bluuebunny/crossref_metadata_2025 huggingface dataset:
Crystallization and preliminary X-ray crystallographic analysis of the ArsM arsenic(III)S-adenosylmethionine methyltransferase
Authors: Marapakala Kavitha , Ajees A. Abdul , Qin Jie , Sankaran Banumathi , Rosen Barry P.
Published: August 2010

Arsenic is the most ubiquitous environmental toxin and carcinogen and consequently ranks first on the Environmental Protection Agency's Superfund Priority List of Hazardous Substances. It is introduced primarily from geochemical sources and is acted on biologically, creating an arsenic biogeocycle. A common biotransformation is methylation to monomethylated, dimethylated and trimethylated species. Methylation is catalyzed by the ArsM (or AS3MT) arsenic(III)S-adenosylmethionine methyltransferase, an enzyme (EC 2.1.1.137) that is found in members of every kingdom from bacteria to humans. ArsM from the thermophilic algaCyanidioschyzonsp. 5508 was expressed, purified and crystallized. Crystals were obtained by the hanging-drop vapor-diffusion method. The crystals belonged to the monoclinic space groupC2, with unit-cell parametersa= 84.85,b= 46.89,c= 100.35 Å, β = 114.25° and one molecule in the asymmetric unit. Diffraction data were collected at the Advanced Light Source and were processed to a resolution of 1.76 Å.
Crystallization and preliminary crystallographic characterization of the PAS domains of EAG and ELK potassium channels
Authors: Adaixo Ricardo , Morais-Cabral João Henrique
Published: August 2010

Per–Arnt–Sim (PAS) domains are ubiquitous in nature; they are ∼130-amino-acid protein domains that adopt a fairly conserved three-dimensional structure despite their low degree of sequence homology. These domains constitute the N-terminus or, less frequently, the C-terminus of a number of proteins, where they exert regulatory functions. PAS-containing proteins generally display two or more copies of this motif. In this work, the crystallization and preliminary analysis of the PAS domains of two eukaryotic potassium channels from the ether-à-go-go (EAG) family are reported.
Crystallization and preliminary X-ray analysis of formate oxidase, an enzyme of the glucose–methanol–choline oxidoreductase family
Authors: Maeda Yoshifumi , Doubayashi Daiju , Ootake Takumi , Oki Masaya , Mikami Bunzo , Uchida Hiroyuki
Published: August 2010

Formate oxidase (FOD), which catalyzes the oxidation of formate to yield carbon dioxide and hydrogen peroxide, belongs to the glucose–methanol–choline oxidoreductase (GMCO) family. FOD fromAspergillus oryzaeRIB40, which has a modified FAD as a cofactor, was crystallized at 293 K by the hanging-drop vapour-diffusion method. The crystal was orthorhombic and belonged to space groupC2221. Diffraction data were collected from a single crystal to 2.4 Å resolution.
Preliminary crystallographic analysis of theEscherichia coliantitoxin MqsA (YgiT/b3021) in complex withmqsRApromoter DNA
Authors: Brown Breann L. , Page Rebecca
Published: August 2010

TheEscherichia coliproteins MqsR and MqsA comprise a novel toxin–antitoxin (TA) system. MqsA, the antitoxin, defines a new family of antitoxins because unlike other antitoxins MqsA is structured throughout its entire sequence, binds zinc and coordinates DNAviaits C-terminal and not its N-terminal domain. In order to understand how bacterial antitoxins, and MqsA in particular, regulate transcription, the MqsA protein was cocrystallized with a 26-mer duplex DNA corresponding to the palindromic region of themqsRApromoter. The merohedrally twinned crystal belonged to space groupP41, with unit-cell parametersa= 60.99,b= 60.99,c= 148.60 Å. A complete data set was collected to a resolution of 2.1 Å. The solvent content of the crystal was consistent with the presence of two MqsA molecules bound to the duplex DNA in the asymmetric unit.
TheCorynebacterium glutamicumaconitase repressor: scratching around for crystals
Authors: García-Nafría Javier , Baumgart Meike , Bott Michael , Wilkinson Anthony J. , Wilson Keith S.
Published: August 2010

Imperfections on the surfaces of crystallization containers are known to influence crystal formation and are thought to do so by helping to overcome the nucleation barrier. The intentional creation of imperfections has been widely applied to induce crystallization of small molecules, but has not been reported for protein crystallization. Here, the crystallization and preliminary X-ray analysis of the TetR-type aconitase repressor are reported. This regulator was the first transcription factor to be identified in the regulation of the tricarboxylic acid cycle inCorynebacterium glutamicum, an organism that is of special industrial interest and is an emerging model organism for Corynebacterineae. Successful crystallization involved introducing manual scratches on the surface of standard commercial plates, which led to a substantial improvement in crystal nucleation and quality.
Crystallization and calcium/sulfur SAD phasing of the human EF-hand protein S100A2
Authors: Koch Michael , Diez Joachim , Wagner Armin , Fritz Günter
Published: August 2010

