bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classifying biotechnology-related policy, regulatory and innovation regimes: A framework for the comparative analysis of genomics policy-making
Authors: Migone Andrea , Howlett Michael 
Published: October 2009

Abstract
An important part of the study of the policy response of government in the area of a novel technology, such as genomics, lies in identifying the technological trajectory followed in the sector and how it intersects or impacts upon existing policy, regulatory and innovation regimes. Part of the challenge in studying the impacts and outcomes of such trajectories, therefore, is their multilayered nature. This has led to the proliferation of different models or frameworks for the analysis of many sectors, each one tackling a specific level and obscuring the linkages between levels and units of analysis. Research into innovations, however, benefits from an understanding of the overall policy and regulatory regimes present in a sector while an understanding of regulatory behaviour is in turn linked to the overall policy framework set up to govern a sector. As such, analyses of both regulation and innovation in a sector such as genomics can profit from an integrated, multi-level approach grounded in the overall nature of the policy regime present in the sphere of activity under examination. We offer such an approach by synthesizing four existing models of policy, regulatory and innovation behaviour that fit the three levels of analysis – the policy regime, regulatory regime and the innovation regime – in the sphere of biotechnology.
NGSView: an extensible open source editor for next-generation sequencing data
Authors: Arner Erik , Hayashizaki Yoshihide , Daub Carsten O. 
Published: October 2009

Abstract
Summary:High-throughput sequencing technologies introduce novel demands on tools available for data analysis. We have developed NGSView (Next Generation Sequence View), a generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. NGSView is available under an open source license and can be extended through a well documented API.
Availability: http://ngsview.sourceforge.net
Contact: arner@gsc.riken.jp
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
Authors: Wang Likun , Feng Zhixing , Wang Xi , Wang Xiaowo , Zhang Xuegong 
Published: October 2009

AbstractSummary: High-throughput RNA sequencing (RNA-seq) is rapidly emerging as a major quantitative transcriptome profiling platform. Here, we present DEGseq, an R package to identify differentially expressed genes or isoforms for RNA-seq data from different samples. In this package, we integrated three existing methods, and introduced two novel methods based on MA-plot to detect and visualize gene expression difference.Availability: The R package and a quick-start vignette is available at http://bioinfo.au.tsinghua.edu.cn/software/degseqContact: xwwang@tsinghua.edu.cn; zhangxg@tsinghua.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.
GTP Is Required for the Microtubule Catastrophe-Inducing Activity of MAP200, a Tobacco Homolog of XMAP215
Authors: Hamada Takahiro , Itoh Tomohiko J. , Hashimoto Takashi , Shimmen Teruo , Sonobe Seiji 
Published: October 2009

AbstractWidely conserved among eukaryotes, the microtubule-associated protein 215 (MAP215) family enhances microtubule dynamic instability. The family member studied most extensively, Xenopus laevis XMAP215, has been reported to enhance both assembly and disassembly parameters, although the mechanism whereby one protein can exert these apparently contradictory effects has not been clarified. Here, we analyze the activity of a plant MAP215 homolog, tobacco (Nicotiana tabacum) MAP200 on microtubule behavior in vitro. We show that, like XMAP215, MAP200 promotes both assembly and disassembly parameters, including microtubule growth rate and catastrophe frequency. When MAP200 is added to tubulin and taxol, strikingly long-coiled structures form. When GDP partially replaces GTP, the increase of catastrophe frequency by MAP200 is strongly diminished, even though this replacement stimulates catastrophe in the absence of MAP200. This implies that MAP200 induces catastrophes by a specific, GTP-requiring pathway. We hypothesize that, in the presence of MAP200, a catastrophe-prone microtubule lattice forms occasionally when elongated but nonadjacent protofilaments make lateral contacts.
The Ectomycorrhizal FungusLaccaria bicolorStimulates Lateral Root Formation in Poplar and Arabidopsis through Auxin Transport and Signaling
Authors: Felten Judith , Kohler Annegret , Morin Emmanuelle , Bhalerao Rishikesh P. , Palme Klaus , Martin Francis , Ditengou Franck A. , Legué Valérie 
Published: October 2009

