Showing papers by "Academy of Sciences of the Czech Republic published in 2008"
••
University of Bergen1, Charles University in Prague2, Academy of Sciences of the Czech Republic3, University of Nottingham4, Boise State University5, Goethe University Frankfurt6, Memorial University of Newfoundland7, Stockholm University8, University of Vienna9, University of Geneva10, Swedish Museum of Natural History11
TL;DR: The Plesovice zircon as discussed by the authors has a concordant U-Pb age with a weighted mean Pb-206/U-238 date of 337.13 +/- 0.37 Ma (ID-TIMS, 95% confidence limits, including tracer calibration uncertainty).
3,694 citations
••
Stephen Richards1, Richard A. Gibbs1, George M. Weinstock1, Susan J. Brown2 +187 more•Institutions (47)
TL;DR: Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products.
Abstract: Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
1,248 citations
••
TL;DR: The Large Ion Collider Experiment (ALICE) as discussed by the authors is a general-purpose, heavy-ion detector at the CERN LHC which focuses on QCD, the strong-interaction sector of the Standard Model.
Abstract: ALICE (A Large Ion Collider Experiment) is a general-purpose, heavy-ion detector at the CERN LHC which focuses on QCD, the strong-interaction sector of the Standard Model. It is designed to address the physics of strongly interacting matter and the quark-gluon plasma at extreme values of energy density and temperature in nucleus-nucleus collisions. Besides running with Pb ions, the physics programme includes collisions with lighter ions, lower energy running and dedicated proton-nucleus runs. ALICE will also take data with proton beams at the top LHC energy to collect reference data for the heavy-ion programme and to address several QCD topics for which ALICE is complementary to the other LHC detectors. The ALICE detector has been built by a collaboration including currently over 1000 physicists and engineers from 105 Institutes in 30 countries. Its overall dimensions are 161626 m3 with a total weight of approximately 10 000 t. The experiment consists of 18 different detector systems each with its own specific technology choice and design constraints, driven both by the physics requirements and the experimental conditions expected at LHC. The most stringent design constraint is to cope with the extreme particle multiplicity anticipated in central Pb-Pb collisions. The different subsystems were optimized to provide high-momentum resolution as well as excellent Particle Identification (PID) over a broad range in momentum, up to the highest multiplicities predicted for LHC. This will allow for comprehensive studies of hadrons, electrons, muons, and photons produced in the collision of heavy nuclei. Most detector systems are scheduled to be installed and ready for data taking by mid-2008 when the LHC is scheduled to start operation, with the exception of parts of the Photon Spectrometer (PHOS), Transition Radiation Detector (TRD) and Electro Magnetic Calorimeter (EMCal). These detectors will be completed for the high-luminosity ion run expected in 2010. This paper describes in detail the detector components as installed for the first data taking in the summer of 2008.
1,218 citations
••
TL;DR: Experimental studies with the real-time iontophoresis method employing the cation tetramethylammonium in normal brain tissue improve the conception of ECS structure and the roles of glia and extracellular matrix in modulating the ECS microenvironment.
Abstract: Diffusion in the extracellular space (ECS) of the brain is constrained by the volume fraction and the tortuosity and a modified diffusion equation represents the transport behavior of many molecule...
1,215 citations
••
01 Jan 2008TL;DR: In the current human-mediated biodiversity crisis, where alien species play an important role, we need to know whether some species are inherently better equipped to become invasive when moved to new areas by humans as mentioned in this paper.
Abstract: Any organism must be equipped for life in a given environment, otherwise it will die. The fundamental question is how well does an organism need to be “equipped”, or what syndrome of traits must it possess to survive and flourish at a given locality. In the current human-mediated biodiversity crisis, where alien species play an important role, we need to know whether some species are inherently better equipped to become invasive when moved to new areas by humans. If so, we can identify such species and consider management options to prevent, or at least reduce the damaging effects of biological invasions. Despite the importance of chance and timing in the establishment and spread of alien plants (Crawley 1989), invasions are clearly not entirely random events (Crawley et al. 1996). Much of the early work on invasions was directed at collating traits associated with invasiveness (Booth et al. 2003). The question of whether is it possible to determine a set of traits that predispose a species to be invasive has been a central theme since the emergence of invasion ecology as a discrete field of study (Richardson and Pysek 2006). Many studies have attempted to profile successful invaders, starting with Herbert Baker’s attempt to identify the traits of an “ideal weed” (Baker 1965), an idea now considered simplistic (Perrins et al. 1993). Baker defined as a weed a plant growing “entirely or predominantly in situations markedly disturbed by man (without, of course, being deliberately cultivated plants)”. To him, weeds included plants that encroached onto agricultural land (agrestals), and those occurring in waste places (ruderals; Baker 1965). There was no explicit reference to the status of the species as being native or alien. Perhaps it was the two species pairs he used to document different traits of “weedy”
960 citations
••
Canterbury of New Zealand1, University of Bern2, CABI3, Helmholtz Centre for Environmental Research - UFZ4, Saint Petersburg State University5, Academy of Sciences of the Czech Republic6, Charles University in Prague7, Institut national de la recherche agronomique8, Autonomous University of Barcelona9, Polish Academy of Sciences10, Spanish National Research Council11
TL;DR: A framework is proposed to facilitate the comparative analysis of invasion pathways by a wide range of taxa in both terrestrial and aquatic ecosystems and helps identify existing gaps in current knowledge of pathways and highlight the limitations of existing legislation to manage introductions of alien species.
