bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermodynamic and dynamic influences in the Far East‐Okhotsk region on stagnant Meiyu‐Baiu
Authors: Wu Chi‐Hua 
Published: June 2017

AbstractWesterly perturbation is enlarged over the Far East‐Okhotsk region in late June and early July and is associated with the largest land‐sea heating contrast surrounding the Sea of Okhotsk. The corresponding characteristics in the lower troposphere are southward deepening of the cold low over northeastern China, and intensification of the Okhotsk high. Coincidentally, the Meiyu‐Baiu coupled with the western North Pacific (WNP) subtropical high is nearly stagnant during this period. By simulations using a global climate model with an intensified Okhotsk surface high in response to cooling Sea of Okhotsk, it is suggested that the enhanced thermal contrast over the Far East‐Okhotsk region can generate an obstacle to Meiyu‐Baiu poleward migration. Corresponding to the intensified Okhotsk high, the WNP subtropical high is strengthened by the high ridge over Taiwan. The East Asian midlatitude westerly jet stream in the northern flank of the WNP subtropical high also strengthens; the consequently enhanced midtropospheric warm temperature advection can regulate the latitude position of the Meiyu‐Baiu. The wave source generated in the upper troposphere is located over the midlatitude WNP (anomalous cyclone) bordering the Sea of Okhotsk, whereas that in the lower troposphere is related to the strengthened westerly in the northern WNP subtropical high. The wave activity propagation consistently indicates the strengthening and equatorward confinement of the westerly jet. Therefore, the intensified Okhotsk high and enlarged westerly perturbation beginning in late June are suggested as an inherently geographic limit of the Far East‐Okhotsk region in regard to Meiyu‐Baiu migration.
Recent Advances and Applications of Nanoscale Infrared Spectroscopy and Imaging
Authors: Unger Miriam , Marcott Curtis 
Published: June 2017

Abstract
In conventional infrared (IR) microspectroscopy, the rule of thumb is that you cannot obtain IR spectra of objects smaller than 5–10 m in size. This is based on the diffraction of radiation, and therefore, the spatial resolution is limited to be on the order of the wavelength of light used to make the measurement. Recently, researchers have developed new techniques that can overcome this limit, where the spatial resolution is not limited by diffraction. In this context, this article will focus on the combination of atomic force microscopy and infrared spectroscopy (AFM‐IR) as well as scattering scanning nearfield optical microscopy (s‐SNOM). Both techniques, AFM‐IR and s‐SNOM, are complementary with different strengths and weaknesses. AFM‐IR directly detects IR radiation absorbed by the sample using the AFM (atomic force microscope) probe tip to sense thermal expansion. This thermal expansion depends primarily on the absorption coefficient of the sample and is largely independent of other optical properties of the AFM tip and the sample. Thus, the AFM‐IR technique is preferred to measure absorption spectra with correlation to conventional IR spectroscopy and, furthermore, can be widely used for studies of soft materials such as polymers and life science samples. On the other hand, s‐SNOM detects radiation scattered by nanometer‐scale regions directly under the AFM probe tip. The scattered field depends on the complex optical constants of both the tip and the sample and contains rich information about nano‐optical phenomena. s‐SNOM is an advanced technique for imaging nanoscale contrast based on optical properties, with diverse applications in advanced materials, devices, and fundamental light/matter interactions. In this article, both the AFM‐IR and s‐SNOM approaches will be described with example applications of how they can be used to chemically characterize materials at the nanoscale.
Process‐Based Laboratory Design
Authors: Schubert Henriette , Kjaergaard Nielsen Flemming 
Published: June 2017

Abstract
The new pharma reality is characterized by fast change and unknown future demands. Often, the laboratories are established before the processes, facility use, and technologies are finalized. Hence, flexible, modular, and changeable laboratory facilities that can be adapted to new research needs or process design are needed. However, planning and designing biopharmaceutical laboratories for research, development, and quality control require understanding of challenges and business drivers to ensure compliant and long‐term laboratory operations.