Human S100A2 is an EF-hand protein and acts as a major tumour suppressor, binding and activating p53 in a Ca2+-dependent manner. Ca2+-bound S100A2 was crystallized and its structure was determined based on the anomalous scattering provided by six S atoms from methionine residues and four calcium ions present in the asymmetric unit. Although the diffraction data were recorded at a wavelength of 0.90 Å, which is usually not assumed to be suitable for calcium/sulfur SAD, the anomalous signal was satisfactory. A nine-atom substructure was determined at 1.8 Å resolution usingSHELXD, andSHELXEwas used for density modification and phase extension to 1.3 Å resolution. The electron-density map obtained was well interpretable and could be used for automated model building byARP/wARP.
Comparison between the orthorhombic and tetragonal forms of the heptamer sequence d[GCG(xT)GCG]/d(CGCACGC)
Authors: Robeyns Koen , Herdewijn Piet , Van Meervelt Luc
Published: August 2010

Cyclohexene nucleic acid (CeNA) building blocks can be introduced into natural DNA sequences without a large conformational influence because of the ability of the six-membered sugar ring to mimic both the C2′-endoand C3′-endoconformations of the naturally occurring ribofuranose sugar ring. The non-self-complementary DNA sequence d[GCG(xT)GCG]/d(CGCACGC) with one incorporated CeNA (xT) moiety crystallizes in two forms: orthorhombic and tetragonal. The tetragonal form, which diffracts to 3 Å resolution, is a kinetically stable polymorph of the orthorhombic form [Robeynset al.(2010),Artificial DNA,1, 1–7], which diffracts to 1.17 Å resolution and is the thermodynamically stable form of the CeNA-incorporated duplex. Here, the two structures are compared, with special emphasis on the differences in crystal packing and the irreversible conversion of the kinetic form into the high-resolution diffracting thermodynamic form.
Leibniz's Two Realms Revisited
Authors: McDonough Jeffrey K.
Published: August 2010

Leibniz speaks, in a variety of contexts, of there being two realms—a “kingdom of power or efficient causes” and “a kingdom of wisdom or final causes.” This essay explores an often overlooked application of Leibniz's famous “two realms doctrine.” The first part turns to Leibniz's work in optics for the roots of his view that nature can be seen as being governed by two complete sets of equipotent laws, with one set corresponding to the efficient causal order of the world, and the other to its teleological order. The second part offers an account of how this picture of lawful over‐determination is to be reconciled with Leibniz's mature metaphysics. The third addresses a line of objection proposed by David Hirschmann to the effect that Leibniz's doctrine undermines his stated commitment to an efficient, broadly mechanical account of the natural world. Finally, the fourth part suggests that Leibniz's thinking about the harmony of final and efficient causes in connection with corporeal nature may help to shed light on his understanding of the teleological unfolding of monads as well.
On What it Takes for There to Be No Fact of the Matter
Authors: Azzouni Jody , Bueno Otávio
Published: August 2010

Philosophers are very fond of making non‐factualist claims—claims to the effect that there is no fact of the matter as to whether something is the case. But can these claims be coherently stated in the context of classical logic? Some care is needed here, we argue, otherwise one ends up denying a tautology or embracing a contradiction. In the end, we think there are only two strategies available to someone who wants to be a non‐factualist about something, and remain within the province of classical logic. But one of these strategies is rather controversial, and the other requires substantially more work than is often supposed. Being a non‐factualist is no easy business, and it may not be the most philosophically perspicuous way to go.
Normative Conflicts and The Logic of ‘Ought’
Authors: Goble Lou
Published: August 2010

On the face of it, normative conflicts are commonplace. Yet standard deontic logic declares them to be logically impossible. That prompts the question, What are the proper principles of normative reasoning if such conflicts are possible? This paper examines several alternatives that have been proposed for a logic of ‘ought’ that can accommodate normative conflicts, and finds all of them unsatisfactory as measured against three criteria of adequacy. It then introduces a new logic that does meet all three criteria, and so allows for the possibility of genuine normative conflicts.
The Ontology of Epistemic Reasons
Authors: Turri John
Published: August 2010

Epistemic reasons are mental states. They are not propositions or non‐mental facts. The discussion proceeds as follows. Section 1 introduces the topic. Section 2 gives two concrete examples of how our topic directly affects the internalism/externalism debate in normative epistemology. Section 3 responds to an argument against the view that reasons are mental states. Section 4 presents two problems for the view that reasons are propositions. Section 5 presents two problems for the view that reasons are non‐mental facts. Section 6 argues that reasons are mental states. Section 7 responds to objections.
Geographies of Subcontracting
Authors: Neo Harvey
Published: August 2010