Abstract: Summary 1. Pathways describe the processes that result in the introduction of alien species from one location to another. A framework is proposed to facilitate the comparative analysis of invasion pathways by a wide range of taxa in both terrestrial and aquatic ecosystems. Comparisons with a range of data helped identify existing gaps in current knowledge of pathways and highlight the limitations of existing legislation to manage introductions of alien species. The scheme aims for universality but uses the European Union as a case study for the regulatory perspectives. 2. Alien species may arrive and enter a new region through three broad mechanisms: importation of a commodity, arrival of a transport vector, and/or natural spread from a neighbouring region where the species is itself alien. These three mechanisms result in six principal pathways: release, escape, contaminant, stowaway, corridor and unaided. 3. Alien species transported as commodities may be introduced as a deliberate release or as an escape from captivity. Many species are not intentionally transported but arrive as a contaminant of a commodity, for example pathogens and pests. Stowaways are directly associated with human transport but arrive independently of a specific commodity, for example organisms transported in ballast water, cargo and airfreight. The corridor pathway highlights the role transport infrastructures play in the introduction of alien species. The unaided pathway describes situations where natural spread results in alien species arriving into a new region from a donor region where it is also alien. 4. Vertebrate pathways tend to be characterized as deliberate releases, invertebrates as contaminants and plants as escapes. Pathogenic micro-organisms and fungi are generally introduced as contaminants of their hosts. The corridor and unaided pathways are often ignored in pathway assessments but warrant further detailed consideration. 5. Synthesis and applications. Intentional releases and escapes should be straightforward to monitor and regulate but, in practice, developing legislation has proved difficult. New introductions continue to occur through contaminant, stowaway, corridor and unaided pathways. These pathways represent special challenges for management and legislation. The present framework should enable these trends to be monitored more clearly and hopefully lead to the development of appropriate regulations or codes of practice to stem the number of future introductions.
867 citations
••
TL;DR: In this article, the silicon pixel tracking system for the ATLAS experiment at the Large Hadron Collider is described and the performance requirements are summarized and detailed descriptions of the pixel detector electronics and the silicon sensors are given.
Abstract: The silicon pixel tracking system for the ATLAS experiment at the Large Hadron Collider is described and the performance requirements are summarized. Detailed descriptions of the pixel detector electronics and the silicon sensors are given. The design, fabrication, assembly and performance of the pixel detector modules are presented. Data obtained from test beams as well as studies using cosmic rays are also discussed.
709 citations
••
TL;DR: An analysis of 2,670 papers dealing with 892 invasive species showed that all major groups of invaders are well studied, but that most information on the mechanisms of invasion has emerged from work on a limited number of the most harmful invaders.
Abstract: Invasive alien species come from most taxonomic groups, and invasion biology is searching for robust cross-taxon generalizations and principles. An analysis of 2670 papers dealing with 892 invasive species showed that all major groups of invaders are well studied, but that most information on the mechanisms of invasion has emerged from work on a limited number of the most harmful invaders. A strong geographical bias, with Africa and Asia understudied, inhibits a balanced understanding of invasion, because we might be lacking knowledge of specific invasion mechanisms from poorly studied, regionally specific habitats. International cooperation is required to achieve a more geographically balanced picture of biological invasions. Invasive species with the greatest impact are best studied, but more studies of species that are naturalized but not (yet) invasive are needed to improve understanding of the mechanisms acting during the naturalization phase of invasions and leading to successful invasion.
