bluuebunny/crossref_metadata_2025 huggingface dataset:
The Background to the Lexical Content of the Nuevo Tesoro Lexicográfico del Español (s. XIV–1726)
Authors: Alvar Ezquerra Manuel
Published: April 2009

This article sets out the sources, both lexicographical and other, used to create the Nuevo Tesoro Lexicográfico del Español (s. XIV–1726). Among these, particular attention is due to the pre-1500 sources, especially the works of Antonio de Nebrija (1444?–1522), because of their importance for subsequent lexicography, including the pioneers of bilingual lexicography who set Spanish alongside another language. Information is also supplied about the number of works and records consulted, the difficulties arising from treating the data, and the method adopted for grouping together variants of the same form. Finally, an indication is given of the interest of the NTLE for the history of lexicography.
Cherokee Classificatory Verbs
Authors: Kilarski Marcin
Published: April 2009

This article examines the role played by the Cherokee verbs for ‘wash’, first cited in 1820 by John Pickering (1777–1848), in studies which postulated lexical redundancy and the lack of generic terms in ‘primitive’ languages. Like the more well-known “Eskimo words for ‘snow’”, the Cherokee verbs provide an example of misanalysis of the complexity of polysynthetic morphology and negligence in the presentation of data from ‘exotic’ languages. In addition, the accounts of the verbs for ‘wash’ demonstrate a misinterpretation of the function of the Cherokee classificatory verbs. In the article the author traces the description of the verbs in 19th and 20th century studies in linguistics, psychology, sociology and anthropology, with the aim of illustrating the claims made about the lexical and grammatical properties of American Indian languages, and the cognitive and cultural characteristics of the American Indians, in particular their inability to express abstract notions and the absence of moral and social values.
Book Review
Authors: Smith Hans-Jørgen
Published: April 2009

Cardiovascular MRI: 150 Multiple Choice Questions and Answers. By P. G. Danias. Totowa, NJ: Humana Press, 2008. ISBN 978-1-934115-59-6. 192 pages, 230 illustrations. Price (paperback): USD 69.95
Book Review
Authors: Jørgensen Finn Stener
Published: April 2009

Ultrasonography in Obstetrics and Gynecology - A Practical Approach to Clinical Problems. Second edition. Edited by C. B. Benson & E. I. Bluth. New York/Stuttgart: Thieme Medical Publishers, 2008. ISBN: 978-1-58890-612-0 (US); ISBN: 978-3-13- 125362-0 (rest of the world). 260 pages. Price (paperback): USD 79.95/EUR 69.95
SOCIAL STATUS AND RELIGIOSITY IN CHRISTIAN EUROPE
Authors: Flere Sergej , Klanjšek Rudi
Published: April 2009

The relationship between social status and religiosity could be illuminating in the explanation of religiosity. This has been suggested by numerous sociologically minded authors. Although not consistent across all national samples, findings from the current study, based on World Values Survey data (1999–2001), did indicate the predominance of a moderate but positive association between low social status and high religiosity among European countries with a Christian heritage. Consequently, the results lent limited support to the classical deprivation thesis, since in none of the samples analyzed could a positive association between high social status and high religiosity could be found.
When underadditivity of factor effects in the Psychological Refractory Period paradigm implies a bottleneck: Evidence from psycholinguistics
Authors: Besner Derek , Reynolds Mike , O'Malley Shannon
Published: April 2009

The Psychological Refractory Period (PRP) paradigm is a dual-task procedure that can be used to examine the resource demands of specific cognitive processes. Inferences about the underlying processes are typically based on performance in the second of two speeded tasks. If the effect of a factor manipulated in Task 2 decreases as the stimulus onset asynchrony (SOA) between tasks decreases ( underadditivity), the normative inference is that the effect of this factor occurs prior to a limited-capacity central processing mechanism. In contrast, if the effect of a factor is additive with SOA then the inference is that this indexes a process that either uses a limited-capacity central processing mechanism or occurs after some process that uses this mechanism. A heretofore unidentified exception to this logic arises when Task 2 involves two separate processes that operate in parallel, but compete. Interference with one process in Task 2 because of work on Task 1 will eliminate or reduce competition within Task 2 and is hence manifest as an underadditive interaction with decreasing SOA. This is illustrated here by reference to a PRP experiment in which the ubiquitous effect of spelling-to-sound regularity on reading aloud time is eliminated at a short SOA and by consideration of three converging lines of investigation in the PRP paradigm when Task 2 involves reading aloud.
Short article: Eye movements when reading text messaging (txt msgng)
Authors: Perea Manuel , Acha Joana , Carreiras Manuel
Published: April 2009

The growing popularity of mobile-phone technology has led to changes in the way people—particularly younger people—communicate. A clear example of this is the advent of Short Message Service (SMS) language, which includes orthographic abbreviations (e.g., omitting vowels, as in wk, week) and phonetic respelling (e.g., using u instead of you). In the present study, we examined the pattern of eye movements during reading of SMS sentences (e.g., my hols wr gr8), relative to normally written sentences, in a sample of skilled “texters”. SMS sentences were created by using (mostly) orthographic or phonological abbreviations. Results showed that there is a reading cost—both at a local level and at a global level—for individuals who are highly expert in SMS language. Furthermore, phonological abbreviations resulted in a greater cost than orthographic abbreviations.
Short article: Negations in syllogistic reasoning: Evidence for a heuristic–analytic conflict
Authors: Stupple Edward J. N. , Waterhouse Eleanor F.
Published: April 2009

