bluuebunny/crossref_metadata_2025 huggingface dataset:
Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage
Authors: Hollibaugh James T , Gifford Scott , Sharma Shalabh , Bano Nasreen , Moran Mary Ann
Published: November 2010

Quantitative PCR (qPCR) analysis revealed elevated relative abundance (1.8% of prokaryotes) of marine group 1 Crenarchaeota (MG1C) in two samples of southeastern US coastal bacterioplankton, collected in August 2008, compared with samples collected from the same site at different times (mean 0.026%). We analyzed the MG1C sequences in metatranscriptomes from these samples to gain an insight into the metabolism of MG1C population growing in the environment, and for comparison with ammonia-oxidizing bacteria (AOB) in the same samples. Assemblies revealed low diversity within sequences assigned to most individual MG1C open reading frames (ORFs) and high homology with ‘Candidatus Nitrosopumilus maritimus’ strain SCM1 genome sequences. Reads assigned to ORFs for ammonia uptake and oxidation accounted for 37% of all MG1C transcripts. We did not recover any reads for Nmar_1354–Nmar_1357, proposed to encode components of an alternative, nitroxyl-based ammonia oxidation pathway; however, reads from Nmar_1259 and Nmar_1667, annotated as encoding a multicopper oxidase with homology to nirK, were abundant. Reads assigned to two homologous ORFs (Nmar_1201 and Nmar_1547), annotated as hypothetical proteins were also abundant, suggesting that their unknown function is important to MG1C. Superoxide dismutase and peroxiredoxin-like transcripts were more abundant in the MG1C transcript pool than in the complete metatranscriptome, suggesting an enhanced response to oxidative stress by the MG1C population. qPCR indicated low AOB abundance (0.0010% of prokaryotes), and we found no transcripts related to ammonia oxidation and only one RuBisCO transcript among the transcripts assigned to AOB, suggesting they were not responding to the same environmental cues as the MG1C population.
The Neonatal Microbiome and Necrotizing Enterocolitis.
Authors: Weinstock George , Tarr Phillip , Warner Barbara , Sodergren Erica , Shannon William , Hamvas Aaron , Magrini Vincent
Published: November 2010

Necrotizing enterocolitis (NEC) is a devastating disorder that affects approximately 10% of premature infants. Its mortality remains high (15-30%), and its cause remains unknown. About 80% of cases occur within 35 days of birth among hospitalized newborns of low birth weight. Probiotics diminish the incidence and severity of NEC, and NEC does not occur antepartum. NEC affects a readily identifiable at-risk group, has a tightly defined interval before its onset, occurs in an organ system that is intimately associated with a microbial population in flux, has a plausible association with the intestinal microbiota, and cohorts at risk have rarely been studied in large numbers, or prospectively. This disorder, therefore, provides a unique opportunity to explore the role of the human enteric microbiome in a devastating disease. Moreover, NEC epidemiology and age-incidence present an ability to enroll and study cohorts that are highly likely to provide valuable pathophysiologic and microbiologic insights.In this project, we will identify and quantify the microbial components of stool and its products before and at the onset of NEC. In doing so, we will test the overarching hypothesis that NEC is a direct or indirect consequence of the enteric biomass, its products, or both. We will use multicenter cohorts of premature infants at high risk of developing NEC, extend our research on this disease currently sponsored by the Washington University Institute of Clinical and Translational Sciences, and continue our longstanding collaborations with the Genome Center at Washington University and the Washington University Digestive Diseases Research Core Center (Informatics Core). The Aims of this proposal are to (1) conduct a case cohort study in which we compare clinical data and biological specimens from cases and well-matched controls; (2) determine if the kind and density of intestinal biomass, its gene content, and transcriptional activity are associated with, and potential determinants of, NEC; and (3) determine if host risk alleles for intestinal inflammation play a role in the development of NEC. These efforts will be accomplished using subjects from three collaborating neonatal intensive care units (NICUs), focusing on the critical, instructive, and understudied pre-NEC stage of illness, and formulating a data repository that will be a resource for investigators worldwide who wish to focus their efforts on NEC, its precipitants, and its prevention and cure.
Visualizing Keyboard Pattern Passwords
Authors: Schweitzer Dino , Boleng Jeff , Hughes Colin , Murphy Louis
Published: November 2010

Passwords are fundamental security vulnerabilities in many systems. Several researchers have investigated the trade-off between password memorability versus resiliency to cracking and have looked at alternative systems such as graphical passwords and biometrics. To create stronger passwords, many systems enforce rules regarding the required length and types of characters passwords must contain. Another suggested approach is to use passphrases to combat dictionary attacks. One common ‘trick’ used to remember passwords that conform to complex rules is to select a pattern of keys on the keyboard. Although appearing random, the pattern is easy to remember. The purpose of this research was to investigate how often patterns are used, whether patterns could be classified into common categories, and whether those categories could be used to attack and defeat pattern-based passwords. Visualization techniques were used to collect data and assist in pattern categorization. The approach successfully identified 2 out of 11 passwords in a real-world password file that were not discovered with a traditional dictionary attack. This article will present the approach used to collect and categorize patterns, and describe the resulting attack method that successfully identified passwords in a live system.
Acoustic streaming induced elimination of nonspecifically bound proteins from a surface acoustic wave biosensor: Mechanism prediction using fluid-structure interaction models
Authors: Sankaranarayanan Subramanian K. R. S. , Singh Reetu , Bhethanabotla Venkat R.
Published: November 2010

