bluuebunny/crossref_metadata_2025 huggingface dataset:
The Last Frontier: The Importance of Kant's Geography
Authors: Louden Robert B
Published: April 2014

The first full English translation of Friedrich Theodor Rink's edition of Kant's Physical Geography was finally published in 2012, and several significant transcriptions of Kant's classroom lectures on physical geography are still forthcoming in volume 26 of the German Academy edition of his Collected Writings. Why has Kant's work on geography suffered from so much neglect? Contrary to received scholarly wisdom, I argue that the main cause of the neglect is not Rink's editorial sloppiness. Rather, Kant's Geography is simply not viewed as being as important as his ethics, logic, metaphysics, theology, and anthropology. In my paper I argue that Kant's Geography deserves our respect, and I present four key reasons for taking it seriously.
How lexical ambiguity distributes activation to semantic neighbors
Authors: Jorge-Botana Guillermo , Olmos Ricardo
Published: April 2014

The role which the diversity of a word’s contexts plays in lexical access is currently the object of research. Vector-space models such as Latent Semantic Analysis (LSA) are useful to examine this role. Having an objective, discrete model of lexical representation allows us to objectify parameters in order to define contextual focalization in a more measurable way. In the first part of our study, we investigate whether certain empirical data on ambiguity can be modeled by means of an exclusively symbolic single representation model such as LSA and an excitatory-inhibitory mechanism such as the Construction-­Integration framework. Our observations support the idea that some ambiguity effects could be explained by the contextual distribution using such a model. In the second part, we put abstract and concrete words to the test. Our LSA model (exclusively symbolic) and the excitatory-inhibitory mechanism can also explain the penalty paid by abstract words as they activate other words through semantic similarity and the advantage of concrete words in naming and semantic judgments, though it does not account for the advantage of concrete words in lexical decision tasks. The results of this second part are then discussed within the framework of the embodied/symbolic view of the language process.
Overgeneralization in the processing of complex forms in Valley Zapotec child language
Authors: Stemberger Joseph Paul , Chávez-Peón Mario E.
Published: April 2014

Models of language learning and processing differ in their level of emphasis on the storage of individual meaningful units versus combinations of meaningful units. While there is evidence for the storage of larger stretches of speech, a separate issue is how much such stored forms contribute to processing, as compared to morphologically simpler forms. We examine the acquisition of one aspect of the phonology of Valley Zapotec: complementarity of segmental length based on subsegmental features: vowels before fortis consonants are short (VCː), and vowels before lenis consonants are long (VːC). This complementarity is found for fortis consonants in morphologically simple forms with final stress (simple nouns, verbs with full subject noun), but not in morphologically complex forms with a final unstressed syllable (diminutive nouns, verbs with pronominal subject clitic). During one period of development, Zapotec-learning children overgeneralize the complementarity from morphologically simple to morphologically complex forms (with u-shaped learning likely). The child’s processing of complex forms in language production is based more on simple forms than on the complex forms themselves. We identify five possible explanations of these results. Insofar as combinations of morphemes are stored at this young age, they are relatively ineffective at influencing processing during language production.
Word frequency of written Urdu
Authors: Khan Quratulain H. , Buchanan Lori
Published: April 2014

Performance on word processing tasks is known to be influenced by the frequency with which words occur in a language. Large and robust effects of word frequency occur across languages and the processes thought to be sensitive to word frequency are considered fundamentally important characteristics of the mental lexicon. To our knowledge, word frequency data is non-existent for Urdu. This important language has characteristics that make it appealing to psycholinguists. Unfortunately, most of the Urdu published electronically is in the form of image files rather than text and therefore, has been largely inaccessible by programs designed to generate word counts. Consequently, unlike other important orthographies (e.g., English) orthographic word frequencies in Urdu are not readily available. We describe here a database that addresses this methodological gap. We have constructed a word frequency database for written Urdu and describe that development. We also describe data from simple tests of the effects of Urdu word frequency to demonstrate that our measure results in effects considered to be the hallmark of frequency effects. The frequency counts from this database will help psycholinguists and cognitive psychologists conduct and control future studies on the mental lexicon using Urdu. This database can be downloaded from http://web2.uwindsor.ca/psychology/urdufrequency/
Formats for other-initiation of repair across languages
Authors: Dingemanse Mark , Blythe Joe , Dirksmeyer Tyko
Published: April 2014

In conversation, people have to deal with problems of speaking, hearing, and understanding. We report on a cross-linguistic investigation of the conversational structure of other-initiated repair (also known as collaborative repair, feedback, requests for clarification, or grounding sequences). We take stock of formats for initiating repair across languages (comparable to Englishhuh?, who?, y’mean X?, etc.) and find that different languages make available a wide but remarkably similar range of linguistic resources for this function. We exploit the patterned variation as evidence for several underlying concerns addressed by repair initiation: characterising trouble, managing responsibility, and handling knowledge. The concerns do not always point in the same direction and thus provide participants in interaction with alternative principles for selecting one format over possible others. By comparing conversational structures across languages, this paper contributes to pragmatic typology: the typology of systems of language use and the principles that shape them.
Variation in pronominal indexing
Authors: Fedden Sebastian , Brown Dunstan , Kratochvíl František , Robinson Laura C. , Schapper Antoinette
Published: April 2014