An experiment utilizing response time measures was conducted to test dominant processing strategies in syllogistic reasoning with the expanded quantifier set proposed by Roberts (2005). Through adding negations to existing quantifiers it is possible to change problem surface features without altering logical validity. Biases based on surface features such as atmosphere, matching, and the probability heuristics model (PHM; Chater & Oaksford, 1999; Wetherick & Gilhooly, 1995) would not be expected to show variance in response latencies, but participant responses should be highly sensitive to changes in the surface features of the quantifiers. In contrast, according to analytic accounts such as mental models theory and mental logic (e.g., Johnson-Laird & Byrne, 1991; Rips, 1994) participants should exhibit increased response times for negated premises, but not be overly impacted upon by the surface features of the conclusion. Data indicated that the dominant response strategy was based on a matching heuristic, but also provided evidence of a resource-demanding analytic procedure for dealing with double negatives. The authors propose that dual-process theories offer a stronger account of these data whereby participants employ competing heuristic and analytic strategies and fall back on a heuristic response when analytic processing fails.
Short article: Irrelevant speech effects and statistical learning
Authors: Neath Ian , Guérard Katherine , Jalbert Annie , Bireta Tamra J. , Surprenant Aimée M.
Published: April 2009

Immediate serial recall of visually presented verbal stimuli is impaired by the presence of irrelevant auditory background speech, the so-called irrelevant speech effect. Two of the three main accounts of this effect place restrictions on when it will be observed, limiting its occurrence either to items processed by the phonological loop (the phonological loop hypothesis) or to items that are not too dissimilar from the irrelevant speech (the feature model). A third, the object-oriented episodic record (O-OER) model, requires only that the memory task involves seriation. The present studies test these three accounts by examining whether irrelevant auditory speech will interfere with a task that does not involve the phonological loop, does not use stimuli that are compatible with those to be remembered, but does require seriation. Two experiments found that irrelevant speech led to lower levels of performance in a visual statistical learning task, offering more support for the O-OER model and posing a challenge for the other two accounts.
Azimuthally non-uniform equilibrium of field-reversed configuration sustained by rotating magnetic field with spatial high-harmonic components
Authors: Inomoto Michiaki , Yambe Kiyoyuki , Kitano Katsuhisa , Okada Shigefumi
Published: April 2009

Field-reversed configurations (FRCs) sustained by rotating magnetic fields (RMFs) with spatial high-harmonic components have been studied in a metal flux conserver of the FRC injection experiment apparatus. In the RMF-FRC equilibrium, significant azimuthal variation of the axial magnetic field, the electron density and the electron rotation velocity are observed. This deformation of the core FRC plasma is brought about by the strong azimuthal non-uniformity of the RMF and the configuration is consistent with the continuity of the electron flow flux and the magnetic field reversal conditions. The RMF with spatial high-harmonic components provides quasi-steady current drive of high-beta and singly-connected FRC plasmas without destructive modes and will be helpful in reducing the particle loss and thermal load when applied to the fusion core plasma.
Cargo-Mediated Regulation of a Rapid Rab4-Dependent Recycling Pathway
Authors: Yudowski Guillermo A. , Puthenveedu Manojkumar A. , Henry Anastasia G. , von Zastrow Mark
Published: April 2009

Membrane trafficking is well known to regulate receptor-mediated signaling processes, but less is known about whether signaling receptors conversely regulate the membrane trafficking machinery. We investigated this question by focusing on the beta-2 adrenergic receptor (B2AR), a G protein-coupled receptor whose cellular signaling activity is controlled by ligand-induced endocytosis followed by recycling. We used total internal reflection fluorescence microscopy (TIR-FM) and tagging with a pH-sensitive GFP variant to image discrete membrane trafficking events mediating B2AR endo- and exocytosis. Within several minutes after initiating rapid endocytosis of B2ARs by the adrenergic agonist isoproterenol, we observed bright “puffs” of locally increased surface fluorescence intensity representing discrete Rab4-dependent recycling events. These events reached a constant frequency in the continuous presence of isoproterenol, and agonist removal produced a rapid (observed within 1 min) and pronounced (≈twofold) increase in recycling event frequency. This regulation required receptor signaling via the cAMP-dependent protein kinase (PKA) and a specific PKA consensus site located in the carboxyl-terminal cytoplasmic tail of the B2AR itself. B2AR-mediated regulation was not restricted to this membrane cargo, however, as transferrin receptors packaged in the same population of recycling vesicles were similarly affected. In contrast, net recycling measured over a longer time interval (10 to 30 min) was not detectably regulated by B2AR signaling. These results identify rapid regulation of a specific recycling pathway by a signaling receptor cargo.
Down-Regulation of a Manganese Transporter in the Face of Metal Toxicity
Authors: Jensen Laran T. , Carroll Mark C. , Hall Matthew D. , Harvey Christopher J. , Beese Sara E. , Culotta Valeria C.
Published: April 2009

