bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome
Authors: Cockram James , White Jon , Zuluaga Diana L. , Smith David , Comadran Jordi , Macaulay Malcolm , Luo Zewei , Kearsey Mike J. , Werner Peter , Harrap David , Tapsell Chris , Liu Hui , Hedley Peter E. , Stein Nils , Schulte Daniela , Steuernagel Burkhard , Marshall David F. , Thomas William T. B. , Ramsay Luke , Mackay Ian , Balding David J. ,   The AGOUEB Consortium, Waugh Robbie , O'Sullivan Donal M. ,   Members of the AGOUEB Consortium, Booer Chris , Pike Steve , Hamilton Graeme , Jellis Graham , Davies Nigel , Ross Anne , Bury Paul , Habgood Rodney , Klose Steve , Vequaud Dominique , Christerson Therese , Brosnan James , Newton Adrian , Russell Joanne , Shaw Paul , Bayles Rosemary , Wang Minghui
Published: November 2010

Although commonplace in human disease genetics, genome-wide association (GWA) studies have only relatively recently been applied to plants. Using 32 phenotypes in the inbreeding crop barley, we report GWA mapping of 15 morphological traits across ∼500 cultivars genotyped with 1,536 SNPs. In contrast to the majority of human GWA studies, we observe high levels of linkage disequilibrium within and between chromosomes. Despite this, GWA analysis readily detected common alleles of high penetrance. To investigate the potential of combining GWA mapping with comparative analysis to resolve traits to candidate polymorphism level in unsequenced genomes, we fine-mapped a selected phenotype (anthocyanin pigmentation) within a 140-kb interval containing three genes. Of these, resequencing the putative anthocyanin pathway gene
HvbHLH1
identified a deletion resulting in a premature stop codon upstream of the basic helix-loop-helix domain, which was diagnostic for lack of anthocyanin in our association and biparental mapping populations. The methodology described here is transferable to species with limited genomic resources, providing a paradigm for reducing the threshold of map-based cloning in unsequenced crops.
Bidirectional binding of invariant chain peptides to an MHC class II molecule
Authors: Günther Sebastian , Schlundt Andreas , Sticht Jana , Roske Yvette , Heinemann Udo , Wiesmüller Karl-Heinz , Jung Günther , Falk Kirsten , Rötzschke Olaf , Freund Christian
Published: November 2010

T-cell recognition of peptides bound to MHC class II (MHCII) molecules is a central event in cell-mediated adaptive immunity. The current paradigm holds that prebound class II-associated invariant chain peptides (CLIP) and all subsequent antigens maintain a canonical orientation in the MHCII binding groove. Here we provide evidence for MHCII-bound CLIP inversion. NMR spectroscopy demonstrates that the interconversion from the canonical to the inverse alignment is a dynamic process, and X-ray crystallography shows that conserved MHC residues form a hydrogen bond network with the peptide backbone in both orientations. The natural catalyst HLA-DM accelerates peptide reorientation and the exchange of either canonically or inversely bound CLIP against antigenic peptide. Thus, noncanonical MHC-CLIP displays the hallmarks of a structurally and functionally intact antigen-presenting complex.
Considerations for parameter optimization and sensitivity in climate models
Authors: Neelin J. David , Bracco Annalisa , Luo Hao , McWilliams James C. , Meyerson Joyce E.
Published: November 2010

Climate models exhibit high sensitivity in some respects, such as for differences in predicted precipitation changes under global warming. Despite successful large-scale simulations, regional climatology features prove difficult to constrain toward observations, with challenges including high-dimensionality, computationally expensive simulations, and ambiguity in the choice of objective function. In an atmospheric General Circulation Model forced by observed sea surface temperature or coupled to a mixed-layer ocean, many climatic variables yield rms-error objective functions that vary smoothly through the feasible parameter range. This smoothness occurs despite nonlinearity strong enough to reverse the curvature of the objective function in some parameters, and to imply limitations on multimodel ensemble means as an estimator of global warming precipitation changes. Low-order polynomial fits to the model output spatial fields as a function of parameter (quadratic in model field, fourth-order in objective function) yield surprisingly successful metamodels for many quantities and facilitate a multiobjective optimization approach. Tradeoffs arise as optima for different variables occur at different parameter values, but with agreement in certain directions. Optima often occur at the limit of the feasible parameter range, identifying key parameterization aspects warranting attention—here the interaction of convection with free tropospheric water vapor. Analytic results for spatial fields of leading contributions to the optimization help to visualize tradeoffs at a regional level, e.g., how mismatches between sensitivity and error spatial fields yield regional error under minimization of global objective functions. The approach is sufficiently simple to guide parameter choices and to aid intercomparison of sensitivity properties among climate models.
Organocatalysis
Authors: Jacobsen Eric N. , MacMillan David W. C.
Published: November 2010

The use of small-molecule organic catalysts in organic synthesis has flourished over the past decade. Examples of defining concepts and cutting-edge results are provided in the papers in this Special Feature.
Retrieval induces reconsolidation of fear extinction memory
Authors: Rossato Janine I. , Bevilaqua Lia R. , Izquierdo Iván , Medina Jorge H. , Cammarota Martín
Published: December 2010