Biosensors typically operate in liquid media for detection of biomarkers and suffer from fouling resulting from nonspecific binding of protein molecules to the device surface. In the current work, using a coupled field finite element fluid-structure interaction simulation, we have identified that fluid motion induced by high intensity sound waves, such as those propagating in these sensors, can lead to the efficient removal of the nonspecifically bound proteins thereby eliminating sensor fouling. We present a computational analysis of the acoustic-streaming phenomenon induced biofouling elimination by surface acoustic-waves (SAWs) propagating on a lithium niobate piezoelectric crystal. The transient solutions generated from the developed coupled field fluid solid interaction model are utilized to predict trends in acoustic-streaming induced forces for varying design parameters such as voltage intensity, device frequency, fluid viscosity, and density. We utilize these model predictions to compute the various interaction forces involved and thereby identify the possible mechanisms for removal of nonspecifically-bound proteins. For the range of sensor operating conditions simulated, our study indicates that the SAW motion acts as a body force to overcome the adhesive forces of the fouling proteins to the device surface whereas the acoustic-streaming induced hydrodynamic forces prevent their reattachment. The streaming velocity fields computed using the finite element models in conjunction with the proposed particle removal mechanism were used to identify the optimum conditions that lead to improved removal efficiency. We show that it is possible to tune operational parameters such as device frequency and input voltage to achieve effective elimination of biofouling proteins in typical biosensing media. Our simulation results agree well with previously reported experimental observations. The findings of this work have significant implications in designing reusable, selective, and highly sensitive biosensors.
Enhancement of the nucleation of smooth and dense nanocrystalline diamond films by using molybdenum seed layers
Authors: Buijnsters J. G. , Vázquez L. , van Dreumel G. W. G. , ter Meulen J. J. , van Enckevort W. J. P. , Celis J. P.
Published: November 2010

A method for the nucleation enhancement of nanocrystalline diamond (NCD) films on silicon substrates at low temperature is discussed. A sputter deposition of a Mo seed layer with thickness 50 nm on Si substrates was applied followed by an ultrasonic seeding step with nanosized detonation diamond powders. Hot-filament chemical vapor deposition (HF-CVD) was used to nucleate and grow NCD films on substrates heated up at 550 °C. The nucleation of diamond and the early stages of NCD film formation were investigated at different methane percentages in methane/hydrogen gas mixtures by atomic force microscopy, micro-Raman spectroscopy, scanning electron microscopy, and grazing incidence x-ray analyses in order to gain specific insight in the nucleation process of NCD films. The nucleation kinetics of diamond on the Mo-coated Si substrates was found to be up to ten times higher than on blank Si substrates. The enhancement of the nucleation of diamond on thin Mo interlayers results from two effects, namely, (a) the nanometer rough Mo surface shows an improved embedding of ultrasonically introduced nanosized diamond seeds that act as starting points for the diamond nucleation during HF-CVD and (b) the rapid carbonization of the Mo surface causes the formation of Mo2C onto which diamond easily nucleates. The diamond nucleation density progressively increases at increasing methane percentages and is about 5×1010 cm−2 at 4.0% methane. The improved nucleation kinetics of diamond on Mo interlayers facilitates the rapid formation of NCD films possessing a very low surface roughness down to ∼6 nm, and allows a submicron thickness control.
Structural and magnetic properties of epitaxial Fe3O4/ZnO and ZnO/Fe3O4 bilayers grown on c-Al2O3 substrate
Authors: Master Ridhi , Choudhary R. J. , Phase D. M.
Published: November 2010

In the present work, we report the growth and properties of pulsed laser deposited epitaxial bilayer structures of Fe3O4/ZnO and ZnO/Fe3O4 on single crystal Al2O3 (0001) substrates. In order to check the structural compatibility of these structures we annealed these samples at different temperatures. Interface between the two layers plays an important role in determining the structural and magnetic properties. X-ray diffraction (XRD) studies revealed the (111) and (0001) oriented growth of Fe3O4 ZnO layers, respectively, in both the bilayers. Phi-scan shows the epitaxial nature of individual layer in both the bilayers. Raman spectra and XRD indicate the formation of ZnFe2O4 at the interface after annealing of ZnO/Fe3O4 bilayer. Magnetization measurements are in correlation with the structural results. The results indicate that Fe3O4/ZnO bilayer is more stable and has sharper interface than the other bilayer.
Changes in chemical properties of 48 intensively grazed, rain-fed dairy paddocks on sandy soils over 11 years of liming in south-western Australia
Authors: Bolland M. D. A. , Russell W. K.
Published: November 2010