669 citations
••
TL;DR: The energy spectrum of cosmic rays above 2.5 x 10;{18} eV, derived from 20,000 events recorded at the Pierre Auger Observatory, is described and the hypothesis of a single power law is rejected with a significance greater than 6 standard deviations.
Abstract: The energy spectrum of cosmic rays above 2.5 x 10;{18} eV, derived from 20,000 events recorded at the Pierre Auger Observatory, is described. The spectral index gamma of the particle flux, J proportional, variantE;{-gamma}, at energies between 4 x 10;{18} eV and 4 x 10;{19} eV is 2.69+/-0.02(stat)+/-0.06(syst), steepening to 4.2+/-0.4(stat)+/-0.06(syst) at higher energies. The hypothesis of a single power law is rejected with a significance greater than 6 standard deviations. The data are consistent with the prediction by Greisen and by Zatsepin and Kuz'min.
648 citations
••
TL;DR: The citation history of Elton’s book is examined using the Web of Science to find the shift in the distribution of topics/concepts cited with reference to Elton over time follows the same trend as for biogeography and ecology in general.
Abstract: The publication, in 1958, of Charles Elton’s book The ecology of invasions by animals and plants launched the systematic study of biological invasions. Invasion ecology has grown to become an important multi-disciplinary subfield of ecology with growing links to many other disciplines. This paper examines the citation history of Elton’s book using the Web of Science. We also examine Elton’s influence in shaping the current research agenda in invasion ecology, for which we use the 28 papers in a special issue of Diversity and Distributions (Volume 14: 2) as a representative sample. After 50 years, Elton’s book remains the most cited single source in the field (> 1500 citations), and is cited more often every year (> 100 times) than any other invasion-related publication, including influential papers in journals. Most citations to Elton’s book refer to particular topics/concepts covered in the book, rather than citing it as a general reference about invasions. The shift in the distribution of topics/concepts cited with reference to Elton over time follows the same trend as for biogeography and ecology in general (increasing emphasis on analytical studies, multi-scale analyses, multi-disciplinary studies, etc.).
628 citations
••
Cancer Research UK1, University of Edinburgh2, Imperial College Healthcare3, University of Birmingham4, Imperial College London5, University of London6, University of Leeds7, Princess Anne Hospital8, University of Oxford9, University of Kiel10, University of Greifswald11, University of Cambridge12, Leiden University13, University of Melbourne14, Cancer Council Victoria15, University of Barcelona16, University of Santiago de Compostela17, German Cancer Research Center18, Karolinska Institutet19, Academy of Sciences of the Czech Republic20, University of Hong Kong21, University of Extremadura22, Complutense University of Madrid23, University of Helsinki24
TL;DR: Genetic data provide further evidence for the 'common-disease common-variant' model of CRC predisposition and identify two previously unreported associations.
Abstract: To identify colorectal cancer (CRC) susceptibility alleles, we conducted a genome-wide association study. In phase 1, we genotyped 550,163 tagSNPs in 940 familial colorectal tumor cases (627 CRC, 313 high-risk adenoma) and 965 controls. In phase 2, we genotyped 42,708 selected SNPs in 2,873 CRC cases and 2,871 controls. In phase 3, we evaluated 11 SNPs showing association at P < 10(-4) in a joint analysis of phases 1 and 2 in 4,287 CRC cases and 3,743 controls. Two SNPs were taken forward to phase 4 genotyping (10,731 CRC cases and 10,961 controls from eight centers). In addition to the previously reported 8q24, 15q13 and 18q21 CRC risk loci, we identified two previously unreported associations: rs10795668, located at 10p14 (P = 2.5 x 10(-13) overall; P = 6.9 x 10(-12) replication), and rs16892766, at 8q23.3 (P = 3.3 x 10(-18) overall; P = 9.6 x 10(-17) replication), which tags a plausible causative gene, EIF3H. These data provide further evidence for the 'common-disease common-variant' model of CRC predisposition.
••
TL;DR: The possible functions of cathepsin D and its various forms in cells and organisms during physiological and pathological conditions are reviewed.
