contamination of the library by sequences derived from host cells or other fungal cell types. RT-PCR confirmed that genes identified in the FACS-purified hyphae were also expressed in planta. The method has wide applicability for isolating the infection structures of other plant pathogens, and will facilitate cell-specific transcriptome analysis via deep sequencing and microarray hybridization, as well as proteomic analyses.

Identifying specific interstellar polycyclic aromatic hydrocarbons

International Nuclear Information System (INIS)

Mulas, Giacomo; Malloci, Giuliano; Porceddu, Ignazio

2005-01-01

Interstellar Polycyclic Aromatic Hydrocarbons (PAHs) have been thought to be ubiquitous for more than twenty years, yet no single species in this class has been identified in the Interstellar Medium (ISM) to date. The unprecedented sensitivity and resolution of present Infrared Space Observatory (ISO) and forthcoming Herschel observations in the far infrared spectral range will offer a unique way out of this embarrassing impasse

Recognition of plant parts with problem-specific algorithms

Science.gov (United States)

Schwanke, Joerg; Brendel, Thorsten; Jensch, Peter F.; Megnet, Roland

1994-06-01

Automatic micropropagation is necessary to produce cost-effective high amounts of biomass. Juvenile plants are dissected in clean- room environment on particular points on the stem or the leaves. A vision-system detects possible cutting points and controls a specialized robot. This contribution is directed to the pattern- recognition algorithms to detect structural parts of the plant.

Investigations regarding the lowering of specific intellectual property risks identified in the production process

Directory of Open Access Journals (Sweden)

Pakocs Ramona

2017-01-01

Full Text Available The main purpose of this research is to decrease the emergence of specific intellectual property risks within the production process as well as increasing risk management performance of IP by preventing them. In order to achieve this, previous studies regarding the main specific intellectual property risks from industrial companies were analyzed together with their managerial methods as well as the possibility of reducing their emergence. As a result of the research conducted were identified five types of intellectual property risks that have a high potential of emergence in the production process, namely: the risk of production of goods in violation of IP rights; the know-how, production knowledge and trade secret disclosure risk; the technological risk of unprotected utility models; the technological risk of unprotected integrated circuits topographies and finally the risk of product counterfeit. In order to achieve the main purpose of our investigation, we have proposed new formulas for estimating the specific intellectual property risks identified in the production process. Their purpose was to minimalize the risk’s negative effects on industrial companies and to increase the managerial performance from the intellectual property domain through a new type of management appropriately named: intellectual property management. The research is finalized with a case study regarding the lapse of rights of a patented invention. Based on a case analysis, it was proved that the exploitation of an invention without a contract represents a counterfeit.

Auxiliary feedwater system risk-based inspection guide for the South Texas Project nuclear power plant

International Nuclear Information System (INIS)

Bumgardner, J.D.; Nickolaus, J.R.; Moffitt, N.E.; Gore, B.F.; Vo, T.V.

1993-12-01

In a study sponsored by the US Nuclear Regulatory Commission (NRC), Pacific Northwest Laboratory has developed and applied a methodology for deriving plant-specific risk-based inspection guidance for the auxiliary feedwater (AFW) system at pressurized water reactors that have not undergone probabilistic risk assessment (PRA). This methodology uses existing PRA results and plant operating experience information. Existing PRA-based inspection guidance information recently developed for the NRC for various plants was used to identify generic component failure modes. This information was then combined with plant-specific and industry-wide component information and failure data to identify failure modes and failure mechanisms for the AFW system at the selected plants. South Texas Project was selected as a plant for study. The product of this effort is a prioritized listing of AFW failures which have occurred at the plant and at other PWRs. This listing is intended for use by the NRC inspectors in preparation of inspection plans addressing AFW risk important components at the South Texas Project plant

Auxiliary feedwater system risk-based inspection guide for the H. B. Robinson nuclear power plant

International Nuclear Information System (INIS)

Moffitt, N.E.; Lloyd, R.C.; Gore, B.F.; Vo, T.V.; Garner, L.W.

1993-08-01

In a study sponsored by the US Nuclear Regulatory Commission (NRC), Pacific Northwest Laboratory has developed and applied a methodology for deriving plant-specific risk-based inspection guidance for the auxiliary feedwater (AFW) system at pressurized water reactors that have not undergone probabilistic risk assessment (PRA). This methodology uses existing PRA results and plant operating experience information. Existing PRA-based inspection guidance information recently developed for the NRC for various plants was used to identify generic component failure modes. This information was then combined with plant-specific and industry-wide component information and failure data to identify failure modes and failure mechanisms for the AFW system at the selected plants. H. B. Robinson was selected as one of a series of plants for study. The product of this effort is a prioritized listing of AFW failures which have occurred at the plant and at other PWRs. This listing is intended for use by NRC inspectors in the preparation of inspection plans addressing AFW risk-important components at the H. B. Robinson plant

Auxiliary feedwater system risk-based inspection guide for the J.M. Farley Nuclear Power Plant

International Nuclear Information System (INIS)

Vo, T.V.; Pugh, R.; Gore, B.F.; Harrison, D.G.

1990-10-01

In a study sponsored by the US Nuclear Regulatory Commission (NRC), Pacific Northwest Laboratory has developed and applied a methodology for deriving plant-specific risk-based inspection guidance for the auxiliary feedwater (AFW) system at pressurized water reactors that have not undergone probabilistic risk assessment(PRA). This methodology uses existing PRA results and plant operating experience information. Existing PRA-based inspection guidance recently developed for the NRC for various plants was used to identify generic component failure modes. This information was then combined with plant-specific and industry-wide component information and failure data to identify failure modes and failure mechanisms for the AFW system at the selected plants. J. M. Farley was selected as the second plant for study. The product of this effort is a prioritized listing of AFW failures which have occurred at the plant and at other PWRs. This listing is intended for use by NRC inspectors in the preparation of inspection plans addressing AFW risk-important at the J. M. Farley plant. 23 refs., 1 fig., 1 tab

Reviewing PSA-based analyses to modify technical specifications at nuclear power plants

International Nuclear Information System (INIS)

Samanta, P.K.; Martinez-Guridi, G.; Vesely, W.E.

1995-12-01

Changes to Technical Specifications (TSs) at nuclear power plants (NPPs) require review and approval by the United States Nuclear Regulatory Commission (USNRC). Currently, many requests for changes to TSs use analyses that are based on a plant's probabilistic safety assessment (PSA). This report presents an approach to reviewing such PSA-based submittals for changes to TSs. We discuss the basic objectives of reviewing a PSA-based submittal to modify NPP TSs; the methodology of reviewing a TS submittal, and the differing roles of a PSA review, a PSA Computer Code review, and a review of a TS submittal. To illustrate this approach, we discuss our review of changes to allowed outage time (AOT) and surveillance test interval (STI) in the TS for the South Texas Project Nuclear Generating Station. Based on this experience gained, a check-list of items is given for future reviewers; it can be used to verify that the submittal contains sufficient information, and also that the review has addressed the relevant issues. Finally, recommended steps in the review process and the expected findings of each step are discussed

An HTS-compatible 3D colony formation assay to identify tumor-specific chemotherapeutics.

Science.gov (United States)

Horman, Shane R; To, Jeremy; Orth, Anthony P

2013-12-01

There has been increasing interest in the development of cellular behavior models that take advantage of three-dimensional (3D) cell culture. To enable assessment of differential perturbagen impacts on cell growth in 2D and 3D, we have miniaturized and adapted for high-throughput screening (HTS) the soft agar colony formation assay, employing a laser-scanning cytometer to image and quantify multiple cell types simultaneously. The assay is HTS compatible, providing high-quality, image-based, replicable data for multiple, co-cultured cell types. As proof of concept, we subjected colorectal carcinoma colonies in 3D soft agar to a mini screen of 1528 natural product compounds. Hit compounds from the primary screen were rescreened in an HTS 3D co-culture matrix containing colon stromal cells and cancer cells. By combining tumor cells and normal, nontransformed colon epithelial cells in one primary screening assay, we were able to obtain differential IC50 data, thereby distinguishing tumor-specific compounds from general cytotoxic compounds. Moreover, we were able to identify compounds that antagonized tumor colony formation in 3D only, highlighting the importance of this assay in identifying agents that interfere with 3D tumor structural growth. This screening platform provides a fast, simple, and robust method for identification of tumor-specific agents in a biologically relevant microenvironment.

GABA signalling modulates plant growth by directly regulating the activity of plant-specific anion transporters.

Science.gov (United States)

Ramesh, Sunita A; Tyerman, Stephen D; Xu, Bo; Bose, Jayakumar; Kaur, Satwinder; Conn, Vanessa; Domingos, Patricia; Ullah, Sana; Wege, Stefanie; Shabala, Sergey; Feijó, José A; Ryan, Peter R; Gilliham, Matthew; Gillham, Matthew

2015-07-29

The non-protein amino acid, gamma-aminobutyric acid (GABA) rapidly accumulates in plant tissues in response to biotic and abiotic stress, and regulates plant growth. Until now it was not known whether GABA exerts its effects in plants through the regulation of carbon metabolism or via an unidentified signalling pathway. Here, we demonstrate that anion flux through plant aluminium-activated malate transporter (ALMT) proteins is activated by anions and negatively regulated by GABA. Site-directed mutagenesis of selected amino acids within ALMT proteins abolishes GABA efficacy but does not alter other transport properties. GABA modulation of ALMT activity results in altered root growth and altered root tolerance to alkaline pH, acid pH and aluminium ions. We propose that GABA exerts its multiple physiological effects in plants via ALMT, including the regulation of pollen tube and root growth, and that GABA can finally be considered a legitimate signalling molecule in both the plant and animal kingdoms.

Peptide aptamers: The versatile role of specific protein function inhibitors in plant biotechnology.

Science.gov (United States)

Colombo, Monica; Mizzotti, Chiara; Masiero, Simona; Kater, Martin M; Pesaresi, Paolo

2015-11-01

In recent years, peptide aptamers have emerged as novel molecular tools that have attracted the attention of researchers in various fields of basic and applied science, ranging from medicine to analytical chemistry. These artificial short peptides are able to specifically bind, track, and inhibit a given target molecule with high affinity, even molecules with poor immunogenicity or high toxicity, and represent a remarkable alternative to antibodies in many different applications. Their use is on the rise, driven mainly by the medical and pharmaceutical sector. Here we discuss the enormous potential of peptide aptamers in both basic and applied aspects of plant biotechnology and food safety. The different peptide aptamer selection methods available both in vivo and in vitro are introduced, and the most important possible applications in plant biotechnology are illustrated. In particular, we discuss the generation of broad-based virus resistance in crops, "reverse genetics" and aptasensors in bioassays for detecting contaminations in food and feed. Furthermore, we suggest an alternative to the transfer of peptide aptamers into plant cells via genetic transformation, based on the use of cell-penetrating peptides that overcome the limits imposed by both crop transformation and Genetically Modified Organism commercialization. © 2015 Institute of Botany, Chinese Academy of Sciences.

Proceedings of a NEA/CSNI-UNIPEDE specialist meeting on improving technical specifications for nuclear power plants

Energy Technology Data Exchange (ETDEWEB)

NONE

1987-07-01

This CSNI specialist meeting on improving technical specifications for nuclear power plants is sponsored by the OECD Nuclear Energy Agency jointly with UNIPEDE. Technical specifications for nuclear power plants are in a way a prescription which has a direct bearing on the success or failure of the particular installation, and on the success or failure of fission energy around the world. It is therefore highly important that these prescriptions are made as clear and as concise as possible and that it distinguishes requirements which are essential for public health and safety, from the many others which are less important accordingly. The conference was held in september 1987 in madrid (Spain); it is composed of about 40 papers grouped into 8 sessions: invited papers (6 papers), international survey results (1 paper), limiting conditions for operation (8 papers), maintenance and testing (4 papers), actions statements and allowed outage times (8 papers), methodology and technical justification (8 papers), future trends and alternative approaches (4 papers), and a final panel

Multifactor dimensionality reduction analysis identifies specific nucleotide patterns promoting genetic polymorphisms

Directory of Open Access Journals (Sweden)

Arehart Eric

2009-03-01

Full Text Available Abstract Background The fidelity of DNA replication serves as the nidus for both genetic evolution and genomic instability fostering disease. Single nucleotide polymorphisms (SNPs constitute greater than 80% of the genetic variation between individuals. A new theory regarding DNA replication fidelity has emerged in which selectivity is governed by base-pair geometry through interactions between the selected nucleotide, the complementary strand, and the polymerase active site. We hypothesize that specific nucleotide combinations in the flanking regions of SNP fragments are associated with mutation. Results We modeled the relationship between DNA sequence and observed polymorphisms using the novel multifactor dimensionality reduction (MDR approach. MDR was originally developed to detect synergistic interactions between multiple SNPs that are predictive of disease susceptibility. We initially assembled data from the Broad Institute as a pilot test for the hypothesis that flanking region patterns associate with mutagenesis (n = 2194. We then confirmed and expanded our inquiry with human SNPs within coding regions and their flanking sequences collected from the National Center for Biotechnology Information (NCBI database (n = 29967 and a control set of sequences (coding region not associated with SNP sites randomly selected from the NCBI database (n = 29967. We discovered seven flanking region pattern associations in the Broad dataset which reached a minimum significance level of p ≤ 0.05. Significant models (p Conclusion The present study represents the first use of this computational methodology for modeling nonlinear patterns in molecular genetics. MDR was able to identify distinct nucleotide patterning around sites of mutations dependent upon the observed nucleotide change. We discovered one flanking region set that included five nucleotides clustered around a specific type of SNP site. Based on the strongly associated patterns identified in

Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer.