At its simplest, ‘subcontracting’ occurs when a company outsources some of its operations and functions to others. These contracts include production, service support, and in some cases, research and design. Yet, the nature of subcontracting as a mode of economic production varies dramatically across different industries, spatial scales, places, and impacts. In view of the immense scope of this topic, in this article, I hope to highlight and illuminate a few significant strands and key contentions of the subcontracting literature. First, I will illustrate the varieties and increasing complexity of subcontracting since its early roots in the pre‐industrialization era. Second, I will attempt to explain why firms choose to subcontract. Third, I will also mention briefly other cognate concepts (e.g. ‘trust’ and ‘agglomeration’) which play a role in explaining the nature of subcontracting relationships. Where possible, I will also discuss the extent to which subcontracting relationships are inequitable. Finally, I will use the case study of contract farming in the livestock industry to illustrate the various contentions surrounding subcontracting as a form of economic production and organization.
The Internationalisation of Managerial Environmentalism: Globalisation, Diffusion and Territorialisation
Authors: Perkins Richard
Published: August 2010

A remarkable feature of the past half century has been the emergence, diversification and diffusion of managerial environmentalism across large parts of the globe. This article examines how globalisation has been implicated in these internationalisation processes and outcomes. A central theme is that the ways in which aspects of managerial environmentalism have diffused are complex, multi‐dimensional and defy simple generalisations about the constituent mechanisms and spatialities. Moreover, the international diffusion of environmental innovations has been shaped by the domestic geographies of place, resulting in uneven and hybrid patterns of managerial environmentalism across space.
Development, Application and Place of Neutral Theory in Ecology and Biogeography
Authors: Perry George L.W. , Groeneveld Jürgen , Miller Ben P.
Published: August 2010

Classical ecological theory predicts that ecological communities should only contain as many species as there are resources. Many ecosystems, however, seem to contain many more species than classical theory allows. Understanding this paradox is central to community ecology and biogeography. Niche‐based models consider that differences and trade‐offs between species’ life history traits stabilise species interactions and so allow coexistence. In stark contrast, neutral models assume that individuals at the same trophic level interact identically with conspecifics and heterospecifics (i.e. all species are equivalent), and this equivalence allows coexistence. Despite it seeming unlikely that species are equivalent, neutral models do predict some of the macroscopic properties of ecological communities surprisingly well. Although there are many neutral models, the best‐known neutral model in the context of community ecology is that described by Hubbell (2001) in the Unified Neutral Theory of Biodiversity. We review the development of neutral theory in ecology and biogeography, consider its predictions and how they can be evaluated, and look at how neutral theory may develop in the future. This article focuses on species‐rich plant communities, as they are, for the most part, the test‐bed for the recent development and application of neutral models, but we also consider the application of neutral approaches to other taxonomic groups and ecosystem types.
The Geography of Insurgency
Authors: Lohman Andrew D. , Flint Colin
Published: August 2010

In recent years geographers and scholars from other disciplines have made substantial contributions to the literature on political violence, civil war and conflict within states through asking spatial questions: where is conflict likely to occur and how will it spread or diffuse? In this article, we provide a survey of the approaches, theories and methodologies used to address these questions and suggest avenues for advancing the spatial analysis of conflict. We argue that such conflicts are best conceived as an insurgency, defined as a violent political process to assert power and control over territorial space. After exploring the contributions of qualitative approaches (critical and feminist geopolitics) to our spatial understandings of these political processes, we examine quantitative research addressing these spatial questions. Specifically, we suggest that a network approach provides a useful perspective for understanding the power relations and spatial contestation of an insurgency. This approach also differentiates between escalation and diffusion, which are often treated synonymously in the literature.
Fire in the American South: Vegetation Impacts, History, and Climatic Relations
Authors: Lafon Charles W.
Published: August 2010

Fire plays a key role in many ecosystems of the southeastern U.S. Longleaf pine (Pinus palustris) and Table Mountain pine‐pitch pine (P. pungens–P. rigida) forests along with other ecosystems – including oak (Quercus) forests, grasslands, and spruce‐fir (Picea‐Abies) forests – illustrate the range of fire effects and plant persistence strategies in the American South. Fire history research reveals that fires and fire‐associated vegetation were common before the fire exclusion of the past century. Both lightning and anthropogenic ignitions (caused by American Indians or European settlers) contributed to burning, but their relative importance is debated. The humid climate constrains burning, especially by lightning‐ignited fires, which often occur during moist conditions. Studies of fire climatology indicate the importance of dry conditions (e.g. drought years and relatively dry areas) for widespread burning in this humid region. Landscape fragmentation also influences burning. In the past some fires also likely grew much larger than today because they were unimpeded by roads, farms, and other barriers.
Defining Hyporheic Zones – Advancing Our Conceptual and Operational Definitions of Where Stream Water and Groundwater Meet
Authors: Gooseff Michael N.
Published: August 2010