We examine the role of referential properties and lexical stipulation in three closely related languages of eastern Indonesia, the Alor-Pantar languages Abui, Kamang, and Teiwa. Our focus is on the continuum along which event properties (e.g. volitionality, affectedness) are highly important at one extreme or play virtually no role at the other. These languages occupy different points along this continuum. In Abui, event semantics play the greatest role, while in Teiwa they play the smallest role (the lexical property animacy being dominant in the formation of verb classes). Kamang occupies an intermediate position. Teiwa has conventionalised the relation between a verb and its class along the lines of animacy so that classes become associated with the animacy value of the objects with which the verbs in a given class typically occur. Paying attention to a lexical property like animacy, in contrast with event properties, has meant greater potential for arbitrary classes to emerge.
Semantic fieldwork and lexical universals
Authors: Goddard Cliff , Wierzbicka Anna
Published: April 2014

The main goal of paper is to show how NSM findings about lexical universals (semantic primes) can be applied to semantic analysis in little-described languages. It is argued that using lexical universals as a vocabulary for semantic analysis allows one to formulate meaning descriptions that are rigorous, cognitively authentic, maximally translatable, and free from Anglocentrism. A second goal is to shed light on methodological issues in semantic fieldwork by interrogating some controversial claims about the Dalabon and Pirahã languages. We argue that reductive paraphrase into lexical universals provides a practical procedure for arriving at coherent interpretations of unfamiliar lexical meanings. Other indigenous/endangered languages discussed include East Cree, Arrernte, Kayardild, Karuk, and Maori. We urge field linguists to take the NSM metalanguage, based on lexical universals, into the field with them, both as an aid to lexicogrammatical documentation and analysis and as a way to improve semantic communication with consultants.
Variation as a cognitive device
Authors: Pecman Mojca
Published: April 2014

In Languages for Specific Purposes (LSPs), variation and term formation are often seen as related phenomena, variation being interpreted as a sign of neology. In scientific discourse though, variation can play specific roles, thereby giving a different dimension to neology as a linguistic process than generally implied in terminological studies. The well-known referential function, consisting of creating new designations for naming new concepts, can be set aside in scientific texts to create space for what we define as the cognitive function: a situation where a scientist purposefully employs term variation as a means for theorising and better explaining a given concept. We argue that Halliday’s “grammatical metaphor” and “given-new” information theory provide an interesting background for understanding scientific term formation processes, and the ensuing issue of terminological variation. Consequently, in this article, we try to place the phenomenon of neology and of terminological variation within the framework of discourse analysis, by devising a method for probing sequential behaviour of terminological variants across text sections. Additionally, this study aims to improve building lexical resources within the ARTES terminological and phraseological multilingual database project, which serves as a support for developing lexicographical and translational skills in students in specialised translation.
English and Spanish descriptors in wine tasting terminology
Authors: López-Arroyo Belén , Roberts Roda P.
Published: April 2014

Wine tasting notes constitute a specialized genre in the field of Oenology, with their own rhetoric and language. However, the language of wine tasting notes is by no means as specialized as that of most other specialized genres. Indeed, while there are dozens of terms used to describe and evaluate wines, there are only a limited number of words that are used exclusively or primarily for describing taste. In this study, we will first examine how wine literature attempts to analyze the descriptors used in wine tasting notes. We will then study a number of common wine descriptors in English and Spanish in the context of the nouns that they collocate with, in order to determine how specific or general these descriptors are in their use and meaning. On the basis of their collocability, we will categorize the descriptors into three categories and then analyze the meaning components of those descriptors that fall into the most general category.
Dusildenafil citrateau Viagra® ou l’art délicat de nommer les médicaments
Authors: Faure Pascaline
Published: April 2014

In times past, drugs often derived from plants and were quite naturally named after them. Nowadays, considering the significant economic issues at stake (Dutchen 2009), pharmaceutical companies increasingly entrust brand agencies with the naming of their products (Kenagy 2001). In this article, we offer to analyze the names of some brand and generic drugs, exploiting the French VIDAL dictionary, the British National Formulary and the US FDA corpora, with the aim to bring to light the evolution of lexical trends over the last century. Whilst doing so, we wish to demonstrate that, in the field of pharmacology, the process of naming is nowadays not so much underlain by a legitimate need for clarity and scientificity but rather by marketing strategies some of which prove to be misleading for patients. Considering the now international dimension of the pharmaceutical industry, drug names are often the same around the world. Yet, there are exceptions, which we point out and explain. Furthermore, we deemed interesting to underline the extent to which medicines are part of our everyday life by pointing out nicknames that patients tend to give to their treatments — usually sedatives, neuroleptics and the like — and metaphors they may resort to in English and in French. We conclude with the acknowledgement that medicines are henceforth like any other goods, whose financial stakes are such that, besides developing forceful new names, the pharmaceutical industry goes so far as inventing new diseases (disease mongering) to increase its market share (Even and Debré 2012).
On the elements activating the transmission of specialized knowledge in verbs
Authors: Joan Casademont Anna
Published: April 2014