The purpose of this article is to provide guidance and a methodology that is based on a process and operational driven design approach. The methodology can be used for
QC
laboratory projects, R&D laboratory facilities,
in vivo
animal research, trial facilities, and facilities for development or small‐scale manufacturing of tailored therapies. The focus is on guidance on design development and basis for management decision rather than detailed design and construction guideline. The methodology and principles described can be used globally regardless of local requirements.
Systems Biology: Principles and Applications in Plant Research
Authors: Coruzzi Gloria M. , Burga Alejandro R. , Katari Manpreet S. , Gutiérrez Rodrigo A. 
Published: June 2017

AbstractPlants have played a major role in the geochemical and climatic evolution of our planet. Today, in addition to their fundamental ecological importance plants are essential for humans as the main source of food, provide raw materials for many types of industry and chemicals for medical applications. It is thus daunting to realize how little we understand about plant systems. To date, only approximately 15% of the genes ofArabidopsis thaliana, the most explored model system for plant biologists, have been characterized experimentally. Systems biology offers the opportunity to increase our understanding of plants as living organisms, by generating a holistic view of the organism grounded at the molecular level. In this chapter, we discuss the basics of systems biology, the data and tools we need for systems research and how it can be used to produce an integrated view of plant biology. We finish with a discussion of case studies, published examples of plant systems biology research and their impact on our knowledge of plants as integrated systems.
An Overview of Systems Biology
Authors: Albert Réka , Assmann Sarah M. 
Published: June 2017

AbstractThis chapter provides an overview of three crucial aspects of systems biology: constructing biological networks, analyzing and modelling the structure of biological networks and modelling the dynamics of biological networks. We describe the types of intracellular networks most often studied, and the ‘omic’ information available to synthesize these networks, with a special focus on plant biology. We review the computational methods used to construct or infer (reverse engineer) intracellular networks. We present the graph‐theoretical measures most useful for understanding the organization of biological networks, from the single node level to the global properties of the whole network. A representative sample of biological network models is provided, ranging from static models to dynamic models that incorporate how the status of the nodes changes in time. Throughout the chapter we focus on the biological predictions possible by combining experimental, theoretical and computational methods.
Proteomics: Setting the Stage for Systems Biology
Authors: Peck Scott C. 
Published: June 2017

Abstract
Proteomics is a broadly defined discipline. Loosely, the early definition referred to the goal of studying ‘all proteins produced by a genome’. The reality is that this goal has never been achieved because of the complexity of the proteome, and most studies actually deal with sub‐proteomes – for example, proteins from a particular organelle or with a specific modification. This distinction, however, does not detract from the increasing importance of proteomics in systems biology. Rather, the study of sub‐proteomes merely emphasizes the combinatorial complexity that can be achieved by the variety of protein forms produced by the genome. The underlying paradigm is that each form of a protein may be functionally distinct, meaning that a more detailed understanding of how a protein changes in form, location or activity during development or a response is required to understand its role in a biological process. This level of understanding is the current goal of proteomic studies.
From the Ionome to the Genome: Identifying the Gene Networks that Control the Mineral Content Of Plants
Authors: Guerinot Mary Lou , Baxter Ivan , Salt David E. 
Published: June 2017

AbstractHere we describe ionomics, the quantitative and simultaneous measurement of the elemental composition of living organisms, and its application to the study of plant mineral nutrition. We detail the analytical and bioinformatic approaches that allow for high‐throughput screening of the ionome and how they have been applied to the model plantArabidopsis thalianato elucidate genetic and biochemical pathways necessary for proper ion homeostasis. Ionomics should help us understand which genes are responsible for the ability of plants to adapt to environments that vary widely in mineral content and how these genes ultimately control the ionome of the plant.
Development and Systems Biology: Riding the Genomics Wave towards a Systems Understanding of Root Development
Authors: Brady Siobhan M. , Benfey Philip N. 
Published: June 2017