AbstractThe early phase of the interaction between tree roots and ectomycorrhizal fungi, prior to symbiosis establishment, is accompanied by a stimulation of lateral root (LR) development. We aimed to identify gene networks that regulate LR development during the early signal exchanges between poplar (Populus tremula × Populus alba) and the ectomycorrhizal fungus Laccaria bicolor with a focus on auxin transport and signaling pathways. Our data demonstrated that increased LR development in poplar and Arabidopsis (Arabidopsis thaliana) interacting with L. bicolor is not dependent on the ability of the plant to form ectomycorrhizae. LR stimulation paralleled an increase in auxin accumulation at root apices. Blocking plant polar auxin transport with 1-naphthylphthalamic acid inhibited LR development and auxin accumulation. An oligoarray-based transcript profile of poplar roots exposed to molecules released by L. bicolor revealed the differential expression of 2,945 genes, including several components of polar auxin transport (PtaPIN and PtaAUX genes), auxin conjugation (PtaGH3 genes), and auxin signaling (PtaIAA genes). Transcripts of PtaPIN9, the homolog of Arabidopsis AtPIN2, and several PtaIAAs accumulated specifically during the early interaction phase. Expression of these rapidly induced genes was repressed by 1-naphthylphthalamic acid. Accordingly, LR stimulation upon contact with L. bicolor in Arabidopsis transgenic plants defective in homologs of these genes was decreased or absent. Furthermore, in Arabidopsis pin2, the root apical auxin increase during contact with the fungus was modified. We propose a model in which fungus-induced auxin accumulation at the root apex stimulates LR formation through a mechanism involving PtaPIN9-dependent auxin redistribution together with PtaIAA-based auxin signaling.
Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencing
Authors: Hsieh Li-Ching , Lin Shu-I. , Shih Arthur Chun-Chieh , Chen June-Wei , Lin Wei-Yi , Tseng Ching-Ying , Li Wen-Hsiung , Chiou Tzyy-Jen 
Published: October 2009

Abstract
Recent studies have demonstrated the important role of plant microRNAs (miRNAs) under nutrient deficiencies. In this study, deep sequencing of Arabidopsis (Arabidopsis thaliana) small RNAs was conducted to reveal miRNAs and other small RNAs that were differentially expressed in response to phosphate (Pi) deficiency. About 3.5 million sequence reads corresponding to 0.6 to 1.2 million unique sequence tags from each Pi-sufficient or Pi-deficient root or shoot sample were mapped to the Arabidopsis genome. We showed that upon Pi deprivation, the expression of miR156, miR399, miR778, miR827, and miR2111 was induced, whereas the expression of miR169, miR395, and miR398 was repressed. We found cross talk coordinated by these miRNAs under different nutrient deficiencies. In addition to miRNAs, we identified one Pi starvation-induced DICER-LIKE1-dependent small RNA derived from the long terminal repeat of a retrotransposon and a group of 19-nucleotide small RNAs corresponding to the 5′ end of tRNA and expressed at a high level in Pi-starved roots. Importantly, we observed an increased abundance of TAS4-derived trans-acting small interfering RNAs (ta-siRNAs) in Pi-deficient shoots and uncovered an autoregulatory mechanism of PAP1/MYB75 via miR828 and TAS4-siR81(−) that regulates the biosynthesis of anthocyanin. This finding sheds light on the regulatory network between miRNA/ta-siRNA and its target gene. Of note, a substantial amount of miR399* accumulated under Pi deficiency. Like miR399, miR399* can move across the graft junction, implying a potential biological role for miR399*. This study represents a comprehensive expression profiling of Pi-responsive small RNAs and advances our understanding of the regulation of Pi homeostasis mediated by small RNAs.
An ABC Transporter Mutation Alters Root Exudation of Phytochemicals That Provoke an Overhaul of Natural Soil Microbiota
Authors: Badri Dayakar V. , Quintana Naira , El Kassis Elie G. , Kim Hye Kyong , Choi Young Hae , Sugiyama Akifumi , Verpoorte Robert , Martinoia Enrico , Manter Daniel K. , Vivanco Jorge M. 
Published: October 2009