There is a growing recognition of the importance of connections between streams and adjacent alluvial aquifers. The exchange of water, mass, and energy between these locations influences stream ecosystem structure and function by facilitating nutrient cycling, respiration, stream temperature buffering, and survival of macroinvertebrates. Near‐surface aquifers that interact with surface water have been termed ‘hyporheic zones’, yet there are several accepted definitions of this term (biological, geochemical, and hydrological definitions), which do not necessarily agree with each other. Biologists refer to it as the subsurface inhabited by hyporheos (‘stream’ macroinvertebrates observed in the subsurface). Hydrologists support a conceptual model that suggests a ‘flow‐through’ subsurface region containing flowpaths that originate and terminate at the stream. Geochemical definition suggests that the hyporheic zone is a mixing zone between surface water and deep‐sourced groundwater, with intermediate conditions between these end members. Temporal and spatial scales over which we seek to define hyporheic zones constrain our ability to do so. It is recognized that stream water exchanges through the subsurface over many timescales. Proposed here is a definition based on the timescale of flow through the hyporheic zone, in which residence times of interest are explicitly distinguished and referred to – e.g. ‘the 24‐h hyporheic zone’. Thus the ‘component’ of the hyporheic zone that is of interest can be related to specific rates of processes of interest (e.g. denitrification rate). Adoption of this approach will reduce ambiguity in hyporheic science and hopefully contribute to interdisciplinary scientific advancements.
Precipitation Measurement and the Advancement Toward Global Observations
Authors: Durkee Josh
Published: August 2010

Precipitation is an important variable in the global hydrologic cycle that helps to sustain life, influences a variety of daily activities, and plays a critical role in the Earth’s energy balance. Our understanding of precipitation, especially in forecast applications, hazards mitigation, and water resources are among the leading challenges in the scientific community. Over the last 50 years, the science of precipitation observation and measurement, particularly at fglobal scales, has advanced quite rapidly since the age of basic precipitation collection at the surface. Scientists have developed numerous techniques to estimate precipitation at the surface and from space, but not without their drawbacks. This article presents an overview of the advantages and limitations of some of the more mainstream techniques of precipitation measurement, and the march toward a relatively high quality, full global precipitation observation network.
Geography and the Politics of Climate Policy
Authors: Bailey Ian , Compston Hugh
Published: August 2010

Despite widespread recognition that many of the severest obstacles to climate policy are political (in the form of resistance from political parties, business groups and electorates) rather than scientific, technological or economic and a growing literature on the spatial dimensions of climate governance, geographical research has yet systematically to address how geographical thinking can inform the development of political strategies to assist governments to overcome political opposition to climate policy. In this article we argue for, and explore the outlines of, such a geographical contribution to understanding and reinvigorating the politics of climate change. We particularly draw attention to the importance of context and of how geographical theorisations on the politics of scale and networks can assist in evaluating future political strategies for climate policy.
Remote Sensing as a Tool for Tropical Ecology
Authors: Balzotti Chris S. , Petersen Steven L. , Terry Richard E. , Scherer Andrew K. , Golden Charles
Published: August 2010

Tropical forests provide important habitat for a tremendous diversity of plant and animal species. However, limitations in measuring and monitoring the structure and function of tropical forests has caused these systems to remain poorly understood. Remote‐sensing technology has provided a powerful tool for quantification of structural patterns and associating these with resource use. Satellite and aerial platforms can be used to collect remotely sensed images of tropical forests that can be applied to ecological research and management. The purpose of this article is to highlight the resources available for tropical forest remote sensing and to present a case‐study that demonstrates its application to a neotropical forest located in the Petén region of northern Guatemala.
Racial Quotas and the Culture War in Brazilian Academia
Authors: Bailey Stanley R. , Peria Michelle
Published: August 2010

Dozens of Brazilian universities recently adopted racial quotas for negros, read Afro‐Brazilians, in higher education. Anyone familiar with the Brazilian context will recognize this step as a paradigm shift in the state’s approach to ‘race’. State discourse in past decades touted a mixed‐race population not beset by overt discriminatory practices. In response to this new approach, two well‐defined clusters of professors in Brazil’s universities authored several dueling manifestos supporting and opposing race‐based affirmative action. This article suggests a ‘culture war’ framing of the debate and delineates the contrasting historic ideologies of racialism and antiracialism that inform the divergent racial worldviews of each academic camp. It then explores four points of contention from the manifestos that characterize their conflicting perspectives. They differ in terms of (1) their images of the Brazilian nation, (2) their diagnoses of the mechanisms behind non‐white underrepresentation in Brazilian universities, (3) their prognoses for a remedy via racial quotas, and (4) their motivations for entering the debate. At the same time, the article locates some possible common ground.
Inequalities in Transnational Families
Authors: Dreby Joanna , Adkins Timothy
Published: August 2010

Over the past two decades, interest in the transnational lifestyles of contemporary migrants has grown significantly. In this article, we focus not on transnational identities, processes or structures, but rather on the emergent literature on transnational families in the context of migration to the United States. Transnational family studies broadly fall into two thematic camps: 1) those that describe transnational households as cooperative units in the face of economic, political and legal constraint and 2) those that show how the conditions that lead family members to live apart exacerbate and create new sources of conflict within families. Whether highlighting family conflict or cooperation, contemporary transnational family studies differ theoretically from prior research on immigrant families. Instead of focusing on immigrant incorporation, this literature demonstrates how global structures of inequality at the macro‐level affect the everyday lives of transnational family members, as well as how individual action reproduces or challenges these broader social inequalities.
Art as Propaganda: Bringing Du Bois into the Sociology of Art
Authors: Kidd Dustin , Jackson Christina
Published: August 2010