AbstractSystems biology approaches have recently garnered much interest in plant biology, primarily due to the massive increase of data obtained using genomic approaches. One advantage of using these approaches is the elucidation of emergent behaviour, or a complex pattern, which results from the interaction of simple components. The use of systems biology approaches to understand root development at various scales, including transcriptional networks that regulate cell identity, dynamic cellular behaviour that contributes to root growth and physical root architecture will be explored.
Vascular Morphogenesis During Root Development
Authors: Campilho Ana , Lindgren Ove , Helariutta Ykä 
Published: June 2017

Abstract
The root vascular cylinder consists of two conductive tissues, phloem and xylem. The vascular pattern, the way these two tissues are arranged, is often dynamic during ontogeny. In this chapter, we will first describe the current knowledge on how the vascular pattern is established anatomically. Then we review the most recent advances on understanding the gene functions behind the patterning, cell proliferation and differentiation related to the establishment of the vascular tissue types. It seems that during these processes the hormonal and genetic controls are tightly integrated. Finally, we discuss the power of some genome‐wide approaches for further understanding of the integrated view on vascular development.
Adventitious Root Formation: New Insights and Perspectives
Authors: Geiss Gaia , Gutierrez Laurent , Bellini Catherine 
Published: June 2017

AbstractThe root system of a plant consists of the primary, lateral and adventitious roots. Lateral roots always develop from roots whereas adventitious roots form from stem or leaf‐derived cells. Adventitious rooting is an essential step in the vegetative propagation of economically important horticultural and woody species. It allows clonal propagation and rapid fixation of superior genotypes prior to their introduction into production or breeding programs. Problems associated with rooting of cuttings frequently result in significant economic losses. Development of adventitious roots is a complex process that is affected by multiple factors including phytohormones, light, nutritional status, associated stress responses such as wounding, and genetic characteristics. How endogenous and environmental factors interact to control adventitious root formation is still poorly understood, although significant progress has been made in the understanding of the molecular control of root and lateral root development. In this review, we will summarize the current knowledge on the physiological aspects of AR formation and highlight the recent progress made in the identification of putative molecular players involved in the control of adventitious rooting.
Root Gravitropism
Authors: Swarup Ranjan , Bennett Malcolm J. 
Published: June 2017

Abstract

Gravity represents a critical environmental signal for land plants that profoundly influences their growth and development. Plants correct changes in their orientation employing a differential growth response, termed gravitropism. Root gravitropism can be divided into several successive phases:
gravity perception
,
gravitropic signal transmission
,
gravitropic response
and a fourth phase that we term
gravitropic signal attenuation
which serves to prevent further root bending. Gravity perception induces the formation of a lateral auxin gradient. A large number of the auxin‐related components that make up the gravitropic signalling and response machinery have been identified in the model plant
Arabidopsis thaliana
highlighting the central importance of this signal. The past 5 years have also seen several important breakthroughs which have led to the identification of the root cells and tissues that transport, and respond to, the lateral auxin gradient. The review will focus on these recent advances in our understanding about the molecular and cellular mechanisms that regulate root gravitropism.
Molecular and Genetic Dissection of Cereal Root System Development
Authors: Hochholdinger Frank , Zimmermann Roman 
Published: June 2017

Abstract
Monocotyledonous cereal root systems have a complex organization and are composed of primary and seminal roots that are preformed during embryogenesis and roots that emerge postembryonically either from other roots (lateral roots) or from nodal structures of the shoot (shoot‐borne roots). In recent years, a number of specific mutants affected in cereal root system development, mainly in maize, rice and barley, have been identified. These mutants are impaired in root formation during embryogenesis, in primary root elongation, in root hair formation, in shoot‐borne root initiation and in lateral root initiation and elongation. Recently, for some of these mutants the corresponding genes have been cloned and functionally characterized. In addition, these mutants have also been deployed for comparative proteome and transcriptome analyses to dissect the molecular networks involved in cereal root formation.
When Plants Socialize: Symbioses and Root Development
Authors: Péret Benjamin , Svistoonoff Sergio , Laplaze Laurent 
Published: June 2017