Abstract
Root exudates influence the surrounding soil microbial community, and recent evidence demonstrates the involvement of ATP-binding cassette (ABC) transporters in root secretion of phytochemicals. In this study, we examined effects of seven Arabidopsis (Arabidopsis thaliana) ABC transporter mutants on the microbial community in native soils. After two generations, only the Arabidopsis abcg30 (Atpdr2) mutant had significantly altered both the fungal and bacterial communities compared with the wild type using automated ribosomal intergenic spacer analysis. Similarly, root exudate profiles differed between the mutants; however, the largest variance from the wild type (Columbia-0) was observed in abcg30, which showed increased phenolics and decreased sugars. In support of this biochemical observation, whole-genome expression analyses of abcg30 roots revealed that some genes involved in biosynthesis and transport of secondary metabolites were up-regulated, while some sugar transporters were down-regulated compared with genome expression in wild-type roots. Microbial taxa associated with Columbia-0 and abcg30 cultured soils determined by pyrosequencing revealed that exudates from abcg30 cultivated a microbial community with a relatively greater abundance of potentially beneficial bacteria (i.e. plant-growth-promoting rhizobacteria and nitrogen fixers) and were specifically enriched in bacteria involved in heavy metal remediation. In summary, we report how a single gene mutation from a functional plant mutant influences the surrounding community of soil organisms, showing that genes are not only important for intrinsic plant physiology but also for the interactions with the surrounding community of organisms as well.
Protein Phosphatases 2C Regulate the Activation of the Snf1-Related Kinase OST1 by Abscisic Acid inArabidopsis
Authors: Vlad Florina , Rubio Silvia , Rodrigues Americo , Sirichandra Caroline , Belin Christophe , Robert Nadia , Leung Jeffrey , Rodriguez Pedro L. , Laurière Christiane , Merlot Sylvain 
Published: October 2009

AbstractThe plant hormone abscisic acid (ABA) orchestrates plant adaptive responses to a variety of stresses, including drought. This signaling pathway is regulated by reversible protein phosphorylation, and genetic evidence demonstrated that several related protein phosphatases 2C (PP2Cs) are negative regulators of this pathway in Arabidopsis thaliana. Here, we developed a protein phosphatase profiling strategy to define the substrate preferences of the HAB1 PP2C implicated in ABA signaling and used these data to screen for putative substrates. Interestingly, this analysis designated the activation loop of the ABA activated kinase OST1, related to Snf1 and AMPK kinases, as a putative HAB1 substrate. We experimentally demonstrated that HAB1 dephosphorylates and deactivates OST1 in vitro. Furthermore, HAB1 and the related PP2Cs ABI1 and ABI2 interact with OST1 in vivo, and mutations in the corresponding genes strongly affect OST1 activation by ABA. Our results provide evidence that PP2Cs are directly implicated in the ABA-dependent activation of OST1 and further suggest that the activation mechanism of AMPK/Snf1-related kinases through the inhibition of regulating PP2Cs is conserved from plants to human.
Cotranslational Proteolysis Dominates Glutathione Homeostasis to Support Proper Growth and Development
Authors: Frottin Frédéric , Espagne Christelle , Traverso José A. , Mauve Caroline , Valot Benoît , Lelarge-Trouverie Caroline , Zivy Michel , Noctor Graham , Meinnel Thierry , Giglione Carmela 
Published: October 2009

Abstract
The earliest proteolytic event affecting most proteins is the excision of the initiating Met (NME). This is an essential and ubiquitous cotranslational process tightly regulated in all eukaryotes. Currently, the effects of NME on unknown complex cellular networks and the ways in which its inhibition leads to developmental defects and cell growth arrest remain poorly understood. Here, we provide insight into the earliest molecular mechanisms associated with the inhibition of the NME process in Arabidopsis thaliana. We demonstrate that the developmental defects induced by NME inhibition are caused by an increase in cellular proteolytic activity, primarily induced by an increase in the number of proteins targeted for rapid degradation. This deregulation drives, through the increase of the free amino acids pool, a perturbation of the glutathione homeostasis, which corresponds to the earliest limiting, reversible step promoting the phenotype. We demonstrate that these effects are universally conserved and that the reestablishment of the appropriate glutathione status restores growth and proper development in various organisms. Finally, we describe a novel integrated model in which NME, protein N-α-acylation, proteolysis, and glutathione homeostasis operate in a sequentially regulated mechanism that directs both growth and development.
ARABIDOPSIS TRITHORAX-RELATED7 Is Required for Methylation of Lysine 4 of Histone H3 and for Transcriptional Activation of FLOWERING LOCUS C
Authors: Tamada Yosuke , Yun Jae-Young , Woo Seung chul , Amasino Richard M. 
Published: October 2009