The nonreinforced expression of long-tem memory may lead to two opposite protein synthesis-dependent processes: extinction and reconsolidation. Extinction weakens consolidated memories, whereas reconsolidation allows incorporation of additional information into them. Knowledge about these two processes has accumulated in recent years, but their possible interaction has not been evaluated yet. Here, we report that inhibition of protein synthesis in the CA1 region of the dorsal hippocampus after retrieval of fear extinction impedes subsequent reactivation of the extinction memory trace without affecting its storage or that of the initial fear memory. Our results suggest that extinction memory is susceptible to a retrieval-induced process similar to reconsolidation in the hippocampus.
Language variation and linguistic description in 16th-century France
Authors: Kibbee Douglas A.
Published: November 2010

The first French grammarians to consider the French language condemned variation – historical variation, geographical variation, and sociolinguistic variation. For the French language to be first among vernacular languages, it had to have fixity, to be governed by absolute rules. How can one determine if a lexical item, pronunciation feature, or morphological feature should be accepted? Some would study the best authors, but the list of such authors is a matter of debate. Others would define the ‘true French’ geographically, but they tend to choose their own regions. Ultimately, the choice depends on a sense of ‘usage’ which is in harmony with the ‘naïve puissance’ of the language, the pursuit of which may ultimately lead to a reunification of word and object, a unity lost at the Tower of Babel. The grammarians’ attacks on variation serve biblical as well as political destiny.
Phonetics and phonology 1949–1989
Authors: Sara Solomon I.
Published: November 2010

Phonetics and Phonology have had noticeable developments in the last forty years: phonetics from the articulatory descriptions of sounds of Pike’s Phonetics (1943), to a physiological set of distinctive features of Chomsky & Halle’s The Sound Pattern of English (1968); the acoustic displays of Potter’s Visible Speech (1947) to a set of acoustic distinctive features in Jakobson, Fant, Halle’s Preliminaries (1951). Suprasegmental characterizations have developed from impressionistic labels of tone, stress, length and intonation to an experimentally quantifiable set of parameters characterizing these aspects of speech in a unified manner in Lehiste’s Suprasegmentals (1970). Phonology progressed from the autonomous to the integrated, and from the structural to the transformational/generative, from Pike’s Phonemics (1947), and Trubetzkoy’s Grundzüge (1939) to a complex system of levels/tiers/strata that represent speech in a more detailed, holistic and integrated manner. Current approaches recognize not only the features and segments of the speech continuum, but the rules that organize these into the phonological system. Approaches to the explanation of this organization have been many: the segmental/sequential approach of American phonemicists, Praguian phonologists and early generativists developed into a phonological component that consists of segments, organized into syllables that pattern into rhythmic feet which constitute the geometry of the sequence as a multi level/tier/stratum. These developments are all considered generative, but labelled Natural-Generative, Autosegmental-Genera-tive, Non-Linear-Generative, Metrical-Generative, etc. ‘Generative’ is kept to maintain the twin characteristics of being integrated and rule governed. There has been a shift in the paradigm: from segments to features and from structural to transformational with significant developments in both paradigms in the last forty years.
The beginnings of phonology in Italy
Authors: Albano Leoni Federico
Published: November 2010

It is known that structural phonology (and, more generally, structural linguistics) began in Italy later than in other European countries. In the general opinion, this was due to the hegemony of Benedetto Croces’s philosophy during the years between World War I and his death in 1952. This paper shows how an early attempt to give a structural description of Italian phonology (Porru 1939) encountered an exceptionally harsh review (Pisani 1939), which appears to have been motivated more by personal and academic considerations than by philosophical or theoretical grounds. The authority of Pisani seemed to discourage any other attempt by Italian linguists to join European structuralism until about 1950. In fact, in that year two articles appeared (by no other than Pisani and by Devoto) which seemed to mark the end of a prohibition. The conclusion that may be drawn from this episode is that the development of sciences depends not only on general theoretical and cultural frames but also on actions and choices of individuals.
‘Core’ and ‘Periphery’ in Historical Perspective
Authors: Joseph John E.
Published: November 2010

This article traces the changing fortunes of Chomsky’s concepts of ‘core’ and ‘periphery’, from the beginnings of Government and Binding Theory in the late 1970s to the incipient minimalism of the early 1990s. Ten different characterizations of core and periphery are found in Chomsky’s work of the period, which alternatively questions the need for the distinction and promotes it to central theoretical status. Core and periphery are found to pertain to several different conceptual and phenomenological levels: universality, systematicity, typology, and historicity. Furthermore, they covertly recapitulate some of the oldest dichotomies of linguistic thought: nature/convention, analogy/anomaly, synchronic/diachronic, and marked/unmarked. The conclusions reached support recent changes in the theory which greatly reduce the prominence of the core/periphery distinction.
Las Osservationi de Giovanni Miranda
Authors: Blanch Juan M. Lope
Published: November 2010