Abstract: For years, it has been held that cathepsin D (CD) is involved in rather non-specific protein degradation in a strongly acidic milieu of lysosomes. Studies with CD knock-out mice revealed that CD is not necessary for embryonal development, but it is indispensable for postnatal tissue homeostasis. Mutation that abolishes CD enzymatic activity causes neuronal ceroid lipofuscinosis (NCL) characterized by severe neurodegeneration, developmental regression, visual loss and epilepsy in both animals and humans. In the last decade, however, an increasing number of studies demonstrated that enzymatic function of CD is not restricted solely to acidic milieu of lysosomes with important consequences in regulation of apoptosis. In addition to CD enzymatic activity, it has been shown that apoptosis is also regulated by catalytically inactive mutants of CD which suggests that CD interacts with other important molecules and influences cell signaling. Moreover, procathepsin D (pCD), secreted from cancer cells, acts as a mitogen on both cancer and stromal cells and stimulates their pro-invasive and pro-metastatic properties. Numerous studies found that pCD/CD level represents an independent prognostic factor in a variety of cancers and is therefore considered to be a potential target of anti-cancer therapy. Studies dealing with functions of cathepsin D are complicated by the fact that there are several simultaneous forms of CD in a cell—pCD, intermediate enzymatically active CD and mature heavy and light chain CD. It became evident that these forms may differently regulate the above-mentioned processes. In this article, we review the possible functions of CD and its various forms in cells and organisms during physiological and pathological conditions.
••
Scripps Institution of Oceanography1, University of Barcelona2, Hokkaido University3, United States Department of Energy4, California Institute of Technology5, École normale supérieure de Lyon6, University of Oxford7, University of Genoa8, Johns Hopkins University9, University of South Florida10, University of St Andrews11, Washington University in St. Louis12, University of Milan13, Discovery Institute14, Uppsala University15, Tokyo Metropolitan University16, Tokai University17, University of California, Berkeley18, Okinawa Institute of Science and Technology19, University of Tokyo20, Academy of Sciences of the Czech Republic21, IBM22, Max Planck Society23, University of Maryland, College Park24, University of Toronto25, University of Lausanne26, University of Victoria27, University of Tsukuba28, Kyoto University29, Osaka University30, Nagahama Institute of Bio-Science and Technology31, Sun Yat-sen University32, Juntendo University33, Children's Hospital Oakland Research Institute34
TL;DR: The results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.
Abstract: Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates--a very wide phylogenetic distance In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates
••
TL;DR: A molecular mechanism for the oxidation of aniline is proposed in this paper, which explains the specific features of polyaniline oligomerization and polymerization in various acidity ranges.
Abstract: Polyaniline is one of the most important conducting and responsive polymers. A molecular mechanism for the oxidation of aniline is proposed. This mechanism explains the specific features of aniline oligomerization and polymerization in various acidity ranges. The formation of polyaniline precipitates, colloids and thin films is reviewed and discussed on the basis of the chemistry of aniline oxidation. The generation of nanostructures, i.e. granules, nanotubes, nanowires and microspheres, is also considered. Oligomers containing phenazine constitutional units play an important role in self-assembly to form templates. Polyaniline chains then grow from these templates and produce the various individual morphologies. Copyright © 2008 Society of Chemical Industry
••
TL;DR: In this paper, a database of 52 480 vegetation plots from three regions of Europe: Catalonia (Mediterranean-submediterranean region), Czech Republic (subcontinental) and Great Britain (oceanic) was used to classify plant species into neophytes, archaeophytes and natives, and calculated the proportion of each group in 33 habitats described by the EUNIS classification.
Abstract: Summary 1. Although invasions by alien plants are major threats to the biodiversity of natural habitats, individual habitats vary considerably in their susceptibility to invasion. Therefore the risk assessment procedures, which are used increasingly by environmental managers to inform effective planning of invasive plant control, require reliable quantitative information on the extent to which different habitats are susceptible to invasion. It is also important to know whether the levels of invasion in different habitats are locally specific or consistent among regions with contrasting climate, flora and history of human impact. 2. We compiled a database of 52 480 vegetation plots from three regions of Europe: Catalonia (Mediterranean‐submediterranean region), Czech Republic (subcontinental) and Great Britain (oceanic). We classified plant species into neophytes, archaeophytes and natives, and calculated the proportion of each group in 33 habitats described by the European Nature Information System (EUNIS) classification. 3. Of 545 alien species found in the plots, only eight occurred in all three regions. Despite this large difference in species composition, patterns of habitat invasions were highly consistent between regions. None or few aliens were found in environmentally extreme and nutrient-poor habitats, e.g. mires, heathlands and high-mountain grasslands. Many aliens were found in frequently disturbed habitats with fluctuating nutrient availability, e.g. in man-made habitats. Neophytes were also often found in coastal, littoral and riverine habitats. 4. Neophytes were found commonly in habitats also occupied by archaeophytes. Thus, the number of archaeophytes can be considered as a good predictor of the neophyte invasion risk. However, neophytes had stronger affinity to wet habitats and disturbed woody vegetation while archaeophytes tended to be more common in dry to mesic open habitats. 5. Synthesis and applications. The considerable inter-regional consistency of the habitat invasion patterns suggests that habitats can be used as a good predictor for the invasion risk assessment. This finding opens promising perspectives for the use of spatially explicit information on habitats, including scenarios of future land-use change, to identify the areas of highest risk of invasion.