Abstract
In the winter-annual accessions of Arabidopsis thaliana, presence of an active allele of FRIGIDA (FRI) elevates expression of FLOWERING LOCUS C (FLC), a repressor of flowering, and thus confers a vernalization requirement. FLC activation by FRI involves methylation of Lys 4 of histone H3 (H3K4) at FLC chromatin. Many multicellular organisms that have been examined contain two classes of H3K4 methylases, a yeast (Saccharomyces cerevisiae) Set1 class and a class related to Drosophila melanogaster Trithorax. In this work, we demonstrate that ARABIDOPSIS TRITHORAX-RELATED7 (ATXR7), a putative Set1 class H3K4 methylase, is required for proper FLC expression. The atxr7 mutation partially suppresses the delayed flowering of a FRI-containing line. The rapid flowering of atxr7 is associated with reduced FLC expression and is accompanied by decreased H3K4 methylation and increased H3K27 methylation at FLC. Thus, ATXR7 is required for the proper levels of these histone modifications that set the level of FLC expression to create a vernalization requirement in winter-annual accessions. Previously, it has been reported that lesions in ATX1, which encodes a Trithorax class H3K4 methylase, partially suppress the delayed flowering of winter-annual Arabidopsis. We show that the flowering phenotype of atx1 atxr7 double mutants is additive relative to those of single mutants. Therefore, both classes of H3K4 methylases appear to be required for proper regulation of FLC expression.
Arabidopsis Decapping 5 Is Required for mRNA Decapping, P-Body Formation, and Translational Repression during Postembryonic Development
Authors: Xu Jun , Chua Nam-Hai 
Published: October 2009

Abstract
Eukaryotic processing bodies (P-bodies) are implicated in mRNA storage and mRNA decapping. We previously found that a decapping complex comprising Decapping 1 (DCP1), DCP2, and Varicose in Arabidopsis thaliana is essential for postembryonic development, but the underlying mechanism is poorly understood. Here, we characterized Arabidopsis DCP5, a homolog of human RNA-associated protein 55, as an additional P-body constituent. DCP5 associates with DCP1 and DCP2 and is required for mRNA decapping in vivo. In spite of its association with DCP2, DCP5 has no effect on DCP2 decapping activity in vitro, suggesting that the effect on decapping in vivo is indirect. In knockdown mutant dcp5-1, not only is mRNA decapping compromised, but the size of P-bodies is also significantly decreased. These results indicate that DCP5 is required for P-body formation, which likely facilitates efficient decapping. During wild-type seed germination, mRNAs encoding seed storage proteins (SSPs) are translationally repressed and degraded. By contrast, in dcp5-1, SSP mRNAs are translated, leading to accumulation of their products in germinated seedlings. In vitro experiments using wheat germ extracts confirmed that DCP5 is a translational repressor. Our results showed that DCP5 is required for translational repression and P-body formation and plays an indirect role in mRNA decapping.
The role of robots in the food industry: a review
Authors: Bogue Robert 
Published: October 2009

PurposeThe purpose of this paper is to provide a review of present‐day and anticipated future applications of robots in the food industry.Design/methodology/approachThe paper discusses the use of robots in the agriculture and farming, processing and packaging and retail sectors of the industry. Examples are given of specific applications and development activities.FindingsRobots are being developed for many agriculture and farming applications but with the exception of milking robots, most still remain at the research/prototype stage. Food processing and packaging is the best developed sector of the industry and most uses entail picking, packing and palletising, although meat cutting is a growing application. Robots are few in the food retail sector although a number of innovative, niche products have recently been launched.Originality/valueThis paper reviews the use of robots throughout the food chain and considers possible future applications.
In quest of mobility – Honda to develop walking assist devices
Authors: Kusuda Yoshihiro 
Published: October 2009