The yeast Smf1p Nramp manganese transporter is posttranslationally regulated by environmental manganese. Smf1p is stabilized at the cell surface with manganese starvation, but is largely degraded in the vacuole with physiological manganese through a mechanism involving the Rsp5p adaptor complex Bsd2p/Tre1p/Tre2p. We now describe an additional level of Smf1p regulation that occurs with toxicity from manganese, but not other essential metals. This regulation is largely Smf1p-specific. As with physiological manganese, toxic manganese triggers vacuolar degradation of Smf1p by trafficking through the multivesicular body. However, regulation by toxic manganese does not involve Bsd2p/Tre1p/Tre2p. Toxic manganese triggers both endocytosis of cell surface Smf1p and vacuolar targeting of intracellular Smf1p through the exocytic pathway. Notably, the kinetics of vacuolar targeting for Smf1p are relatively slow with toxic manganese and require prolonged exposures to the metal. Down-regulation of Smf1p by toxic manganese does not require transport activity of Smf1p, whereas such transport activity is needed for Smf1p regulation by manganese starvation. Furthermore, the responses to manganese starvation and manganese toxicity involve separate cellular compartments. We provide evidence that manganese starvation is sensed within the lumen of the secretory pathway, whereas manganese toxicity is sensed within an extra-Golgi/cytosolic compartment of the cell.
LKB1 Catalytic Activity Contributes to Estrogen Receptor α Signaling
Authors: Nath-Sain Suchita , Marignani Paola A.
Published: April 2009

The tumor suppressor serine-threonine kinase LKB1 is mutated in Peutz-Jeghers syndrome (PJS) and in epithelial cancers, including hormone-sensitive organs such as breast, ovaries, testes, and prostate. Clinical studies in breast cancer patients show low LKB1 expression is related to poor prognosis, whereas in PJS, the risk of breast cancer is similar to the risk from germline mutations in breast cancer (BRCA) 1/BRCA2. In this study, we investigate the role of LKB1 in estrogen receptor α (ERα) signaling. We demonstrate for the first time that LKB1 binds to ERα in the cell nucleus in which it is recruited to the promoter of ERα-responsive genes. Furthermore, LKB1 catalytic activity enhances ERα transactivation compared with LKB1 catalytically deficient mutants. The significance of our discovery is that we demonstrate for the first time a novel functional link between LKB1 and ERα. Our discovery places LKB1 in a coactivator role for ERα signaling, broadening the scientific scope of this tumor suppressor kinase and laying the groundwork for the use of LKB1 as a target for the development of new therapies against breast cancer.
Nuclear Fusion and Genome Encounter during Yeast Zygote Formation
Authors: Tartakoff Alan Michael , Jaiswal Purnima
Published: April 2009

When haploid cells of Saccharomyces cerevisiae are crossed, parental nuclei congress and fuse with each other. To investigate underlying mechanisms, we have developed assays that evaluate the impact of drugs and mutations. Nuclear congression is inhibited by drugs that perturb the actin and tubulin cytoskeletons. Nuclear envelope (NE) fusion consists of at least five steps in which preliminary modifications are followed by controlled flux of first outer and then inner membrane proteins, all before visible dilation of the waist of the nucleus or coalescence of the parental spindle pole bodies. Flux of nuclear pore complexes occurs after dilation. Karyogamy requires both the Sec18p/NSF ATPase and ER/NE luminal homeostasis. After fusion, chromosome tethering keeps tagged parental genomes separate from each other. The process of NE fusion and evidence of genome independence in yeast provide a prototype for understanding related events in higher eukaryotes.
Functional Overlap of Microtubule Assembly Factors in Chromatin-Promoted Spindle Assembly
Authors: Groen Aaron C. , Maresca Thomas J. , Gatlin Jesse C. , Salmon Edward D. , Mitchison Timothy J.
Published: April 2009

Distinct pathways from centrosomes and chromatin are thought to contribute in parallel to microtubule nucleation and stabilization during animal cell mitotic spindle assembly, but their full mechanisms are not known. We investigated the function of three proposed nucleation/stabilization factors, TPX2, γ-tubulin and XMAP215, in chromatin-promoted assembly of anastral spindles in Xenopus laevis egg extract. In addition to conventional depletion-add back experiments, we tested whether factors could substitute for each other, indicative of functional redundancy. All three factors were required for microtubule polymerization and bipolar spindle assembly around chromatin beads. Depletion of TPX2 was partially rescued by the addition of excess XMAP215 or EB1, or inhibiting MCAK (a Kinesin-13). Depletion of either γ-tubulin or XMAP215 was partially rescued by adding back XMAP215, but not by adding any of the other factors. These data reveal functional redundancy between specific assembly factors in the chromatin pathway, suggesting individual proteins or pathways commonly viewed to be essential may not have entirely unique functions.
pySolo: a complete suite for sleep analysis in Drosophila
Authors: Gilestro Giorgio F. , Cirelli Chiara
Published: April 2009

Summary: pySolo is a multiplatform software for analysis of sleep and locomotor activity in Drosophila melanogaster. pySolo provides a user-friendly graphic interface and it has been developed with the specific aim of being accessible, portable, fast and easily expandable through an intuitive plug-in structure. Support for development of additional plug-ins is provided through a community website.

Availability: Software and documentation are located at http://www.pysolo.net. pySolo is a free software released under the GNU General Public License.