Giovanni Miranda’s Osservationi della Lingua Castigliana (Venice, 1566) was the best pedagogical grammar of Spanish of its time; and since it served as a model to French, English, and German grammarians it was important well beyond Italy. Because it was essentially a practical teaching work, one finds in it few theoretical pronouncements. Theory, however, is not totally absent from his book, as becomes obvious in the discussion of the concept of ‘sentence’ or of the ‘parts of speech’, but as a whole the work deals with questions that were thought to be essential to the learner of a language, mostly morphology and certain peculiarities of Castilian grammar and usage. The work is divided into four parts: I, the article, the noun, the adjective, and the pronoun; II, the verb, whose conjugation is dealt with exhaustively; III, the non-inflectional parts of speech in Spanish; and IV, spelling and pronunciation. Throughout the work the author discusses related semantic, lexical, and phraseological subjects, and uses proverbs, anecdotes, and very short stories to illustrate colloquial usage of Spanish. Miranda’s Osservationi were influenced by Giovanni Mario Alessandri d’Urbino’s Paragone della Lingua Toscana et Castigliana (Naples, 1560). Miranda the format of the Paragone, but greatiy expands on it. The Osservationi della Lingua Castigliana can be said to be the first effective pedagogical grammar of Spanish written for speakers of other languages.
Sobre la formación del corpus de autoridades en la Gramática Española
Authors: Lliteras Poncel Margarita
Published: November 2010

In the Spanish tradition, descriptive grammars based both factually and methodologically on a corpus gleaned from identified contemporary sources, mostly taken from literature, do not appear until the several editions (11831–81847) of the grammar of Vicente Salvâ (1786–1849), and later in that of Andrés Bello (11847–1860). A small part of Salvá’s corpus does come from medieval and renaissance authors, but these are used only to illustrate diachronic change in Spanish. Salvá’s empirical and descriptive approach, and that of other 19th-century Spanish and Spanish American grammarians that follow him, leads to specialization within the wider field of grammar and, as is shown here, syntax is the area that profits the most, both in depth and in size or extension. There is no precedent for this grammaticographical tradition in the Renaissance, when a literary corpus is used only for those parts of the texts that traditionally dealt with metrics and versification. Renaissance grammarians derived the authority of their texts from the transfer of the rules of Latin grammar into Spanish, not from the language of the literary canon. During the 18th-century Enlightenment grammars based on a literary corpus begin to appear, but the authors from whose works the corpus is taken are those of a previous (non-contemporary) period. As shown in this article, it is in the 18th century that descriptivism results in an increase in the importance of syntax, although that increment in size is minor by comparison with that which takes place during the 19th century beginning with the works of Salvá.
La historificación de la lingüística histórica
Authors: del Valle José
Published: November 2010

The main tenet of this article is that Spanish philologist Ramón Menéndez Pidal’s (1869–1968) theoretical approach to the history of the language, as developed in his Manual de gramática histórica española (1904) and in Orígenes del español (1926), was a result not only of a highly original interpretation of the linguistic theories available to him and a need to improve their explanatory power, but also from an interplay between this theory and the ideological context from which it emerged. This ideological context, which I maintain is critical for the understanding of the full implications of Menéndez Pidal’s linguistic approach, has been assumed by traditional historiography to be outside the scope of linguistics. It is claimed here that the Spanish philologist’s scholarly accomplishments, justly praised by his disciples and hispanists in general, did not occur in a social vacuum, but were instead well entrenched in a specific intellectual, social, and historical context. Menéndez Pidal lived and worked in a period in which Spain, like other 19th-century liberal democracies, was building its identity as a nation-state. In this period, the construction of the Spanish nation was threatened by centrifugal forces (e.g., the articulation of Basque, Catalan, and Galician nationalisms) that challenged Spain’s unitary political and cultural identity. It is precisely against the backdrop of this socio-political landscape that Menéndez Pidal’s use of the neogrammarian model of convergence in the Manual, his scrupulous philological examination of old documents in Orígenes is interpreted – which, for him, offered proof of Castile’s destiny as the leading force in the history of Spain, including his integrative reworking of the phonetic law converting it into a means by which to perceive the unity underlying dialectal variation.
Learning implicitly to produce avoided behaviours
Authors: Witt Arnaud , Vinter Annie
Published: December 2010

The literature on repetition processing reveals an intriguing paradox between the particular salience of repetitions, which makes them easy to learn, and a tendency to avoid them when generating sequences. The aim of this experiment was to study the extent to which children can learn to produce these avoided behaviours by means of an artificial grammar paradigm using generation tests with implicit or explicit instructions. The analysis of the control group's performance confirmed the presence of a spontaneous tendency to avoid generating repetitions. A comparison with chance revealed that the children learned to produce repetitions in the explicit test but not in the implicit test. However, a comparison with the control group showed that learning nonetheless occurred in the experimental group with the implicit test. The discussion focused on this antirepetition behavioural bias and how it interacted with the type of information processes elicited by the tests selected for assessing implicit learning effects.
Electronic Prediction Rules for Methicillin-ResistantStaphylococcus aureusColonization
Authors: Robicsek Ari , Beaumont Jennifer L. , Wright Marc-Oliver , Thomson Richard B. , Kaul Karen L. , Peterson Lance R.
Published: December 2010

Background.

Considerable hospital resources are dedicated to minimizing the number of methicillin-resistantStaphylococcus aureus(MRSA) infections. One tool that is commonly used to achieve this goal is surveillance for MRSA colonization. This process is costly, and false-positive test results lead to isolation of individuals who do not carry MRSA. The performance of this technique would improve if patients who are at high risk of colonization could be readily targeted.

Methods.

Five MRSA colonization prediction rules of varying complexity were derived in a population of 23,314 patients who were consecutively admitted to a US hospital and tested for colonization. Rules incorporated only prospectively collected, structured electronic data found in a patient's record within 1 day of hospital admission. These rules were tested in a validation cohort of 26,650 patients who were admitted to 2 other hospitals.

