bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular interactions between multihaem cytochromes: probing the protein–protein interactions between pentahaem cytochromes of a nitrite reductase complex
Authors: Lockwood Colin , Butt Julea N. , Clarke Thomas A. , Richardson David J. 
Published: January 2011

The cytochrome c nitrite reductase NrfA is a 53 kDa pentahaem enzyme that crystallizes as a decahaem homodimer. NrfA catalyses the reduction of NO2− to NH4+ through a six electron reduction pathway that is of major physiological significance to the anaerobic metabolism of enteric and sulfate reducing bacteria. NrfA receives electrons from the 21 kDa pentahaem NrfB donor protein. This requires that redox complexes form between the NrfA and NrfB pentahaem cytochromes. The formation of these complexes can be monitored using a range of methodologies for studying protein–protein interactions, including dynamic light scattering, gel filtration, analytical ultracentrifugation and visible spectroscopy. These methods have been used to show that oxidized NrfA exists in dynamic monomer–dimer equilibrium with a Kd (dissociation constant) of 4 μM. Significantly, the monomeric and dimeric forms of NrfA are equally active for either the six electron reduction of NO2− or HSO3−. When mixed together, NrfA and NrfB exist in equilibrium with NrfAB, which is described by a Kd of 50 nM. Thus, since NrfA and NrfB are present in micromolar concentrations in the periplasmic compartment, it is likely that NrfB remains tightly associated with its NrfA redox partner under physiological conditions.
Advances in 15N-tracing experiments: new labelling and data analysis approaches
Authors: Rütting Tobias , Huygens Dries , Staelens Jeroen , Müller Christoph , Boeckx Pascal 
Published: January 2011

To obtain an in-depth understanding of soil nitrogen dynamics, it is necessary to quantify a variety of simultaneously occurring gross nitrogen transformation processes. In order to do so, most studies apply 15N in a disturbed soil–microbial–root system and quantify gross rates based on the principles of 15N isotope dilution. However, this approach has several shortcomings. First, studying disturbed soil provides only limited information on in situ soil nitrogen dynamics. Secondly, the analytical data analysis allows the quantification of total production and consumption rates of the labelled pool, but does not provide information on process-specific transformation rates. Combining in situ15N isotope labelling over 1–2 weeks with numerical data analysis allows determining process-specific gross nitrogen transformations in undisturbed soils under field conditions in the presence of live roots and their associated microbial communities. This has the potential to increase our understanding of nitrogen dynamics in the soil environment.
Urinary glycan markers for disease
Authors: Alonzi Dominic S. , Su Ying-Hsiu , Butters Terry D. 
Published: January 2011

Robust assays for the isolation and characterization of urinary FOS (free oligosaccharides) have been developed to screen patients for altered protein and/or lipid glycosylation. A FOS analysis can therefore identify potential biomarkers for hepatocellular carcinoma, since variations in glycosylation as a result of tumorigenecity should be detectable in the FOS of patients. HCC (hepatocellular carcinoma) accounts for 80–90% of all liver cancers. It occurs more often in men than women and occurs mostly in people 50–60 years old. The disease is more common in parts of Africa and Asia than in North or South America and Europe. Using a combination of solid-phase extraction techniques and affinity chromatography, followed by separation of urinary FOS by NP (normal phase)-HPLC and HIAX (hydrophilic interaction and anion-exchange)-HPLC, more than 200 different species have been identified in patient samples. The high incidence of small sialylated oligosaccharides in HCC patients suggests that pro-inflammatory markers may be detected as early indicators of disease progression. In addition, the methods developed here to isolate and analyse excreted glycoprotein- and glycosphingolipid-bound oligosaccharides have been used to characterize changes in metabolic processes that underlie a number of human genetic disorders. The ability to predict disease status in microlitre amounts of readily available non-invasive urine samples indicates that rapid methods for screening can be developed.
Allostery in the ferredoxin protein motif does not involve a conformational switch
Authors: Nechushtai Rachel , Lammert Heiko , Michaeli Dorit , Eisenberg-Domovich Yael , Zuris John A. , Luca Maria A. , Capraro Dominique T. , Fish Alex , Shimshon Odelia , Roy Melinda , Schug Alexander , Whitford Paul C. , Livnah Oded , Onuchic José N. , Jennings Patricia A. 
Published: January 2011

Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain plant-type ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron–sulfur cluster (∼20
Å
), it leads to a significant change in the redox potential of the iron–sulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron–sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.
Breeding crops for tolerance to salinity, waterlogging and inundation.
Authors: Mullan D. J. , Barrett-Lennard E. G. 
Published: January 2011