••
Colorado State University1, University of Georgia2, Landcare Research3, Canadian Forest Service4, Agriculture and Agri-Food Canada5, Queen Mary University of London6, Macquarie University7, Academy of Sciences of the Czech Republic8, University of Jena9, University of Giessen10, Kenya Methodist University11, Forestry Tasmania12, Institut de recherche pour le développement13, University of Lethbridge14, Cardiff University15, Universiti Malaysia Sabah16, International Center for Tropical Agriculture17, Pontifical Xavierian University18, University of Puerto Rico19, Xishuangbanna Tropical Botanical Garden20
TL;DR: Inclusion of soil animals will improve the predictive capabilities of region- or biome-scale decomposition models, soil animal influences on decomposition are important at the regional scale when attempting to predict global change scenarios, and the statistical relationship between decomposition rates and climate, at the global scale, is robust against changes in soil faunal abundance and diversity.
Abstract: Climate and litter quality are primary drivers of terrestrial decomposition and, based on evidence from multisite experiments at regional and global scales, are universally factored into global decomposition models. In contrast, soil animals are considered key regulators of decomposition at local scales but their role at larger scales is unresolved. Soil animals are consequently excluded from global models of organic mineralization processes. Incomplete assessment of the roles of soil animals stems from the difficulties of manipulating invertebrate animals experimentally across large geographic gradients. This is compounded by deficient or inconsistent taxonomy. We report a global decomposition experiment to assess the importance of soil animals in C mineralization, in which a common grass litter substrate was exposed to natural decomposition in either control or reduced animal treatments across 30 sites distributed from 43°S to 68°N on six continents. Animals in the mesofaunal size range were recovered from the litter by Tullgren extraction and identified to common specifications, mostly at the ordinal level. The design of the trials enabled faunal contribution to be evaluated against abiotic parameters between sites. Soil animals increase decomposition rates in temperate and wet tropical climates, but have neutral effects where temperature or moisture constrain biological activity. Our findings highlight that faunal influences on decomposition are dependent on prevailing climatic conditions. We conclude that (1) inclusion of soil animals will improve the predictive capabilities of region- or biome-scale decomposition models, (2) soil animal influences on decomposition are important at the regional scale when attempting to predict global change scenarios, and (3) the statistical relationship between decomposition rates and climate, at the global scale, is robust against changes in soil faunal abundance and diversity.
••
TL;DR: In this paper, the Pierre Auger Observatory data was used to confirm the anisotropy of the arrival direction of the highest-energy cosmic rays with the highest energy, which are correlated with the positions of relatively nearby active galactic nuclei (AGN) at a confidence level of more than 99%.
••
TL;DR: One of the most important findings in this study is that, according to symmetry adapted perturbation theory (SAPT) analyses, halogen bonds are largely dependent on both electrostatic and dispersion type interactions.
Abstract: In recent years it has been recognized that, because of their unique properties, halogen bonds have tremendous potential in the development of new pharmaceutical compounds and materials. In this study we investigate the phenomenon of halogen bonding by carrying out ab initio calculations on the halomethane-formaldehyde complexes as well as the fluorine substituted FnH3-nCX···OCH2 dimers, where the halogen bonding halogens (X) are chlorine, bromine, and iodine. Coupled cluster (CCSD(T)/aug-cc-pVTZ) calculations indicate that the binding energies for these type of interactions lie in the range between −1.05 kcal/mol (H3CCl···OCH2) and −3.72 kcal/mol (F3CI···OCH2). One of the most important findings in this study is that, according to symmetry adapted perturbation theory (SAPT) analyses, halogen bonds are largely dependent on both electrostatic and dispersion type interactions. As the halogen atom involved in halogen bonding becomes larger the interaction strength for this type of interaction also gets large...
••
TL;DR: A newly cultured organism that has ultrastructural features typical for alveolates, is phylogenetically related to apicomplexans, and contains a photosynthetic plastid that shares an origin with the apicoplasts is described.