Soil testing was conducted during 1999–2009 to determine lime and fertiliser phosphorus (P), potassium (K), and sulfur (S) requirements of intensively grazed, rain-fed, ryegrass dairy pastures in 48 paddocks on sand to sandy loam soils in the Mediterranean-type climate of south-western Australia. The study demonstrated that tissue testing was required in conjunction with soil testing to confirm decisions based on soil testing, and to assess management decisions for elements not covered by soil testing. Soil testing for pH was reliable for indicating paddocks requiring lime to ameliorate soil acidity, and to monitor progress of liming. Soil P testing proved reliable for indicating when P fertiliser applications were required, with no P being required when soil-test P was above the critical value for that soil, and when no P was applied, tissue testing indicated that P remained adequate for ryegrass production. Soil testing could not be used to determine paddocks requiring fertiliser K and S, because both elements can leach below the root-zone, with rainfall determining the extent of leaching and magnitude of the decrease in pasture production resulting from deficiency, which cannot be predicted. The solution is to apply fertiliser K and S each year, and use tissue testing to improve fertiliser K and S management. Research has shown that, for dairy and other grazing industries in the region, laboratories need measure and report every year soil pH and soil-test P only, together with measuring every 3–5 years the P-buffering index (estimating P sorption of soil), organic carbon content, and electrical conductivity.
High-throughput sequencing reveals a simple model of nucleosome energetics
Authors: Locke George , Tolkunov Denis , Moqtaderi Zarmik , Struhl Kevin , Morozov Alexandre V.
Published: November 2010

We use genome-wide nucleosome maps to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of finite-size particles in an arbitrary external potential and arrays of DNA-bound histone octamers. We derive an analytical solution to infer free energies of nucleosome formation directly from nucleosome occupancies measured in high-throughput experiments. The sequence-specific part of free energies is then captured by fitting them to a sum of energies assigned to individual nucleotide motifs. We have developed hierarchical models of increasing complexity and spatial resolution, establishing that nucleosome occupancies can be explained by systematic differences in mono- and dinucleotide content between nucleosomal and linker DNA sequences, with periodic dinucleotide distributions and longer sequence motifs playing a minor role. Furthermore, similar sequence signatures are exhibited by control experiments in which nucleosome-free genomic DNA is either sonicated or digested with micrococcal nuclease, making it possible that current predictions based on high-throughput nucleosome-positioning maps are biased by experimental artifacts.
Wingless-type family member 5A (Wnt-5a) stimulates synaptic differentiation and function of glutamatergic synapses
Authors: Varela-Nallar Lorena , Alfaro Iván E. , Serrano Felipe G. , Parodi Jorge , Inestrosa Nibaldo C.
Published: November 2010

Growing evidence indicates that Wingless-type (Wnt) signaling plays an important role in the maturation of the central nervous system. We report here that Wingless-type family member 5A (Wnt-5a) is expressed early in development and stimulates dendrite spine morphogenesis, inducing de novo formation of spines and increasing the size of the preexisting ones in hippocampal neurons. Wnt-5a increased intracellular calcium concentration in dendritic processes and the amplitude of NMDA spontaneous miniature currents. Acute application of Wnt-5a increased the amplitude of field excitatory postsynaptic potentials (fEPSP) in hippocampal slices, an effect that was prevented by calcium-channel blockers. The physiological relevance of our findings is supported by studies showing that Wnt scavengers decreased spine density, miniature excitatory postsynaptic currents, and fEPSP amplitude. We conclude that Wnt-5a stimulates different aspects of synaptic differentiation and plasticity in the mammalian central nervous system.
Role for a somatically diversified lectin in resistance of an invertebrate to parasite infection
Authors: Hanington Patrick C. , Forys Michelle A. , Dragoo Jerry W. , Zhang Si-Ming , Adema Coen M. , Loker Eric S.
Published: November 2010

Invertebrates lack adaptive immune systems homologous to those of vertebrates, yet it is becoming increasingly clear that they can produce diversified antigen recognition molecules. We have previously noted that the snail
Biomphalaria glabrata
produces a secreted lectin, fibrinogen-related protein 3 (FREP3), unusual among invertebrate defense molecules because it is somatically diversified by gene conversion and point mutation. Here we implicate FREP3 in playing a central role in resistance to a major group of snail pathogens, digenetic trematodes. FREP3 is up-regulated in three models of resistance of
B. glabrata
to infection with
Schistosoma mansoni
or
Echinostoma paraensei
, and functions as an opsonin favoring phagocytosis by hemocytes. Knock-down of FREP3 in resistant snails using siRNA-mediated interference resulted in increased susceptibility to
E. paraensei
, providing a direct link between a gastropod immune molecule and resistance to trematodes. FREP3 up-regulation is also associated with heightened responsiveness following priming with attenuated digenetic trematodes (acquired resistance) in this model invertebrate immune system.
Centrosomal protein of 192 kDa (Cep192) promotes centrosome-driven spindle assembly by engaging in organelle-specific Aurora A activation
Authors: Joukov Vladimir , De Nicolo Arcangela , Rodriguez Alison , Walter Johannes C. , Livingston David M.
Published: November 2010