In this paper we propose an analysis of phraseological verbs in specialized discourse in order to establish syntactic and semantic characteristics likely to indicate the transmission of specialized knowledge. By adopting and adapting theoretical and descriptive proposals existing for general language, we consider elements from the relation between the verb and its arguments (such as argument structure and thematic roles) and aspects from the arguments themselves (such as semantic features and termhood). Through the detection of combined features and behaviour patterns of occurrences, we are able to more specifically establish which characteristics allow us to recognise the terminological use of phraseological verbs and which kind of information is the more relevant to its conveyance.
Guaranteed lower bounds for eigenvalues
Authors: Carstensen Carsten , Gedicke Joscha
Published: April 2014

This paper introduces fully computable two-sided bounds on the eigenvalues of the Laplace operator on arbitrarily coarse meshes based on some approximation of the corresponding eigenfunction in the nonconforming Crouzeix-Raviart finite element space plus some postprocessing. The efficiency of the guaranteed error bounds involves the global mesh-size and is proven for the large class of graded meshes. Numerical examples demonstrate the reliability of the guaranteed error control even with an inexact solve of the algebraic eigenvalue problem. This motivates an adaptive algorithm which monitors the discretisation error, the maximal mesh-size, and the algebraic eigenvalue error. The accuracy of the guaranteed eigenvalue bounds is surprisingly high with efficiency indices as small as 1.4.
On non-detects in qPCR data
Authors: McCall Matthew N. , McMurray Helene R. , Land Hartmut , Almudevar Anthony
Published: April 2014

Motivation: Quantitative real-time PCR (qPCR) is one of the most widely used methods to measure gene expression. Despite extensive research in qPCR laboratory protocols, normalization and statistical analysis, little attention has been given to qPCR non-detects—those reactions failing to produce a minimum amount of signal.

Results: We show that the common methods of handling qPCR non-detects lead to biased inference. Furthermore, we show that non-detects do not represent data missing completely at random and likely represent missing data occurring not at random. We propose a model of the missing data mechanism and develop a method to directly model non-detects as missing data. Finally, we show that our approach results in a sizeable reduction in bias when estimating both absolute and differential gene expression.

Availability and implementation: The proposed algorithm is implemented in the R package, nondetects. This package also contains the raw data for the three example datasets used in this manuscript. The package is freely available at http://mnmccall.com/software and as part of the Bioconductor project.

Contact:  mccallm@gmail.com
Rainfastness of Prothioconazole + Tebuconazole for Fusarium Head Blight and Deoxynivalenol Management in Soft Red Winter Wheat
Authors: Andersen K. F. , Morris L. , Derksen R. C. , Madden L. V. , Paul P. A.
Published: April 2014

Fungicides are most warranted for control of Fusarium head blight (FHB), a disease of wheat caused by the fungal pathogen Fusarium graminearum, when wet, rainy conditions occur during anthesis. However, it is unclear whether rainfall directly following application affects fungicide efficacy against FHB and its associated toxin, deoxynivalenol (DON). The objective of this study was to determine the rainfastness of the fungicide tebuconazole + prothioconazole and the residual life of tebuconazole when applied to wheat spikes at anthesis in combination with the nonionic surfactant Induce. Three field experiments were conducted during 2012 and 2013 in Wooster, OH. Simulated rainfall of a fixed intensity and duration was applied to separate plots at five different times after the fungicide treatment (0, 60, 105, 150, or 195 min). Spike samples were collected at 4-day intervals after fungicide application and assayed for tebuconazole residue. A similar set of greenhouse experiments was conducted using six post-fungicide-application rainfall timing treatments (0, 15, 30, 60, 120, or 180 min). All experiments were inoculated at anthesis with spores of F. graminearum, and FHB index (IND) and DON were quantified. In four of the five experiments, all fungicide-treated experimental units (EUs) had significantly lower mean IND and DON than the untreated check, regardless of rainfall treatment. Among rainfall treatments, EUs that received the earliest rains after fungicide application tended to have the highest numerical mean IND and DON, but were generally not significantly different from EUs that received later rain or fungicide without rain. In both years, fungicide residue on wheat spikes decreased rapidly with time after application, but the rate of reduction varied somewhat between years, with a half-life of 6 to 9 days. Rainfall treatment did not have a significant effect on the rate of residue reduction or the level of residue at a fixed sampling time after fungicide application. In this study, tebuconazole + prothioconazole mixed with a nonionic surfactant was fairly rainfast for a fixed set of rainfall characteristics, and tebuconazole residue did not persist very long after application on wheat spikes.
Stimulatory Effects of Sublethal Doses of Dimethachlon on Sclerotinia sclerotiorum
Authors: Zhou Feng , Liang Hong-Jie , Di Ya-Li , You Hong , Zhu Fu-Xing
Published: April 2014