Abstract: Many parasitic Apicomplexa, such as Plasmodium falciparum, contain an unpigmented chloroplast remnant termed the apicoplast, which is a target for malaria treatment. However, no close relative of apicomplexans with a functional photosynthetic plastid has yet been described. Here we describe a newly cultured organism that has ultrastructural features typical for alveolates, is phylogenetically related to apicomplexans, and contains a photosynthetic plastid. The plastid is surrounded by four membranes, is pigmented by chlorophyll a, and uses the codon UGA to encode tryptophan in the psbA gene. This genetic feature has been found only in coccidian apicoplasts and various mitochondria. The UGA-Trp codon and phylogenies of plastid and nuclear ribosomal RNA genes indicate that the organism is the closest known photosynthetic relative to apicomplexan parasites and that its plastid shares an origin with the apicoplasts. The discovery of this organism provides a powerful model with which to study the evolution of parasitism in Apicomplexa.
••
TL;DR: A bacterial artificial chromosome (BAC)–based integrated physical map of the largest chromosome, 3B, that alone is 995 megabases is constructed, establishing a template for the remaining wheat chromosomes and demonstrating the feasibility of constructing physical maps in large, complex, polyploid genomes with a chromosome-based approach.
Abstract: As the staple food for 35% of the world's population, wheat is one of the most important crop species. To date, sequence-based tools to accelerate wheat improvement are lacking. As part of the international effort to sequence the 17-billion-base-pair hexaploid bread wheat genome (2n = 6x = 42 chromosomes), we constructed a bacterial artificial chromosome (BAC)-based integrated physical map of the largest chromosome, 3B, that alone is 995 megabases. A chromosome-specific BAC library was used to assemble 82% of the chromosome into 1036 contigs that were anchored with 1443 molecular markers, providing a major resource for genetic and genomic studies. This physical map establishes a template for the remaining wheat chromosomes and demonstrates the feasibility of constructing physical maps in large, complex, polyploid genomes with a chromosome-based approach.
••
TL;DR: A zwitterionic poly(carboxybetaine acrylamide) (polyCBAA) biomimetic material was employed to create a unique biorecognition coating with an ultralow fouling background, enabling the sensitive and specific detection of proteins in blood plasma.
Abstract: A crucial step in the development of implanted medical devices, in vivo diagnostics, and microarrays is the effective prevention of nonspecific protein adsorption from real-world complex media such as blood plasma or serum. In this work, a zwitterionic poly(carboxybetaine acrylamide) (polyCBAA) biomimetic material was employed to create a unique biorecognition coating with an ultralow fouling background, enabling the sensitive and specific detection of proteins in blood plasma. Conditions for surface activation, protein immobilization, and surface deactivation of the carboxylate groups in the polyCBAA coating were determined. An antibody-functionalized polyCBAA surface platform was used to detect a target protein in blood plasma using a sensitive surface plasmon resonance (SPR) sensor. A selective protein was directly detected from 100% human blood plasma with extraordinary specificity and sensitivity. The total nonspecific protein adsorption on the functionalized polyCBAA surface was very low (<3 ng/cm2 ...
••
TL;DR: These habitats experience recurrent disturbances and are rich, at least temporarily, in available nutrients, which supports the hypothesis that fluctuating resources are the major cause of habitat invasibility.
Abstract: Habitats vary considerably in the level of invasion (number or proportion of alien plant species they contain), which depends on local habitat properties, propagule pressure, and climate. To determine the invasibility (susceptibility to invasions) of different habitats, it is necessary to factor out the effects of any confounding variables such as propagule pressure and climate on the level of invasion. We used 20 468 vegetation plots from 32 habitats in the Czech Republic to compare the invasibility of different habitats. Using regression trees, the proportion of alien plants, including archaeophytes (prehistoric to medieval invaders) and neophytes (recent invaders), was related to variables representing habitat properties, propagule pressure, and climate. The propagule pressure was expressed as the proportion of surrounding urban and industrial or agricultural land, human population density, distance from a river, and history of human colonization in the region. Urban and industrial land use had a positive effect on the proportion of both archaeophytes and neophytes. Agricultural land use, higher population density, and longer history of human impact positively affected the proportion of archaeophytes. Disturbed human-made habitats with herbaceous vegetation were most invaded by both groups of aliens. Neophytes were also relatively common in disturbed woody vegetation, such as broad-leaved plantations, forest clearings, and riverine scrub. These habitats also had the highest proportion of aliens after removing the effect of propagule pressure and climate, indicating that they are not only the most invaded, but also most invasible. These habitats experience recurrent disturbances and are rich, at least temporarily, in available nutrients, which supports the hypothesis that fluctuating resources are the major cause of habitat invasibility. The least invaded habitats were mires and alpine-subalpine grasslands and scrub. After removing the effect of propagule pressure and climate, some habitats actually invaded at an intermediate level had very low proportions of aliens. This indicates that these habitats (e.g., dry, wet, and saline grasslands, base-rich fens, and broad-leaved deciduous woodlands) are resistant to invasion.