Centrosomes are primary microtubule (MT)-organizing centers (MTOCs). During mitosis, they dramatically increase their size and MT-nucleating activity and participate in spindle assembly from spindle poles. These events require the serine/threonine kinase, Aurora A (AurA), and the centrosomal protein of 192 kDa (Cep192)/spindle defective 2 (Spd-2), but the underlying mechanism remains unclear. We have found that Cep192, unlike targeting protein for Xklp2 (TPX2), a known MT-localizing AurA activator, is an AurA cofactor in centrosome-driven spindle assembly. Cep192, through a direct interaction, targets AurA to mitotic centrosomes where the locally accumulating AurA forms homodimers or oligomers. The dimerization of endogenous AurA, in the presence of bound Cep192, triggers potent kinase activation that, in turn, drives MT assembly. Depletion of Cep192 or specific interference with AurA-Cep192 binding did not prevent AurA oligomerization on MTs but abrogated AurA recruitment to centrosomes and its activation by either sperm nuclei or anti-AurA antibody (αAurA)-induced dimerization. In these settings, MT assembly by both centrosomes and αAurA-coated beads was also abolished or severely compromised. Hence, Cep192 activates AurA by a mechanism different from that previously described for TPX2. The Cep192-mediated mechanism maximizes AurA activity at centrosomes and appears essential for the function of these organelles as MTOCs.
Participant structure and the on-line production of discourse context
Authors: van Dam-van Isselt Jet
Published: November 2010

Abstract
This paper presents the micro-analysis of one interrupted and unfinished Dutch 'sentence' that was heard in a popular Dutch Talk Show called 'Sonja op Zaterdag'.1 It contains a self-correction that is produced as a change in 'footing' (Goffman 1979). The issue is raised whether the abandonment of the sentence-under-construction should be considered a random, 'performance' type phenomenon or whether it can be accounted for systematically in terms of discourse-level constraints on the interruptability of sentences (cf. Schegloff 1979). I will argue that the latter seems to be the case. Analyses of the data and hypothetical alternatives to it reveal that observed differences can be articulated in a dynamic discourse model in which utterances may themselves produce contextual updates (Polanyi and Scha 1983; Polanyi 1988; applied to classroom data by van Dam van Isselt 1993). It is suggested that the model should be extended to acknowledge 'defective' sentences.
Übersetzung und Sprachwissenschaft — eine Orientierung
Authors: Faiß Klaus
Published: November 2010

Summary — Résumé
Linguistics regards translating as a linguistic discipline. Hence one is justified in asking what relevance linguistics has for the art of translating. With this question in mind, the present article examines various models and approaches in modern linguistics (con-trastive grammar, transformational grammar, tagmemics). It turns out that modern linguistics has given too little attention to the problems of translating. If the claim that translating is to be regarded as a linguistic discipline ist o be uphold, then a re-orientation of linguistics will be necessary. The objective of his re-orientation will be a "textual linguistics". It must be admitted, however, that the question of whether even a fully workable textual linguistics would be able to cope with all the problems of translation cannot be answered at the present stage of research.
La linguistique regarde la traduction comme une de ses branches. On a par conséquent le droit de poser la question de la pertinence de la linguistique pour l'art de traduire. L'article examine, en partant de cette question, les différents modèles de la linguistique moderne (grammaire contrastive, grammaire transformationnelle, tagmémique). Il se trouve que la linguistique moderne a trop peu considéré le problème de la traduction. Si l'idée de la traduction comme une branche linguistique peut se défendre, une réorientation de la linguistique sera nécessaire. L'objet d'une telle réorientation sera une « linguistique textuelle ». Il doit pourtant être admis que la question de savoir si une linguistique textuelle même entièrement efficace sera à même de résoudre tous les problèmes de la traduction ne se laisse pas décider au moment actuel de la recherche.
PRISM with Incarcerated Young People: Optical Illusion or Reflection of Reality?
Authors: Cregg Michelle , Payne Elizabeth
Published: November 2010

The PRISM process was used to assess the presence of situational risk factors for institutional violence in a juvenile custodial setting in the UK. As part of the assessment, interviews were carried out with staff and young people (aged 15 to 17) and records of violence on the unit over the previous two years were analyzed. Results revealed the presence of a number of situational risk factors for violence with differing levels of severity. A number of interventions were devised for the management of violence on the unit. The study provides support for the utility of PRISM within juvenile custodial settings.
The Impact of Relationship Stage on the Determinants of Trust in the Pharmacist–Client Relationship: Results from a Social Marketing Campaign
Authors: Maniscalco Chiara , Daniloski Kim , Brinberg David
Published: November 2010

The relationship between clients and their health care providers has an important impact on health promotion and disease prevention. Perhaps the most important element of patients' relationships with their health care providers is trust. Enhancing clients' trust in their health care provider has been shown to lead to greater adherence to medical advice, continuity of care, and better overall health outcomes. Pharmacists are beginning to take on the role of primary health care providers to meet the increasing need for affordable, quality medical care. As pharmacists begin to dispense medical advice as well as medicine, there is an increased need for research on the determinants of trust in the pharmacist-client relationship. In this article, we conduct in-depth interviews and a large-scale field survey to develop a social marketing campaign to increase clients' trust in their pharmacists. We implement the campaign through a randomized field experiment and find evidence that emphasizing relational benefits in the developing stages of the pharmacist–client relationship increases trust.
SESAME (SEquence Sorter & AMplicon Explorer): genotyping based on high-throughput multiplex amplicon sequencing
Authors: Meglécz Emese , Piry Sylvain , Desmarais Erick , Galan Maxime , Gilles André , Guivier Emmanuel , Pech Nicolas , Martin Jean-François
Published: November 2010