Abstract

During the next century, global climate change is likely to cause substantial increases in the severity with which salinity, waterlogging and inundation affect crop production in many of the world's agricultural regions. In this chapter we address the effects of climate change on these three environmental stresses in terms of their threat to sustainable crop production. The effects of salinity, waterlogging and inundation on crop plants are examined, with a focus also directed towards the exacerbating effects of the complex interactions between these stresses. We identify key plant physiological traits as targets for breeding initiatives. Three possible approaches to the development of crops for saline, waterlogged and inundated soils are considered: (i) selection within crop species; (ii) the development of hybrids between adapted wild species and crop plants; and (iii) the domestication of halophytes. Finally, we detail some of the complex research, development and agricultural issues that need to be addressed by a broad research and development community in order to increase crop production during the foreseeable period of global climate change.
Multi-location testing as a tool to identify plant response to global climate change.
Authors: Braun H. J. , Atlin G. , Payne T. 
Published: January 2011

Abstract

Plant breeding, using the combined potential of conventional, molecular and genetically modified technologies, will provide cultivars with greatly enhanced nutrient and water-use efficiency, enhanced tolerance to heat and drought, resistance to diseases and appropriate end-use and nutritional quality, and, possibly most important, increased ability to cope with the increasing extremes in temperature and precipitation occurring at one location over years. Modern crop cultivars developed by seed companies, international crop research centres and national breeding programmes often exhibit very wide geographical adaptation, as well as broad adaptation to the range of environmental and management conditions that occur within and between a target population of environments, or megaenvironments. To identify such cultivars, multi-location testing done by the International Maize and Wheat Improvement Center (CIMMYT) and the International Rice Research Institute (IRRI) remains the most efficient system. International evaluation networks based on exchange of and free access to germplasm and multi-location testing are therefore a cornerstone in the strategies and efforts to develop wheat, rice and maize germplasm that is adapted to the increasingly variable growing conditions encountered due to global climate change. Information from such trials must be combined with information from managed stress trials. Wide performance adaptation is essential to respond to global climate change, to the vagaries of spatial heterogeneity within farmers' fields and their production input management efficacies, and from unpredictable temporal climatic seasonal variability.
Management of resident soil microbial community structure and function to suppress soilborne disease development.
Authors: Mazzola M. 
Published: January 2011

Abstract

Climate change is likely to alter the distribution and severity of soilborne diseases affecting both intensive and low-input agricultural production systems. Naturally occurring disease suppressive soils have been documented in a variety of cropping systems, and in many instances the biological attributes contributing to suppressiveness have been identified. While these studies have often yielded an understanding of operative mechanisms leading to the suppressive state, significant difficulty has been realized in the transfer of this knowledge into the development of effective field-level disease control practices. Early efforts focused on the inundative application of individual or mixtures of microbial strains recovered from these systems, and known to function in specific soil suppressiveness. However, the introduction of biological agents into non-native soil ecosystems typically fails to yield commercially viable or consistent levels of disease control. Of late, greater emphasis has been placed on manipulation of the cropping system to manage resident beneficial rhizosphere microorganisms as a means to suppress soilborne plant pathogens. One such strategy is the cropping of specific plant species or genotypes, or the application of soil amendments with the goal of selectively enhancing disease suppressive microbial communities. This chapter will briefly review the existence of biologically functional disease suppressive soils, document the research history supporting the potential in managing microbial communities for disease control, describe methods available for the effective manipulation of bioactive populations, and describe specific examples demonstrating the effective application of the approach.
Biotechnology in agriculture.
Authors: Whitford R. , Gilbert M. , Langridge P. 
Published: January 2011

Abstract

Climate change is predicted to result in disruption of many farming systems. The Food and Agriculture Organization (FAO) predicts a 15-20% fall in global agricultural production by 2080. Consequently, adaptation of major crop species to climate change will be the biggest challenge for plant breeders this century. Biotechnology will be important when adapting crops to better tolerate changing stresses. It includes using advanced genetic mapping technologies, like molecular markers, in the breeding and development of new varieties. Molecular markers are used to provide greater focus, accuracy and speed in crop breeding programmes with further advances coming. Genetic modification (GM) techniques are providing access to a diversity of genes, used to develop plant varieties more tolerant to the negative impacts of climate change.
GIS and crop simulation modelling applications in climate change research.
Authors: Hodson D. , White J. 
Published: January 2011