AbstractPlant roots encounter a large variety of living organisms in the soil. Some soil microorganisms associate with plant roots to form symbiotic interactions. In this chapter, we describe the establishment of two widespread and important symbiotic associations: mycorrhizae and actinorhizae; and the developmental changes that they induce both at the site of interaction and on the whole root system.
Legume Root Architecture: A Peculiar Root System
Authors: Gonzalez‐Rizzo Silvina , Laporte Philippe , Crespi Martin , Frugier Florian 
Published: June 2017

AbstractThe soil environmental conditions and symbiotic interactions are the major determinants of legume root architecture. Investigating cues that affect root developmental adaptations to the environment as well as understanding the mechanisms underlying the control of the root architecture are crucial to improve agronomical traits, notably in the legume family. Indeed, legumes are one of the most widespread crops, in terms of number and diversity of cultivated species.Legume roots can develop two types of secondary root organs: lateral roots and nitrogen‐fixing nodules. Lateral root formation is common to all higher plants; however, nodules are present only on legume roots as a result of the symbiotic interaction with nitrogen‐fixing soil bacteria, collectively known as rhizobia. The only nonlegume plants described to be able to interact with rhizobia to form nitrogen‐fixing nodules areParasponiaspp.What makes the legume root system so peculiar? The aim of this chapter is to give an overview of the current knowledge of the development of secondary root organs in legumes. A comparative analysis of their structure and ontogeny will be presented, and the specific and common regulatory mechanisms involved will be described.
Glycosyltransferases of theGT8Family
Authors: Yin Yanbin , Mohnen Debra , Gelineo‐Albersheim Ivana , Xu Ying , Hahn Michael G. 
Published: June 2017

AbstractThe higher plant genomes sequenced to date include numerous genes encoding proteins classified as belonging to CAZy family GT8. The large number and diversity of GT8 proteins in higher plants, which currently constitute more than 65% of the identified eukaryotic GT8 genes, highlight the importance of these proteins in plants. Here we summarize a detailed phylogenetic study of GT8 proteins from three monocot and four dicot plant genomes that clearly divides higher plant GT8 proteins into two distantly related sets of clades, many of which are further divided into statistically well‐supported subclades. One set, the GAUT1 (GAlactUronosylTransferase1)‐related family, includes the GAUT andGAUT‐Like (GATL) proteins, comprising one proven galacturonsyltransferase and multiple additional members strongly implicated in the synthesis of pectins and xylan, two major types of polysaccharides present in plant cell walls. The second set, which includesPlantGlycogenin‐likeStarchInitiationProteins(PGSIPs) andGalactinolSynthases(GolSs), appears not to be directly involved in plant cell wall synthesis. The PGSIPs have been suggested to play a role in priming starch biosynthesis, while the GolSs are key enzymes in the synthesis of the raffinose family of oligosaccharides that play important roles in plant responses to environmental stress. This chapter also summarizes data from biochemical, transcriptional, and mutational studies that provide additional insights into possible functions of higher plant GT8 proteins. However, much work is needed to fully define the roles of GT8 proteins in plants, particularly with respect to their enzymatic function in plant cell wall biosynthesis.
Transport Systems forNO3−andNH4+
Authors: Orsel Mathilde , Miller Anthony J. 
Published: June 2017

AbstractArabidopsistransporter families for both nitrate and ammonium have been identified and characterized in some detail. Gene knockout studies have been very useful for identifying the physiological function of specific genes inArabidopsis. In the post‐genomic era, the identification of genes with orthologous transport functions in other plant species is now relatively easy. However, several key areas of nitrogen transport still require a much better understanding in the model plantArabidopsis, and some of these are described in this chapter.
Plant Metabolomics in a Nutshell: Potential and Future Challenges
Authors: Hall Robert D. 
Published: June 2017