Summary: Characterizing genetic diversity through genotyping short amplicons is central to evolutionary biology. Next-generation sequencing (NGS) technologies changed the scale at which these type of data are acquired. SESAME is a web application package that assists genotyping of multiplexed individuals for several markers based on NGS amplicon sequencing. It automatically assigns reads to loci and individuals, corrects reads if standard samples are available and provides an intuitive graphical user interface (GUI) for allele validation based on the sequences and associated decision-making tools. The aim of SESAME is to help allele identification among a large number of sequences.

Availability: SESAME and its documentation are freely available under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Licence for Windows and Linux from http://www1.montpellier.inra.fr/CBGP/NGS/ or http://tinyurl.com/ngs-sesame.

Contact:  emese.meglecz@univ-provence.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures
Authors: Wang Hong-Qiang , Tuominen Lindsey K. , Tsai Chung-Jui
Published: November 2010

Motivation: The pre-estimate of the proportion of null hypotheses (π0) plays a critical role in controlling false discovery rate (FDR) in multiple hypothesis testing. However, hidden complex dependence structures of many genomics datasets distort the distribution of p-values, rendering existing π0 estimators less effective.

Results: From the basic non-linear model of the q-value method, we developed a simple linear algorithm to probe local dependence blocks. We uncovered a non-static relationship between tests' p-values and their corresponding q-values that is influenced by data structure and π0. Using an optimization framework, these findings were exploited to devise a Sliding Linear Model (SLIM) to more reliably estimate π0 under dependence. When tested on a number of simulation datasets with varying data dependence structures and on microarray data, SLIM was found to be robust in estimating π0 against dependence. The accuracy of its π0 estimation suggests that SLIM can be used as a stand-alone tool for prediction of significant tests.

Availability: The R code of the proposed method is available at http://aspendb.uga.edu/downloads for academic use.

Contact:  cjtsai@warnell.edu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The rocky road from research to operations for satellite ocean-colour data in fishery management
Authors: Wilson Cara
Published: November 2010

Wilson, C. 2011. The rocky road from research to operations for satellite ocean-colour data in fishery management. – ICES Journal of Marine Science, 68: 677–686. The aim of the SAFARI project is to accelerate the assimilation of earth-observation data into fisheries research and management by facilitating the application of rapidly evolving satellite technology. This assumes that these data will be available in future. However, for ocean-colour data, that assumption may not hold because of possible gaps in data continuity. Of the many types of satellite data, ocean colour is the most important to fisheries, because it is the only biological measurement. However, current ocean-colour sensors are all operating beyond their planned design life, and there are potential problems with future launches. Although the research community is aware of the value of satellite ocean-colour data, advocacy from the operational community, fishery management in particular, has been lacking. In the United States, the absence of an easily identifiable operational need for ocean-colour data is largely responsible for the likely gap in data continuity. A range of current and potential operational uses of ocean-colour data, some reasons why these data have been underutilized in fishery management, and what can be done to mitigate them are discussed and outlined.
Learning to understand others' actions
Authors: Press Clare , Heyes Cecilia , Kilner James M.
Published: November 2010

Despite nearly two decades of research on mirror neurons, there is still much debate about what they do. The most enduring hypothesis is that they enable ‘action understanding’. However, recent critical reviews have failed to find compelling evidence in favour of this view. Instead, these authors argue that mirror neurons are produced by associative learning and therefore that they cannot contribute to action understanding. The present opinion piece suggests that this argument is flawed. We argue that mirror neurons may both develop through associative learning
and
contribute to inferences about the actions of others.
Fish mucous cocoons: the ‘mosquito nets’ of the sea
Authors: Grutter Alexandra S. , Rumney Jennifer G. , Sinclair-Taylor Tane , Waldie Peter , Franklin Craig E.
Published: November 2010

Mucus performs numerous protective functions in vertebrates, and in fishes may defend them against harmful organisms, although often the evidence is contradictory. The function of the mucous cocoons that many parrotfishes and wrasses sleep in, while long used as a classical example of antipredator behaviour, remains unresolved. Ectoparasitic gnathiid isopods (Gnathiidae), which feed on the blood of fish, are removed by cleaner fish during the day; however, it is unclear how parrotfish and wrasse avoid gnathiid attacks at night. To test the novel hypothesis that mucous cocoons protect against gnathiids, we exposed the coral reef parrotfishChlorurus sordidus(Scaridae) with and without cocoons to gnathiids overnight and measured the energetic content of cocoons. Fish without mucous cocoons were attacked more by gnathiids than fish with cocoons. The energetic content of mucous cocoons was estimated as 2.5 per cent of the fish's daily energy budget fish. Therefore, mucous cocoons protected against attacks by gnathiids, acting like mosquito nets in humans, a function of cocoons and an efficient physiological adaptation for preventing parasite infestation that is not used by any other animal.
Frugivores and seed dispersal: mechanisms and consequences for biodiversity of a key ecological interaction
Authors: Jordano Pedro , Forget Pierre-Michel , Lambert Joanna E. , Böhning-Gaese Katrin , Traveset Anna , Wright S. Joseph
Published: November 2010