Results.

The prevalence of MRSA at hospital admission was 2.2% and 4.0% in the derivation and validation cohorts, respectively. Multivariable modeling identified predictors of MRSA colonization among demographic, admission-related, pharmacologic, laboratory, physiologic, and historical variables. Five prediction rules varied in their performance, but each could be used to identify the 30% of patients who accounted for greater than 60% of all cases of MRSA colonization and approximately 70% of all MRSA-associated patient-days. Most rules could also identify the 20% of patients with a greater than 8% chance of colonization and the 40% of patients among whom colonization prevalence was 2% or less.

Conclusions.

We report electronic prediction rules that can fully automate triage of patients for MRSA-related hospital admission testing and that offer significant improvements on previously reported rules. The efficiencies introduced may result in savings to infection control programs with little sacrifice in effectiveness.
Impact of Switching from an Open to a Closed Infusion System on Rates of Central Line–Associated Bloodstream Infection: A Meta-analysis of Time-Sequence Cohort Studies in 4 Countries
Authors: Maki Dennis G. , Rosenthal Victor D. , Salomao Reinaldo , Franzetti Fabio , Rangel-Frausto Manuel Sigfrido
Published: December 2010

Background.

We report a meta-analysis of 4 identical time-series cohort studies of the impact of switching from use of open infusion containers (glass bottle, burette, or semirigid plastic bottle) to closed infusion containers (fully collapsible plastic containers) on central line-associated bloodstream infection (CLABSI) rates and all-cause intensive care unit (ICU) mortality in 15 adult ICUs in Argentina, Brazil, Italy, and Mexico.

Methods.

All ICUs used open infusion containers for 6–12 months, followed by switching to closed containers. Patient characteristics, adherence to infection control practices, CLABSI rates, and ICU mortality during the 2 periods were compared by χ2test for each country, and the results were combined using meta-analysis.

Results.

Similar numbers of patients participated in 2 periods (2,237 and 2,136). Patients in each period had comparable Average Severity of Illness Scores, risk factors for CLABSI, hand hygiene adherence, central line care, and mean duration of central line placement. CLABSI incidence dropped markedly in all 4 countries after switching from an open to a closed infusion container (pooled results, from 10.1 to 3.3 CLABSIs per 1,000 central line-days; relative risk [RR], 0.33 [95% confidence interval {CI}, 0.24-0.46];P<.001). All-cause ICU mortality also decreased significantiy, from 22.0 to 16.9 deaths per 100 patients (RR, 0.77 [95% CI, 0.68-0.87];P<.001).

Conclusions.

Switching from an open to a closed infusion container resulted in a striking reduction in the overall CLABSI incidence and all-cause ICU mortality. Data suggest that open infusion containers are associated with a greatiy increased risk of infusion-related bloodstream infection and increased ICU mortality that have been unrecognized. Furthermore, data suggest CLABSIs are associated with significant attributable mortality.
On the irreducibility of locally analytic principal series representations
Authors: Orlik Sascha , Strauch Matthias
Published: December 2010

LetG\mathbf {G}be app-adic connected reductive group with Lie algebrag\mathfrak {g}. For a parabolic subgroupP⊂G\mathbf {P} \subset \mathbf {G}and a finite-dimensional locally analytic representationVVof a Levi subgroup ofP\mathbf {P}, we study the induced locally analyticG\mathbf {G}-representationW=IndPG⁡(V)W = \operatorname {Ind}_{\mathbf {P}}^{\mathbf {G}}(V). Our result is the following criterion concerning the topological irreducibility ofWW: If the Verma moduleU(g)⊗U(p)V′U(\mathfrak {g}) \otimes _{U(\mathfrak {p})} V’associated to the dual representationV′V’is irreducible, thenWWis topologically irreducible as well.
Mechanisms of plasma membrane targeting of formin mDia2 through its amino terminal domains
Authors: Gorelik Roman , Yang Changsong , Kameswaran Vasumathi , Dominguez Roberto , Svitkina Tatyana
Published: December 2010

The formin mDia2 mediates the formation of lamellipodia and filopodia during cell locomotion. The subcellular localization of activated mDia2 depends on interactions with actin filaments and the plasma membrane. We investigated the poorly understood mechanism of plasma membrane targeting of mDia2 and found that the entire N-terminal region of mDia2 preceding the actin-polymerizing formin homology domains 1 and 2 (FH1–FH2) module was potently targeted to the membrane. This localization was enhanced by Rif, but not by other tested small GTPases, and depended on a positively charged N-terminal basic domain (BD). The BD bound acidic phospholipids in vitro, suggesting that in vivo it may associate with the plasma membrane through electrostatic interactions. Unexpectedly, a fragment consisting of the GTPase-binding region and the diaphanous inhibitory domain (G-DID), thought to mediate the interaction with GTPases, was not targeted to the plasma membrane even in the presence of constitutively active Rif. Addition of the BD or dimerization/coiled coil domains to G-DID rescued plasma membrane targeting in cells. Direct binding of Rif to mDia2 N terminus required the presence of both G and DID. These results suggest that the entire N terminus of mDia2 serves as a coincidence detection module, directing mDia2 to the plasma membrane through interactions with phospholipids and activated Rif.
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models
Authors: Fleming Ronan M. T. , Thiele Ines
Published: November 2010

Motivation: In flux balance analysis of genome scale stoichiometric models of metabolism, the principal constraints are uptake or secretion rates, the steady state mass conservation assumption and reaction directionality. Here, we introduce an algorithmic pipeline for quantitative assignment of reaction directionality in multi-compartmental genome scale models based on an application of the second law of thermodynamics to each reaction. Given experimental or computationally estimated standard metabolite species Gibbs energy and metabolite concentrations, the algorithms bounds reaction Gibbs energy, which is transformed to in vivo pH, temperature, ionic strength and electrical potential.