Science.gov (United States)

Tang, Yew Chung; Ho, Szu-Chi; Tan, Elisabeth; Ng, Alvin Wei Tian; McPherson, John R; Goh, Germaine Yen Lin; Teh, Bin Tean; Bard, Frederic; Rozen, Steven G

2018-03-22

-SSL patterns of activity in a large proportion of PTEN-deficient breast cancer cell lines and are potential specific vulnerabilities in PTEN-deficient breast cancer. Furthermore, the NUAK1 PTEN-SSL vulnerability identified by RNA interference techniques can be recapitulated and exploited using the small molecule kinase inhibitor HTH-01-015. Thus, NUAK1 inhibition may be an effective strategy for precision treatment of PTEN-deficient breast tumors.

Subsurface earthworm casts can be important soil microsites specifically influencing the growth of grassland plants.

Science.gov (United States)

Zaller, Johann G; Wechselberger, Katharina F; Gorfer, Markus; Hann, Patrick; Frank, Thomas; Wanek, Wolfgang; Drapela, Thomas

Earthworms (Annelida: Oligochaeta) deposit several tons per hectare of casts enriched in nutrients and/or arbuscular mycorrhizal fungi (AMF) and create a spatial and temporal soil heterogeneity that can play a role in structuring plant communities. However, while we begin to understand the role of surface casts, it is still unclear to what extent plants utilize subsurface casts. We conducted a greenhouse experiment using large mesocosms (volume 45 l) to test whether (1) soil microsites consisting of earthworm casts with or without AMF (four Glomus taxa) affect the biomass production of 11 grassland plant species comprising the three functional groups grasses, forbs, and legumes, (2) different ecological groups of earthworms (soil dwellers- Aporrectodea caliginosa vs. vertical burrowers- Lumbricus terrestris ) alter potential influences of soil microsites (i.e., four earthworms × two subsurface microsites × two AMF treatments). Soil microsites were artificially inserted in a 25-cm depth, and afterwards, plant species were sown in a regular pattern; the experiment ran for 6 months. Our results show that minute amounts of subsurface casts (0.89 g kg -1 soil) decreased the shoot and root production of forbs and legumes, but not that of grasses. The presence of earthworms reduced root biomass of grasses only. Our data also suggest that subsurface casts provide microsites from which root AMF colonization can start. Ecological groups of earthworms did not differ in their effects on plant production or AMF distribution. Taken together, these findings suggest that subsurface earthworm casts might play a role in structuring plant communities by specifically affecting the growth of certain functional groups of plants.

Plant growth stage-specific injury and economic injury level for verde plant bug, Creontiades signatus (Hemiptera: Miridae), on cotton: effect of bloom period of infestation.

Science.gov (United States)

Brewer, Michael J; Anderson, Darwin J; Armstrong, J Scott

2013-10-01

Verde plant bugs, Creontiades signatus Distant (Hemiptera: Miridae), were released onto caged cotton, Cossypium hirsutum L., for a 1-wk period to characterize the effects of insect density and bloom period of infestation on cotton injury and yield in 2011 and 2012, Corpus Christi, TX. When plants were infested during early bloom (10-11 nodes above first white flower), a linear decline in fruit retention and boll load and a linear increase in boll injury were detected as verde plant bug infestation levels increased from an average of 0.5 to 4 bugs per plant. Lint and seed yield per plant showed a corresponding decline. Fruit retention, boll load, and yield were not affected on plants infested 1 wk later at peak bloom (8-9 nodes above first white flower), even though boll injury increased as infestation levels increased. Second-year testing verified boll injury but not yield loss, when infestations occurred at peak bloom. Incidence of cotton boll rot, known to be associated with verde plant bug feeding, was low to modest (verde plant bug were important contributors to yield decline, damage potential was greatest during the early bloom period of infestation, and a simple linear response best described the yield response-insect density relationship at early bloom. Confirmation that cotton after peak bloom was less prone to verde plant bug injury and an early bloom-specific economic injury level were key findings that can improve integrated pest management decision-making for dryland cotton, at least under low-rainfall growing conditions.

Cell type-specific responses to salinity - the epidermal bladder cell transcriptome of Mesembryanthemum crystallinum.

Science.gov (United States)

Oh, Dong-Ha; Barkla, Bronwyn J; Vera-Estrella, Rosario; Pantoja, Omar; Lee, Sang-Yeol; Bohnert, Hans J; Dassanayake, Maheshi

2015-08-01

Mesembryanthemum crystallinum (ice plant) exhibits extreme tolerance to salt. Epidermal bladder cells (EBCs), developing on the surface of aerial tissues and specialized in sodium sequestration and other protective functions, are critical for the plant's stress adaptation. We present the first transcriptome analysis of EBCs isolated from intact plants, to investigate cell type-specific responses during plant salt adaptation. We developed a de novo assembled, nonredundant EBC reference transcriptome. Using RNAseq, we compared the expression patterns of the EBC-specific transcriptome between control and salt-treated plants. The EBC reference transcriptome consists of 37 341 transcript-contigs, of which 7% showed significantly different expression between salt-treated and control samples. We identified significant changes in ion transport, metabolism related to energy generation and osmolyte accumulation, stress signalling, and organelle functions, as well as a number of lineage-specific genes of unknown function, in response to salt treatment. The salinity-induced EBC transcriptome includes active transcript clusters, refuting the view of EBCs as passive storage compartments in the whole-plant stress response. EBC transcriptomes, differing from those of whole plants or leaf tissue, exemplify the importance of cell type-specific resolution in understanding stress adaptive mechanisms. No claim to original US government works. New Phytologist © 2015 New Phytologist Trust.

Sexual Hieracium pilosella plants are better inter-specific, while apomictic plants are better intra-specific competitors

OpenAIRE

Sailer, Christian; Schmid, Bernhard; Stöcklin, Jürg; Grossniklaus, Ueli

2014-01-01

Apomixis, asexual reproduction through seeds, occurs in over 40 plant families. This widespread phenomenon can lead to the fixation of successful genotypes, resulting in a fitness advantage. On the other hand, apomicts are expected to lose their fitness advantage if the environment changes because of their limited evolutionary potential, which is due to low genetic variability and the potential accumulation of deleterious somatic mutations. Nonetheless, some apomicts have been extremely succe...

Attachment of Salmonella strains to a plant cell wall model is modulated by surface characteristics and not by specific carbohydrate interactions.

Science.gov (United States)

Tan, Michelle Sze-Fan; Moore, Sean C; Tabor, Rico F; Fegan, Narelle; Rahman, Sadequr; Dykes, Gary A

2016-09-15

Processing of fresh produce exposes cut surfaces of plant cell walls that then become vulnerable to human foodborne pathogen attachment and contamination, particularly by Salmonella enterica. Plant cell walls are mainly composed of the polysaccharides cellulose, pectin and hemicelluloses (predominantly xyloglucan). Our previous work used bacterial cellulose-based plant cell wall models to study the interaction between Salmonella and the various plant cell wall components. We demonstrated that Salmonella attachment was favoured in the presence of pectin while xyloglucan had no effect on its attachment. Xyloglucan significantly increased the attachment of Salmonella cells to the plant cell wall model only when it was in association with pectin. In this study, we investigate whether the plant cell wall polysaccharides mediate Salmonella attachment to the bacterial cellulose-based plant cell wall models through specific carbohydrate interactions or through the effects of carbohydrates on the physical characteristics of the attachment surface. We found that none of the monosaccharides that make up the plant cell wall polysaccharides specifically inhibit Salmonella attachment to the bacterial cellulose-based plant cell wall models. Confocal laser scanning microscopy showed that Salmonella cells can penetrate and attach within the tightly arranged bacterial cellulose network. Analysis of images obtained from atomic force microscopy revealed that the bacterial cellulose-pectin-xyloglucan composite with 0.3 % (w/v) xyloglucan, previously shown to have the highest number of Salmonella cells attached to it, had significantly thicker cellulose fibrils compared to other composites. Scanning electron microscopy images also showed that the bacterial cellulose and bacterial cellulose-xyloglucan composites were more porous when compared to the other composites containing pectin. Our study found that the attachment of Salmonella cells to cut plant cell walls was not mediated by

Homophilic and Heterophilic Interactions of Type II Cadherins Identify Specificity Groups Underlying Cell-Adhesive Behavior

Directory of Open Access Journals (Sweden)

Julia Brasch

2018-05-01

Full Text Available Summary: Type II cadherins are cell-cell adhesion proteins critical for tissue patterning and neuronal targeting but whose molecular binding code remains poorly understood. Here, we delineate binding preferences for type II cadherin cell-adhesive regions, revealing extensive heterophilic interactions between specific pairs, in addition to homophilic interactions. Three distinct specificity groups emerge from our analysis with members that share highly similar heterophilic binding patterns and favor binding to one another. Structures of adhesive fragments from each specificity group confirm near-identical dimer topology conserved throughout the family, allowing interface residues whose conservation corresponds to specificity preferences to be identified. We show that targeted mutation of these residues converts binding preferences between specificity groups in biophysical and co-culture assays. Our results provide a detailed understanding of the type II cadherin interaction map and a basis for defining their role in tissue patterning and for the emerging importance of their heterophilic interactions in neural connectivity. : Type II cadherins are a family of vertebrate cell adhesion proteins expressed primarily in the CNS. Brasch et al. measure binding between adhesive fragments, revealing homophilic and extensive selective heterophilic binding with specificities that define groups of similar cadherins. Structures reveal common adhesive dimers, with residues governing cell-adhesive specificity. Keywords: cell adhesion, crystal structure, hemophilic specificity, heterophilic specificity, neural patterning, synaptic targeting, cadherin

Recent advances in cross-cultural measurement in psychiatric epidemiology: utilizing 'what matters most' to identify culture-specific aspects of stigma.

Science.gov (United States)

Yang, Lawrence Hsin; Thornicroft, Graham; Alvarado, Ruben; Vega, Eduardo; Link, Bruce George

2014-04-01

While stigma measurement across cultures has assumed growing importance in psychiatric epidemiology, it is unknown to what extent concepts arising from culture have been incorporated. We utilize a formulation of culture-as the everyday interactions that 'matter most' to individuals within a cultural group-to identify culturally-specific stigma dynamics relevant to measurement. A systematic literature review from January 1990 to September 2012 was conducted using PsycINFO, Medline and Google Scholar to identify articles studying: (i) mental health stigma-related concepts; (ii) ≥ 1 non-Western European cultural group. From 5292 abstracts, 196 empirical articles were located. The vast majority of studies (77%) utilized adaptations of existing Western-developed stigma measures to new cultural groups. Extremely few studies (2.0%) featured quantitative stigma measures derived within a non-Western European cultural group. A sizeable amount (16.8%) of studies employed qualitative methods to identify culture-specific stigma processes. The 'what matters most' perspective identified cultural ideals of the everyday activities that comprise 'personhood' of 'preserving lineage' among specific Asian groups, 'fighting hard to overcome problems and taking advantage of immigration opportunities' among specific Latino-American groups, and 'establishing trust among religious institutions due to institutional discrimination' among African-American groups. These essential cultural interactions shaped culture-specific stigma manifestations. Mixed method studies (3.6%) corroborated these qualitative results. Quantitatively-derived, culturally-specific stigma measures were lacking. Further, the vast majority of qualitative studies on stigma were conducted without using stigma-specific frameworks. We propose the 'what matters most' approach to address this key issue in future research.

Neighbor Detection Induces Organ-Specific Transcriptomes, Revealing Patterns Underlying Hypocotyl-Specific Growth.

Science.gov (United States)

Kohnen, Markus V; Schmid-Siegert, Emanuel; Trevisan, Martine; Petrolati, Laure Allenbach; Sénéchal, Fabien; Müller-Moulé, Patricia; Maloof, Julin; Xenarios, Ioannis; Fankhauser, Christian

2016-12-01

In response to neighbor proximity, plants increase the growth of specific organs (e.g., hypocotyls) to enhance access to sunlight. Shade enhances the activity of Phytochrome Interacting Factors (PIFs) by releasing these bHLH transcription factors from phytochrome B-mediated inhibition. PIFs promote elongation by inducing auxin production in cotyledons. In order to elucidate spatiotemporal aspects of the neighbor proximity response, we separately analyzed gene expression patterns in the major light-sensing organ (cotyledons) and in rapidly elongating hypocotyls of Arabidopsis thaliana PIFs initiate transcriptional reprogramming in both organs within 15 min, comprising regulated expression of several early auxin response genes. This suggests that hypocotyl growth is elicited by both local and distal auxin signals. We show that cotyledon-derived auxin is both necessary and sufficient to initiate hypocotyl growth, but we also provide evidence for the functional importance of the local PIF-induced response. With time, the transcriptional response diverges increasingly between organs. We identify genes whose differential expression may underlie organ-specific elongation. Finally, we uncover a growth promotion gene expression signature shared between different developmentally regulated growth processes and responses to the environment in different organs. © 2016 American Society of Plant Biologists. All rights reserved.