We examine WEB Du Bois's writings about the arts in the NAACP journalThe Crisisfrom 1910–1934 in order to construct a Du Boisian social theory of the arts. The key elements of this theoretical framework are: artists, money, freedom, organization, truth, beauty, and propaganda. The most surprising element is propaganda, which for Du Bois meant that art needs to address racial politics. There is a strong sense in Du Bois's writings that art can and should have socially transformative effects. Comparing Du Bois's work to current theories from the sociology of art, we find that Du Bois emphasizes the role of art in social change, while current work treats art primarily as a tool for social reproduction. We argue for expanding the theoretical toolbox of the sociology of the arts through greater consideration of Du Bois's propaganda concept.
Aesthetic Capital: A Research Review on Beauty Perks and Penalties
Authors: Anderson Tammy L. , Grunert Catherine , Katz Arielle , Lovascio Samantha
Published: August 2010

The presence of aesthetically based cultural goods and their ever‐increasing influence in modern society may pose a new conceptual opportunity to sociology. Specifically, how can the discipline forge an understanding of how value associated with beauty returns forms of individual wealth? A new term, i.e. aesthetic capital, might be an answer. Such a concept, we maintain, covers the privileges and wealth people receive from aesthetic traits, such as their face, hair, body, clothes, grooming habits and other markers of beauty. The purpose of our paper is to review the kinds of perks, and penalties, people receive from being deemed beautiful. Our review shows that visually appealing traits greatly impact our lives, in matters of modest importance (friend selection) to great importance (e.g. getting a job and career mobility). Thus, the promise of an aesthetic capital concept lies in enabling sociology to better understand inequality and the socially based forms of wealth available to individuals in modern society.
Exact solutions of a particle in a box with a delta function potential: The factorization method
Authors: Pedram Pouria , Vahabi M.
Published: August 2010

We use the factorization method to find the exact eigenvalues and eigenfunctions for a particle in a box with the delta function potential V(x)=λδ(x−x0). We show that the presence of the potential results in the discontinuity of the corresponding ladder operators. The presence of the delta function potential allows us to obtain the full spectrum in the first step of the factorization procedure even in the weak coupling limit λ→0.
Self-dual electromagnetic fields
Authors: Chubykalo Andrew E. , Espinoza Augusto , Kosyakov B. P.
Published: August 2010

We demonstrate the utility of self-dual fields in electrodynamics. Stable configurations of free electromagnetic fields can be represented as superpositions of standing waves, each possessing zero Poynting vector and zero orbital angular momentum. The standing waves are themselves superpositions of self-dual and anti-self-dual solutions. The idea of self-duality provides additional insights into the geometrical and spectral properties of stable electromagnetic configurations, such as those responsible for the formation of ball lightning.
The equipartition theorem revisited
Authors: Mello Pier A. , Rodríguez Rosalío F.
Published: August 2010

We generalize the equipartition theorem to confined systems of structureless independent molecules by introducing a confining potential, which is usually not done explicitly in most textbooks. We show that if the size of the system is much larger than the range of the confining potential, the generalization is independent of the form of the potential but contains corrections produced by the confinement. We demonstrate the important role played by the walls and show how the boundary terms may be employed to describe their contribution to the pressure exerted on the system.
Classical thermodynamics of particles in harmonic traps
Authors: Ligare Martin
Published: August 2010

I develop simple thermodynamic relations for a system of noninteracting classical particles confined in an isotropic harmonic trap. The volume occupied by the particles in such a trap is not well defined, and the pressure varies with position, indicating that the thermodynamic relations should be expressed in terms of more appropriate variables. I use the effective spring constant of the trap as a state variable and show that the conjugate state variable is proportional to the ensemble average of the mean squared displacement of the particles from the center of the trap. Thermodynamic relations are derived in terms of these variables, including the pressure and thermal equations of state, the entropy, and the heat capacities. I also consider cyclic thermodynamic processes in a harmonically confined gas.
Frequency Analysis Techniques for Identification of Viral Genetic Data
Authors: Trifonov Vladimir , Rabadan Raul
Published: August 2010

Environmental metagenomic samples and samples obtained as an attempt to identify a pathogen associated with the emergence of a novel infectious disease are important sources of novel microorganisms. The low costs and high throughput of sequencing technologies are expected to allow for the genetic material in those samples to be sequenced and the genomes of the novel microorganisms to be identified by alignment to those in a database of known genomes. Yet, for various biological and technical reasons, such alignment might not always be possible. We investigate a frequency analysis technique which on one hand allows for the identification of genetic material without relying on alignment and on the other hand makes possible the discovery of nonoverlapping contigs from the same organism. The technique is based on obtaining signatures of the genetic data and defining a distance/similarity measure between signatures. More precisely, the signatures of the genetic data are the frequencies of
k
-mers occurring in them, with
k
being a natural number. We considered an entropy-based distance between signatures, similar to the Kullback-Leibler distance in information theory, and investigated its ability to categorize negative-sense single-stranded RNA (ssRNA) viral genetic data. Our conclusion is that in this viral context, the technique provides a viable way of discovering genetic relationships without relying on alignment. We envision that our approach will be applicable to other microbial genetic contexts, e.g., other types of viruses, and will be an important tool in the discovery of novel microorganisms.