Results: This cross-platform MATLAB extension to the COnstraint-Based Reconstruction and Analysis (COBRA) toolbox is computationally efficient, extensively documented and open source.

Availability:  http://opencobra.sourceforge.net

Contact:  ronan.mt.fleming@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Granular Packing Influences Bulk Density of DDGS
Authors: Keierleber Christine , Rosentrater Kurt A.
Published: November 2010

As the quantity of ethanol produced continues to increase, the amount of distillers dried grains with solubles (DDGS), the primary coproduct of ethanol manufacturing, has become more widely available. Currently, the main consumer of DDGS is the livestock industry, but new value‐added uses are garnering interest. With the increase in the availability of, and demand for DDGS, transportation has become an important issue because DDGS must be shipped increasingly long distances using railways. Rail transportation is expensive, especially considering the quantities of DDGS that can be loaded onto unit trains. DDGS often has low bulk density and poor flowability characteristics. This study examined compression effects on particle arrangements as quantified by bulk density and compressibility of the DDGS. Mean loose bulk density was 446.18 kg/m3. A linear relationship (R2 = 0.982 for 50 N applied force and R2 = 0.959 for 1 kN applied force) was observed between the applied stress (≈0.0–0.0065 and ≈0.0–0.13 MPa, respectively) and the resulting packed bulk density (≤470.21 and ≤555.03 kg/m3, respectively). Compressive stress increased curvilinearly (R2 = 0.994 for the 50 N load and R2 = 0.997 for the 1 kN load) as the applied strain increased (≈0.0–0.007% and 0.0–24.0%, respectively). As the loading increased, compressibility increased 5.11–19.22%. Bulk restitution after loading was removed was 0.53–0.61. Required storage volume is reduced when the bulk density is increased. But flowability characteristics should improve as the compressibility, and thus the bulk density, of the product is reduced.
Accumulation of Oxygenated Fatty Acids in Oat Lipids During Storage
Authors: Doehlert Douglas C. , Angelikousis Steven , Vick Brady
Published: November 2010

Oxygenated fatty acids were identified in oat grain by gas chromatography‐mass spectrometry. We hypothesized that most of these were the results of lipoxygenase activity. This hypothesis was tested by measuring concentrations of these compounds after hydrothermal treatments and storage of oat groats or oat flour for 22 weeks at 37°C and 65% relative humidity. Steam treatments inactivated lipases, whereas roasting at 106°C did not. Free fatty acids accumulated quickly in untreated or roasted flour, but not in steamed flour or groats. A total of six hydroxy and epoxy fatty acids were identified. Oxidized fatty acids were found in both esterified lipids and free fatty acids, indicating that lipase action was not necessary for lipid oxidation. More oxidation products were found in flour than in groats, and less were found in the steamed treatments. Lipoperoxygenase appeared to be involved in the formation of oxidation products, although nonenzymatic mechanisms may also operate. Hydroxy‐fatty acids are associated with strongly bitter flavors and are undesirable. Results indicate the importance of enzyme inactivation before storage of processed oat products.
Effects of Silicon Applications on Soybean Rust Development Under Greenhouse and Field Conditions
Authors: Lemes E. M. , Mackowiak C. L. , Blount A. , Marois J. J. , Wright D. L. , Coelho L. , Datnoff L. E.
Published: November 2010

Soybean rust (SBR), caused by Phakopsora pachyrhizi, is one of the most destructive fungal diseases affecting soybean production. Silicon (Si) amendments were studied as an alternative strategy to control SBR because this element was reported to suppress a number of plant diseases in other host–pathogen systems. In greenhouse experiments, soybean cultivars inoculated with P. pachyrhizi received soil applications of wollastonite (CaSiO3) (Si at 0, 0.96, and 1.92 t ha–1) or foliar applications of potassium silicate (K2SiO3) (Si at 0, 500, 1,000, or 2,000 mg kg–1). Greenhouse experiment results demonstrated that Si treatments delayed disease onset by approximately 3 days. The area under disease progress curve (AUDPC) of plants receiving Si treatments also was significantly lower than the AUDPC of non-Si-treated plants. For field experiments, an average 3-day delay in disease onset was observed only for soil Si treatments. Reductions in AUDPC of up to 43 and 36% were also observed for soil and foliar Si treatments, respectively. Considering the natural delayed disease onset due to the inability of the pathogen to overwinter in the major soybean production areas of the United States, the delay in disease onset and the final reduction in AUDPC observed by the soil Si treatments used may lead to the development of SBR control practices that can benefit organic and conventional soybean production systems.
Diagnosis of Alagille Syndrome—25 Years of Experience at King's College Hospital
Authors: Subramaniam P , Knisely A , Portmann B , Qureshi SA , Aclimandos WA , Karani JB , Baker AJ
Published: November 2010

Objective:

The aim of the study was to study the clinical and histological features of Alagille syndrome (AGS) at presentation comparing the value of the various modalities before the implementation of genetic diagnosis.