Contact:  gilestro@wisc.edu
Bayesian inference of protein–protein interactions from biological literature
Authors: Chowdhary Rajesh , Zhang Jinfeng , Liu Jun S.
Published: April 2009

Motivation: Protein–protein interaction (PPI) extraction from published biological articles has attracted much attention because of the importance of protein interactions in biological processes. Despite significant progress, mining PPIs from literatures still rely heavily on time- and resource-consuming manual annotations.

Results: In this study, we developed a novel methodology based on Bayesian networks (BNs) for extracting PPI triplets (a PPI triplet consists of two protein names and the corresponding interaction word) from unstructured text. The method achieved an overall accuracy of 87% on a cross-validation test using manually annotated dataset. We also showed, through extracting PPI triplets from a large number of PubMed abstracts, that our method was able to complement human annotations to extract large number of new PPIs from literature.

Availability: Programs/scripts we developed/used in the study are available at http://stat.fsu.edu/~jinfeng/datasets/Bio-SI-programs-Bayesian-chowdhary-zhang-liu.zip

Contact:  jliu@stat.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
MapView: visualization of short reads alignment on a desktop computer
Authors: Bao Hua , Guo Hui , Wang Jinwei , Zhou Renchao , Lu Xuemei , Shi Suhua
Published: April 2009

Summary: We introduce a new visual analytics tool named MapView to facilitate the representation of large-scale short reads alignment data and genetic variation analysis. MapView can handle hundreds of millions of short reads on a desktop computer with limited memory. It supports a compact alignment view for both single-end and paired end short reads, multiple navigation and zoom modes and multi-thread processing. Moreover, MapView offers automated genetic variation detection. MapView has been used in our lab and by over 10 research labs worldwide.

Availability:  http://evolution.sysu.edu.cn/mapview/.

Contact:  baohua100@hotmail.com; lssssh@mail.sysu.edu.cn

Supplementary information:  Supplementary data are available at http://evolution.sysu.edu.cn/mapview/MVF.pdf
ProtVirDB: a database of protozoan virulent proteins
Authors: Ramana Jayashree , Gupta Dinesh
Published: April 2009

Summary: ProtVirDB is a comprehensive and user-friendly web-based knowledgebase of virulent proteins belonging to protozoan species. The database will facilitate research and provide an integrated platform for comparative studies of virulent proteins in different parasitic protozoans and organize them under a unifying classification schema with functional categories. Remarkably, one-third of the protein sequences in the database showed presence of either mono- or hetero-repeats, or both concomitantly—hence reiterating the importance of repeats in parasite virulence mechanisms. A number of useful bioinformatics tools including BLAST and tools for phylogenetic analysis are integrated with the database. With the rapidly burgeoning interest in the pathogenesis mechanisms of protozoans and ongoing genome sequencing projects, we anticipate that the database will be a useful tool for the research community.

Availability:  http://bioinfo.icgeb.res.in/protvirdb

Contact:  dinesh@icgeb.res.in

Supplementary information:  Supplementary data are available at Bioinformatics online
Size-dependent frequency response of sandeel schools
Authors: Johnsen Espen , Pedersen Ronald , Ona Egil
Published: April 2009

Johnsen, E., Pedersen, R., and Ona, E. 2009. Size-dependent frequency response of sandeel schools. – ICES Journal of Marine Science, 66: 1100–1105. Annual Norwegian sandeel surveys have been conducted in the North Sea since 2005 to measure the stock of lesser sandeel (Ammodytes marinus). Target identification is often a major challenge in acoustic surveys, and discriminant analyses have been used to separate echoes accurately from schools of herring, mackerel, and sandeel based on their acoustic-frequency responses measured at 18, 38, 120, and 200 kHz. At two fishing grounds during the 2008 survey, 332 schools were identified as sandeel, based on the characteristics of the acoustic signal, and validated by trawl samples. The schools consisted almost entirely of 1-year-old sandeels on one of the grounds, and 2-year-olds on the other. In this study, the potential of acoustic-frequency responses is advanced to classify the sizes of fish in them. A discriminant analysis using frequency responses as independent variables was able to differentiate between sandeel schools comprising 1- and 2-year-old fish (p < 0.001). Approximately 83% of the 2-year-old fish and 77% of the 1-year-old fish were classified correctly. The frequency responses at 18 and 38 kHz were the most important independent variables. Sandeel landings in the North Sea are normally dominated by 1- and 2-year-old sandeels in the first half of the year. This study revealed that these two age classes could be identified acoustically; a finding that may be important for acoustic surveys of sandeels and for management of the commercial sandeel fishery.
Nursery grounds of the orange roughy around New Zealand
Authors: Dunn M. R. , Rickard G. J. , Sutton P. J. H. , Doonan I. J.
Published: April 2009