IMPORTANCE
Multiple factors contribute to the emergence of novel infectious diseases. Implementation of effective measures against such diseases relies on the rapid identification of novel pathogens. Another important source of novel microorganisms is environmental metagenomic samples. The low costs and high throughput of sequencing technologies provide a method for the identification of novel microorganisms by sequence alignment. There are several obstacles to this method, as follows: our knowledge of biology is biased by an anthropomorphic view, microbial genomic material could be a minuscule fraction of the sample, the sequencing and enrichment technologies can be a source of errors and biases, and finally, microbes have high diversity and high evolutionary rates. As a result, novel microorganisms could have very low genetic similarity to already known genomes, and the identification by alignment could be computationally prohibitive. We investigate a frequency analysis technique which allows for the identification of novel genetic material without relying on alignment.
Emergence and Global Dissemination of Host-Specific
Streptococcus agalactiae
Clones
Authors: Sørensen Uffe B. Skov , Poulsen Knud , Ghezzo Claudia , Margarit Immaculada , Kilian Mogens
Published: August 2010

To examine the global diversity of
Streptococcus agalactiae
(group B streptococci [GBS]) and to elucidate the evolutionary processes that determine its population genetics structure and the reported changes in host tropism and infection epidemiology, we examined a collection of 238 bovine and human isolates from nine countries on five continents. Phylogenetic analysis based on the sequences of 15 housekeeping genes combined with patterns of virulence-associated traits identified a genetically heterogeneous core population from which virulent lineages occasionally emerge as a result of recombination affecting major segments of the genome. Such lineages, like clonal complex 17 (CC17) and two distinct clusters of CC23, are exclusively adapted to either humans or cattle and successfully spread globally. The recent emergence and expansion of the human-associated and highly virulent sequence type 17 (ST17) could conceivably account, in part, for the increased prevalence of neonatal GBS infections after 1960. The composite structure of the
S. agalactiae
genome invalidates phylogenetic inferences exclusively based on multilocus sequence typing (MLST) data and thereby the previously reported conclusion that the human-associated CC17 emerged from the bovine-associated CC67.

IMPORTANCE
Group B streptococci (GBS) (
Streptococcus agalactiae
) have long been recognized as important causes of mastitis in cattle. After 1960, GBS also became the most prevalent cause of invasive and often fatal infections in newborns. At the same time, GBS are carried by a substantial proportion of healthy individuals. The aims of this study were to elucidate the genetic mechanisms that lead to diversification of the GBS population and to examine the relationship between virulence and host preference of evolutionary lineages of GBS. Genetic analysis of GBS isolates from worldwide sources demonstrated epidemic clones adapted specifically to either the human or bovine host. Such clones seem to emerge from a genetically heterogeneous core population as a result of recombination affecting major segments of the genome. Emergence and global spread of certain clones explain, in part, the change in epidemiology of GBS disease and may have implications for prevention.
Membrane Topology Mapping of the O-Antigen Flippase (Wzx), Polymerase (Wzy), and Ligase (WaaL) from Pseudomonas aeruginosa PAO1 Reveals Novel Domain Architectures
Authors: Islam Salim T. , Taylor Véronique L. , Qi Meng , Lam Joseph S.
Published: August 2010

Biosynthesis of B-band lipopolysaccharide (LPS) in
Pseudomonas aeruginosa
follows the Wzy-dependent pathway, requiring the integral inner membrane proteins Wzx (O-antigen [O-Ag] flippase), Wzy (O-Ag polymerase), and WaaL (O-Ag ligase). For an important first step in deciphering the mechanisms of LPS assembly, we set out to map the membrane topology of these proteins. Random and targeted 3′
wzx
,
wzy
, and
waaL
truncations were fused to a
phoA
-
lacZα
dual reporter capable of displaying both alkaline phosphatase and β-galactosidase activity. The results from truncation fusion expression and the corresponding differential enzyme activity ratios allowed for the assignment of specific regions of the proteins to cytoplasmic, transmembrane (TM), or periplasmic loci. Protein orientation in the inner membrane was confirmed via C-terminal fusion to green fluorescent protein. Our data revealed unique TM domain properties in these proteins, particularly for Wzx, indicating the potential for a charged pore. Novel periplasmic and cytoplasmic loop domains were also uncovered, with the latter in Wzy and WaaL revealing tracts consistent with potential Walker A/B motifs.