Patients and Methods:

We performed a retrospective analysis of the records of 117 children diagnosed as having AGS after referral to King's College Hospital between 1980 and 2005.

Results:

Cholestasis was seen in 104 of 117 (89%), characteristic facies in 91 of 117 (77%), posterior embryotoxon in 72 of 117 (61%), butterfly vertebrae in 44 of 117 (39%), heart disease (most often peripheral pulmonary stenosis) in 107 of 117 (91%), and renal disease in 27 of 117 (23%). Serum cholesterol levels of >5 mmol/L were seen in 52 of 86 (60.4%). Liver biopsy showed characteristic features of paucity of interlobular bile ducts in 59 of 77 (76.6%) children younger than 16 weeks of age, in 10 of 14 (71.4%) between 16 weeks and 1 year of age, and in 8 of 12 (66.66%) older than 1 year of age. Other biopsy findings were those of nonspecific hepatitis and biliary features. Iminodiacetic acid scans showed no excretion of isotope into the bowel after 24 hours in 21 of 35 (60%), and small/no gallbladder on ultrasound was seen in 29 of 104 (27.8%). Eleven of 117 (9.4%) had a diagnostic laparotomy and operative cholangiography, 2 proceeding to Kasai portoenterostomy before referral to our unit.

Conclusions:

Clinical features of AGS are not as consistently informative as suggested in the literature. Hypercholesterolaemia is nonspecific but may be a helpful pointer. Histology is not characteristic in 25%; hepatobiliary iminodiacetic acid scan and ultrasound may suggest a false diagnosis of biliary atresia in 60% and 28%, respectively, supporting the concept that infants with liver disease warrant early referral to a specialist centre. The advent of genetic diagnosis will redefine the syndrome with likely effects on the prognosis of the defined group.
Herpes Simplex Virus is Akt-ing in translational control
Authors: Norman Kara L. , Sarnow Peter
Published: December 2010

All viruses depend on the cellular protein synthesis machinery for the production of viral proteins. Thus, viruses have evolved a variety of strategies to avoid innate host responses that inhibit protein synthesis. In this issue of Genes & Development, Chuluunbaatar and colleagues (pp. 2627–2639) demonstrate that Herpes Simplex Virus-1 counteracts this response through viral kinase Us3, which mimics cellular kinase Akt to phosphorylate and repress tuberous sclerosis complex 2 (TSC2), resulting in the activation of mammalian target of rapamycin complex 1 (mTORC1) and enhancement of mRNA translation.
Isolation of Xenopus Oocytes
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M.
Published: December 2010

INTRODUCTION

Xenopus oocytes are obtained from sexually mature females by surgically removing parts of the ovary. The operation is not fatal and can be performed on an anesthetized frog several times during its lifetime. However, a recovery period of 2 wk is recommended between operations. A careful record of all operations performed, including details of oocyte quality, should be kept. A frog that produces one good batch of oocytes; e.g., those that translate injected messenger RNAs (mRNAs) efficiently, should be recorded and used again, because oocyte quality is generally frog-dependent.
Microinjection of Xenopus Oocytes
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M.
Published: December 2010

INTRODUCTION

Xenopus oocytes can be injected with messenger RNA (mRNA) or DNA constructs into the cytoplasm or nucleus, respectively. The cytoplasm can withstand the introduction of up to 50 nL of injected material, and the nucleus can tolerate up to 20 nL. This protocol describes microinjection of both defolliculated and folliculated Xenopus oocytes. Oocytes remain in good condition for a relatively long time, and injections can be continued, if necessary, over a period of days.
Strigolactones Are Transported through the Xylem and Play a Key Role in Shoot Architectural Response to Phosphate Deficiency in Nonarbuscular Mycorrhizal Host Arabidopsis
Authors: Kohlen Wouter , Charnikhova Tatsiana , Liu Qing , Bours Ralph , Domagalska Malgorzata A. , Beguerie Sebastien , Verstappen Francel , Leyser Ottoline , Bouwmeester Harro , Ruyter-Spira Carolien
Published: December 2010

The biosynthesis of the recently identified novel class of plant hormones, strigolactones, is up-regulated upon phosphate deficiency in many plant species. It is generally accepted that the evolutionary origin of strigolactone up-regulation is their function as a rhizosphere signal that stimulates hyphal branching of arbuscular mycorrhizal fungi. In this work, we demonstrate that this induction is conserved in Arabidopsis (Arabidopsis thaliana), although Arabidopsis is not a host for arbuscular mycorrhizal fungi. We demonstrate that the increase in strigolactone production contributes to the changes in shoot architecture observed in response to phosphate deficiency. Using high-performance liquid chromatography, column chromatography, and multiple reaction monitoring-liquid chromatography-tandem mass spectrometry analysis, we identified two strigolactones (orobanchol and orobanchyl acetate) in Arabidopsis and have evidence of the presence of a third (5-deoxystrigol). We show that at least one of them (orobanchol) is strongly reduced in the putative strigolactone biosynthetic mutants more axillary growth1 (max1) and max4 but not in the signal transduction mutant max2. Orobanchol was also detected in xylem sap and up-regulated under phosphate deficiency, which is consistent with the idea that root-derived strigolactones are transported to the shoot, where they regulate branching. Moreover, two additional putative strigolactone-like compounds were detected in xylem sap, one of which was not detected in root exudates. Together, these results show that xylem-transported strigolactones contribute to the regulation of shoot architectural response to phosphate-limiting conditions.
Allelic Variation in the Perennial Ryegrass FLOWERING LOCUS T Gene Is Associated with Changes in Flowering Time across a Range of Populations
Authors: Skøt Leif , Sanderson Ruth , Thomas Ann , Skøt Kirsten , Thorogood Danny , Latypova Galina , Asp Torben , Armstead Ian
Published: November 2010