Dunn, M. R., Rickard, G. J., Sutton, P. J. H., and Doonan, I. J. 2009. Nursery grounds of the orange roughy around New Zealand. – ICES Journal of Marine Science, 66: 871–885. The orange roughy (Hoplostethus atlanticus) is a deep-sea species with a centenarian lifespan, a life-history feature that may enable the stocks to withstand prolonged periods of recruitment failure. Most stocks have been substantially depleted, however, so estimating recruitment has become a priority in setting catch quotas to ensure future sustainability of the fisheries. A description of the nursery grounds of the species off New Zealand is provided, using extensive research-survey data from 12 541 bottom trawls and 713 midwater trawls. The juveniles were initially caught on the seabed, near known spawning grounds, and towards the shallower end of the species' distribution, and not in midwater or the shallower or deeper bottom tows. Densities were greatest at 850-900 m. As juveniles grew, their spatial and depth distribution expanded, both shallower and deeper, with a skew towards deeper water, such that by the onset of maturation, densities were relatively high in 850–1300 m of water. The early nursery grounds were in relatively warm water, but on the south Chatham Rise, appeared to be bounded by the presence of a cold-water front.
Inferring evolutionarily significant units of bacterial diversity from broad environmental surveys of single-locus data
Authors: Barraclough Timothy G. , Hughes Martin , Ashford-Hodges Natalie , Fujisawa Tomochika
Published: April 2009

By far the greatest challenge for diversity studies is to characterize the diversity of prokaryotes, which probably encompasses billions of species, most of which are unculturable. Recent advances in theory and analysis have focused on multi-locus approaches and on combined analysis of molecular and ecological data. However, broad environmental surveys of bacterial diversity still rely on single-locus data, notably 16S ribosomal DNA, and little other detailed information. Evolutionary methods of delimiting species from single-locus data alone need to consider population genetic and macroevolutionary theories for the expected levels of interspecific and intraspecific variation. We discuss the use of a recent evolutionary method, based on the theory of coalescence within independently evolving populations, compared with a traditional approach that uses a fixed threshold divergence to delimit species.
Stability in distribution of mild solutions to stochastic partial differential delay equations with jumps
Authors: Bao Jianhai , Truman Aubrey , Yuan Chenggui
Published: April 2009

The existence, uniqueness and some sufficient conditions for stability in distribution of mild solutions to stochastic partial differential delay equations with jumps are presented. The principle technique of our investigation is to construct a proper approximating strong solution system and carry out a limiting type of argument to pass on stability of strong solutions to mild ones. As a consequence, stability results of Basak
et al
. (

Basak
et al
. 1999

J. Math. Anal. Appl.
202
, 604–622) and Yuan
et al
. (

Yuan
et al
. 2003

Syst. Control Lett.
50
, 195–207) are generalized to cover a class of much more general stochastic partial differential delay equations with jumps in infinite dimensions. In contrast to the almost sure exponential stability in Ichikawa (
Ichikawa 1982
J. Math. Anal. Appl.
90
, 12–44) and Luo & Liu (
Luo & Liu 2008
Stoch. Proc. Appl.
118
, 864–895) and the moment exponential stability in Luo & Liu, we present a new result on the stability in distribution of mild solutions. Finally, an example is given to demonstrate the applicability of our work.
Charge-density waves at intermediate coupling
Authors: Buker Donald W.
Published: April 2009

An electron–phonon theory for a quasi-one-dimensional band of electrons forming a moving incommensurate charge-density wave (CDW) state at zero temperature is presented. A useful analytic expression for the energy gap as a function of electron–phonon coupling is found. The gap is quite a bit larger than the well-known weak-coupling result, even for modest coupling, where the mean-field approximation should still be valid. It is also shown that the form of the Hamiltonian implies that there is no spread at all in the wavevector of the CDW in the vicinity of 2
k
F
. Comparisons of theoretical and experimental values of the energy gap and the lattice displacement amplitude are made for NbSe
3
.
Elastic waves guided by a welded joint in a plate
Authors: Fan Zheng , Lowe Mike J.S.
Published: April 2009

The inspection of large areas of complex structures is a growing interest for industry. An experimental observation on a large welded plate found that the weld can concentrate and guide the energy of a guided wave travelling along the direction of the weld. This is attractive for non-destructive evaluation (NDE) since it offers the potential to quickly inspect for defects such as cracking or corrosion along long lengths of welds. In this paper, a two-dimensional semi-analytical finite-element (SAFE) method is applied to provide a modal study of the elastic waves that are guided by the welded joint in a plate. This brings understanding to the compression wave that was previously observed in the experiment. However, during the study, a shear weld-guided mode, which is non-leaky and almost non-dispersive, has also been discovered. Its characteristics are particularly attractive for NDE, so this is a significant new finding. The properties for both the compression and the shear mode are discussed and compared, and the physical reason for the energy trapping phenomena is then explained. Experiments have been undertaken to validate the existence of the shear weld-guided mode and the accuracy of the FE model, showing very good results.
Reward quality influences the development of learned olfactory biases in honeybees
Authors: Wright Geraldine A. , Choudhary Amir F. , Bentley Michael A.
Published: April 2009

Plants produce flowers with complex visual and olfactory signals, but we know relatively little about the way that signals such as floral scents have evolved. One important factor that may direct the evolution of floral signals is a pollinator's ability to learn. When animals learn to associate two similar signals with different outcomes, biases in their responses to new signals can be formed. Here, we investigated whether or not pollinators develop learned biases towards floral scents that depend on nectar reward quality by training restrained honeybees to learn to associate two similar odour signals with different outcomes using a classical conditioning assay. Honeybees developed learned biases towards odours as a result of differential conditioning, and the extent to which an olfactory bias could be produced depended upon the difference in the quality of the nectar rewards experienced during conditioning. Our results suggest that differences in reward quality offered by flowers influence odour recognition by pollinators, which in turn could influence the evolution of floral scents in natural populations of co-flowering plants.
A single origin of Batesian mimicry among hybridizing populations of admiral butterflies (Limenitis arthemis) rejects an evolutionary reversion to the ancestral phenotype
Authors: Savage Wesley K. , Mullen Sean P.
Published: April 2009