IMPORTANCE
The opportunistic pathogen
Pseudomonas aeruginosa
synthesizes its virulence factor lipopolysaccharide via the Wzy-dependent pathway, requiring translocation, polymerization, and ligation of lipid-linked polysaccharide repeat units by the integral inner membrane proteins Wzx, Wzy, and WaaL, respectively. However, structural evidence to help explain the function of these proteins is lacking. Since membrane proteins are difficult to crystallize, topological mapping is an important first step in identifying exposed and membrane-embedded domains. We mapped the topologies of Wzx, Wzy, and WaaL from
P. aeruginosa
PAO1 by use of truncation libraries of a randomly fused C-terminal reporter capable of different enzyme activities in the periplasm and cytoplasm. Topology maps were created based directly on residue localization data, eliminating the bias associated with reliance on multiple topology prediction algorithms for initial generation of consensus transmembrane domain localizations. Consequently, we have identified novel periplasmic, cytoplasmic, and transmembrane domain properties that would help to explain the proposed functions of Wzx, Wzy, and WaaL.
Percutaneous transluminal angioplasty in a patient with vasospasm secondary to coccidioidal meningitis: case report and review of the literature
Authors: Hu Yin C , Newman C Benjamin , Bristol Ruth , McDougall Cameron G , Albuquerque Felipe C
Published: August 2010

Introduction

Coccidioidomycosis is secondary to infection with fungal speciesCoccidioides immitisorCoccidioides posadasii.One consequence of extrapulmonary coccidioidomycosis dissemination is meningitis, which is associated with high rates of morbidity and mortality if left untreated. Intracranial vasospasm, although rarely described, can occur and may be a result of vasculitic or subacute fibrotic changes. We describe a case of successful percutaneous transluminal angioplasty (PTA) in a patient with severe vasospasm related to coccidioidal meningitis. This is the first report of this endovascular treatment used to treat coccidioidal vasospasm.

Clinical presentation

A patient with a history of pulmonary coccidioidomycosis presented with acute confusion, blurry vision and headache. Serology confirmed basilar meningitis and magnetic resonance angiography demonstrated severe symptomatic vasospasm.

Intervention

Emergent cerebral angiography confirmed severe vasospasm in the right middle cerebral artery and moderate vasospasm in the left middle cerebral artery. Successful PTA was performed under general anesthesia. The patient demonstrated postprocedural angiographic and clinical improvement.

Conclusion

We report the first case of successful PTA performed to treat vasospasm related to coccidioidal meningitis. When vasospasm is clinically symptomatic, PTA is a safe and feasible procedure.
Germination of small-seeded tropical rain forest plants exposed to different spectral compositions
Authors: Metcalfe D. J.
Published: August 2010

Seeds of 11 very small-seeded species with different degrees of shade tolerance as juveniles were tested for their response to neutral shade (6% daylight), green shade (3%), and darkness. Germination was monitored over 46 weeks. All species germinated in daylight to some extent. Species of Pternandra and Urophyllum, commonly found as juveniles in deep shade, germinated to the same percentage in green shade as in daylight, although over a longer time period, and to a lower percentage in the dark. Percentage germination of Gynotroches axillaris and Pellacalyx saccardianus, also found as juveniles in deep shade, was similar in all treatments, but much faster in daylight. Species of Ficus, which are found commonly as seedlings in deep shade but require higher irradiance for onward growth, germinated rapidly in daylight, and to a lower percentage and after a longer time in green shade than in the dark. Melastoma, which establishes in large gaps, germinated only in daylight. As most species can germinate under a spectral composition similar to canopy shade it is likely that they can germinate under a closed canopy in nature and may become established without the formation of even a transient canopy gap provided leaf litter is absent. Keywords: germination, red/far-red ratio, shade tolerance, tropical rain forest.
Relationship between flowering phenology of perennial herbs and meteorological data in deciduous forests of Sweden
Authors: Diekmann Martin
Published: August 2010

The relationship between flowering phenology and meteorological measurements, in particular air temperature, was studied for 29 herbaceous species in four areas of deciduous forest near Uppsala, Sweden. Altogether 16 models were tested for their accuracy of predicting flowering. These were cumulative sum models based on the heat unit concept of an accumulation of (modified) temperatures above a threshold base temperature from a chosen starting date. Average temperature was tested as an alternative method. All models were first applied to a data set from the years 1990 to 1992 and then to an independent test data set from 1993. The accumulation of daily mean air temperatures (degree-days) above 5 °C from January 1 was chosen as the basic reference model. Despite its simplicity, it was a very accurate model in predicting flowering for these species. Only two models were superior to the reference model in both data sets: the summation of degree hours instead of degree-days from optimized starting dates for each species, and the addition of photoperiod (daylength) to daily mean temperature. In general, the models performed better for the late-flowering species than for the early-flowering species. The accuracy of the models was partly dependent on the actual course of temperature accumulation in a year. Keywords: degree-days, full flowering, photoperiod, solar radiation, temperature sum.
Demography and life history of three sympatric species of Botrychium subg. Botrychium in Waterton Lakes National Park, Alberta
Authors: Lesica Peter , Ahlenslager Kathleen
Published: August 2010