The Arabidopsis (Arabidopsis thaliana) FLOWERING LOCUS T (FT) gene and its orthologs in other plant species (e.g. rice [Oryza sativa] OsFTL2/Hd3a) have an established role in the photoperiodic induction of flowering response. The genomic and phenotypic variations associated with the perennial ryegrass (Lolium perenne) ortholog of FT, designated LpFT3, was assessed in a diverse collection of nine European germplasm populations, which together constituted an association panel of 864 plants. Sequencing and genotyping of a series of amplicons derived from the nine populations, containing the complete exon and intron sequences as well as 5′ and 3′ noncoding sequences of LpFT3, identified a total of seven haplotypes. Genotyping assays designed to detect the genomic variation showed that three haplotypes were present in approximately equal proportions and represented 84% of the total, with a fourth representing a further 11%. Of the three major haplotypes, two were predicted to code for identical protein products and the third contained two amino acid substitutions. Association analysis using either a mixed model with a relationship matrix to correct for population structure and relatedness or structured association with further correction using genomic control indicated significant associations between LpFT3 and variation in flowering time. These associations were corroborated in a validation population segregating for the same major alleles. The most “diagnostic” region of genomic variation was situated 5′ of the coding sequence. Analysis of this region identified that the interhaplotype variation was closely associated with sequence motifs that were apparently conserved in the 5′ region of orthologs of LpFT3 from other plant species. These may represent cis-regulatory elements involved in influencing the expression of this gene.
Meiotic Progression inArabidopsisIs Governed by Complex Regulatory Interactions between SMG7, TDM1, and the Meiosis I–Specific Cyclin TAM
Authors: Bulankova Petra , Riehs-Kearnan Nina , Nowack Moritz K. , Schnittger Arp , Riha Karel
Published: December 2010

Meiosis is a modified cell division that produces four haploid nuclei from a single diploid cell in two rounds of chromosome segregation. Here, we analyze the role of Arabidopsis thaliana SUPPRESSOR WITH MORPHOGENETIC EFFECTS ON GENITALIA7 (SMG7), THREE DIVISION MUTANT1 (TDM1), and TARDY ASYNCHRONOUS MEIOSIS (TAM) in meiotic progression. SMG7 is a conserved nonsense-mediated mRNA decay factor that is also, in Arabidopsis, essential for completion of meiosis. Examination of activating CYCLIN DEPENDENT KINASE A;1 phosophorylation at Thr-161 suggests that the meiotic arrest observed in smg7 mutants is likely caused by a failure to downregulate cyclin-dependent kinase (CDK) activity at the end of the second meiotic division. Genetic analysis indicates that SMG7 and TDM1 act in the same pathway to facilitate exit from meiosis. We further demonstrate that the cyclin TAM is specifically expressed in meiosis I and has both stimulatory and inhibitory effects on progression to meiosis II. TAM knockouts skip the second meiotic division producing unreduced gametes, but inactivation of SMG7 or TDM1 alleviates TAM's requirement for entry into meiosis II. We propose a model that meiotic progression in Arabidopsis pollen mother cells is driven by a yet to be identified cyclin-CDK activity that is modulated by regulatory interactions between TDM1, SMG7, and TAM.
Arabidopsis Kinetochore Fiber-Associated MAP65-4 Cross-Links Microtubules and Promotes Microtubule Bundle Elongation
Authors: Fache Vincent , Gaillard Jérémie , Van Damme Daniel , Geelen Danny , Neumann Emmanuelle , Stoppin-Mellet Virginie , Vantard Marylin
Published: December 2010

The acentrosomal plant mitotic spindle is uniquely structured in that it lacks opposing centrosomes at its poles and is equipped with a connective preprophase band that regulates the spatial framework for spindle orientation and mobility. These features are supported by specialized microtubule-associated proteins and motors. Here, we show that Arabidopsis thaliana MAP65-4, a non-motor microtubule associated protein (MAP) that belongs to the evolutionarily conserved MAP65 family, specifically associates with the forming mitotic spindle during prophase and with the kinetochore fibers from prometaphase to the end of anaphase. In vitro, MAP65-4 induces microtubule (MT) bundling through the formation of cross-bridges between adjacent MTs both in polar and antipolar orientations. The association of MAP65-4 with an MT bundle is concomitant with its elongation. Furthermore, MAP65-4 modulates the MT dynamic instability parameters of individual MTs within a bundle, mainly by decreasing the frequency of catastrophes and increasing the frequency of rescue events, and thereby supports the progressive lengthening of MT bundles over time. These properties are in line with its role of initiating kinetochore fibers during prospindle formation.
Ability of radial arterial palpation and observation of the pulse oximetry trace to estimate non‐invasive systolic pressure in healthy volunteers and in women undergoing spinal anaesthesia for elective caesarean section*
Authors: Sabharwal A. , Strickland T. , Yentis S. M.
Published: November 2010