Batesian mimicry is a fundamental example of adaptive phenotypic evolution driven by strong natural selection. Given the potentially dramatic impacts of selection on individual fitness, it is important to understand the conditions under which mimicry is maintained versus lost. Although much empirical and theoretical work has been devoted to the maintenance of Batesian mimicry, there are no conclusive examples of its loss in natural populations. Recently, it has been proposed that non-mimetic populations of the polytypicLimenitis arthemisspecies complex represent an evolutionary loss of Batesian mimicry, and a reversion to the ancestral phenotype. Here, we evaluate this conclusion using segregating amplified fragment length polymorphism markers to investigate the history and fate of mimicry among forms of theL. arthemiscomplex and closely related NearcticLimenitisspecies. In contrast to the previous finding, our results support a single origin of mimicry within theL. arthemiscomplex and the retention of the ancestral white-banded form in non-mimetic populations. Our finding is based on a genome-wide sampling approach to phylogeny reconstruction that highlights the challenges associated with inferring the evolutionary relationships among recently diverged species or populations (i.e. incomplete lineage sorting, introgressive hybridization and/or selection).
No sex in fungus-farming ants or their crops
Authors: Himler Anna G. , Caldera Eric J. , Baer Boris C. , Fernández-Marín Hermógenes , Mueller Ulrich G.
Published: April 2009

Asexual reproduction imposes evolutionary handicaps on asexual species, rendering them prone to extinction, because asexual reproduction generates novel genotypes and purges deleterious mutations at lower rates than sexual reproduction. Here, we report the first case of complete asexuality in ants, the fungus-growing ant
Mycocepurus smithii
, where queens reproduce asexually but workers are sterile, which is doubly enigmatic because the clonal colonies of
M. smithii
also depend on clonal fungi for food. Degenerate female mating anatomy, extensive field and laboratory surveys, and DNA fingerprinting implicate complete asexuality in this widespread ant species. Maternally inherited bacteria (e.g.
Wolbachia
,
Cardinium
) and the fungal cultivars can be ruled out as agents inducing asexuality.
M. smithii
societies of clonal females provide a unique system to test theories of parent–offspring conflict and reproductive policing in social insects. Asexuality of both ant farmer and fungal crop challenges traditional views proposing that sexual farmer ants outpace coevolving sexual crop pathogens, and thus compensate for vulnerabilities of their asexual crops. Either the double asexuality of both farmer and crop may permit the host to fully exploit advantages of asexuality for unknown reasons or frequent switching between crops (symbiont reassociation) generates novel ant–fungus combinations, which may compensate for any evolutionary handicaps of asexuality in
M. smithii
.
Immunological serotype interactions and their effect on the epidemiological pattern of dengue
Authors: Recker Mario , Blyuss Konstantin B. , Simmons Cameron P. , Hien Tran Tinh , Wills Bridget , Farrar Jeremy , Gupta Sunetra
Published: April 2009

Long-term epidemiological data reveal multi-annual fluctuations in the incidence of dengue fever and dengue haemorrhagic fever, as well as complex cyclical behaviour in the dynamics of the four serotypes of the dengue virus. It has previously been proposed that these patterns are due to the phenomenon of the so-called antibody-dependent enhancement (ADE) among dengue serotypes, whereby viral replication is increased during secondary infection with a heterologous serotype; however, recent studies have implied that this positive reinforcement cannot account for the temporal patterns of dengue and that some form of cross-immunity or external forcing is necessary. Here, we show that ADE alone can produce the observed periodicities and desynchronized oscillations of individual serotypes if its effects are decomposed into its two possible manifestations: enhancement of susceptibility to secondary infections and increased transmissibility from individuals suffering from secondary infections. This decomposition not only lowers the level of enhancement necessary for realistic disease patterns but also reduces the risk of stochastic extinction. Furthermore, our analyses reveal a time-lagged correlation between serotype dynamics and disease incidence rates, which could have important implications for understanding the irregular pattern of dengue epidemics.
Liver cirrhosis caused by Exophiala dermatitidis
Authors: Hong Ki Ho , Kim Jeong Won , Jang Se Jin , Yu Eunsil , Kim Eui-Chong
Published: April 2009

We report a case of liver cirrhosis caused byExophiala dermatitidisin a previously healthy child. The infecting organism was initially mistaken as capsule-deficientCryptococcus neoformans.
Development of an assay for the detection and quantification of the measles virus nucleoprotein (N) gene using real-time reverse transcriptase PCR
Authors: Akiyama Miho , Kimura Hirokazu , Tsukagoshi Hiroyuki , Taira Katsuya , Mizuta Katsumi , Saitoh Mika , Nagano Manami , Sutoh Asuka , Noda Masahiro , Morita Yukio , Sakatsume Osamu , Okabe Nobuhiko , Tashiro Masato
Published: April 2009