Growth and virulence stimulations of sublethal doses of fungicides on plant-pathogenic fungi and oomycetes have been reported and the stimulatory effects are potentially relevant to plant disease management. Sclerotinia sclerotiorum is one of the most devastating and economically important necrotrophic fungal phytopathogens, capable of infecting more than 400 species of plants worldwide. In order to study stimulatory effects of sublethal doses of fungicides on S. sclerotiorum, 55 dimethachlon-sensitive isolates and 3 dimethachlon-resistant isolates of S. sclerotiorum were assayed to determine effects of sublethal doses of dimethachlon on mycelial growth rate on potato dextrose agar (PDA) media and virulence on oilseed rape plants. Results showed that all 3 dimethachlon-resistant isolates and 13 of the 55 sensitive isolates exhibited stimulatory responses to sublethal doses of dimethachlon. Dimethachlon-resistant isolates grew significantly (P < 0.05) faster on PDA media amended with dimethachlon at 0.5 to 4 μg/ml than on fungicide-free PDA media. As for virulence on detached leaves of oilseed rape plants, lesion diameters of dimethachlon-resistant isolates after growth on PDA media amended with dimethachlon at 0.5 to 2 μg/ml were significantly larger (P < 0.05) than the control. The maximum stimulatory effects were 42.40 to 59.80%. In pot experiments, for both dimethachlon-sensitive and -resistant isolates, significant (P < 0.05) virulence stimulations were observed after spraying with dimethachlon at a concentration of 2 μg/ml. After growing on dimethachlon-amended PDA media, H2O2 sensitivity of S. sclerotiorum decreased significantly (P < 0.05) compared with the nonamended PDA control.
A Latent Period Duration Model for Wheat Stem Rust
Authors: Nopsa John F. Hernandez , Pfender William F.
Published: April 2014

Wheat stem rust (WSR), caused by Puccinia graminis subsp. graminis Pers., is a highly destructive disease of wheat and several other small grains. The discovery of P. graminis subsp. graminis race Ug99, which overcomes previously effective resistance in wheat, raises concerns for global wheat production and food security. There is currently no mathematical model that describes the duration of the WSR latent period based on temperature or heat units. A study using P. graminis subsp. graminis race GFCDC in ‘Stephens’ wheat was conducted at a range of temperatures (from 4.7 to 33.4°C), to determine their effect on latent period duration. There were significant differences in latent period duration among temperatures, and temperatures above 30°C generally were not conducive for pustule development. A mathematical model to predict latent period duration based on temperature was formulated; the model can be applied to data consisting of varying temperature readings measured at any desired time increment. The model was validated in outdoor experiments under natural conditions on Stephens and ‘McNair’ wheat. In field and outdoor experiments, the latent period durations predicted with the model were within 16 h of the observed latent period, and most fell into the 99% confidence interval of the observations. For experiments conducted on field-grown plants, no significant differences were found between predicted and observed latent period duration. Factorial experiments conducted under growth chamber conditions, using four wheat cultivars (Stephens, McNair 701, ‘Scout 66’, and ‘Kingbird’) and four P. graminis subsp. graminis races (GCCNC, GCCSC, QFCSC, and GFCDC) at three temperatures (5, 15 and 30°C) showed significant differences among cultivars at each temperature. A quantitative model for latent period duration could help in estimating epidemic development, and also in improving our understanding of WSR epidemiology.
A computational model for the formation of lamin-B mitotic spindle envelope and matrix
Authors: Shi Changji , Channels Wilbur E. , Zheng Yixian , Iglesias Pablo A.
Published: April 2014

Recent reports show that, after nuclear envelope breakdown, lamin-B, a component of the nuclear lamina in interphase, localizes around the mitotic spindle as a membranous network. How this process occurs, however, and how it influences mitotic spindle morphogenesis is unclear. Here, we develop a computational model based on a continuum description to represent the abundance and location of various molecular species involved during mitosis, and use the model to test a number of hypotheses regarding the formation of the mitotic matrix. Our model illustrates that freely diffusible nuclear proteins can be captured and transported to the spindle poles by minus-end-directed microtubule (MT) motors. Moreover, simulations show that these proteins can be used to build a shell-like region that envelopes the mitotic spindle, which helps to improve the focusing of the mitotic spindle by spatially restricting MT polymerization and limiting the effective diffusion of the free MTs. Simulations also confirm that spatially dependent regulation of the spindle network through the Ran system improves spindle focusing and morphology. Our results agree with experimental observations that lamin-B reorganizes around the spindle and helps to maintain spindle morphology.
Control of cell growth, division and death: information processing in living cells
Authors: Tyson John J. , Novak Bela
Published: April 2014

By way of surface receptor molecules and internal surveillance mechanisms, the living cell receives information about its external environment and internal state. In light of this information, the cell must determine its most appropriate course of action under the circumstances and initiate the relevant response pathways. Typical responses include growth and division, sexual reproduction, movement, differentiation and programmed cell death. Similar to a digital computer that uses bistable electrical switches to store and process information, the living cell uses bistable biochemical switches to implement its decision-making capabilities. In this review article, we describe some of the lines of thought that led, over the last 50 years, to our current understanding of cellular information processing, particularly related to cell growth, division and death.
Modelling mammalian cellular quiescence
Authors: Yao Guang
Published: April 2014