Species-specific effects of live roots and shoot litter on soil decomposer abundances do not forecast plant litter-nitrogen uptake.

Science.gov (United States)

Saj, Stéphane; Mikola, Juha; Ekelund, Flemming

2009-08-01

Plant species produce litter of varying quality and differ in the quality and quantity of compounds they release from live roots, which both can induce different decomposer growth in the soil. To test whether differences in decomposer growth can forecast the amount of N species acquire from plant litter, as suggested by theory, we grew individuals of three grassland plants-Holcus lanatus, Plantago lanceolata and Lotus corniculatus-in soils into which (15)N-labelled litter of either Holcus, Plantago or Lotus was added. We measured the effects of live roots and litter of each species on soil microbes and their protozoan and nematode feeders, and to link decomposer growth and plant nutrient uptake, we measured the amount of N taken up by plants from the added litter. We hypothesised that those species that induce the highest growth of microbes, and especially that of microbial feeders, will also take up the highest amount of N from the litter. We found, however, that although numbers of bacterial-feeding Protozoa and nematodes were on average lower after addition of Holcus than Plantago or Lotus litter, N uptake was higher from Holcus litter. Further, although the effects on Protozoa and bacterial- and fungal-feeding nematodes did not differ between the live plants, litter-N uptake differed, with Holcus being the most efficient compared to Plantago and Lotus. Hence, although microbes and their feeders unquestionably control N mineralization in the soil, and their growth differs among plant species, these differences cannot predict differences in litter-N uptake among plant species. A likely reason is that for nutrient uptake, other species-specific plant traits, such as litter chemistry, root proliferation ability and competitiveness for soil N, override in significance the species-specific ability of plants to induce decomposer growth.

Auxiliary feedwater system risk-based inspection guide for the Byron and Braidwood nuclear power plants

International Nuclear Information System (INIS)

Moffitt, N.E.; Gore, B.F.; Vo, T.V.

1991-07-01

In a study sponsored by the US Nuclear Regulatory Commission (NRC), Pacific Northwest Laboratory has developed and applied a methodology for deriving plant-specific risk-based inspection guidance for the auxiliary feedwater (AFW) system at pressurized water reactors that have not undergone probabilistic risk assessment (PRA). This methodology uses existing PRA results and plant operating experience information. Existing PRA-based inspection guidance information recently developed for the NRC for various plants was used to identify generic component failure modes. This information was then combined with plant-specific and industry-wide component information and failure data to identify failure modes and failure mechanisms for the AFW system at the selected plants. Byron and Braidwood were selected for the fourth study in this program. The produce of this effort is a prioritized listing of AFW failures which have occurred at the plants and at other PWRs. This listing is intended for use by NRC inspectors in the preparation of inspection plans addressing AFW risk-important components at the Byron/Braidwood plants. 23 refs., 1 fig., 1 tab

An expert botanical feature extraction technique based on phenetic features for identifying plant species.

Directory of Open Access Journals (Sweden)

Hoshang Kolivand

Full Text Available In this paper, we present a new method to recognise the leaf type and identify plant species using phenetic parts of the leaf; lobes, apex and base detection. Most of the research in this area focuses on the popular features such as the shape, colour, vein, and texture, which consumes large amounts of computational processing and are not efficient, especially in the Acer database with a high complexity structure of the leaves. This paper is focused on phenetic parts of the leaf which increases accuracy. Detecting the local maxima and local minima are done based on Centroid Contour Distance for Every Boundary Point, using north and south region to recognise the apex and base. Digital morphology is used to measure the leaf shape and the leaf margin. Centroid Contour Gradient is presented to extract the curvature of leaf apex and base. We analyse 32 leaf images of tropical plants and evaluated with two different datasets, Flavia, and Acer. The best accuracy obtained is 94.76% and 82.6% respectively. Experimental results show the effectiveness of the proposed technique without considering the commonly used features with high computational cost.

An expert botanical feature extraction technique based on phenetic features for identifying plant species

Science.gov (United States)

Fern, Bong Mei; Rahim, Mohd Shafry Mohd; Sulong, Ghazali; Baker, Thar; Tully, David

2018-01-01

In this paper, we present a new method to recognise the leaf type and identify plant species using phenetic parts of the leaf; lobes, apex and base detection. Most of the research in this area focuses on the popular features such as the shape, colour, vein, and texture, which consumes large amounts of computational processing and are not efficient, especially in the Acer database with a high complexity structure of the leaves. This paper is focused on phenetic parts of the leaf which increases accuracy. Detecting the local maxima and local minima are done based on Centroid Contour Distance for Every Boundary Point, using north and south region to recognise the apex and base. Digital morphology is used to measure the leaf shape and the leaf margin. Centroid Contour Gradient is presented to extract the curvature of leaf apex and base. We analyse 32 leaf images of tropical plants and evaluated with two different datasets, Flavia, and Acer. The best accuracy obtained is 94.76% and 82.6% respectively. Experimental results show the effectiveness of the proposed technique without considering the commonly used features with high computational cost. PMID:29420568

Anti-gout Potential of Malaysian Medicinal Plants

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Fazleen I. Abu Bakar

2018-03-01

Full Text Available Gout is a type of arthritis that causes painful inflammation in one or more joints. In gout, elevation of uric acid in the blood triggers the formation of crystals, causing joint pain. Malaysia is a mega-biodiversity country that is rich in medicinal plants species. Therefore, its flora might offer promising therapies for gout. This article aims to systematically review the anti-gout potential of Malaysian medicinal plants. Articles on gout published from 2000 to 2017 were identified using PubMed, Scopus, ScienceDirect, and Google Scholar with the following keyword search terms: “gout,” “medicinal plants,” “Malaysia,” “epidemiology,” “in vitro,” and “in vivo.” In this study, 85 plants were identified as possessing anti-gout activity. These plants had higher percentages of xanthine oxidase inhibitory activity (>85%; specifically, the Momordica charantia, Chrysanthemum indicum, Cinnamomum cassia, Kaempferia galanga, Artemisia vulgaris, and Morinda elliptica had the highest values, due to their diverse natural bioactive compounds, which include flavonoids, phenolics, tannin, coumarins, luteolin, and apigenin. This review summarizes the anti-gout potential of Malaysian medicinal plants but the mechanisms, active compounds, pharmacokinetics, bioavailability, and safety of the plants still remain to be elucidated.

Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins.

Science.gov (United States)

Le, Nguyen-Quoc-Khanh; Ho, Quang-Thai; Ou, Yu-Yen

2017-09-05

In several years, deep learning is a modern machine learning technique using in a variety of fields with state-of-the-art performance. Therefore, utilization of deep learning to enhance performance is also an important solution for current bioinformatics field. In this study, we try to use deep learning via convolutional neural networks and position specific scoring matrices to identify electron transport proteins, which is an important molecular function in transmembrane proteins. Our deep learning method can approach a precise model for identifying of electron transport proteins with achieved sensitivity of 80.3%, specificity of 94.4%, and accuracy of 92.3%, with MCC of 0.71 for independent dataset. The proposed technique can serve as a powerful tool for identifying electron transport proteins and can help biologists understand the function of the electron transport proteins. Moreover, this study provides a basis for further research that can enrich a field of applying deep learning in bioinformatics. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

De Novo Assembly and Characterization of the Transcriptome of the Parasitic Weed Dodder Identifies Genes Associated with Plant Parasitism1[C][W][OPEN

Science.gov (United States)

Ranjan, Aashish; Ichihashi, Yasunori; Farhi, Moran; Zumstein, Kristina; Townsley, Brad; David-Schwartz, Rakefet; Sinha, Neelima R.

2014-01-01

Parasitic flowering plants are one of the most destructive agricultural pests and have major impact on crop yields throughout the world. Being dependent on finding a host plant for growth, parasitic plants penetrate their host using specialized organs called haustoria. Haustoria establish vascular connections with the host, which enable the parasite to steal nutrients and water. The underlying molecular and developmental basis of parasitism by plants is largely unknown. In order to investigate the process of parasitism, RNAs from different stages (i.e. seed, seedling, vegetative strand, prehaustoria, haustoria, and flower) were used to de novo assemble and annotate the transcriptome of the obligate plant stem parasite dodder (Cuscuta pentagona). The assembled transcriptome was used to dissect transcriptional dynamics during dodder development and parasitism and identified key gene categories involved in the process of plant parasitism. Host plant infection is accompanied by increased expression of parasite genes underlying transport and transporter categories, response to stress and stimuli, as well as genes encoding enzymes involved in cell wall modifications. By contrast, expression of photosynthetic genes is decreased in the dodder infective stages compared with normal stem. In addition, genes relating to biosynthesis, transport, and response of phytohormones, such as auxin, gibberellins, and strigolactone, were differentially expressed in the dodder infective stages compared with stems and seedlings. This analysis sheds light on the transcriptional changes that accompany plant parasitism and will aid in identifying potential gene targets for use in controlling the infestation of crops by parasitic weeds. PMID:24399359

Technical specifications, Callaway Plant, Unit No. 1. Appendix A to license No. NPF-25 (Docket No. STN 50-483)

International Nuclear Information System (INIS)

Anderson, F.D.

1984-06-01

Technical specifications are presented for the limiting conditions for operation and surveillance requirements for the reactor core, reactivity control systems, power distribution limits, instrumentation, reactor coolant system, emergency core cooling systems, containment systems, plant systems, electrical power systems, refueling operations, special test exceptions, radioactive effluents, radiological environmental monitoring; design features of the site, containment, core, coolant system, and fuel storage; and plant staff organization

Co-evolution of insect proteases and plant protease inhibitors.

Science.gov (United States)

Jongsma, Maarten A; Beekwilder, Jules

2011-08-01

Plants are at the basis of the food chain, but there is no such thing as a "free lunch" for herbivores. To promote reproductive success, plants evolved multi-layered defensive tactics to avoid or discourage herbivory. To the detriment of plants, herbivores, in turn, evolved intricate strategies to find, eat, and successfully digest essential plant parts to raise their own offspring. In this battle the digestive tract is the arena determining final victory or defeat as measured by growth or starvation of the herbivore. Earlier, specific molecular opponents were identified as proteases and inhibitors: digestive proteases of herbivores evolved structural motifs to occlude plant protease inhibitors, or alternatively, the insects evolved proteases capable of specifically degrading the host plant inhibitors. In response plant inhibitors evolved hyper-variable and novel protein folds to remain active against potential herbivores. At the level of protease regulation in herbivorous insects, it was shown that inhibition-insensitive digestive proteases are up-regulated when sensitive proteases are inhibited. The way this regulation operates in mammals is known as negative feedback by gut-luminal factors, so-called 'monitor peptides' that are sensitive to the concentration of active enzymes. We propose that regulation of gut enzymes by endogenous luminal factors has been an open invitation to plants to "hijack" this regulation by evolving receptor antagonists, although yet these plant factors have not been identified. In future research the question of the co-evolution of insect proteases and plant inhibitors should, therefore, be better approached from a systems level keeping in mind that evolution is fundamentally opportunistic and that the plant's fitness is primarily improved by lowering the availability of essential amino acids to an herbivore by any available mechanism.

Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of Oncidium Gower Ramsey

Directory of Open Access Journals (Sweden)

Tung Shu-Yun

2011-04-01

Full Text Available Abstract Background Orchids comprise one of the largest families of flowering plants and generate commercially important flowers. However, model plants, such as Arabidopsis thaliana do not contain all plant genes, and agronomic and horticulturally important genera and species must be individually studied. Results Several molecular biology tools were used to isolate flower-specific gene promoters from Oncidium 'Gower Ramsey' (Onc. GR. A cDNA library of reproductive tissues was used to construct a microarray in order to compare gene expression in flowers and leaves. Five genes were highly expressed in flower tissues, and the subcellular locations of the corresponding proteins were identified using lip transient transformation with fluorescent protein-fusion constructs. BAC clones of the 5 genes, together with 7 previously published flower- and reproductive growth-specific genes in Onc. GR, were identified for cloning of their promoter regions. Interestingly, 3 of the 5 novel flower-abundant genes were putative trypsin inhibitor (TI genes (OnTI1, OnTI2 and OnTI3, which were tandemly duplicated in the same BAC clone. Their promoters were identified using transient GUS reporter gene transformation and stable A. thaliana transformation analyses. Conclusions By combining cDNA microarray, BAC library, and bombardment assay techniques, we successfully identified flower-directed orchid genes and promoters.