••
TL;DR: The combinations of optical micro‐manipulation with other techniques and their classical and emerging applications to non‐contact optical separation and sorting of micro‐ and nanoparticle suspensions, compositional and structural analysis of specimens, and quantification of force interactions at the microscopic scale are reviewed.
Abstract: We review the combinations of optical micro-manipulation with other techniques and their classical and emerging applications to non-contact optical separation and sorting of micro- and nanoparticle suspensions, compositional and structural analysis of specimens, and quantification of force interactions at the microscopic scale. The review aims at inspiring researchers, especially those working outside the optical micro-manipulation field, to find new and interesting applications of these methods.
••
TL;DR: The identities of differentially expressed proteins identified in human, mouse, and rat tissues published in three recent volumes of Proteomics are compiled and the appearance of the most predominant proteins in the dataset is calculated.
Abstract: After reading many 2-DE-based articles featuring lists of the differentially expressed proteins, one starts experiencing a disturbing deja vu. The same proteins seem to predominate regardless of the experiment, tissue or species. To quantify the occurrence of individual differentially expressed proteins in 2-DE experiment reports, we compiled the identities of differentially expressed proteins identified in human, mouse, and rat tissues published in three recent volumes of Proteomics and calculated the appearance of the most predominant proteins in the dataset. The most frequently identified protein is a highly abundant glycolytic enzyme enolase 1, differentially expressed in nearly every third experiment on both human and rodent tissues. Heat-shock protein 27 (HSP27) and heat-shock protein 60 (HSP60) were differentially expressed in about 30 percent of human and rodent samples, respectively. Considering protein families as units, keratins and peroxiredoxins are the most frequently identified molecules, with at least one member of the group being differentially expressed in about 40 percent of all experiments. We suggest that the frequent identification of these proteins must be considered in the interpretation of any 2-DE studies. We consider if these commonly observed changes represent common cellular stress responses or are a reflection of the technical limitations of 2-DE.
••
TL;DR: In this paper, three mesoporous silica materials with different pore sizes and pore connectivity were prepared and functionalized with aminopropyl (AP) ligands by post-synthesis treatment.
••
TL;DR: In this paper, the authors address the question: under which circumstances can we rely upon spontaneous succession and when are technical measures more effective in restoration programs? To answer this question, the position of a disturbed site along the productivity-stress gradient was considered.
Abstract: We address the question: under which circumstances can we rely upon spontaneous succession and when are technical measures more effective in restoration programs? To answer this question, the position of a disturbed site along the productivity–stress gradient was considered. The probability of attaining a target stage by spontaneous succession decreases toward both ends of the productivity–stress gradient, whereas the acceptance of technical measures generally increases. In correspondence with that, the monetary cost of restoration increases toward the ends of the gradient. Therefore, spontaneous succession is advocated especially if environmental site conditions are not very extreme.
••
TL;DR: The principles behind epigenetic compartmentalization and the functional consequences of chromatin arrangement within interphase nuclei are summarized.
Abstract: Epigenetic modifications, such as acetylation, phosphorylation, methylation, ubiquitination, and ADP ribosylation, of the highly conserved core histones, H2A, H2B, H3, and H4, influence the genetic potential of DNA. The enormous regulatory potential of histone modification is illustrated in the vast array of epigenetic markers found throughout the genome. More than the other types of histone modification, acetylation and methylation of specific lysine residues on N-terminal histone tails are fundamental for the formation of chromatin domains, such as euchromatin, and facultative and constitutive heterochromatin. In addition, the modification of histones can cause a region of chromatin to undergo nuclear compartmentalization and, as such, specific epigenetic markers are non-randomly distributed within interphase nuclei. In this review, we summarize the principles behind epigenetic compartmentalization and the functional consequences of chromatin arrangement within interphase nuclei.
••
TL;DR: In this paper, aniline was oxidized with ammonium peroxydisulfate in solutions of strong acid (0.1 M sulfuric acid), weak acid ( 0.4 M acetic acid), or alkali (0 2 M ammonium hydroxide).