PurposeThe purpose of this paper is to describe new walking assist devices Honda is developing.Design/methodology/approachThe exhibition, press release and interview are described. The features of the walking assist devices are presented.FindingsThe paper finds that Honda is developing walking assist devices for elderly and disabled people based on its expertise in autonomous walking obtained through the development of Advanced Step in Innovative Mobility.Originality/valueThis paper highlights the value of the walking assist devices.
Development of an inspection robot for long‐distance transmission pipeline on‐site overhaul
Authors: Yuan Jianming , Wu Xinjun , Kang Yihua , Huang Chen 
Published: October 2009

PurposeDamage of oil and gas long‐distance transmission pipelines caused by corrosion, stresses, geological change, and other factors can result in catastrophic failures. The purpose of this paper is to describe a mobile out‐pipe inspection robot for the pipeline inspection.Design/methodology/approachThis paper adapts to the requirements of long‐distance transmission pipelines on‐site overhaul, the robot developed in this paper utilizes a local magnetic flux leakage testing method for the pipeline inspection. Detection, walking, attachment, steering, and control units are designed for the robot.FindingsThe detection apparatus of the robot plays dual roles as detection and attachment unit. So, the structure of the robot is relatively simple and it is relatively small in size and relatively light.Practical implicationsA prototype of the robot has been manufactured according to the design. Results of the test in lab show the robot can be used to inspect pipe.Originality/valueThe robot is able to scan and inspect the pipeline along the planned route automatically.
A miniature wall climbing robot with biomechanical suction cups
Authors: Hu Bingshan , Wang Liwen , Zhao Yanzheng , Fu Z. 
Published: October 2009

PurposeWall climbing robots' volume is needed to be very small in fields that workspace is limited, such as anti‐terror scouting, industry pipe network inspecting and so on. The purpose of this paper is to design a miniature wall climbing robot with biomechanical suction cups actuated by shape memory alloy (SMA) actuators.Design/methodology/approachBased on characteristics of biologic suction apparatuses, the biomechanical suction cup is designed first. Theory analysis of the suction cup is made considering elastic plate's deflection and SMAs constitutive model. A triangular close linkage locomotion mechanism is chosen for the miniature robot because of its simple structure and control. The robot's gait, kinematics, and control system are all illustrated in this paper.FindingsExperiments indicate that the suction cup can be used as an adhesion mechanism for miniature wall climbing robots, and the miniature robot prototype with biomechanical suction cups can move in straight line and turn with a fixed angle on an inclined glass wall.Originality/valueThis paper describes how a miniature wall climbing robot with biomechanical suction cups actuated by SMA without any air pump is designed.
Analysis of the effects of time delays on the teleoperation of a mobile robot in various modes of operation
Authors: Sanders David 
Published: October 2009

PurposeThe purpose of this paper is to investigate the effect of time delay on the ability of a human operator to complete a task with a teleoperated mobile‐robot using two systems, two different ways of interacting with the mobile‐robots and several different environments.Design/methodology/approachTeleoperators are observed completing a series of tasks using a joystick to control a mobile‐robot while time delays are introduced to the system. They sit at a computer and view scenes remotely on a screen. Cameras are either mounted on the robot or mounted externally so that they view both the environment and robot. Teleoperators complete the tests both with and without sensors. One robot system uses an umbilical cable and one uses a radio link.FindingsIn simple environments, a teleoperator may perform better without a sensor system to assist them but as time delays are introduced then there are more failures. In more complicated environments or when time delays are longer, then teleoperators perform better with a sensor system to assist. Teleoperators may also tend to perform better with a radio link than with an umbilical connection.Research limitations/implicationsTeleoperated systems rely heavily on visual feedback and experienced operators. This paper investigates the effect of introducing a delay to the delivery of that visual feedback.Practical implicationsThe paper suggests that in simple environments with short time delays then the amount of sensor support should be small but in more complicated environments or with longer delays then more sensor support needs to be provided.Originality/valueResults from imposing time delays on a teleoperated mobile‐robot are presented. Effects on the task of different ways of viewing activity on a computer display are presented, that is with cameras mounted on the robot or cameras mounted externally to view both the environment and robot. Results from using sensors to assist teleoperators are presented. The paper suggests that the amount of sensor support should be varied depending on circumstances.