Cellular quiescence is a reversible non-proliferating state. The reactivation of ‘sleep-like’ quiescent cells (e.g. fibroblasts, lymphocytes and stem cells) into proliferation is crucial for tissue repair and regeneration and a key to the growth, development and health of higher multicellular organisms, such as mammals. Quiescence has been a primarily phenotypic description (i.e. non-permanent cell cycle arrest) and poorly studied. However, contrary to the earlier thinking that quiescence is simply a passive and dormant state lacking proliferating activities, recent studies have revealed that cellular quiescence is actively maintained in the cell and that it corresponds to a collection of heterogeneous states. Recent modelling and experimental work have suggested that an Rb-E2F bistable switch plays a pivotal role in controlling the quiescence–proliferation balance and the heterogeneous quiescent states. Other quiescence regulatory activities may crosstalk with and impinge upon the Rb-E2F bistable switch, forming a gene network that controls the cells’ quiescent states and their dynamic transitions to proliferation in response to noisy environmental signals. Elucidating the dynamic control mechanisms underlying quiescence may lead to novel therapeutic strategies that re-establish normal quiescent states, in a variety of hyper- and hypo-proliferative diseases, including cancer and ageing.
The balance between cell cycle arrest and cell proliferation: control by the extracellular matrix and by contact inhibition
Authors: Gérard Claude , Goldbeter Albert
Published: April 2014

To understand the dynamics of the cell cycle, we need to characterize the balance between cell cycle arrest and cell proliferation, which is often deregulated in cancers. We address this issue by means of a detailed computational model for the network of cyclin-dependent kinases (Cdks) driving the mammalian cell cycle. Previous analysis of the model focused on how this balance is controlled by growth factors (GFs) or the levels of activators (oncogenes) and inhibitors (tumour suppressors) of cell cycle progression. Supra-threshold changes in the level of any of these factors can trigger a switch in the dynamical behaviour of the Cdk network corresponding to a bifurcation between a stable steady state, associated with cell cycle arrest, and sustained oscillations of the various cyclin/Cdk complexes, corresponding to cell proliferation. Here, we focus on the regulation of cell proliferation by cellular environmental factors external to the Cdk network, such as the extracellular matrix (ECM), and contact inhibition, which increases with cell density. We extend the model for the Cdk network by including the phenomenological effect of both the ECM, which controls the activation of the focal adhesion kinase (FAK) that promotes cell cycle progression, and cell density, which inhibits cell proliferation via the Hippo/YAP pathway. The model shows that GFs and FAK activation are capable of triggering in a similar dynamical manner the transition to cell proliferation, while the Hippo/YAP pathway can arrest proliferation once cell density passes a critical threshold. The results account for the dependence or independence of cell proliferation on serum and/or cell anchorage to ECM. Whether the balance in the Cdk network is tilted towards cell cycle arrest or proliferation depends on the direction in which the threshold associated with the bifurcation is passed once the cell integrates the multiple, internal or external signals that promote or impede progression in the cell cycle.
It is not the parts, but how they interact that determines the behaviour of circadian rhythms across scales and organisms
Authors: DeWoskin Daniel , Geng Weihua , Stinchcombe Adam R. , Forger Daniel B.
Published: April 2014

Biological rhythms, generated by feedback loops containing interacting genes, proteins and/or cells, time physiological processes in many organisms. While many of the components of the systems that generate biological rhythms have been identified, much less is known about the details of their interactions. Using examples from the circadian (daily) clock in three organisms,Neurospora,Drosophilaand mouse, we show, with mathematical models of varying complexity, howinteractionsamong (i) promoter sites, (ii) proteins forming complexes, and (iii) cells can have a drastic effect on timekeeping. Inspired by the identification of many transcription factors, for example as involved in theNeurosporacircadian clock, that can both activate and repress, we show how these multiple actions can cause complex oscillatory patterns in a transcription–translation feedback loop (TTFL). Inspired by the timekeeping complex formed by the NMO–PER–TIM–SGG complex that regulates the negative TTFL in theDrosophilacircadian clock, we show how the mechanism of complex formation can determine the prevalence of oscillations in a TTFL. Finally, we note that most mathematical models of intracellular clocks model a single cell, but compare with experimental data from collections of cells. We find that refitting the most detailed model of the mammalian circadian clock, so that the coupling between cells matches experimental data, yields different dynamics and makes an interesting prediction that also matches experimental data: individual cells are bistable, and network coupling removes this bistability and causes the network to be more robust to external perturbations. Taken together, we propose that the interactions between components in biological timekeeping systems are carefully tuned towards proper function. We also show how timekeeping can be controlled by novel mechanisms at different levels of organization.
A queueing approach to multi-site enzyme kinetics
Authors: Hochendoner Philip , Ogle Curtis , Mather William H.
Published: April 2014