The 5th Symposium on Frugivores and Seed Dispersal, held in Montpellier (France), 13–18 June 2010, brought together more than 220 researchers exemplifying a wide diversity of approaches to the study of frugivory and dispersal of seeds. Following Ted Fleming and Alejandro Estrada's initiative in 1985, this event was a celebration of the 25th anniversary of the first meeting in Veracruz, Mexico. Frugivory and seed dispersal are active research areas that have diversified in multiple directions since 1985 to include evolution (e.g. phylogenetic diversity and dispersal adaptations), physiology (e.g. sensory cues and digestion), landscape ecology (movement patterns), molecular ecology (e.g. gene flow, genetic diversity and structure), community ecology (e.g. mutualistic interaction networks) and conservation biology (effects of hunting, fragmentation, invasion and extinction), among others. This meeting provided an opportunity to assess conceptual and methodological progress, to present ever more sophisticated insights into frugivory in animals and dispersal patterns in plants, and to report the advances made in examining the mechanisms and consequences of seed dispersal for plants and frugivores.
The statistical mechanics of a polygenic character under stabilizing selection, mutation and drift
Authors: de Vladar Harold P. , Barton Nick H.
Published: November 2010

By exploiting an analogy between population genetics and statistical mechanics, we study the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. This requires us to track only four macroscopic variables, instead of the distribution of all the allele frequencies that influence the trait. These macroscopic variables are the expectations of: the trait mean and its square, the genetic variance, and of a measure of heterozygosity, and are derived from a generating function that is in turn derived by maximizing an entropy measure. These four macroscopics are enough to accurately describe the dynamics of the trait mean and of its genetic variance (and in principle of any other quantity). Unlike previous approaches that were based on an infinite series of moments or cumulants, which had to be truncated arbitrarily, our calculations provide a well-defined approximation procedure. We apply the framework to abrupt and gradual changes in the optimum, as well as to changes in the strength of stabilizing selection. Our approximations are surprisingly accurate, even for systems with as few as five loci. We find that when the effects of drift are included, the expected genetic variance is hardly altered by directional selection, even though it fluctuates in any particular instance. We also find hysteresis, showing that even after averaging over the microscopic variables, the macroscopic trajectories retain a memory of the underlying genetic states.
Electroporation and lysis of marine microalga
Karenia brevis
for RNA extraction and amplification
Authors: Bahi M. M. , Tsaloglou M.-N. , Mowlem M. , Morgan H.
Published: November 2010

We describe here a simple device for dielectrophoretic concentration of marine microalga
Karenia brevis
non-motile cells, followed by electric field-mediated lysis for RNA extraction. The lysate was purified using magnetic beads and pure RNA extracted. RNA quality was assessed off-chip by nucleic acid sequence-based amplification and the optimum conditions for lysis were determined. This procedure will form part of an integrated microfluidic system that is being developed with sub-systems for performing cell concentration and lysis, RNA extraction/purification and real-time quantitative RNA detection. The integrated system and its components could be used for a large range of applications including
in situ
harmful algal bloom detection, transcriptomics and point-of-care diagnostics.
A two-layer approach to modelling the transformation of dilute pyroclastic currents into dense pyroclastic flows
Authors: Doyle Emma E. , Hogg Andrew J. , Mader Heidy M.
Published: November 2010

Most models of volcanic ash flows assume that the flow is either dilute or dense, with dynamics dominated by fluid turbulence or particle collisions, respectively. However, most naturally occurring flows feature both of these end members. To this end, a two-layer model for the formation of dense pyroclastic basal flows from dilute, collapsing volcanic eruption columns is presented. Depth-averaged, constant temperature, continuum conservation equations to describe the collapsing dilute current are derived. A dense basal flow is then considered to form at the base of this current owing to sedimentation of particles and is modelled as a granular avalanche of constant density. We present results which show that the two-layer model can predict much larger maximum runouts than would be expected from single-layer models, based on either dilute or dense conditions, as the dilute surge can outrun the dense granular flow, or vice versa, depending on conditions.
Environmental, pharmacological and genetic influences on the spread of drug-resistant malaria
Authors: Antao Tiago , Hastings Ian M.
Published: November 2010

Plasmodium falciparum
malaria is subject to artificial selection from antimalarial drugs that select for drug-resistant parasites. We describe and apply a flexible new approach to investigate how epistasis, inbreeding, selection heterogeneity and multiple simultaneous drug deployments interact to influence the spread of drug-resistant malaria. This framework recognizes that different human ‘environments’ within which treatment may occur (such as semi- and non-immune humans taking full or partial drug courses) influence the genetic interactions between parasite loci involved in resistance. Our model provides an explanation for how the rate of spread varies according to different malaria transmission intensities, why resistance might stabilize at intermediate frequencies and also identifies several factors that influence the decline of resistance after a drug is removed. Results suggest that studies based on clinical outcomes might overestimate the spread of resistant parasites, especially in high-transmission areas. We show that when transmission decreases, prevalence might decrease without a corresponding change in frequency of resistance and that this relationship is heavily influenced by the extent of linkage disequilibrium between loci. This has important consequences on the interpretation of data from areas where control is being successful and suggests that reducing transmission might have less impact on the spread of resistance than previously expected.
Hunting at the highway: traffic noise reduces foraging efficiency in acoustic predators
Authors: Siemers Björn M. , Schaub Andrea
Published: November 2010