We assessed the ability of palpating the radial arterial pulse and observing the oximeter trace to estimate the automated non‐invasive systolic pressure reading in 20 healthy female volunteers and 20 parturients undergoing spinal anaesthesia for elective caesarean section. Using real‐time values of cuff pressure during inflation/deflation, the pressure was recorded when the manually palpated radial arterial pulse or pulse oximeter waveform disappeared and reappeared. The actual measured systolic pressure was noted and the results compared using Bland–Altman analysis. In the volunteers, the bias/precision for radial arterial palpation was −12.9/22.1 mmHg (inflation) and −9.7/16.7 mmHg (deflation), and for oximetry 29.5/18.8 mmHg (inflation) and −20.7/21.7 mmHg (deflation). In the parturients, the bias/precision was −19.0/47.6 mmHg (inflation) and −15.5/51.0 mmHg (deflation) for arterial palpation, and 22.6/16.1 mmHg (inflation) and −14.2/19.9 mmHg (deflation) for oximetry. Our results suggest that neither method is accurate at estimating the non‐invasive systolic pressure, with all except oximetry (inflation) underestimating it by approximately 10–20 mmHg and with poor precision.
Debris flow burial of ancient wall system in the Upper Po River valley
Authors: Mahaney William C. , Tricart Pierre , Barendregt Rene W. , Carcaillet Christopher , Rabufetti Davide , Kalm Volli
Published: November 2010

The regrouping area, where Hannibal is thought to have reformed his army after forging a path through a massive rockfall in the Cottian Alps, has been reshaped by a blanket of sediment deposited from debris flows following heavy rain in spring, 2008. Analysis of precipitation data for the period mid‐May to mid‐June, 2008, shows that 722 mm of rain fell at 2150 m, falling off to half that amount at 3325 m on the flanks of Mon Viso. Following exhaustive analysis of environmental factors connected with the invasion of Italy at the start of the Second Punic War (218 bc), identification of the regrouping area for the Carthaginian Army centred on the presence of an ancient stone wall system which possibly dates from Hannibalic times. Lichen cover, lichen diameters, weathering characteristics, degree to which boulders had sunk into the resident soil, and presence of ancient hearths all combined to make this area a choice locale for reconstructive geoarchaeology. Large scale mass wasting off a prominent bedrock bar adjacent to the wall system in the Upper Po River Valley resulted in burial of most of the prominent wall structures which will complicate any exploration geoarchaeology attempts in future.
Classic localities explained 6: Tobago
Authors: Donovan Stephen K. , Jackson Trevor A.
Published: November 2010

The island of Tobago is only about 40 km in length and to the geologist is a demonstration of the old saying that good things come in small packages. Situated in the southeast corner of the Caribbean Plate, it is the eastern extremity of the Caribbean Mountain System of northern South America, and is divided into three geologic provinces, one metamorphic, one igneous and one sedimentary.
Emulsifying properties and structural characteristics of β‐conglycinin and dextran conjugates synthesised in a pressurised liquid system
Authors: Xu Cai‐ hong , Yu Shu‐ juan , Yang Xiao‐quan , Qi Jun‐ru , Lin Hua , Zhao Zhen‐gang
Published: December 2010

The purpose of this study was to characterise the Maillard reaction in a pressurised liquid system containing β‐conglycinin and dextran. The rate of browning and the free amino content in this liquid system, with an initial pH of 7.2, were measured after reaction under atmospheric pressure and at 10 MPa. The secondary and tertiary structures of the conjugates were analysed by circular dichroism, showing that the increased pressure accelerated the reaction rate of the free amino groups and reduced the rate of browning. Significant structural changes occurred in the tertiary structure of the conjugates. Additionally, the emulsifying properties of the β‐conglycinin–dextran conjugates produced were studied. The emulsifying properties of the conjugates produced at 10 MPa were higher than those made at atmospheric pressure.
Effects of radiation process on total protein and amino acids composition of raw and processed pearl millet flour during storage
Authors: Mohamed ElShazali Ahmed , Mohamed Ahmed Isam A. , Yagoub Abu ElGasim A. , Babiker Elfadil E.
Published: December 2010

The present work describes radiation‐induced effects during storage on total protein and amino acids composition of raw and processed flour of two pearl millet cultivars (Ashana and Dembi). The protein content of the whole raw flour was 14.46% and 13.38% for Ashana and Dembi cultivars, respectively. Dehulling of the grains reduced the protein content to 13.38% and 12.67% for the cultivars, respectively. Storage of the radiated whole and dehulled flour for 60 days slightly reduced the protein content even after cooking. The effect of radiation process in combination with the treatments applied to the grains and/or flour on amino acids contents was found to be varying between the cultivars. Most of the amino acids were stable against all treatments except leucine, glutamic acid and phenylalanine. Regardless of the storage period and processing method, amino acid contents of Ashana cultivar were increased after radiation process compared to that of Dembi cultivar.