We developed a new quantification method for the measles virus (MeV) nucleoprotein (N) gene using real-time reverse transcriptase PCR. This method allowed us to quantify 101–107 copies per reaction (corresponding to 5×10−1–5×105 copies μl−1) of the MeV N gene. We also quantified the MeV N gene from the throat swabs of 22 patients with measles as well as the MeV genotypes A, D3, D5, D9 and H1 in viral suspensions derived from MeV-infected cells. As a result, 3.9×103–5.2×106 copies ml−1and 7.4×107–2.0×108 copies ml−1of the MeV genomes (N gene) were detected in the throat swabs and viral suspensions, respectively. No other viruses (enteroviruses, respiratory syncytial virus, human metapneumovirus or mumps virus) were detected in the assay. The results suggest that this method is applicable to the detection and quantification of some genotypes of MeV.
Peritonitis due to Neosartorya pseudofischeri in an elderly patient undergoing peritoneal dialysis successfully treated with voriconazole
Authors: Ghebremedhin B. , Bluemel A. , Neumann K.-H. , Koenig B. , Koenig W.
Published: April 2009

Aspergillusperitonitis is a rare life-threatening complication of peritoneal dialysis (PD). We report a case of symptomaticNeosartorya pseudofischeriperitonitis in a 60-year-old woman treated by continuous ambulatory peritoneal dialysis (CAPD) for 13 months, who performed peritoneal exchanges independently. This is believed to be the first published case ofN. pseudofischeriin an elderly patient. Comprehensive treatment included early removal of the PD catheter and the use of voriconazole (200 mg Vfend twice daily) for a period of 5 weeks. This case supports the need for more effective prophylaxis and treatment of non-Candidafungal infections in CAPD patients. Our conclusions from this case and a review of the literature are that infection with this fungus can cause substantial morbidity and is best treated with prompt catheter removal, aggressive antifungal therapy with voriconazole or amphotericin B, and vigilant observation for complications. Our report describes for what is believed to be the first time the administration of voriconazole to treat aNeosartoryaperitonitis case.
Evaluation of laccases and melanization in clinical and environmental Cryptococcus neoformans samples by non-denaturing PAGE
Authors: Pereira Cristiane B. , Bueno Frank L. , Dias Amanda L. T. , Brigagão Maísa R. P. L. , Paula Claudete R. , Siqueira Antonio M.
Published: April 2009

The increased incidence of infections caused by the opportunistic pathogen Cryptococcus neoformans, which mainly affects immunocompromised patients but can also infect immunocompetent individuals, has needed additional studies on this micro-organism's pathogenicity and factors related to virulence, such as enzyme production, for a better understanding of the aetiology of cryptococcosis. The aim of this study was to verify the applicability of non-denaturing PAGE for analysis of laccases by quantification of the amount of melanin pigment produced by clinical and environmental strains of C. neoformans. After incubation of the gel with the substrate l-dopa, strains produced melanin spots of a bright brown to black colour. Quantification of these spots was performed by densitometry analysis and the amount of melanin produced was calculated and compared among the strains. All strains showed laccase activity. Serotype B strains showed a higher melanin intensity than serotype A strains. Over half of the clinical strains (56.2 %) showed the lowest melanin intensities, suggesting that melanin production may not be the main virulence factor against host defence. The clinical strain ICB 88 revealed two melanin spots on the gel, indicating the presence of two laccase isoforms. The environmental strains showed the highest values of melanin intensity, which may be related to previous exposure to environmental stress conditions.
Probiotics to minimize the disruption of faecal microbiota in healthy subjects undergoing antibiotic therapy
Authors: Engelbrektson Anna , Korzenik Joshua R. , Pittler Arlyn , Sanders Mary E. , Klaenhammer Todd R. , Leyer Gregory , Kitts Christopher L.
Published: April 2009

A novel combination of culturing and DNA-based terminal restriction fragment length polymorphism (TRFLP) analysis was used to investigate the effect of probiotics on antibiotic-induced gut microbiota alterations to determine if a probiotic preparation containing bifidobacteria and lactobacilli, taken during and after antibiotic therapy, can minimize antibiotic disturbance of faecal microbiota. Healthy subjects administered amoxicillin/clavulanate were randomized and concomitantly received a placebo or probiotic mixture. The primary end point was similarity of faecal microbiota as determined by culturing and TRFLP from subjects taking probiotics compared to those taking a placebo measured by comparing data from baseline to post-treatment for each subject. TRFLP analysis revealed a high subject to subject variation in the baseline faecal microbiota. The most common antibiotic-induced disturbance was a relative increase inClostridium,Eubacterium,BacteroidesandEnterobacteraceae. The mean similarity to the baseline increased over time in both treatment groups, although the probiotic group was less disturbed according to both TRFLP and culture data. The culture method revealed that post-antibiotic faecal microbiota in probiotic-consuming subjects were more similar to the baseline microbiota than the control group (P=0.046). Changes inEnterobactereaceae(P=0.006) andBifidobacterium(P=0.030) counts were significantly different between the groups. Analysis of TRFLP data reinforced the trend between groups but was not statistically significant (P=0.066). This study indicates this mixture of probiotics promotes a more rapid return to pre-antibiotic baseline faecal bacterial microbiota.
Choosing the road less traveled by: a ligand–receptor system that controls target recognition by Drosophila motor axons
Authors: Zinn Kai
Published: April 2009