Noise pollution from human traffic networks and industrial activity impacts vast areas of our planet. While anthropogenic noise effects on animal communication are well documented, we have very limited understanding of noise impact on more complex ecosystem processes, such as predator–prey interactions, albeit urgently needed to devise mitigation measures. Here, we show that traffic noise decreases the foraging efficiency of an acoustic predator, the greater mouse-eared bat (Myotis myotis). These bats feed on large, ground-running arthropods that they find by listening to their faint rustling sounds. We measured the bats' foraging performance on a continuous scale of acoustically simulated highway distances in a behavioural experiment, designed to rule out confounding factors such as general noise avoidance. Successful foraging bouts decreased and search time drastically increased with proximity to the highway. At 7.5 m to the road, search time was increased by a factor of five. From this increase, we predict a 25-fold decrease in surveyed ground area and thus in foraging efficiency for a wild bat. As most of the bats' prey are predators themselves, the noise impact on the bats' foraging performance will have complex effects on the food web and ultimately on the ecosystem stability. Similar scenarios apply to other ecologically important and highly protected acoustic predators, e.g. owls. Our study provides the empirical basis for quantitative predictions of anthropogenic noise impacts on ecosystem processes. It highlights that an understanding of the effects of noise emissions and other forms of ‘sensory pollution’ are crucially important for the assessment of environmental impact of human activities.
Cyanobacterial systematics and nomenclature as featured in the International Bulletin of Bacteriological Nomenclature and Taxonomy / International Journal of Systematic Bacteriology / International Journal of Systematic and Evolutionary Microbiology
Authors: Oren Aharon
Published: November 2010

Surprisingly few papers on cyanobacteria have been published in the International Bulletin of Bacteriological Nomenclature and Taxonomy / International Journal of Systematic Bacteriology / International Journal of Systematic and Evolutionary Microbiology (IBBNT/IJSB/IJSEM) during its 60 years of existence. The first papers featuring the group appeared in volume 28 and, in the 32 years that have passed since, 42 articles on cyanobacteria have been published in the journal. Very few of these papers deal with the description of new taxa and this is understandable in view of the current difficulty in validly publishing new names of cyanobacteria under the rules of the International Code of Nomenclature of Prokaryotes (ICNP). Other papers discuss the problems of the nomenclature of the group under the International Code of Botanical Nomenclature (ICBN)/ICNP and the ICBN. The largest group of articles on cyanobacteria consists of papers on systematics, in which isolates are compared using different approaches, without any implications for the nomenclature of the group under either Code. The fact that on average these papers have been highly cited shows that IJSEM and its predecessors have been an excellent framework for publications on cyanobacteria and should remain so in the future.
Pontirhabdus pectinivorans gen. nov., sp. nov., isolated from seawater
Authors: Yi Hana , Cho Jang-Cheon , Chun Jongsik
Published: November 2010

A yellow-coloured, rod-shaped, Gram-reaction-negative and aerobic bacterial strain, designated JC2675T, was isolated from a seawater sample from Jeju Island, Korea. The isolate required sea salts for growth. Gliding motility was observed. Flexirubin-type pigments were absent. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JC2675T represented a distinct phyletic line that reflected a novel generic status within the family Flavobacteraceae with relatively low gene sequence similarities (<95.7 %) to other recognized genera. The predominant isoprenoid quinone (MK-6) and DNA G+C content (30 mol%) were consistent with the assignment of the novel strain to the family Flavobacteriaceae, but overall phenotypic traits demonstrated that the novel strain was not closely affiliated with any previously described genus. Based on data from a study using a polyphasic taxonomic approach, it is proposed that strain JC2675T represents a new genus and novel species belonging to the family Flavobacteriaceae, for which the name Pontirhabdus pectinivorans gen. nov., sp. nov. is proposed. The type strain of the type species is JC2675T ( = KACC 14153T = JCM 17107T).
Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase
Authors: Vorobev Alexey V. , Baani Mohamed , Doronina Nina V. , Brady Allyson L. , Liesack Werner , Dunfield Peter F. , Dedysh Svetlana N.
Published: November 2010