Abstract

The challenges that climate change presents to humanity require an unprecedented ability to predict the responses of crops to environment and management. Geographic information systems (GIS) and crop simulation models are two powerful and highly complementary tools that are increasingly used for such predictive analyses. The role of both technologies in predicting future situations centres around extrapolation. For GIS, extrapolation from the past based on correlation in a very loose sense plays an important role. For crop models, extrapolation based on how known processes respond to factors of interest (i.e. simulation) is a key factor. GIS and crop models can be integrated, providing predictions that combine the spatial perspective of GIS with the stronger representation of temporal processes of simulation models. This chapter reviews the use of these two tools for predicting impacts of climate change and examining options for adaptation. Increasingly, downscaled outputs from a range of global general circulation models under differing future scenarios are used as key inputs for both tools. Examples are given for major food crops and key agricultural zones, with a bias towards tropical and subtropical regions. Consideration is also given to factors limiting efficient application of the tools to climate change research. Both technologies will see increasing use in climate change research and in applications of research in decision making. Credible studies of crop responses to climate involve dealing with large sets of data and potentially millions of simulations, especially if adaptation is considered. While the computational challenges are daunting, the greater challenge is how to devise efficient protocols for selecting the most meaningful scenarios, interpreting the results and summarizing outputs for decision makers.
Co-publication with Journal of Physics: Conference Series
Authors: Takahashi M , Saito H 
Published: January 2011

Invited papers from ISAMMA 2010 (Sendai, Japan, 12–16 July 2010)
A selection of papers, invited by the conference organisers and peer reviewed by the journal, are published here in a special issue of Journal of Physics D: Applied Physics.
The bulk of the papers presented at the conference, after peer review, are published separately in

Journal of Physics: Conference Series.
Polymer materials with spatially graded morphologies: preparation, characterization and utilization
Authors: Fujiki Daisuke , Jing Chuanming , Van-Pham Dan-Thuy , Nakanishi Hideyuki , Norisuye Tomohisa , Tran-Cong-Miyata Qui 
Published: January 2011

Abstract
Experimental studies on polymer materials with spatially graded structures are reviewed in this paper. A wide variety of principles and experimental methods utilized to prepare and control these specific structures of polymer materials are summarized and discussed. In particular, the method of using light to generate and control these gradient morphologies in the micrometer scales is summarized with great detail for binary polymer mixtures. Finally, recent studies on copolymers with various gradient compositions at nanometer length scales are also summarized in this review.
On adapted coordinate systems
Authors: Ikromov Isroil , Müller Detlef 
Published: January 2011

The notion of an adapted coordinate system for a given real-analytic function, introduced by V. I. Arnol’d, plays an important role, for instance, in the study of asymptotic expansions of oscillatory integrals. In two dimensions, A. N. Varchenko gave sufficient conditions for the adaptness of a given coordinate system and proved the existence of an adapted coordinate system for analytic functions without multiple components. Varchenko’s proof is based on a two-dimensional resolution of singularities result.

In this article, we present a more elementary approach to these results, which is based on the Puiseux series expansion of roots of the given function. This approach is inspired by the work of D. H. Phong and E. M. Stein on the Newton polyhedron and oscillatory integral operators. It applies to arbitrary real-analytic functions, and even to arbitrary smooth functions of finite type. In particular, we show that Varchenko’s conditions are in fact necessary and sufficient for the adaptedness of a given coordinate system and that adapted coordinates always exist in two dimensions, even in the smooth, finite type setting. For analytic functions, a construction of adapted coordinates by means of Puiseux series expansions of roots has already been carried out in work by D. H. Phong, E. M. Stein and J. A. Sturm on the growth and stability of real-analytic function, as we learned after the completion of this paper. In contrast to their work, however, our proof more closely follows Varchenko’s algorithm for the construction of an adapted coordinate system, which turns out to be useful for the extension to the smooth setting.
Identity-by-descent filtering of exome sequence data for disease–gene identification in autosomal recessive disorders
Authors: Rödelsperger Christian , Krawitz Peter , Bauer Sebastian , Hecht Jochen , Bigham Abigail W. , Bamshad Michael , de Condor Birgit Jonske , Schweiger Michal R. , Robinson Peter N. 
Published: January 2011