MDEP Design-Specific Common Position CP-APR1400WG-01. Common position addressing Fukushima Daiichi nuclear power plant accident

International Nuclear Information System (INIS)

2016-05-01

The MDEP APR1400 Working Group (APR1400WG) members consist of members from Republic of Korea, United Arab Emirates, and the United States. A main objectives of MDEP is to encourage convergence of code, standard and safety goals with exploring the opportunities for harmonization of regulatory practice and cooperation on safety review of APR-1400 specific designs. This common position addressing is aimed at sharing knowledge, information and experience on safety improvement related to lessons learned from the Fukushima Daiichi NPP Accident or Fukushima Daiichi NPP Accident-related issues amongst APR-1400 WG member states to achieve the MEDP goal. Because not all of these Regulators have completed the regulatory review of their APR1400 applications yet, this paper identifies common preliminary approaches to address potential safety improvements for APR1400 plants, as well as common general expectations for new nuclear power plants, as related to lessons learned from the Fukushima Daiichi NPP Accident or Fukushima Daiichi NPP Accident-related issues. While some asymmetry exists among those of three Regulators in terms of design, regulatory practice and licensing milestone sharing information and common understanding on post-Fukushima Daiichi NPP Accident enhancement would be promote resilient design for countering beyond design extreme external event like Fukushima Daiichi NPP nuclear disaster. This common position paper aims at identifying characteristics of post-Fukushima Daiichi NPP Accident enhancements putting in place by each country and setting common position to achieve balanced and harmonized APR-1400 design. After the safety reviews of the APR1400 design applications that are currently in review are completed, the regulators will update this paper to reflect their safety conclusions regarding the APR1400 design and how the design could be enhanced to address Fukushima Daiichi NPP Accident-related issues. The common preliminary approaches are organised into

Safety of Nuclear Power Plants: Design. Specific Safety Requirements (Spanish Edition); Seguridad de las centrales nucleares: Diseno. Requisitos de seguridad especificos

Energy Technology Data Exchange (ETDEWEB)

NONE

2012-04-15

This publication is a revision of Safety Requirements No. NS-R-1, Safety of Nuclear Power Plants: Design. It establishes requirements applicable to the design of nuclear power plants and elaborates on the safety objective, safety principles and concepts that provide the basis for deriving the safety requirements that must be met for the design of a nuclear power plant. It will be useful for organizations involved in the design, manufacture, construction, modification, maintenance, operation and decommissioning of nuclear power plants, as well as for regulatory bodies. Contents: 1. Introduction; 2. Applying the safety principles and concepts; 3. Management of safety in design; 4. Principal technical requirements; 5. General plant design; 6. Design of specific plant systems.

Phytoplasmal infection derails genetically preprogrammed meristem fate and alters plant architecture

OpenAIRE

Wei, Wei; Davis, Robert Edward; Nuss, Donald L.; Zhao, Yan

2013-01-01

In higher plants, the destiny of apical meristems (stem cells) is specific organogenesis, which determines the pattern of plant growth, and therefore morphotype and fertility. We found that bacterial infection can derail the meristems from their genetically preprogrammed destiny, altering plant morphogenesis. We identified four abnormal growth patterns, symptoms, in tomato infected with a cell wall-less bacterium, and found that each symptom corresponds to a distinct phase in meristem fate de...

Natural radionuclides in soil profiles surrounding the largest coal-fired power plant in Serbia

Directory of Open Access Journals (Sweden)

Tanić Milan N.

2016-01-01

Full Text Available This study evaluates the influence of the largest Serbian coal-fired power plant on radionuclide concentrations in soil profiles up to 50 cm in depth. Thirty soil profiles were sampled from the plant surroundings (up to 10 km distance and analyzed using standard methods for soil physicochemical properties and gamma ray spectrometry for specific activities of natural radionuclides (40K, 226Ra and 232Th. Spatial and vertical distribution of radionuclides was determined and analyzed to show the relations between the specific activities in the soil and soil properties and the most influential factors of natural radionuclide variability were identified. The radiological indices for surface soil were calculated and radiological risk assessment was performed. The measured specific activities were similar to values of background levels for Serbia. The sampling depth did not show any significant influence on specific activities of natural radionuclides. The strongest predictor of specific activities of the investigated radionuclides was soil granulometry. All parameters of radiological risk assessment were below the recommended values and adopted limits. It appears that the coal-fired power plant does not have a significant impact on the spatial and vertical distribution of natural radionuclides in the area of interest, but technologically enhanced natural radioactivity as a consequence of the plant operations was identified within the first 1.5 km from the power plant. [Projekat Ministarstva nauke Republike Srbije br. III43009 i br. III41005

Nuclear plant aging research program

International Nuclear Information System (INIS)

Eissenberg, D.M.

1987-01-01

The U.S. Nuclear Regulatory Commission, Office of Nuclear Regulatory Research, has established the Nuclear Plant Aging Research (NPAR) program in its Division of Engineering Technology. Principal contractors for this program include Oak Ridge National Laboratory, Brookhaven National Laboratory, Idaho National Engineering Laboratory, and Pacific Northwest Laboratory. The program goals are: to identify and characterize time-dependent degradation (aging) of nuclear plant safety-related electrical and mechanical components which could lead to loss of safety function; to identify and recommend methods for detecting and trending aging effects prior to loss of safety function so that timely maintenance can be implemented; and to recommend maintenance practices for mitigating the effects of aging. Research activities include prioritization of system and component aging in nuclear plants, characterization of aging degradation of specific components including identification of functional indicators useful for trending degradation, and testing of practical methods and devices for measuring the functional indicators. Aging assessments have been completed on electric motors, snubbers, motor-operated valves, and check valves. Testing of trending methods and devices for motor-operated valves and check valves is in progress

Genome Evolution of Plant-Parasitic Nematodes.

Science.gov (United States)

Kikuchi, Taisei; Eves-van den Akker, Sebastian; Jones, John T

2017-08-04

Plant parasitism has evolved independently on at least four separate occasions in the phylum Nematoda. The application of next-generation sequencing (NGS) to plant-parasitic nematodes has allowed a wide range of genome- or transcriptome-level comparisons, and these have identified genome adaptations that enable parasitism of plants. Current genome data suggest that horizontal gene transfer, gene family expansions, evolution of new genes that mediate interactions with the host, and parasitism-specific gene regulation are important adaptations that allow nematodes to parasitize plants. Sequencing of a larger number of nematode genomes, including plant parasites that show different modes of parasitism or that have evolved in currently unsampled clades, and using free-living taxa as comparators would allow more detailed analysis and a better understanding of the organization of key genes within the genomes. This would facilitate a more complete understanding of the way in which parasitism has shaped the genomes of plant-parasitic nematodes.

The Willow Microbiome is Influenced by Soil Petroleum-Hydrocarbon Concentration with Plant Compartment-Specific Effects

Directory of Open Access Journals (Sweden)

Stacie Tardif

2016-09-01

Full Text Available The interaction between plants and microorganisms, which is the driving force behind the decontamination of petroleum hydrocarbon (PHC contamination in phytoremediation technology, is poorly understood. Here, we aimed at characterizing the variations between plant compartments in the microbiome of two willow cultivars growing in contaminated soils. A field experiment was set-up at a former petrochemical plant in Canada and, after two growing seasons, bulk soil, rhizosphere soil, roots and stems samples of two willow cultivars (Salix purpurea cv. FishCreek and Salix miyabeana cv. SX67 growing at three PHC contamination concentrations were taken. DNA was extracted and bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS regions were amplified and sequenced using an Ion Torrent Personal Genome Machine. Following multivariate statistical analyses, the level of PHC-contamination appeared as the primary factor influencing the willow microbiome with compartment-specific effects, with significant differences between the responses of bacterial and fungal communities. Increasing PHC contamination levels resulted in shifts in the microbiome composition, favoring putative hydrocarbon degraders and microorganisms previously reported as associated with plant health. These shifts were less drastic in the rhizosphere, root and stem tissues as compared to bulk soil, probably because the willows provided a more controlled environment and thus protected microbial communities against increasing contamination levels. Insights from this study will help to devise optimal plant microbiomes for increasing the efficiency of phytoremediation technology.

Data integration aids understanding of butterfly–host plant networks

Science.gov (United States)

Muto-Fujita, Ai; Takemoto, Kazuhiro; Kanaya, Shigehiko; Nakazato, Takeru; Tokimatsu, Toshiaki; Matsumoto, Natsushi; Kono, Mayo; Chubachi, Yuko; Ozaki, Katsuhisa; Kotera, Masaaki

2017-01-01

Although host-plant selection is a central topic in ecology, its general underpinnings are poorly understood. Here, we performed a case study focusing on the publicly available data on Japanese butterflies. A combined statistical analysis of plant–herbivore relationships and taxonomy revealed that some butterfly subfamilies in different families feed on the same plant families, and the occurrence of this phenomenon more than just by chance, thus indicating the independent acquisition of adaptive phenotypes to the same hosts. We consequently integrated plant–herbivore and plant–compound relationship data and conducted a statistical analysis to identify compounds unique to host plants of specific butterfly families. Some of the identified plant compounds are known to attract certain butterfly groups while repelling others. The additional incorporation of insect–compound relationship data revealed potential metabolic processes that are related to host plant selection. Our results demonstrate that data integration enables the computational detection of compounds putatively involved in particular interspecies interactions and that further data enrichment and integration of genomic and transcriptomic data facilitates the unveiling of the molecular mechanisms involved in host plant selection. PMID:28262809

Identification of a Fungal 1,8-Cineole Synthase from Hypoxylon sp. with Specificity Determinants in Common with the Plant Synthases*

Science.gov (United States)

Shaw, Jeffrey J.; Berbasova, Tetyana; Sasaki, Tomoaki; Jefferson-George, Kyra; Spakowicz, Daniel J.; Dunican, Brian F.; Portero, Carolina E.; Narváez-Trujillo, Alexandra; Strobel, Scott A.

2015-01-01

Terpenes are an important and diverse class of secondary metabolites widely produced by fungi. Volatile compound screening of a fungal endophyte collection revealed a number of isolates in the family Xylariaceae, producing a series of terpene molecules, including 1,8-cineole. This compound is a commercially important component of eucalyptus oil used in pharmaceutical applications and has been explored as a potential biofuel additive. The genes that produce terpene molecules, such as 1,8-cineole, have been little explored in fungi, providing an opportunity to explore the biosynthetic origin of these compounds. Through genome sequencing of cineole-producing isolate E7406B, we were able to identify 11 new terpene synthase genes. Expressing a subset of these genes in Escherichia coli allowed identification of the hyp3 gene, responsible for 1,8-cineole biosynthesis, the first monoterpene synthase discovered in fungi. In a striking example of convergent evolution, mutational analysis of this terpene synthase revealed an active site asparagine critical for water capture and specificity during cineole synthesis, the same mechanism used in an unrelated plant homologue. These studies have provided insight into the evolutionary relationship of fungal terpene synthases to those in plants and bacteria and further established fungi as a relatively untapped source of this important and diverse class of compounds. PMID:25648891

Identifying functional cancer-specific miRNA-mRNA interactions in testicular germ cell tumor.

Science.gov (United States)

Sedaghat, Nafiseh; Fathy, Mahmood; Modarressi, Mohammad Hossein; Shojaie, Ali

2016-09-07

Testicular cancer is the most common cancer in men aged between 15 and 35 and more than 90% of testicular neoplasms are originated at germ cells. Recent research has shown the impact of microRNAs (miRNAs) in different types of cancer, including testicular germ cell tumor (TGCT). MicroRNAs are small non-coding RNAs which affect the development and progression of cancer cells by binding to mRNAs and regulating their expressions. The identification of functional miRNA-mRNA interactions in cancers, i.e. those that alter the expression of genes in cancer cells, can help delineate post-regulatory mechanisms and may lead to new treatments to control the progression of cancer. A number of sequence-based methods have been developed to predict miRNA-mRNA interactions based on the complementarity of sequences. While necessary, sequence complementarity is, however, not sufficient for presence of functional interactions. Alternative methods have thus been developed to refine the sequence-based interactions using concurrent expression profiles of miRNAs and mRNAs. This study aims to find functional cancer-specific miRNA-mRNA interactions in TGCT. To this end, the sequence-based predicted interactions are first refined using an ensemble learning method, based on two well-known methods of learning miRNA-mRNA interactions, namely, TaLasso and GenMiR++. Additional functional analyses were then used to identify a subset of interactions to be most likely functional and specific to TGCT. The final list of 13 miRNA-mRNA interactions can be potential targets for identifying TGCT-specific interactions and future laboratory experiments to develop new therapies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Fungal and plant gene expression in arbuscular mycorrhizal symbiosis.

Science.gov (United States)

Balestrini, Raffaella; Lanfranco, Luisa

2006-11-01

Arbuscular mycorrhizas (AMs) are a unique example of symbiosis between two eukaryotes, soil fungi and plants. This association induces important physiological changes in each partner that lead to reciprocal benefits, mainly in nutrient supply. The symbiosis results from modifications in plant and fungal cell organization caused by specific changes in gene expression. Recently, much effort has gone into studying these gene expression patterns to identify a wider spectrum of genes involved. We aim in this review to describe AM symbiosis in terms of current knowledge on plant and fungal gene expression profiles.

Survey of operating experience from LERs to identify aging trends

International Nuclear Information System (INIS)

Murphy, G.A.