Abstract

In just 10 years, plant metabolomics has been transformed from a purely theoretical concept into a highly valued and widely exploited technology. Moving on from the many and wide‐ranging hopes, enthused upon in a multitude of early reviews, metabolomics for plant research has already proved itself despite the technology still experiencing certain limitations. We have a long road to travel before we reach our desired destination – a very happy place where large‐scale, (semi‐)automated, unbiased multiplex analyses of plant materials, leading to exhaustive lists of named metabolites become possible. This biochemical Holy Grail will, by definition, never be reached. Nevertheless, continued advances in hardware, software and biostatistics are enabling us to generate ever‐advancing, detailed insights into the chemical composition of plants and how this is influenced by genetical and environmental perturbation. There continues to be a major driving force behind further developments, spurred on by myriad existing and potentially new applications in both applied and fundamental plant science. It is no longer so much a case of
hope springs eternal
but rather,
who dares wins
!
Sphingolipid α‐Hydroxylase (
Scs7p
)
Authors: Malkowski Michael G 
Published: June 2017

Abstract
Sphingolipid α‐hydroxylase (Scs7p) is a membrane‐bound protein belonging to the hydroxylase/desaturase family of enzymes that utilize a dimetal center to hydroxylate or desaturate lipid‐based substrates. Scs7p specifically hydroxylates the α‐carbon of the very‐long‐chain fatty acid moiety of sphingolipid precursor molecules that are prevalent in the myelin sheath and epidermis, where they play a stabilizing role. The core structure of Scs7p consists of a helical catalytic cap domain that sits atop four transmembrane helices that anchor the enzyme in the endoplasmic reticulum. Ten highly conserved histidine residues are responsible for coordinating the metal atoms within the core of the enzyme. Comparison of Scs7p structure and substrate‐binding model to the structure of stearoyl‐CoA desaturase reveals significant differences in the architecture of the enzymes within the catalytic cap domain. These differences provide insight into the different mechanisms of substrate binding and recognition of substrates by hydroxylase and desaturase enzymes.
Bestimmung des Radikal‐Radikal‐Abstands in lichtaktiven Proteinen im angeregten Zustand und dessen Bedeutung für die biologische Magnetorezeption
Authors: Nohr Daniel , Paulus Bernd , Rodriguez Ryan , Okafuji Asako , Bittl Robert , Schleicher Erik , Weber Stefan 
Published: June 2017

AbstractDurch Licht erzeugte, kurzlebige Radikalpaare sind Reaktionsintermediate in Photolyasen und Cryptochromen. Cryptochrome spielen wahrscheinlich bei der Magnetfeldwahrnehmung durch Zugvögel und beim magnetfeldabhängigen Verhalten von Insekten eine Rolle. Wir haben transiente Zustände im Cryptochrom aus Drosophila melanogaster und im strukturverwandten DNA‐Reparaturenzym DNA‐Photolyase aus Escherichia coli untersucht. Mithilfe eines Puls‐EPR‐Verfahrens konnten die beiden Beiträge zur Spin‐Spin‐Wechselwirkung, die Austauschwechselwirkung und die magnetische Dipol‐Dipol‐Kopplung, direkt bestimmt werden. Anhand dieser Größen wurden in beiden Proteinen die Radikalpaarpartner identifiziert, und es konnten Aussagen über die potenzielle Effizienz des Radikalpaars im Drosophila‐Cryptochrom als Magnetorezeptor getroffen werden. Weiterhin wurden Beweise für eine erweiterte Elektrontransferkaskade in diesem Protein erbracht: Der Tryptophanrest W394 ist ein essentieller Bestandteil für die Photoreduktion des Flavin‐Kofaktors und für die Bildung eines Radikalpaars mit einer für eine Magnetfeldsensibilität ausreichend langen Lebenszeit.
Narrative Therapy with Pre‐schoolers – Unfolding the Story
Authors: Stiefel Ingeborg , Anson Jenny , Hinchcliffe Davida 
Published: June 2017

This paper describes an application of Narrative Therapy to working with pre‐school aged children in the family setting. Techniques have been specifically tailored and adapted to meet the developmental needs of this age group and assist with therapeutic engagement through all phases of therapy. We focus on three components: theme‐development, externalising the problem or helper, and multi‐sensory communication. Two cases are presented, which illustrate the therapeutic work with 4 year old children.