Abstract
Motivation: Next-generation sequencing and exome-capture technologies are currently revolutionizing the way geneticists screen for disease-causing mutations in rare Mendelian disorders. However, the identification of causal mutations is challenging due to the sheer number of variants that are identified in individual exomes. Although databases such as dbSNP or HapMap can be used to reduce the plethora of candidate genes by filtering out common variants, the remaining set of genes still remains on the order of dozens.
Results: Our algorithm uses a non-homogeneous hidden Markov model that employs local recombination rates to identify chromosomal regions that are identical by descent (IBD = 2) in children of consanguineous or non-consanguineous parents solely based on genotype data of siblings derived from high-throughput sequencing platforms. Using simulated and real exome sequence data, we show that our algorithm is able to reduce the search space for the causative disease gene to a fifth or a tenth of the entire exome.
Availability: An R script and an accompanying tutorial are available at http://compbio.charite.de/index.php/ibd2.html.
Contact: peter.robinson@charite.de
Quality control and preprocessing of metagenomic datasets
Authors: Schmieder Robert , Edwards Robert 
Published: January 2011

Abstract
Summary: Here, we present PRINSEQ for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets. Summary statistics of FASTA (and QUAL) or FASTQ files are generated in tabular and graphical form and sequences can be filtered, reformatted and trimmed by a variety of options to improve downstream analysis.
Availability and Implementation: This open-source application was implemented in Perl and can be used as a stand alone version or accessed online through a user-friendly web interface. The source code, user help and additional information are available at http://prinseq.sourceforge.net/.
Contact: rschmied@sciences.sdsu.edu; redwards@cs.sdsu.edu
Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis
Authors: Ren Maozhi , Qiu Shuqing , Venglat Prakash , Xiang Daoquan , Feng Li , Selvaraj Gopalan , Datla Raju 
Published: January 2011

Abstract
Target of rapamycin (TOR) is a central regulator of cell growth, cell death, nutrition, starvation, hormone, and stress responses in diverse eukaryotes. However, very little is known about TOR signaling and the associated functional domains in plants. We have taken a genetic approach to dissect TOR functions in Arabidopsis (Arabidopsis thaliana) and report here that the kinase domain is essential for the role of TOR in embryogenesis and 45S rRNA expression. Twelve new T-DNA insertion mutants, spanning 14.2 kb of TOR-encoding genomic region, have been characterized. Nine of these share expression of defective kinase domain and embryo arrest at 16 to 32 cell stage. However, three T-DNA insertion lines affecting FATC domain displayed normal embryo development, indicating that FATC domain was dispensable in Arabidopsis. Genetic complementation showed that the TOR kinase domain alone in tor-10/tor-10 mutant background can rescue early embryo lethality and restore normal development. Overexpression of full-length TOR or kinase domain in Arabidopsis displayed developmental abnormalities in meristem, leaf, root, stem, flowering time, and senescence. We further show that TOR, especially the kinase domain, plays a role in ribosome biogenesis by activating 45S rRNA production. Of the six putative nuclear localization sequences in the kinase domain, nuclear localization sequence 6 was identified to confer TOR nuclear targeting in transient expression assays. Chromatin immunoprecipitation studies revealed that the HEAT repeat domain binds to 45S rRNA promoter and the 5′ external transcribed spacer elements motif. Together, these results show that TOR controls the embryogenesis, postembryonic development, and 45S rRNA production through its kinase domain in Arabidopsis.
Excision and Episomal Replication of Cauliflower mosaic virus Integrated into a Plant Genome
Authors: Squires Julie , Gillespie Trudi , Schoelz James E. , Palukaitis Peter 
Published: January 2011

Abstract
Transgenic Arabidopsis (Arabidopsis thaliana) plants containing a monomeric copy of the cauliflower mosaic virus (CaMV) genome exhibited the generation of infectious, episomally replicating virus. The circular viral genome had been split within the nonessential gene II for integration into the Arabidopsis genome by Agrobacterium tumefaciens-mediated transformation. Transgenic plants were assessed for episomal infections at flowering, seed set, and/or senescence. The infections were confirmed by western blot for the CaMV P6 and P4 proteins, electron microscopy for the presence of icosahedral virions, and through polymerase chain reaction across the recombination junction. By the end of the test period, a majority of the transgenic Arabidopsis plants had developed episomal infections. The episomal form of the virus was infectious to nontransgenic plants, indicating that no essential functions were lost after release from the Arabidopsis chromosome. An analysis of the viral genomes recovered from either transgenic Arabidopsis or nontransgenic turnip (Brassica rapa var rapa) revealed that the viruses contained deletions within gene II, and in some cases, the deletions extended to the beginning of gene III. In addition, many of the progeny viruses contained small regions of nonviral sequence derived from the flanking transformation vector. The nature of the nucleotide sequences at the recombination junctions in the circular progeny virus indicated that most were generated by nonhomologous recombination during the excision event. The release of the CaMV viral genomes from an integrated copy was not dependent upon the application of environmental stresses but occurred with greater frequency with either age or the late stages of plant maturation.