1985-01-01

The results of a study using the Oak Ridge National Laboratory's Nuclear Operations Analysis Center computer files of operating experience reports [licensee event reports (LERs), abnormal occurrences, etc.] are summarized in this study, specific time-related degradation mechanisms are identified as possible causes of a reportable occurrence. Data collected on domestic commercial nuclear power plants covering 1969 to 1982 yielded over 5800 events attributable to possible age related failures. Of these events, 2795 were attributable to instrument drift and are addressed separately in the report. The remaining events (3098) were reviewed, and data were collected for each event, which identified the specific system, component, and subpart: the information included the age-related mechanism, severity of the failure, and method of detection of the failure. About two-thirds of the failures were judged to be degraded, with one-third listed as catastrophic

Transcriptional plant responses critical for resistance towards necrotrophic pathogens

Directory of Open Access Journals (Sweden)

Rainer P. Birkenbihl

2011-11-01

Full Text Available Plant defenses aimed at necrotrophic pathogens appear to be genetically complex. Despite the apparent lack of a specific recognition of such necrotrophs by products of major R genes, biochemical, molecular, and genetic studies, in particular using the model plant Arabidopsis, have uncovered numerous host components critical for the outcome of such interactions. Although the JA signaling pathway plays a central role in plant defense towards necrotrophs additional signaling pathways contribute to the plant response network. Transcriptional reprogramming is a vital part of the host defense machinery and several key regulators have recently been identified. Some of these transcription factors positively affect plant resistance whereas others play a role in enhancing host susceptibility towards these phytopathogens.

Secondary plant succession on disturbed sites at Yucca Mountain, Nevada

Energy Technology Data Exchange (ETDEWEB)

Angerer, J.P.; Ostler, W.K.; Gabbert, W.D.; Schultz, B.W.

1994-12-01

This report presents the results of a study of secondary plant succession on disturbed sites created during initial site investigations in the late 1970s and early 1980s at Yucca Mountain, NV. Specific study objectives were to determine the rate and success of secondary plant succession, identify plant species found in disturbances that may be suitable for site-specific reclamation, and to identify environmental variables that influence succession on disturbed sites. During 1991 and 1992, fifty seven disturbed sites were located. Vegetation parameters, disturbance characteristics and environmental variables were measured at each site. Disturbed site vegetation parameters were compared to that of undisturbed sites to determine the status of disturbed site plant succession. Vegetation on disturbed sites, after an average of ten years, was different from undisturbed areas. Ambrosia dumosa, Chrysothamnus teretifolius, Hymenoclea salsola, Gutierrezia sarothrae, Atriplex confertifolia, Atriplex canescens, and Stephanomeria pauciflora were the most dominant species across all disturbed sites. With the exception of A. dumosa, these species were generally minor components of the undisturbed vegetation. Elevation, soil compaction, soil potassium, and amounts of sand and gravel in the soil were found to be significant environmental variables influencing the species composition and abundance of perennial plants on disturbed sites. The recovery rate for disturbed site secondary succession was estimated. Using a linear function (which would represent optimal conditions), the recovery rate for perennial plant cover, regardless of which species comprised the cover, was estimated to be 20 years. However, when a logarithmic function (which would represent probable conditions) was used, the recovery rate was estimated to be 845 years. Recommendations for future studies and site-specific reclamation of disturbances are presented.

Secondary plant succession on disturbed sites at Yucca Mountain, Nevada

International Nuclear Information System (INIS)

Angerer, J.P.; Ostler, W.K.; Gabbert, W.D.; Schultz, B.W.

1994-12-01

This report presents the results of a study of secondary plant succession on disturbed sites created during initial site investigations in the late 1970s and early 1980s at Yucca Mountain, NV. Specific study objectives were to determine the rate and success of secondary plant succession, identify plant species found in disturbances that may be suitable for site-specific reclamation, and to identify environmental variables that influence succession on disturbed sites. During 1991 and 1992, fifty seven disturbed sites were located. Vegetation parameters, disturbance characteristics and environmental variables were measured at each site. Disturbed site vegetation parameters were compared to that of undisturbed sites to determine the status of disturbed site plant succession. Vegetation on disturbed sites, after an average of ten years, was different from undisturbed areas. Ambrosia dumosa, Chrysothamnus teretifolius, Hymenoclea salsola, Gutierrezia sarothrae, Atriplex confertifolia, Atriplex canescens, and Stephanomeria pauciflora were the most dominant species across all disturbed sites. With the exception of A. dumosa, these species were generally minor components of the undisturbed vegetation. Elevation, soil compaction, soil potassium, and amounts of sand and gravel in the soil were found to be significant environmental variables influencing the species composition and abundance of perennial plants on disturbed sites. The recovery rate for disturbed site secondary succession was estimated. Using a linear function (which would represent optimal conditions), the recovery rate for perennial plant cover, regardless of which species comprised the cover, was estimated to be 20 years. However, when a logarithmic function (which would represent probable conditions) was used, the recovery rate was estimated to be 845 years. Recommendations for future studies and site-specific reclamation of disturbances are presented

Coupling genetics and proteomics to identify aphid proteins associated with vector-specific transmission of polerovirus (luteoviridae).

Science.gov (United States)

Yang, Xiaolong; Thannhauser, T W; Burrows, Mary; Cox-Foster, Diana; Gildow, Fred E; Gray, Stewart M

2008-01-01

Cereal yellow dwarf virus-RPV (CYDV-RPV) is transmitted specifically by the aphids Rhopalosiphum padi and Schizaphis graminum in a circulative nonpropagative manner. The high level of vector specificity results from the vector aphids having the functional components of the receptor-mediated endocytotic pathways to allow virus to transverse the gut and salivary tissues. Studies of F(2) progeny from crosses of vector and nonvector genotypes of S. graminum showed that virus transmission efficiency is a heritable trait regulated by multiple genes acting in an additive fashion and that gut- and salivary gland-associated factors are not genetically linked. Utilizing two-dimensional difference gel electrophoresis to compare the proteomes of vector and nonvector parental and F(2) genotypes, four aphid proteins (S4, S8, S29, and S405) were specifically associated with the ability of S. graminum to transmit CYDV-RPV. The four proteins were coimmunoprecipitated with purified RPV, indicating that the aphid proteins are capable of binding to virus. Analysis by mass spectrometry identified S4 as a luciferase and S29 as a cyclophilin, both of which have been implicated in macromolecular transport. Proteins S8 and S405 were not identified from available databases. Study of this unique genetic system coupled with proteomic analysis indicated that these four virus-binding aphid proteins were specifically inherited and conserved in different generations of vector genotypes and suggests that they play a major role in regulating polerovirus transmission.

CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems.

Directory of Open Access Journals (Sweden)

Lihua J Zhu

Full Text Available CRISPR-Cas systems are a diverse family of RNA-protein complexes in bacteria that target foreign DNA sequences for cleavage. Derivatives of these complexes have been engineered to cleave specific target sequences depending on the sequence of a CRISPR-derived guide RNA (gRNA and the source of the Cas9 protein. Important considerations for the design of gRNAs are to maximize aimed activity at the desired target site while minimizing off-target cleavage. Because of the rapid advances in the understanding of existing CRISPR-Cas9-derived RNA-guided nucleases and the development of novel RNA-guided nuclease systems, it is critical to have computational tools that can accommodate a wide range of different parameters for the design of target-specific RNA-guided nuclease systems. We have developed CRISPRseek, a highly flexible, open source software package to identify gRNAs that target a given input sequence while minimizing off-target cleavage at other sites within any selected genome. CRISPRseek will identify potential gRNAs that target a sequence of interest for CRISPR-Cas9 systems from different bacterial species and generate a cleavage score for potential off-target sequences utilizing published or user-supplied weight matrices with position-specific mismatch penalty scores. Identified gRNAs may be further filtered to only include those that occur in paired orientations for increased specificity and/or those that overlap restriction enzyme sites. For applications where gRNAs are desired to discriminate between two related sequences, CRISPRseek can rank gRNAs based on the difference between predicted cleavage scores in each input sequence. CRISPRseek is implemented as a Bioconductor package within the R statistical programming environment, allowing it to be incorporated into computational pipelines to automate the design of gRNAs for target sequences identified in a wide variety of genome-wide analyses. CRISPRseek is available under the GNU General

Ethnopharmacological survey: a selection strategy to identify medicinal plants for a local phytotherapy program

Directory of Open Access Journals (Sweden)

Flávia Liparini Pereira

2012-06-01

Full Text Available Ethnopharmacological studies are important for documenting and protecting cultural and traditional knowledge associated with the medical use of biodiversity. In this paper, we present a survey on medicinal plants used by locals in a community of Nova Viçosa, Viçosa, MG, Brazil, as a strategy to select medicinal plants for a phytotherapy-based local healthcare program. Eleven knowledgeable local informants were chosen by snowball sampling and interviewed about the use of medicinal plants. Plant samples were collected, herborised and then identified using traditional techniques and specialised literature. We sampled 107 medicinal plant species belonging to 86 genera and 39 families, predominantly Asteraceae with 16 species. Costus spicatus (Jacq. Sw, M. pulegium L., Rosmarinus officinalis L. and Ruta graveolens L. were found to have Consensus of Main Use corrected (CMUc values above 50%, which were in agreement with the traditional uses described by the informants. However, species with CMUc values equal to or above 20%, combined with the scientific information survey, were also used to select medicinal plants for the phytotherapy-based local healthcare program. The selection of medicinal plants based on the CMUc index from this particular community, in combination with the scientific survey, appears to be an effective strategy for the implementation of phytotherapy programs.Estudos etnofarmacológicos são importantes no registro e na preservação de conhecimentos de uma cultura tradicional associada ao uso medicinal da biodiversidade. No presente trabalho, foi realizado o levantamento das plantas medicinais utilizadas por conhecedores populares na comunidade de Nova Viçosa, Viçosa, Minas Gerais, Brasil, como ferramenta para auxiliar na seleção de espécies vegetais visando à implantação de um programa de fitoterapia local na comunidade estudada. Participaram 11 conhecedores escolhidos por amostragem Bola de Neve e submetidos a

Nuclear plant aging research - an overview (electrical and mechanical components)

International Nuclear Information System (INIS)

Vora, J.P.

1985-01-01

As the operating nuclear power plants advance in age there must be a conscious national and international effort to understand the influence and safety implications of aging and service wear of components and structures in nuclear power plants and develop measures which are practical and cost effective for timely mitigation of aging degradation that could significantly affect plant safety. The Office of Nuclear Regulatory Research has, therefore, initiated a multi-year, multi-disciplinary program on Nuclear Plant Aging Research (NPAR). The overall goals identified for the program are as follows: 1) to identify and characterize aging and service wear effects associated with electrical and mechanical components, interfaces, and systems whose failure could impair plant safety; 2) to identify and recommend methods of inspection, surveillance and condition monitoring of electrical and mechanical components and systems which will be effective in detecting significant aging effects prior to loss of safety function so that timely maintenance and repair or replacement can be implemented; and, 3) to identify and recommend acceptable maintenance practices which can be undertaken to mitigate the effects of aging and to diminish the rate and extent of degradation caused by aging and service wear. The specific research activities to be implemented to achieve these goals are described

Plant Acyl-CoA:Lysophosphatidylcholine Acyltransferases (LPCATs) Have Different Specificities in Their Forward and Reverse Reactions*

Science.gov (United States)

Lager, Ida; Yilmaz, Jenny Lindberg; Zhou, Xue-Rong; Jasieniecka, Katarzyna; Kazachkov, Michael; Wang, Peng; Zou, Jitao; Weselake, Randall; Smith, Mark A.; Bayon, Shen; Dyer, John M.; Shockey, Jay M.; Heinz, Ernst; Green, Allan; Banas, Antoni; Stymne, Sten

2013-01-01

Acyl-CoA:lysophosphatidylcholine acyltransferase (LPCAT) enzymes have central roles in acyl editing of phosphatidylcholine (PC). Plant LPCAT genes were expressed in yeast and characterized biochemically in microsomal preparations of the cells. Specificities for different acyl-CoAs were similar for seven LPCATs from five different species, including species accumulating hydroxylated acyl groups in their seed oil, with a preference for C18-unsaturated acyl-CoA and low activity with palmitoyl-CoA and ricinoleoyl (12-hydroxyoctadec-9-enoyl)-CoA. We showed that Arabidopsis LPCAT1 and LPCAT2 enzymes catalyzed the acylation and de-acylation of both sn positions of PC, with a preference for the sn-2 position. When acyl specificities of the Arabidopsis LPCATs were measured in the reverse reaction, sn-2-bound oleoyl, linoleoyl, and linolenoyl groups from PC were transferred to acyl-CoA to a similar extent. However, a ricinoleoyl group at the sn-2-position of PC was removed 4–6-fold faster than an oleoyl group in the reverse reaction, despite poor utilization in the forward reaction. The data presented, taken together with earlier published reports on in vivo lipid metabolism, support the hypothesis that plant LPCAT enzymes play an important role in regulating the acyl-CoA composition in plant cells by transferring polyunsaturated and hydroxy fatty acids produced on PC directly to the acyl-CoA pool for further metabolism or catabolism. PMID:24189065

Lineage-specific evolutionary rate in plants: Contributions of a screening for Cereus (Cactaceae).