Two strains of aerobic methanotrophic bacteria, AR4T and SOP9, were isolated from acidic (pH 3.8–4.0) Sphagnum peat bogs in Russia. Another phenotypically similar isolate, strain LAY, was obtained from an acidic (pH 4.0) forest soil in Germany. Cells of these strains were Gram-negative, non-pigmented, non-motile, thin rods that multiplied by irregular cell division and formed rosettes or amorphous cell conglomerates. Similar to Methylocella species, strains AR4T, SOP9 and LAY possessed only a soluble form of methane monooxygenase (sMMO) and lacked intracytoplasmic membranes. Growth occurred only on methane and methanol; the latter was the preferred growth substrate. mRNA transcripts of sMMO were detectable in cells when either methane or both methane and methanol were available. Carbon was assimilated via the serine and ribulose-bisphosphate (RuBP) pathways; nitrogen was fixed via an oxygen-sensitive nitrogenase. Strains AR4T, SOP9 and LAY were moderately acidophilic, mesophilic organisms capable of growth between pH 3.5 and 7.2 (optimum pH 4.8–5.2) and at 4–33 °C (optimum 20–23 °C). The major cellular fatty acid was 18 : 1ω7c and the quinone was Q-10. The DNA G+C content was 55.6–57.5 mol%. The isolates belonged to the family Beijerinckiaceae of the class Alphaproteobacteria and were most closely related to the sMMO-possessing methanotrophs of the genus Methylocella (96.4–97.0 % 16S rRNA gene sequence similarity), particulate MMO (pMMO)-possessing methanotrophs of the genus Methylocapsa (96.1–97.0 %), facultative methylotrophs of the genus Methylovirgula (96.1–96.3 %) and non-methanotrophic organotrophs of the genus Beijerinckia (96.5–97.0 %). Phenotypically, strains AR4T, SOP9 and LAY were most similar to Methylocella species, but differed from members of this genus by cell morphology, greater tolerance of low pH, detectable activities of RuBP pathway enzymes and inability to grow on multicarbon compounds. Therefore, we propose a novel genus and species, Methyloferula stellata gen. nov., sp. nov., to accommodate strains AR4T, SOP9 and LAY. Strain AR4T ( = DSM 22108T  = LMG 25277T  = VKM B-2543T) is the type strain of Methyloferula stellata.
Protein kinase Mζ is essential for the induction and maintenance of dopamine-induced long-term potentiation in apical CA1 dendrites
Authors: Navakkode Sheeja , Sajikumar Sreedharan , Sacktor Todd Charlton , Frey Julietta U.
Published: November 2010

Dopaminergic D1/D5-receptor-mediated processes are important for certain forms of memory as well as for a cellular model of memory, hippocampal long-term potentiation (LTP) in the CA1 region of the hippocampus. D1/D5-receptor function is required for the induction of the protein synthesis-dependent maintenance of CA1-LTP (L-LTP) through activation of the cAMP/PKA-pathway. In earlier studies we had reported a synergistic interaction of D1/D5-receptor function and N-methyl-D-aspartate (NMDA)-receptors for L-LTP. Furthermore, we have found the requirement of the atypical protein kinase C isoform, protein kinase Mζ (PKMζ) for conventional electrically induced L-LTP, in which PKMζ has been identified as a LTP-specific plasticity-related protein (PRP) in apical CA1-dendrites. Here, we investigated whether the dopaminergic pathway activates PKMζ. We found that application of dopamine (DA) evokes a protein synthesis-dependent LTP that requires synergistic NMDA-receptor activation and protein synthesis in apical CA1-dendrites. We identified PKMζ as a DA-induced PRP, which exerted its action at activated synaptic inputs by processes of synaptic tagging.
The GDC1 Gene Encodes a Novel Ankyrin Domain-Containing Protein That Is Essential for Grana Formation in Arabidopsis
Authors: Cui Yong-Lan , Jia Qi-Shi , Yin Qian-Qian , Lin Guan-Nan , Kong Meng-Meng , Yang Zhong-Nan
Published: November 2010

In land-plant chloroplasts, the grana play multiple roles in photosynthesis, including the potential increase of photosynthetic capacity in light and enhancement of photochemical efficiency in shade. However, the molecular mechanisms of grana formation remain elusive. Here, we report a novel gene, Grana-Deficient Chloroplast1 (GDC1), required for chloroplast grana formation in Arabidopsis (Arabidopsis thaliana). In the chloroplast of knockout mutant gdc1-3, only stromal thylakoids were observed, and they could not stack together to form appressed grana. The mutant exhibited seedling lethality with pale green cotyledons and true leaves. Further blue native-polyacrylamide gel electrophoresis analysis indicated that the trimeric forms of Light-Harvesting Complex II (LHCII) were scarcely detected in gdc1-3, confirming previous reports that the LHCII trimer is essential for grana formation. The Lhcb1 protein, the major component of the LHCIIb trimer, was substantially reduced, and another LHCIIb trimer component, Lhcb2, was slightly reduced in the gdc1-3 mutant, although their transcription levels were not altered in the mutant. This suggests that defective LHCII trimer formation in gdc1-3 is due to low amounts of Lhcb1 and Lhcb2. GDC1 encodes a chloroplast protein with an ankyrin domain within the carboxyl terminus. It was highly expressed in Arabidopsis green tissues, and its expression was induced by photosignaling pathways. Immunoblot analysis of the GDC1-green fluorescent protein (GFP) fusion protein in 35S::GDC1-GFP transgenic plants with GFP antibody indicates that GDC1 is associated with an approximately 440-kD thylakoid protein complex instead of the LHCII trimer. This shows that GDC1 may play an indirect role in LHCII trimerization during grana formation.