Multi-site enzymes, defined as where multiple substrate molecules can bind simultaneously to the same enzyme molecule, play a key role in a number of biological networks, with the
Escherichia coli
protease ClpXP a well-studied example. These enzymes can form a low latency ‘waiting line’ of substrate to the enzyme's catalytic core, such that the enzyme molecule can continue to collect substrate even when the catalytic core is occupied. To understand multi-site enzyme kinetics, we study a discrete stochastic model that includes a single catalytic core fed by a fixed number of substrate binding sites. A natural queueing systems analogy is found to provide substantial insight into the dynamics of the model. From this, we derive exact results for the probability distribution of the enzyme configuration and for the distribution of substrate departure times in the case of identical but distinguishable classes of substrate molecules. Comments are also provided for the case when different classes of substrate molecules are not processed identically.
Agaribacter marinus gen. nov., sp. nov., an agar-degrading bacterium from surface seawater
Authors: Teramoto Maki , Nishijima Miyuki
Published: April 2014

A Gram-stain-negative, motile, mesophilic, aerobic, rod-shaped bacterium, strain 8-8T, was isolated from surface seawater at Muroto, Kochi, Japan. The strain exhibited agar-degrading activity. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family

Alteromonadaceae

and clustered distantly with members of the genus

Glaciecola

(≤94.0 % similarity). The DNA G+C content was 41.8 mol%. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c and the major hydroxy fatty acid was C12 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified polar lipid; lysophosphatidylethanolamine and unidentified polar lipids were found as minor components. The major quinone was Q-8. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 8-8T represents a novel species of a new genus, for which the name Agaribacter marinus gen. nov., sp. nov. is proposed. The type strain of Agaribacter marinus is 8-8T ( = NBRC 110023T = LMG 28167T).
Hanseniaspora nectarophila sp. nov., a yeast species isolated from ephemeral flowers
Authors: Čadež Neža , Pagnocca Fernando C. , Raspor Peter , Rosa Carlos A.
Published: April 2014

Seven apiculate yeast strains that were isolated from the flowers of Syphocampylus corymbiferus Pohl in Brazil are genetically, morphologically and phenotypically distinct from recognized species of the genera Hanseniaspora and Kloeckera. Genetic discontinuities between the novel strains and their closest relatives were found using a networking approach based on the concatenated sequences of the rRNA gene (internal transcribed spacer and D1/D2 of the LSU), and the protein-coding genes for actin and translation elongation factor-1α. Phylogenetic analysis based on the rRNA and the actin gene placed the novel species represented by the strains in close relationship to Hanseniaspora meyeri and Hanseniaspora clermontiae. PCR fingerprinting with microsatellite primers confirmed the genetic heterogeneity of the novel species. The name Hanseniaspora nectarophila sp. nov. is proposed, with UFMG POG a.1T ( = ZIM 2311T = CBS 13383T) as the type strain; MycoBank no. MB807210. As the current description of the genus does not allow the presence of multilateral budding, an emended diagnosis of the genus Hanseniaspora Zikes is proposed.
Pedobacter huanghensis sp. nov. and Pedobacter
glacialis sp. nov., isolated from Arctic glacier foreland
Authors: Qiu Xia , Qu Zhihao , Jiang Fan , Ren Lvzhi , Chang Xulu , Kan Wenjing , Fang Chengxiang , Peng Fang
Published: April 2014

Two psychrotolerant, Gram-stain-negative, rod-shaped bacterial strains, designed M1-27T and 8-24T, were subjected to polyphasic taxonomic studies. Strain M1-27T was isolated from the foreland of the Midtre Lovénbreen glacier, whereas strain 8-24T was isolated from the foreland of the Austre Lovénbreen glacier. Both were Arctic glacier forelands, near Ny-Ålesund, Svalbard Archipelago, Norway. Strains M1-27T and 8-24T exhibited 16S rRNA gene sequence similarities of 91.0–96.0 % and 92.3–96.7 %, respectively, to type strains of recognized species of the genus

Pedobacter

. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains were grouped with members of the genus

Pedobacter,
but represented distinct taxa. Both strains contained MK-7 as the predominant menaquinone. The DNA G+C contents of strains M1-27T and 8-24T were 43.8 % and 39.4 %, respectively. The phenotypic characteristics, biochemical properties and polygenetic analysis, clearly indicated that strains M1-27T ( = CCTCC AB 2012936T = LMG 28205T) and 8-24T ( = CCTCC AB 2012941T = NRRL B-59993T) represent two novel species of the genus

Pedobacter

, for which the names Pedobacter huanghensis sp. nov. and Pedobacter glacialis sp. nov., respectively, are proposed.
Nanoscale characterization of effect of l-arginine on Streptococcus mutans biofilm adhesion by atomic force microscopy
Authors: Sharma Shivani , Lavender Stacey , Woo JungReem , Guo Lihong , Shi Wenyuan , Kilpatrick-Liverman LaTonya , Gimzewski James K.
Published: April 2014