Science.gov (United States)

Romeiro-Brito, Monique; Moraes, Evandro M; Taylor, Nigel P; Zappi, Daniela C; Franco, Fernando F

2016-01-01

Predictable chloroplast DNA (cpDNA) sequences have been listed for the shallowest taxonomic studies in plants. We investigated whether plastid regions that vary between closely allied species could be applied for intraspecific studies and compared the variation of these plastid segments with two nuclear regions. We screened 16 plastid and two nuclear intronic regions for species of the genus Cereus (Cactaceae) at three hierarchical levels (species from different clades, species of the same clade, and allopatric populations). Ten plastid regions presented interspecific variation, and six of them showed variation at the intraspecific level. The two nuclear regions showed both inter- and intraspecific variation, and in general they showed higher levels of variability in almost all hierarchical levels than the plastid segments. Our data suggest no correspondence between variation of plastid regions at the interspecific and intraspecific level, probably due to lineage-specific variation in cpDNA, which appears to have less effect in nuclear data. Despite the heterogeneity in evolutionary rates of cpDNA, we highlight three plastid segments that may be considered in initial screenings in plant phylogeographic studies.

The foundations of plant intelligence.

Science.gov (United States)

Trewavas, Anthony

2017-06-06

Intelligence is defined for wild plants and its role in fitness identified. Intelligent behaviour exhibited by single cells and systems similarity between the interactome and connectome indicates neural systems are not necessary for intelligent capabilities. Plants sense and respond to many environmental signals that are assessed to competitively optimize acquisition of patchily distributed resources. Situations of choice engender motivational states in goal-directed plant behaviour; consequent intelligent decisions enable efficient gain of energy over expenditure. Comparison of swarm intelligence and plant behaviour indicates the origins of plant intelligence lie in complex communication and is exemplified by cambial control of branch function. Error correction in behaviours indicates both awareness and intention as does the ability to count to five. Volatile organic compounds are used as signals in numerous plant interactions. Being complex in composition and often species and individual specific, they may represent the plant language and account for self and alien recognition between individual plants. Game theory has been used to understand competitive and cooperative interactions between plants and microbes. Some unexpected cooperative behaviour between individuals and potential aliens has emerged. Behaviour profiting from experience, another simple definition of intelligence, requires both learning and memory and is indicated in the priming of herbivory, disease and abiotic stresses.

Role of the plant-specific endoplasmic reticulum stress-inducible gene TIN1 in the formation of pollen surface structure in Arabidopsis thaliana

KAUST Repository

Iwata, Yuji; Nishino, Tsuneyo; Iwano, Megumi; Takayama, Seiji; Koizumi, Nozomu

2012-01-01

Accumulation of unfolded proteins in the endoplasmic reticulum (ER) of eukaryotic cells triggers the transcriptional activation of ER-resident molecular chaperones and folding enzymes to maintain cellular homeostasis. This process is known as the ER stress response or the unfolded protein response. We have identified tunicamycin induced 1 (TIN1), a plant-specific ER stress-inducible Arabidopsis thaliana gene. The TIN1 protein is localized in the ER; however, its molecular function has yet to be clarified. In this study, we performed functional analysis of TIN1 in planta. RT-PCR analysis showed that TIN1 is highly expressed in pollen. Analysis using the β-glucuronidase reporter gene demonstrated that the TIN1 promoter is active throughout pollen development, peaking at the time of flowering and in an ovule of an open flower. Although a T-DNA insertion mutant of TIN1 grows normally under ambient laboratory conditions, abnormal pollen surface morphology was observed under a scanning electron microscope. Based on the current and previous observations, a possible physiological function of TIN1 during pollen development is discussed. © 2012 The Japanese Society for Plant Cell and Molecular Biology.

The Verticillium-specific protein VdSCP7 localizes to the plant nucleus and modulates immunity to fungal infections.

Science.gov (United States)

Zhang, Lisha; Ni, Hao; Du, Xuan; Wang, Sheng; Ma, Xiao-Wei; Nürnberger, Thorsten; Guo, Hui-Shan; Hua, Chenlei

2017-07-01

Fungal pathogens secrete effector proteins to suppress plant basal defense for successful colonization. Resistant plants, however, can recognize effectors by cognate R proteins to induce effector-triggered immunity (ETI). By analyzing secretomes of the vascular fungal pathogen Verticillium dahliae, we identified a novel secreted protein VdSCP7 that targets the plant nucleus. The green fluorescent protein (GFP)-tagged VdSCP7 gene with either a mutated nuclear localization signal motif or with additional nuclear export signal was transiently expressed in Nicotiana benthamiana, and investigated for induction of plant immunity. The role of VdSCP7 in V. dahliae pathogenicity was characterized by gene knockout and complementation, and GFP labeling. Expression of the VdSCP7 gene in N. benthamiana activated both salicylic acid and jasmonate signaling, and altered the plant's susceptibility to the pathogens Botrytis cinerea and Phytophthora capsici. The immune response activated by VdSCP7 was highly dependent on its initial extracellular secretion and subsequent nuclear localization in plants. Knockout of the VdSCP7 gene significantly enhanced V. dahliae aggressiveness on cotton. GFP-labeled VdSCP7 is secreted by V. dahliae and accumulates in the plant nucleus. We conclude that VdSCP7 is a novel effector protein that targets the host nucleus to modulate plant immunity, and suggest that plants can recognize VdSCP7 to activate ETI during fungal infection. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Major intrinsic proteins (MIPs) in plants: a complex gene family with major impacts on plant phenotype.

Science.gov (United States)

Forrest, Kerrie L; Bhave, Mrinal

2007-10-01

The ubiquitous cell membrane proteins called aquaporins are now firmly established as channel proteins that control the specific transport of water molecules across cell membranes in all living organisms. The aquaporins are thus likely to be of fundamental significance to all facets of plant growth and development affected by plant-water relations. A majority of plant aquaporins have been found to share essential structural features with the human aquaporin and exhibit water-transporting ability in various functional assays, and some have been shown experimentally to be of critical importance to plant survival. Furthermore, substantial evidence is now available from a number of plant species that shows differential gene expression of aquaporins in response to abiotic stresses such as salinity, drought, or cold and clearly establishes the aquaporins as major players in the response of plants to conditions that affect water availability. This review summarizes the function and regulation of these genes to develop a greater understanding of the response of plants to water insufficiency, and particularly, to identify tolerant genotypes of major crop species including wheat and rice and plants that are important in agroforestry.

Technical Specification action statements requiring shutdown

International Nuclear Information System (INIS)

Mankamo, T.; Kim, I.S.; Samanta, P.K.

1993-11-01

When safety systems fail during power operation, the limiting conditions for operation (LCOs) and associated action statements of technical specifications typically require that the plant be shut down within the limits of allowed outage time (AOT). However, when a system needed to remove decay heat, such as the residual heat removal (RHR) system, is inoperable or degraded, shutting down the plant may not necessarily be preferable, from a risk perspective, to continuing power operation over a usual repair time, giving priority to the repairs. The risk impact of the basic operational alternatives, i.e., continued operation or shutdown, was evaluated for failures in the RHR and standby service water (SSW) systems of a boiling-water reactor (BWR) nuclear power plant. A complete or partial failure of the SSW system fails or degrades not only the RHR system but other front-line safety systems supported by the SSW system. This report presents the methodology to evaluate the risk impact of LCOs and associated AOT; the results of risk evaluation from its application to the RHR and SSW systems of a BWR; the findings from the risk-sensitivity analyses to identify alternative operational policies; and the major insights and recommendations to improve the technical specifications action statements

Transcriptome Analysis of Mycobacteria-Specific CD4+ T Cells Identified by Activation-Induced Expression of CD154.

Science.gov (United States)

Kunnath-Velayudhan, Shajo; Goldberg, Michael F; Saini, Neeraj K; Johndrow, Christopher T; Ng, Tony W; Johnson, Alison J; Xu, Jiayong; Chan, John; Jacobs, William R; Porcelli, Steven A

2017-10-01

Analysis of Ag-specific CD4 + T cells in mycobacterial infections at the transcriptome level is informative but technically challenging. Although several methods exist for identifying Ag-specific T cells, including intracellular cytokine staining, cell surface cytokine-capture assays, and staining with peptide:MHC class II multimers, all of these have significant technical constraints that limit their usefulness. Measurement of activation-induced expression of CD154 has been reported to detect live Ag-specific CD4 + T cells, but this approach remains underexplored and, to our knowledge, has not previously been applied in mycobacteria-infected animals. In this article, we show that CD154 expression identifies adoptively transferred or endogenous Ag-specific CD4 + T cells induced by Mycobacterium bovis bacillus Calmette-Guérin vaccination. We confirmed that Ag-specific cytokine production was positively correlated with CD154 expression by CD4 + T cells from bacillus Calmette-Guérin-vaccinated mice and show that high-quality microarrays can be performed from RNA isolated from CD154 + cells purified by cell sorting. Analysis of microarray data demonstrated that the transcriptome of CD4 + CD154 + cells was distinct from that of CD154 - cells and showed major enrichment of transcripts encoding multiple cytokines and pathways of cellular activation. One notable finding was the identification of a previously unrecognized subset of mycobacteria-specific CD4 + T cells that is characterized by the production of IL-3. Our results support the use of CD154 expression as a practical and reliable method to isolate live Ag-specific CD4 + T cells for transcriptomic analysis and potentially for a range of other studies in infected or previously immunized hosts. Copyright © 2017 by The American Association of Immunologists, Inc.

Hillslope characterization: Identifying key controls on local-scale plant communities' distribution using remote sensing and subsurface data fusion.

Science.gov (United States)

Falco, N.; Wainwright, H. M.; Dafflon, B.; Leger, E.; Peterson, J.; Steltzer, H.; Wilmer, C.; Williams, K. H.; Hubbard, S. S.

2017-12-01

Mountainous watershed systems are characterized by extreme heterogeneity in hydrological and pedological properties that influence biotic activities, plant communities and their dynamics. To gain predictive understanding of how ecosystem and watershed system evolve under climate change, it is critical to capture such heterogeneity and to quantify the effect of key environmental variables such as topography, and soil properties. In this study, we exploit advanced geophysical and remote sensing techniques - coupled with machine learning - to better characterize and quantify the interactions between plant communities' distribution and subsurface properties. First, we have developed a remote sensing data fusion framework based on the random forest (RF) classification algorithm to estimate the spatial distribution of plant communities. The framework allows the integration of both plant spectral and structural information, which are derived from multispectral satellite images and airborne LiDAR data. We then use the RF method to evaluate the estimated plant community map, exploiting the subsurface properties (such as bedrock depth, soil moisture and other properties) and geomorphological parameters (such as slope, curvature) as predictors. Datasets include high-resolution geophysical data (electrical resistivity tomography) and LiDAR digital elevation maps. We demonstrate our approach on a mountain hillslope and meadow within the East River watershed in Colorado, which is considered to be a representative headwater catchment in the Upper Colorado Basin. The obtained results show the existence of co-evolution between above and below-ground processes; in particular, dominant shrub communities in wet and flat areas. We show that successful integration of remote sensing data with geophysical measurements allows identifying and quantifying the key environmental controls on plant communities' distribution, and provides insights into their potential changes in the future

Nuclear Plant Aging Research (NPAR) program plan

International Nuclear Information System (INIS)

1985-07-01

The nuclear plant aging research described in this plan is intended to resolve issues related to the aging and service wear of equipment and systems at commercial reactor facilities and their possible impact on plant safety. Emphasis has been placed on identification and characterization of the mechansims of material and component degradation during service and evaluation of methods of inspection, surveillance, condition monitoring and maintenance as means of mitigating such effects. Specifically the goals of the program are as follows: (1) to identify and characterize aging and service wear effects which, if unchecked, could cause degradation of structures, components, and systems and thereby impair plant safety; (2) to identify methods of inspection, surveillance and monitoring, or of evaluating residual life of structures, components, and systems, which will assure timely detection of significant aging effects prior to loss of safety function; and (3) to evaluate the effectiveness of storage, maintenance, repair and replacement practices in mitigating the rate and extent of degradation caused by aging and service wear

Alternative approaches to risk-based technical specifications

International Nuclear Information System (INIS)

Atefi, B.; Gallagher, D.W.; Liner, R.T.; Lofgren, E.V.

1987-01-01

Four alternative risk-based approaches to Technical Specifications are identified. These are: a Probabilistic Risk Assessment (PRA) oriented approach; a reliability goal-oriented approach; an approach based on configuration control; a data-oriented approach. Based on preliminary results, the PRA-oriented approach, which has been developed further than the other approaches, seems to offer a logical, quantitative basis for setting Allowed Outage Times (AOTs) and Surveillance Test Intervals (STIs) for some plant components and systems. The most attractive feature of this approach is that it directly links the AOTs and STIs with the risk associated with the operation of the plant. This would focus the plant operator's and the regulatory agency's attention on the most risk-significant components of the plant. A series of practical issues related to the level of detail and content of the plant PRAs, requirements for the review of these PRAs, and monitoring cf the plant's performance by the regulatory agency must be resolved before the approach could be implemented. Future efforts will examine the other three approaches and their practicality before firm conclusions are drawn regarding the viability of any of these approaches

Functional analyses of plant-specific histone deacetylases

NARCIS (Netherlands)

Li, Huchen

2017-01-01

Plants have a sessile lifestyle. To ensure survival, they develop a potential to respond to environmental cues to set up an adaptive growth and development. This adaptation involves transcriptional reprogramming of the genome through chromatin-based mechanisms relying on the dynamic interplay of

When do plants modify fluvial processes? Plant-hydraulic interactions under variable flow and sediment supply rates

Science.gov (United States)

Manners, Rebecca B.; Wilcox, Andrew C.; Kui, Li; Lightbody, Anne F.; Stella, John C.; Sklar, Leonard S.