In this issue of Genes & Development, Siebert and colleagues (pp. 1052–1062) define a ligand–receptor system that controls motor axon guidance and target recognition in the Drosophila embryo. The beaten path (beat) and sidestep (side) genes were known to be important regulators of motor axon guidance. Siebert and colleagues now show that Beat and Side are cell surface proteins that physically interact with each other, and that Beat-expressing motor axon growth cones reach their targets via recognition of Side-expressing pathways.
Drosophila motor axons recognize and follow a Sidestep-labeled substrate pathway to reach their target fields
Authors: Siebert Matthias , Banovic Daniel , Goellner Bernd , Aberle Hermann
Published: April 2009

During development of the Drosophila nervous system, migrating motor axons contact and interact with different cell types before reaching their peripheral muscle fields. The axonal attractant Sidestep (Side) is expressed in most of these intermediate targets. Here, we show that motor axons recognize and follow Side-expressing cell surfaces from the ventral nerve cord to their target region. Contact of motor axons with Side-expressing cells induces the down-regulation of Side. In the absence of Side, the interaction with intermediate targets is lost. Misexpression of Side in side mutants strongly attracts motor axons to ectopic sites. We provide evidence that, on motor axons, Beaten path Ia (Beat) functions as a receptor or part of a receptor complex for Side. In beat mutants, motor axons no longer recognize Side-expressing cell surfaces. Furthermore, Beat interacts with Side both genetically and biochemically. These results suggest that the tracing of Side-labeled cell surfaces by Beat-expressing growth cones is a major principle of motor axon guidance in Drosophila.
A Specialized Outer Layer of the Primary Cell Wall Joins Elongating Cotton Fibers into Tissue-Like Bundles
Authors: Singh Bir , Avci Utku , Eichler Inwood Sarah E. , Grimson Mark J. , Landgraf Jeff , Mohnen Debra , Sørensen Iben , Wilkerson Curtis G. , Willats William G.T. , Haigler Candace H.
Published: April 2009

Cotton (Gossypium hirsutum) provides the world's dominant renewable textile fiber, and cotton fiber is valued as a research model because of its extensive elongation and secondary wall thickening. Previously, it was assumed that fibers elongated as individual cells. In contrast, observation by cryo-field emission-scanning electron microscopy of cotton fibers developing in situ within the boll demonstrated that fibers elongate within tissue-like bundles. These bundles were entrained by twisting fiber tips and consolidated by adhesion of a cotton fiber middle lamella (CFML). The fiber bundles consolidated via the CFML ultimately formed a packet of fiber around each seed, which helps explain how thousands of cotton fibers achieve their great length within a confined space. The cell wall nature of the CFML was characterized using transmission electron microscopy, including polymer epitope labeling. Toward the end of elongation, up-regulation occurred in gene expression and enzyme activities related to cell wall hydrolysis, and targeted breakdown of the CFML restored fiber individuality. At the same time, losses occurred in certain cell wall polymer epitopes (as revealed by comprehensive microarray polymer profiling) and sugars within noncellulosic matrix components (as revealed by gas chromatography-mass spectrometry analysis of derivatized neutral and acidic glycosyl residues). Broadly, these data show that adhesion modulated by an outer layer of the primary wall can coordinate the extensive growth of a large group of cells and illustrate dynamic changes in primary wall structure and composition occurring during the differentiation of one cell type that spends only part of its life as a tissue.
A Comparative Study of the Involvement of 17 Arabidopsis Myosin Family Members on the Motility of Golgi and Other Organelles
Authors: Avisar Dror , Abu-Abied Mohamad , Belausov Eduard , Sadot Einat , Hawes Chris , Sparkes Imogen A.
Published: April 2009

Gene families with multiple members are predicted to have individuals with overlapping functions. We examined all of the Arabidopsis (Arabidopsis thaliana) myosin family members for their involvement in Golgi and other organelle motility. Truncated fragments of all 17 annotated Arabidopsis myosins containing either the IQ tail or tail domains only were fused to fluorescent markers and coexpressed with a Golgi marker in two different plants. We tracked and calculated Golgi body displacement rate in the presence of all myosin truncations and found that tail fragments of myosins MYA1, MYA2, XI-C, XI-E, XI-I, and XI-K were the best inhibitors of Golgi body movement in the two plants. Tail fragments of myosins XI-B, XI-F, XI-H, and ATM1 had an inhibitory effect on Golgi bodies only in Nicotiana tabacum, while tail fragments of myosins XI-G and ATM2 had a slight effect on Golgi body motility only in Nicotiana benthamiana. The best myosin inhibitors of Golgi body motility were able to arrest mitochondrial movement too. No exclusive colocalization was found between these myosins and Golgi bodies in our system, although the excess of cytosolic signal observed could mask myosin molecules bound to the surface of the organelle. From the preserved actin filaments found in the presence of enhanced green fluorescent protein fusions of truncated myosins and the motility of myosin punctae, we conclude that global arrest of actomyosin-derived cytoplasmic streaming had not occurred. Taken together, our data suggest that the above myosins are involved, directly or indirectly, in the movement of Golgi and mitochondria in plant cells.