A major aetiological factor of dental caries is the pathology of the dental plaque biofilms. The amino acid l-arginine (Arg) is found naturally in saliva as a free molecule or as a part of salivary peptides and proteins. Plaque bacteria metabolize Arg to produce alkali and neutralize glycolytic acids, promoting a less cariogenous oral microbiome. Here, we explored an alternative and complementary mechanism of action of Arg using atomic force microscopy. The nanomechanical properties of Streptococcus mutans biofilm extracellular matrix were characterized under physiological buffer conditions. We report the effect of Arg on the adhesive behaviour and structural properties of extracellular polysaccharides in S. mutans biofilms. High-resolution imaging of biofilm surfaces can reveal additional structural information on bacterial cells embedded within the surrounding extracellular matrix. A dense extracellular matrix was observed in biofilms without Arg compared to those grown in the presence of Arg. S. mutans biofilms grown in the presence of Arg could influence the production and/or composition of extracellular membrane glucans and thereby affect their adhesion properties. Our results suggest that the presence of Arg in the oral cavity could influence the adhesion properties of S. mutans to the tooth surface.
Calcineurin phosphatase and phospholipase C are required for developmental and pathological functions in the citrus fungal pathogen Alternaria alternata
Authors: Tsai Hsieh-Chin , Chung Kuang-Ren
Published: April 2014

Excessive Ca2+or compounds interfering with phosphoinositide cycling have been found to inhibit the growth of the tangerine pathotype ofAlternaria alternata, suggesting a crucial role of Ca2+homeostasis in this pathotype. The roles ofPLC1, a phospholipase C-coding gene andCAL1, a calcineurin phosphatase-coding gene were investigated. Targeted gene disruption showed that bothPLC1andCAL1were required for vegetative growth, conidial formation and pathogenesis in citrus. Fungal strains lackingPLC1orCAL1exhibited extremely slow growth and induced small lesions on calamondin leaves. Δplc1mutants produced fewer conidia, which germinated at slower rates than wild-type. Δcal1mutants produced abnormal hyphae and failed to produce any mature conidia, but instead produced highly melanized bulbous hyphae with distinct septae. Fluorescence microscopy using Fluo-3 dye as a Ca2+indicator revealed that the Δplc1mutant hyphae emitted stronger cytosolic fluorescence, and the Δcal1mutant hyphae emitted less cytosolic fluorescence, than those of wild-type. Infection assessed on detached calamondin leaves revealed that application of CaCl2or neomycin 24 h prior to inoculation provided protection againstAlt. alternata. These data indicate that a dynamic equilibrium of cellular Ca2+is critical for developmental and pathological processes ofAlt. alternata.
Sky1 regulates the expression of sulfur metabolism genes in response to cisplatin
Authors: Rodríguez-Lombardero Silvia , Vizoso-Vázquez Ángel , Lombardía Luis J. , Becerra Manuel , González-Siso M. Isabel , Cerdán M. Esperanza
Published: April 2014

Cisplatin is commonly used in cancer therapy and yeast cells are also sensitive to this compound. We present a transcriptome analysis discriminating between RNA changes induced by cisplatin treatment, which are dependent on or independent ofSKY1function – a gene whose deletion increases resistance to the drug. Gene expression changes produced by addition of cisplatin to W303 and W303-Δsky1cells were recorded using DNA microarrays. The data, validated by quantitative PCR, revealed 122 differentially expressed genes: 69 upregulated and 53 downregulated. Among the upregulated genes, those related to sulfur metabolism were over-represented and partially dependent on Sky1. Deletions ofMET4or other genes encoding co-regulators of the expression of sulfur-metabolism-related genes, with the exception ofMET28, did not modify the cisplatin sensitivity of yeast cells. One of the genes with the highest cisplatin-induced upregulation wasSEO1, encoding a putative permease of sulfur compounds. We also measured the platinum, sulfur and glutathione content in W303, W303-Δsky1and W303-Δseo1cells after cisplatin treatment, and integration of the data suggested that these transcriptional changes might represent a cellular response that allowed chelation of cisplatin with sulfur-containing amino acids and also helped DNA repair by stimulating purine biosynthesis. The transcription pattern of stimulation of sulfur-containing amino acids and purine synthesis decreased, or even disappeared, in the W303-Δsky1strain.
Autoregulation of the Kluyveromyces lactis pyruvate decarboxylase gene KlPDC1 involves the regulatory gene RAG3
Authors: Ottaviano Daniela , Micolonghi Chiara , Tizzani Lorenza , Lemaire Marc , Wésolowski-Louvel Micheline , De Stefano Maria Egle , Ranieri Danilo , Bianchi Michele M.
Published: April 2014

In the yeast Kluyveromyces lactis, the pyruvate decarboxylase gene KlPDC1 is strongly regulated at the transcription level by different environmental factors. Sugars and hypoxia act as inducers of transcription, while ethanol acts as a repressor. Their effects are mediated by gene products, some of which have been characterized. KlPDC1 transcription is also strongly repressed by its product – KlPdc1 – through a mechanism called autoregulation. We performed a genetic screen that allowed us to select and identify the regulatory gene RAG3 as a major factor in the transcriptional activity of the KlPDC1 promoter in the absence of the KlPdc1 protein, i.e. in the autoregulatory mechanism. We also showed that the two proteins Rag3 and KlPdc1 interact, co-localize in the cell and that KlPdc1 may control Rag3 nuclear localization.
Multiple personalities of the RNA polymerase active centre
Authors: Zenkin Nikolay
Published: April 2014

Transcription in all living organisms is accomplished by highly conserved multi-subunit RNA polymerases (RNAPs). Our understanding of the functioning of the active centre of RNAPs has transformed recently with the finding that a conserved flexible domain near the active centre, the trigger loop (TL), participates directly in the catalysis of RNA synthesis and serves as a major determinant for fidelity of transcription. It also appears that the TL is involved in the unique ability of RNAPs to exchange catalytic activities of the active centre. In this phenomenon the TL is replaced by a transcription factor which changes the amino acid content and, as a result, the catalytic properties of the active centre. The existence of a number of transcription factors that act through substitution of the TL suggests that the RNAP has several different active centres to choose from in response to external or internal signals.