2015-02-01

Flow and sediment regimes shape alluvial river channels; yet the influence of these abiotic drivers can be strongly mediated by biotic factors such as the size and density of riparian vegetation. We present results from an experiment designed to identify when plants control fluvial processes and to investigate the sensitivity of fluvial processes to changes in plant characteristics versus changes in flow rate or sediment supply. Live seedlings of two species with distinct morphologies, tamarisk (Tamarix spp.) and cottonwood (Populus fremontii), were placed in different configurations in a mobile sand-bed flume. We measured the hydraulic and sediment flux responses of the channel at different flow rates and sediment supply conditions representing equilibrium (sediment supply = transport rate) and deficit (sediment supply plant species and configuration. Species-specific traits controlled the hydraulic response: compared to cottonwood, which has a more tree-like morphology, the shrubby morphology of tamarisk resulted in less pronation and greater reductions in near-bed velocities, Reynolds stress, and sediment flux rates. Under sediment-deficit conditions, on the other hand, abiotic factors dampened the effect of variations in plant characteristics on the hydraulic response. We identified scenarios for which the highest stem-density patch, independent of abiotic factors, dominated the fluvial response. These results provide insight into how and when plants influence fluvial processes in natural systems.

Detection of plant microRNAs in honey.

Directory of Open Access Journals (Sweden)

Angelo Gismondi

Full Text Available For the first time in the literature, our group has managed to demonstrate the existence of plant RNAs in honey samples. In particular, in our work, different RNA extraction procedures were performed in order to identify a purification method for nucleic acids from honey. Purity, stability and integrity of the RNA samples were evaluated by spectrophotometric, PCR and electrophoretic analyses. Among all honey RNAs, we specifically revealed the presence of both plastidial and nuclear plant transcripts: RuBisCO large subunit mRNA, maturase K messenger and 18S ribosomal RNA. Surprisingly, nine plant microRNAs (miR482b, miR156a, miR396c, miR171a, miR858, miR162a, miR159c, miR395a and miR2118a were also detected and quantified by qPCR. In this context, a comparison between microRNA content in plant samples (i.e. flowers, nectars and their derivative honeys was carried out. In addition, peculiar microRNA profiles were also identified in six different monofloral honeys. Finally, the same plant microRNAs were investigated in other plant food products: tea, cocoa and coffee. Since plant microRNAs introduced by diet have been recently recognized as being able to modulate the consumer's gene expression, our research suggests that honey's benefits for human health may be strongly correlated to the bioactivity of plant microRNAs contained in this matrix.

Genome-Wide Analysis, Classification, Evolution, and Expression Analysis of the Cytochrome P450 93 Family in Land Plants.

Directory of Open Access Journals (Sweden)

Hai Du

Full Text Available Cytochrome P450 93 family (CYP93 belonging to the cytochrome P450 superfamily plays important roles in diverse plant processes. However, no previous studies have investigated the evolution and expression of the members of this family. In this study, we performed comprehensive genome-wide analysis to identify CYP93 genes in 60 green plants. In all, 214 CYP93 proteins were identified; they were specifically found in flowering plants and could be classified into ten subfamilies-CYP93A-K, with the last two being identified first. CYP93A is the ancestor that was derived in flowering plants, and the remaining showed lineage-specific distribution-CYP93B and CYP93C are present in dicots; CYP93F is distributed only in Poaceae; CYP93G and CYP93J are monocot-specific; CYP93E is unique to legumes; CYP93H and CYP93K are only found in Aquilegia coerulea, and CYP93D is Brassicaceae-specific. Each subfamily generally has conserved gene numbers, structures, and characteristics, indicating functional conservation during evolution. Synonymous nucleotide substitution (dN/dS analysis showed that CYP93 genes are under strong negative selection. Comparative expression analyses of CYP93 genes in dicots and monocots revealed that they are preferentially expressed in the roots and tend to be induced by biotic and/or abiotic stresses, in accordance with their well-known functions in plant secondary biosynthesis.

A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation.

Directory of Open Access Journals (Sweden)

Warren D Anderson

2017-07-01

Full Text Available Multiple physiological systems interact throughout the development of a complex disease. Knowledge of the dynamics and connectivity of interactions across physiological systems could facilitate the prevention or mitigation of organ damage underlying complex diseases, many of which are currently refractory to available therapeutics (e.g., hypertension. We studied the regulatory interactions operating within and across organs throughout disease development by integrating in vivo analysis of gene expression dynamics with a reverse engineering approach to infer data-driven dynamic network models of multi-organ gene regulatory influences. We obtained experimental data on the expression of 22 genes across five organs, over a time span that encompassed the development of autonomic nervous system dysfunction and hypertension. We pursued a unique approach for identification of continuous-time models that jointly described the dynamics and structure of multi-organ networks by estimating a sparse subset of ∼12,000 possible gene regulatory interactions. Our analyses revealed that an autonomic dysfunction-specific multi-organ sequence of gene expression activation patterns was associated with a distinct gene regulatory network. We analyzed the model structures for adaptation motifs, and identified disease-specific network motifs involving genes that exhibited aberrant temporal dynamics. Bioinformatic analyses identified disease-specific single nucleotide variants within or near transcription factor binding sites upstream of key genes implicated in maintaining physiological homeostasis. Our approach illustrates a novel framework for investigating the pathogenesis through model-based analysis of multi-organ system dynamics and network properties. Our results yielded novel candidate molecular targets driving the development of cardiovascular disease, metabolic syndrome, and immune dysfunction.

Uptake of plant-derived specific alkaloids allows males of a butterfly to copulate.

Science.gov (United States)

Honda, Keiichi; Matsumoto, Junya; Sasaki, Ken; Tsuruta, Yoshiaki; Honda, Yasuyuki

2018-04-03

Certain butterflies utilize plant-acquired alkaloids for their own chemical defense and/or for producing male sex pheromone; a trait known as pharmacophagy. Males of the danaine butterfly, Parantica sita, have been reported to ingest pyrrolizidine alkaloids (PAs) as adults to produce two PA-derived sex pheromone components, viz. danaidone (major) and 7R-hydroxydanaidal. We found, however, that not all PAs that can be precursors for the pheromone serve for mating success of males. Here we show that although the sex pheromone is regarded as a requisite for successful mating, uptake of specific PA(s) (lycopsamine-type PAs) is also imperative for the males to achieve copulation. The increase in the levels of two biogenic amines, octopamine and/or serotonin, in the brain and thoracic ganglia of males fed with specific PA(s) suggested that these alkaloids most likely enhance male mating activity. The results can present new evidence for the evolutionary provenance of pharmacophagous acquisition of PAs in PA-adapted insects.

Machine-learning identifies substance-specific behavioral markers for opiate and stimulant dependence.

Science.gov (United States)

Ahn, Woo-Young; Vassileva, Jasmin

2016-04-01

Recent animal and human studies reveal distinct cognitive and neurobiological differences between opiate and stimulant addictions; however, our understanding of the common and specific effects of these two classes of drugs remains limited due to the high rates of polysubstance-dependence among drug users. The goal of the current study was to identify multivariate substance-specific markers classifying heroin dependence (HD) and amphetamine dependence (AD), by using machine-learning approaches. Participants included 39 amphetamine mono-dependent, 44 heroin mono-dependent, 58 polysubstance dependent, and 81 non-substance dependent individuals. The majority of substance dependent participants were in protracted abstinence. We used demographic, personality (trait impulsivity, trait psychopathy, aggression, sensation seeking), psychiatric (attention deficit hyperactivity disorder, conduct disorder, antisocial personality disorder, psychopathy, anxiety, depression), and neurocognitive impulsivity measures (Delay Discounting, Go/No-Go, Stop Signal, Immediate Memory, Balloon Analogue Risk, Cambridge Gambling, and Iowa Gambling tasks) as predictors in a machine-learning algorithm. The machine-learning approach revealed substance-specific multivariate profiles that classified HD and AD in new samples with high degree of accuracy. Out of 54 predictors, psychopathy was the only classifier common to both types of addiction. Important dissociations emerged between factors classifying HD and AD, which often showed opposite patterns among individuals with HD and AD. These results suggest that different mechanisms may underlie HD and AD, challenging the unitary account of drug addiction. This line of work may shed light on the development of standardized and cost-efficient clinical diagnostic tests and facilitate the development of individualized prevention and intervention programs for HD and AD. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Water vulnerabilities for existing coal-fired power plants.

Energy Technology Data Exchange (ETDEWEB)

Elcock, D.; Kuiper, J.; Environmental Science Division

2010-08-19

This report was funded by the U.S. Department of Energy's (DOE's) National Energy Technology Laboratory (NETL) Existing Plants Research Program, which has an energy-water research effort that focuses on water use at power plants. This study complements the Existing Plants Research Program's overall research effort by evaluating water issues that could impact power plants. Water consumption by all users in the United States over the 2005-2030 time period is projected to increase by about 7% (from about 108 billion gallons per day [bgd] to about 115 bgd) (Elcock 2010). By contrast, water consumption by coal-fired power plants over this period is projected to increase by about 21% (from about 2.4 to about 2.9 bgd) (NETL 2009b). The high projected demand for water by power plants, which is expected to increase even further as carbon-capture equipment is installed, combined with decreasing freshwater supplies in many areas, suggests that certain coal-fired plants may be particularly vulnerable to potential water demand-supply conflicts. If not addressed, these conflicts could limit power generation and lead to power disruptions or increased consumer costs. The identification of existing coal-fired plants that are vulnerable to water demand and supply concerns, along with an analysis of information about their cooling systems and related characteristics, provides information to help focus future research and development (R&D) efforts to help ensure that coal-fired generation demands are met in a cost-effective manner that supports sustainable water use. This study identified coal-fired power plants that are considered vulnerable to water demand and supply issues by using a geographical information system (GIS) that facilitated the analysis of plant-specific data for more than 500 plants in the NETL's Coal Power Plant Database (CPPDB) (NETL 2007a) simultaneously with 18 indicators of water demand and supply. Two types of demand indicators were

Identifying context-specific competencies required by community Australian Football sports trainers.

Science.gov (United States)

Donaldson, Alex; Finch, Caroline F

2012-08-01

First-aid is a recommended injury prevention and risk management strategy in community sport; however, little is known about the sport-specific competencies required by first-aid providers. To achieve expert consensus on the competencies required by community Australian Football (community-AF) sports trainers. A three-round online Delphi process. Community-AF. 16 Australian sports first-aid and community-AF experts. Rating of competencies as either 'essential', 'expected', 'ideal' or 'not required'. Results After Round 3, 47 of the 77 (61%) competencies were endorsed as 'essential' or 'expected' for a sports trainer to effectively perform the activities required to the standards expected at a community-AF club by ≥75% of experts. These competencies covered: the role of the sports trainer; the responsibilities of the sports trainer; emergency management; injury and illness assessment and immediate management; taping; and injury prevention and risk management. Four competencies (5%) were endorsed as 'ideal' or 'not required' by ≥85% of experts and were excluded from further consideration. The 26 competencies where consensus was not reached were retained as second-tier, optional competencies. Sports trainers are important members of on-field first-aid teams, providing support to both injured players and other sports medicine professionals. The competencies identified in this study provide the basis of a proposed two-tiered community-AF-specific sports trainer education structure that can be implemented by the peak sports body. This includes six mandatory modules, relating to the 'required' competencies, and a further six optional modules covering competencies on which consensus was not reached.

Flavin-containing monooxygenases in plants: looking beyond detox.

Science.gov (United States)

Schlaich, Nikolaus L

2007-09-01

Flavin-containing monooxygenases (FMOs) are known in bacteria, yeast and mammals where they catalyze the transfer of one atom of molecular O(2) to low molecular weight substrates. The predominant physiological function of animal FMOs appears to be detoxification of a vast spectrum of xenobiotics but until recently very little was known about the function of FMOs in plants. In the last two to three years, genetic and biochemical characterization has shown that plant FMOs can catalyze specific steps in the biosynthesis of auxin or in the metabolism of glucosinolates, and, furthermore, have a role in pathogen defence. Thus, plant FMOs hint that further FMO functions might be identified also in non-plant organisms and could stimulate novel research in this area.

Auxiliary feedwater system risk-based inspection guide for the Beaver Valley, Units 1 and 2 nuclear power plants

International Nuclear Information System (INIS)

Lloyd, R.C.; Vehec, T.A.; Moffitt, N.E.; Gore, B.F.; Vo, T.V.; Rossbach, L.W.; Sena, P.P. III

1993-02-01

In a study sponsored by the US Nuclear Regulatory Commission (NRC), Pacific Northwest Laboratory has developed and applied a methodology for deriving plant-specific risk-based inspection guidance for the auxiliary feedwater (AFW) system at pressurized water reactors that have not undergone probabilistic risk assessment (PRA). This methodology uses existing PRA results and plant operating experience information. Existing PRA-based inspection guidance information recently developed for the NRC for various plants was used to identify generic component failure modes. This information was then combined with plant-specific and industry-wide component information and failure data to identify failure modes and failure mechanisms for the AFW system at the selected plants. Beaver Valley Units 1 and 2 were selected as two of a series of plants for study. The product of this effort is a prioritized listing of AFW failures which have occurred at the plant and at other PWRs. This listing is intended for use by NRC inspectors in the preparation of inspection plans addressing AFW risk-important components at Beaver Valley Units 1 and 2

Chemical fingerprinting identifies Echium vulgare, Eupatorium cannabinum and Senecio spp. as plant species mainly responsible for pyrrolizidine alkaloids in bee-collected pollen.