We followed the fate of mapped sporophytes of Botrychium paradoxum, Botrychium hesperium, and their hybrid Botrychium × watertonense in permanent plots for 6 years in Waterton Lakes National Park, Alberta. All three species had half-lives of approximately 3 years or less. Botrychium paradoxum had higher rates of recruitment and mortality leading to less stable population sizes than B. hesperium, perhaps contributing to the former's relative rarity. All species demonstrated prolonged dormancy whereby plants remain below ground for 1 or more years before reappearing. Surveys and monitoring studies for these and probably other species of Botrychium are more difficult owing to prolonged dormancy. Short lifespan and association with disturbed habitats suggests that these ferns may require natural disturbance regimes for long-term persistence. Keywords: Botrychium, demography, life history, rare plants, prolonged dormancy, Waterton Lakes National Park.
Polar transverse expansion of pericycle cells in auxin-treated adventitious roots of onion (Allium cepa)
Authors: Pulgarin A. , Casero P. J. , Casimiro I. , Lloret P. G.
Published: August 2010

The exogenous application of an auxin (α-naphthaleneacetic acid) to adventitious roots of Allium cepa L. changes the polarity of growth from longitudinal to transverse. Promotion of transverse growth by this auxin involves cortical and pericycle cells located in the elongation zone of these roots. Transverse auxin-promoted expansion of cortical tissue is very marked. Within the vascular cylinder, pericycle cells react to treatment in different ways, according to their location with respect to the vascular system. In terms of cross-sectional area and radial diameter increases, the most marked response to auxin treatment occurs in pericycle cells adjacent to xylem poles. Auxin treatment also promotes cell divisions in pericycle and cortical tissues. The pattern of divisions in the pericycle is very similar to that occurring during lateral root development. Nevertheless, lateral roots do not develop along the distalmost 3 mm of auxin-treated roots. In this region the pericycle simply becomes a multilayered tissue. The microtubules are proposed as a conceivable means to control changes in the polarity of expansion and promotion of periclinal divisions in this experimental system. Keywords: Allium cepa, growth polarity, naphthaleneacetic acid, pericycle, plane of division, root cortex.
Changes in protein biosynthesis during the differentiation ofPisolithus–Eucalyptus grandisectomycorrhiza
Authors: Burgess Treena , Dell Bernie
Published: August 2010

Protein biosynthesis in Pisolithus – Eucalyptus grandis ectomycorrhiza was related to the stage of ectomycorrhizal development using two-dimensional polyacrylamide gel electrophoresis of proteins labelled by in vivo incorporation of35S radiolabelled amino acids. Nineteen-day-old seedlings were radiolabelled and the primary root was divided into 1-cm segments. With increasing distance from the tip of the primary root, the lateral roots developed as follows: segment 1, no lateral tips; segment 2, three lateral tips, 1–4 days old; segment 3, five lateral tips, 3–8 days old; segment 4, five lateral tips, 7–12 days old. Six-day-old ectomycorrhizas were fully formed with a mantle and Hartig net. During ectomycorrhizal development, there was a decrease in all plant proteins and differential accumulation of fungal proteins. The apical segment of the primary root had a biosynthesis profile very similar to that of noninoculated roots. By contrast, the other segments of the primary root, with attached lateral roots, had biosynthesis profiles that were similar to those of the free-living hyphae. Thus, plant biosynthesis was shown to be predominantly associated with the primary root meristem. The domination of the fungal partner in the protein biosynthesis of developing ectomycorrhiza is probably a consequence of stimulated fungal growth and the corresponding decrease in plant meristematic activity. Ectomycorrhizal development was associated with a differential accumulation of fungal polypeptides and the appearance of a group of symbiosis-related acid fungal polypeptides between 27 and 37 kDa. As the polypeptides were present in a similar magnitude throughout ectomycorrhizal development (lateral tips 1–12 days old), it is suggested that they function as structural proteins associated with mantle formation. Keywords: ectomycorrhizal development, Eucalyptus, Pisolithus, protein biosynthesis, symbiosis-related polypeptides.
Intensive production of juvenile cuttings by mother microplant culture inHydrangea macrophylla"Leuchtfeuer"
Authors: Galopin Gilles , Beaujard François , Gendraud Michel
Published: August 2010

The vegetative propagation of hydrangea (Hydrangea macrophylla "Leuchtfeuer") should be explored through the architectural concepts of woody plants. The formation and continued culture of mother microplants in the greenhouse with high relative humidity and long days make up the new propagation method. Vegetative growth is characterized by the prolific production of homogenous cuttings as basal shoots in which the morphology of the axis is similar to that of plants produced by germination. There is considerable capacity for high levels of production, and it is a possible alternative to in vitro and traditional propagation. The morphogenetic basis of the functioning of these cultures is discussed in relation to juvenility and differentiation in woody plants. Keywords: morphogenesis, Hydrangea macrophylla, vegetative propagation, juvenility.