A video of this Prize Lecture, presented at the Society for General Microbiology Annual Conference 2014, can be viewed via this link: https://www.youtube.com/watch?v=79Z7iXVEPo4
Trimeric knob protein specifically distinguishes neutralizing antibodies to different human adenovirus species: potential application for adenovirus seroepidemiology
Authors: Yu Bin , Dong Jianing , Wang Chu , Wang Zhen , Gao Lei , Zhang Haihong , Wu Jiaxin , Kong Wei , Yu Xianghui
Published: April 2014

Adenoviruses (Ads) are non-enveloped DNA viruses that have been extensively studied and used as vectors for gene therapy and several potential vaccines. There are 57 Ad serotypes in seven species (A–G), and Ad neutralizing antibody (NAb) titres can vary by serotype and geographical location. Until now serotype- and species-specific antibodies have been detected by neutralization or haemagglutination inhibition assays. These expensive and cumbersome methods of adenovirus typing have mainly been used in epidemiological studies. Our prior work demonstrated that NAbs against the fiber protein are commonly generated during natural Ad infection in humans and the trimeric knob is preferentially recognized by fiber-induced NAbs. In this study, we expressed nine trimeric knob proteins from representative Ad serotypes of human Ad (HAdV)-A–F in Escherichia coli and found no cross-reactivity of these recombinant proteins with rabbit hyperimmune sera (among HAdV-A–F or within HAdV-C). Results of the ELISA based on Ad2 and Ad5 (both HAdV-C) knob proteins were consistent with those of neutralization assays, indicating that the trimeric knob protein would be a good candidate antigen for detecting Ad serotype-specific NAbs in sera from naturally infected subjects. We also demonstrated the primary seroepidemiology of nine Ad serotypes in 274 children using the knob-based ELISA. These results have potential implications for epidemiology of Ad serotypes and future development of Ad-based vaccines and gene therapy.
Structural basis of a novel activity of bacterial 6-pyruvoyltetrahydropterin synthase homologues distinct from mammalian 6-pyruvoyltetrahydropterin synthase activity
Authors: Seo Kyung Hye , Zhuang Ningning , Park Young Shik , Park Ki Hun , Lee Kon Ho
Published: April 2014

Escherichia coli6-carboxytetrahydropterin synthase (eCTPS), a homologue of 6-pyruvoyltetrahydropterin synthase (PTPS), possesses a much stronger catalytic activity to cleave the side chain of sepiapterinin vitrocompared with genuine PTPS activity and catalyzes the conversion of dihydroneopterin triphosphate to 6-carboxy-5,6,7,8-tetrahydropterinin vivo. Crystal structures of wild-type apo eCTPS and of a Cys27Ala mutant eCTPS complexed with sepiapterin have been determined to 2.3 and 2.5 Å resolution, respectively. The structures are highly conserved at the active site and the Zn2+binding site. However, comparison of the eCTPS structures with those of mammalian PTPS homologues revealed that two specific residues, Trp51 and Phe55, that are not found in mammalian PTPS keep the substrate bound by stacking it with their side chains. Replacement of these two residues by site-directed mutagenesis to the residues Met and Leu, which are only found in mammalian PTPS, converted eCTPS to the mammalian PTPS activity. These studies confirm that these two aromatic residues in eCTPS play an essential role in stabilizing the substrate and in the specific enzyme activity that differs from the original PTPS activity. These aromatic residues Trp51 and Phe55 are a key signature of bacterial PTPS enzymes that distinguish them from mammalian PTPS homologues.
IR laser-induced protein crystal transformation
Authors: Kiefersauer Reiner , Grandl Brigitte , Krapp Stephan , Huber Robert
Published: April 2014

A method and the design of instrumentation, and its preliminary practical realisation, including test experiments, with the object of inducing phase changes of biomolecular crystals by controlled dehydration through heating with infrared (IR) light are described. The aim is to generate and select crystalline phases through transformation in the solid state which have improved order (higher resolution in X-ray diffraction experiments) and reduced mosaic spread (more uniformly aligned mosaic blocks) for diffraction data collection and analysis. The crystal is heated by pulsed and/or constant IR laser irradiation. Loss of crystal water following heating and its reabsorption through equilibration with the environment is measured optically by a video system. Heating proved superior to traditional controlled dehydration by humidity change for the test cases CODH (carbon monoxide dehydrogenase) and CLK2 (a protein kinase). Heating with IR light is experimentally simple and offers an exploration of a much broader parameter space than the traditional method, as it allows the option of varying the rate of phase changes through modification of the IR pulse strength, width and repeat frequency. It impacts the crystal instantaneously, isotropically and homogeneously, and is therefore expected to cause less mechanical stress.