Science.gov (United States)

Kast, Christina; Kilchenmann, Verena; Reinhard, Hans; Droz, Benoit; Lucchetti, Matteo Angelo; Dübecke, Arne; Beckh, Gudrun; Zoller, Otmar

2018-02-01

Various studies have shown that bee-collected pollen sold as nutritional supplements may contain toxic pyrrolizidine alkaloids (PAs) and, thus, pose a potential health risk for consumers. The level of contamination may vary according to its geographical and botanical origin. Here, the PA content of pollen produced in Switzerland was studied and 32 commercially available bee-collected pollen supplements produced between 2010 and 2014 were analysed. In addition, at what time period bees collect PA-containing pollen was investigated. Hence, this study looked into the occurrence of PAs in pollen samples collected daily during two-to-three consecutive seasons. Furthermore, the PA spectrum in pollen was compared to the spectrum found in flower heads of PA-plants to unambiguously identify plants responsible for PA contamination of pollen. The PA concentration of commercial and daily collected pollen was determined by target analysis using an HPLC-MS/MS system, allowing the detection of 18 different PAs and PA N-oxides found in the genera Echium, Eupatorium and Senecio, while the comparison of the PA spectrum in pollen and flower heads was performed by LC-HR-MS, allowing the detection of all PA types in a sample, including saturated, non-carcinogenic PAs. Of the commercially available pollen, 31% contained PAs with a mean concentration of 319 ng/g, mainly Echium- and Eupatorium-type PAs, while the PA concentrations were below the limit of quantitation (LOQ) in 69% of the pollen samples. Bees collected pollen containing Echium-type PAs mainly in June and July, while they gathered pollen containing Eupatorium-type PAs from mid-July to August. Senecio-type PAs appeared from June to September. Comparison of the PA array in pollen and plants identified E. vulgare and E. cannabinum as the main plants responsible for PA contamination of Swiss bee-collected pollen, and to a lesser extent also identified plants belonging to the genus Senecio.

Plant Translation Factors and Virus Resistance

Directory of Open Access Journals (Sweden)

Hélène Sanfaçon

2015-06-01

Full Text Available Plant viruses recruit cellular translation factors not only to translate their viral RNAs but also to regulate their replication and potentiate their local and systemic movement. Because of the virus dependence on cellular translation factors, it is perhaps not surprising that many natural plant recessive resistance genes have been mapped to mutations of translation initiation factors eIF4E and eIF4G or their isoforms, eIFiso4E and eIFiso4G. The partial functional redundancy of these isoforms allows specific mutation or knock-down of one isoform to provide virus resistance without hindering the general health of the plant. New possible targets for antiviral strategies have also been identified following the characterization of other plant translation factors (eIF4A-like helicases, eIF3, eEF1A and eEF1B that specifically interact with viral RNAs and proteins and regulate various aspects of the infection cycle. Emerging evidence that translation repression operates as an alternative antiviral RNA silencing mechanism is also discussed. Understanding the mechanisms that control the development of natural viral resistance and the emergence of virulent isolates in response to these plant defense responses will provide the basis for the selection of new sources of resistance and for the intelligent design of engineered resistance that is broad-spectrum and durable.

Identifying Issues in Applying Integrated Project Delivery to Domestic Nuclear Power Plant Construction Projects

Energy Technology Data Exchange (ETDEWEB)

Kim, Young Joo [Korean Nuclear Society, Daejeon (Korea, Republic of)

2016-05-15

Integrated Project Delivery (IPD) is defined as that people, systems, business structures, and practices of key stakeholders are incorporated into a single-team, with a single process, which executes a project in a way of optimizing the project's outcome, increasing values delivered to the end user, reducing waste, and maximizing efficiency throughout the phases of engineering to construction. The researcher had carried out literature review in terms of IPD to identify major characteristics of IPD which are presented in the following section and had compared such characteristics against peculiarities of nuclear power plant (NPP) construction projects in order to shed light on obstacles in possible application of IPD method to domestic NPP construction projects in the coming days. In this research, three (3) major characteristics of IPD were identified: 1) key stakeholders signing one balanced contract, forming de facto one body, sharing risk and reward 2) an integrated project team being formed in the early stage of a project and providing input to minimize time and cost loss from rework downstream 3) team members co-locating, having open and direct communication, making decisions on time, and pursuing the success of the project itself.

Mercury emissions and coal-fired power plants: Understanding the problems and identifying solutions

International Nuclear Information System (INIS)

Davis, S.E.

1997-01-01

Electric utility emissions contribute to an array of air quality concerns, most notably ground-level ozone, acid deposition, global warming, and fine particulate pollution. More recently, electric utility emissions of air toxics such as mercury have been linked to serious ecological health effects, especially in fish-eating birds. Another issue that is gaining attention is that of eutrophication in marine waters from nitrogen oxide emissions. Coal-fired power plants warrant special consideration, particularly in regards to mercury. Coal-fired power plants currently represent over 30% of controllable anthropogenic emissions in the US and are expected to emit nearly half of all anthropogenic emissions in the US by 2010. However, because the human health threshold for mercury is not known with certainty and mercury control technologies such as activated carbon injection are extremely expensive, mercury emissions from electric utilities have not been addressed in the US through either regulation or voluntary initiatives. The Center is beginning to evaluate the viability of no- or low-regrets measures that may be more consistent with the current state of the science on human and ecological health effects. The Center is also looking at options to reduce eutophication. Specifically, the Center has: hosted a workshop to assess the viability of low-cost mercury control options for electric utilities, developed a proposal to undertake a mercury banking initiative, worked to reduce compliance costs associated with multiple and conflicting regulations, and investigated the potential benefits and workability of NOx trading between air and water sources These activities are described in greater detail in the Center's paper

GSHSite: exploiting an iteratively statistical method to identify s-glutathionylation sites with substrate specificity.

Directory of Open Access Journals (Sweden)

Yi-Ju Chen

Full Text Available S-glutathionylation, the covalent attachment of a glutathione (GSH to the sulfur atom of cysteine, is a selective and reversible protein post-translational modification (PTM that regulates protein activity, localization, and stability. Despite its implication in the regulation of protein functions and cell signaling, the substrate specificity of cysteine S-glutathionylation remains unknown. Based on a total of 1783 experimentally identified S-glutathionylation sites from mouse macrophages, this work presents an informatics investigation on S-glutathionylation sites including structural factors such as the flanking amino acids composition and the accessible surface area (ASA. TwoSampleLogo presents that positively charged amino acids flanking the S-glutathionylated cysteine may influence the formation of S-glutathionylation in closed three-dimensional environment. A statistical method is further applied to iteratively detect the conserved substrate motifs with statistical significance. Support vector machine (SVM is then applied to generate predictive model considering the substrate motifs. According to five-fold cross-validation, the SVMs trained with substrate motifs could achieve an enhanced sensitivity, specificity, and accuracy, and provides a promising performance in an independent test set. The effectiveness of the proposed method is demonstrated by the correct identification of previously reported S-glutathionylation sites of mouse thioredoxin (TXN and human protein tyrosine phosphatase 1b (PTP1B. Finally, the constructed models are adopted to implement an effective web-based tool, named GSHSite (http://csb.cse.yzu.edu.tw/GSHSite/, for identifying uncharacterized GSH substrate sites on the protein sequences.

Knowns and unknowns of plasma membrane protein degradation in plants.

Science.gov (United States)

Liu, Chuanliang; Shen, Wenjin; Yang, Chao; Zeng, Lizhang; Gao, Caiji

2018-07-01

Plasma membrane (PM) not only creates a physical barrier to enclose the intracellular compartments but also mediates the direct communication between plants and the ever-changing environment. A tight control of PM protein homeostasis by selective degradation is thus crucial for proper plant development and plant-environment interactions. Accumulated evidences have shown that a number of plant PM proteins undergo clathrin-dependent or membrane microdomain-associated endocytic routes to vacuole for degradation in a cargo-ubiquitination dependent or independent manner. Besides, several trans-acting determinants involved in the regulation of endocytosis, recycling and multivesicular body-mediated vacuolar sorting have been identified in plants. More interestingly, recent findings have uncovered the participation of selective autophagy in PM protein turnover in plants. Although great progresses have been made to identify the PM proteins that undergo dynamic changes in subcellular localizations and to explore the factors that control the membrane protein trafficking, several questions remain to be answered regarding the molecular mechanisms of PM protein degradation in plants. In this short review article, we briefly summarize recent progress in our understanding of the internalization, sorting and degradation of plant PM proteins. More specifically, we focus on discussing the elusive aspects underlying the pathways of PM protein degradation in plants. Copyright © 2018 Elsevier B.V. All rights reserved.

Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants.

Science.gov (United States)

Li, Xinguo; Wu, Harry X; Southerton, Simon G

2010-06-21

Wood is a valuable natural resource and a major carbon sink. Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Although genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. We use comparative genomics to examine evolution of the xylem transcriptome to gain insights into xylem evolution. The xylem transcriptome is highly conserved in conifers, but considerably divergent in angiosperms. The functional domains of genes in the xylem transcriptome are moderately to highly conserved in vascular plants, suggesting the existence of a common ancestral xylem transcriptome. Compared to the total transcriptome derived from a range of tissues, the xylem transcriptome is relatively conserved in vascular plants. Of the xylem transcriptome, cell wall genes, ancestral xylem genes, known proteins and transcription factors are relatively more conserved in vascular plants. A total of 527 putative xylem orthologs were identified, which are unevenly distributed across the Arabidopsis chromosomes with eight hot spots observed. Phylogenetic analysis revealed that evolution of the xylem transcriptome has paralleled plant evolution. We also identified 274 conifer-specific xylem unigenes, all of which are of unknown function. These xylem orthologs and conifer-specific unigenes are likely to have played a crucial role in xylem evolution. Conifers have highly conserved xylem transcriptomes, while angiosperm xylem transcriptomes are relatively diversified. Vascular plants share a common ancestral xylem transcriptome. The xylem transcriptomes of vascular plants are more conserved than the total transcriptomes. Evolution of the xylem transcriptome has largely followed the trend of plant evolution.

Cell-specific vacuolar calcium storage mediated by CAX1 regulates apoplastic calcium concentration, gas exchange, and plant productivity in Arabidopsis.

Science.gov (United States)

Conn, Simon J; Gilliham, Matthew; Athman, Asmini; Schreiber, Andreas W; Baumann, Ute; Moller, Isabel; Cheng, Ning-Hui; Stancombe, Matthew A; Hirschi, Kendal D; Webb, Alex A R; Burton, Rachel; Kaiser, Brent N; Tyerman, Stephen D; Leigh, Roger A

2011-01-01

The physiological role and mechanism of nutrient storage within vacuoles of specific cell types is poorly understood. Transcript profiles from Arabidopsis thaliana leaf cells differing in calcium concentration ([Ca], epidermis 60 mM) were compared using a microarray screen and single-cell quantitative PCR. Three tonoplast-localized Ca(2+) transporters, CAX1 (Ca(2+)/H(+)-antiporter), ACA4, and ACA11 (Ca(2+)-ATPases), were identified as preferentially expressed in Ca-rich mesophyll. Analysis of respective loss-of-function mutants demonstrated that only a mutant that lacked expression of both CAX1 and CAX3, a gene ectopically expressed in leaves upon knockout of CAX1, had reduced mesophyll [Ca]. Reduced capacity for mesophyll Ca accumulation resulted in reduced cell wall extensibility, stomatal aperture, transpiration, CO(2) assimilation, and leaf growth rate; increased transcript abundance of other Ca(2+) transporter genes; altered expression of cell wall-modifying proteins, including members of the pectinmethylesterase, expansin, cellulose synthase, and polygalacturonase families; and higher pectin concentrations and thicker cell walls. We demonstrate that these phenotypes result from altered apoplastic free [Ca(2+)], which is threefold greater in cax1/cax3 than in wild-type plants. We establish CAX1 as a key regulator of apoplastic [Ca(2+)] through compartmentation into mesophyll vacuoles, a mechanism essential for optimal plant function and productivity.

Plant walkdown

International Nuclear Information System (INIS)

Kostov, M.

2000-01-01

This report covers the following: preparatory steps for performing plant walk-down; the objective of the first plant walk-down; plant walk-down procedures; earthquake screening evaluation; walk-down documentation; second plant walk-down. The following objectives concerning the plant walk-down(s) were achieved. The plant system configuration is verified in order to proceed with event tree and fault tree analyses. Systems interactions, other types of dependencies or plant unique features are identified. he safety related components that are judged to generically possess high capacities (i.e., larger than the earthquake review level) have been verified to contain no weaknesses. Further analyses needed to establish the capacities of remaining safety-related components are identified and necessary field data are obtained. Information on components is obtained to assist in HCLPF (fragility) evaluation and peer review of the seismic margin study

Thermal insulation system design and fabrication specification (nuclear) for the Clinch River Breeder Reactor plant

International Nuclear Information System (INIS)