Abstract: Aniline was oxidized with ammonium peroxydisulfate in solutions of strong acid (0.1 M sulfuric acid), weak acid (0.4 M acetic acid), or alkali (0.2 M ammonium hydroxide). The properties of the oxidation products and their morphology are controlled by the initial acidity of the medium and the acidity profile during the oxidation; the acidity increases because sulfuric acid is a byproduct. Conducting polyaniline nanogranules, nanotubes, or nonconducting oligoaniline microspheres were obtained, respectively. FTIR spectra suggest that the oligomers produced by the oxidation of neutral aniline molecules at the beginning of oxidation are similar, regardless of the acidity of the medium. Neutral aniline molecules, prevailing under alkaline conditions, are easily oxidized to aniline oligomers composed of ortho- and para-coupled aniline constitutional units. Ortho-coupled units are further converted by oxidative intramolecular cyclization to phenazines. It is proposed that, in acidic media, N-phenylphenazine units...
••
TL;DR: 3xTg-AD mice have an impaired ability to generate new neurones in the DG of the hippocampus, the severity of which increases with age and might be directly associated with the known cognitive impairment observed from 6 months of age onwards.
Abstract: It has become generally accepted that new neurones are added and integrated mainly in two areas of the mammalian CNS, the subventricular zone and the subgranular zone (SGZ) of the dentate gyrus (DG) of the hippocampus, which is of central importance in learning and memory. The newly generated cells display neuronal morphology, are able to generate action potentials and receive functional synaptic inputs, i.e. their properties are similar to those found in mature neurones. Alzheimer's disease (AD) is the primary and widespread cause of dementia and is an age-related, progressive and irreversible neurodegenerative disease that deteriorates cognitive functions. Here, we have used male and female triple transgenic mice (3xTg-AD) harbouring three mutant genes (β-amyloid precursor protein, presenilin-1 and tau) and their respective non-transgenic (non-Tg) controls at 2, 3, 4, 6, 9 and 12 months of age to establish the link between AD and neurogenesis. Using immunohistochemistry we determined the area density of proliferating cells within the SGZ of the DG, measured by the presence of phosphorylated Histone H3 (HH3), and their possible co-localisation with GFAP to exclude a glial phenotype. Less than 1% of the HH3 labeled cells co-localised with GFAP. Both non-Tg and 3xTg-AD showed an age-dependent decrease in neurogenesis. However, male 3xTg-AD mice demonstrated a further reduction in the production of new neurones from 9 months of age (73% decrease) and a complete depletion at 12 months, when compared to controls. In addition, female 3xTg-AD mice showed an earlier but equivalent decrease in neurogenesis at 4 months (reduction of 63%) with an almost inexistent rate at 12 months (88% decrease) compared to controls. This reduction in neurogenesis was directly associated with the presence of β-amyloid plaques and an increase in the number of β-amyloid containing neurones in the hippocampus; which in the case of 3xgTg females was directly correlated. These results suggest that 3xTg-AD mice have an impaired ability to generate new neurones in the DG of the hippocampus, the severity of which increases with age and might be directly associated with the known cognitive impairment observed from 6 months of age onwards . The earlier reduction of neurogenesis in females, from 4 months, is in agreement with the higher prevalence of AD in women than in men. Thus it is conceivable to speculate that a recovery in neurogenesis rates in AD could help to rescue cognitive impairment.
••
CERN1, Pennsylvania State University2, University of Siena3, Instituto Politécnico Nacional4, University of Genoa5, University of Helsinki6, University of Manchester7, Czech Technical University in Prague8, Academy of Sciences of the Czech Republic9, National Institute of Chemical Physics and Biophysics10, Case Western Reserve University11
TL;DR: The TOTEM Experiment as discussed by the authors measured the total pp cross-section with the luminosity-independent method and studied elastic and diffractive scattering at the LHC using two tracking telescopes, T1 and T2.
Abstract: The TOTEM Experiment will measure the total pp cross-section with the luminosity-independent method and study elastic and diffractive scattering at the LHC. To achieve optimum forward coverage for charged particles emitted by the pp collisions in the interaction point IP5, two tracking telescopes, T1 and T2, will be installed on each side in the pseudorapidity region 3.1 ≤ |η| ≤ 6.5, and Roman Pot stations will be placed at distances of ±147 m and ±220 m from IP5. Being an independent experiment but technically integrated into CMS, TOTEM will first operate in standalone mode to pursue its own physics programme and at a later stage together with CMS for a common physics programme. This article gives a description of the TOTEM apparatus and its performance.