bluuebunny/crossref_metadata_2025 huggingface dataset:
Australia’s rangelands: a future vision
Authors: Fitzhardinge Guy
Published: February 2012

The rangelands of Australia and their communities can be represented as a diverse and interrelated complex of social and ecological systems. For the development of a sustainable future for both social and ecological systems, thinking needs to be at a level that accommodates the interaction of all systems and not just part of them. Historical trends show that continued emphasis on increased production in agriculture does little to improve the real wealth of the industry in the long term. Changing community attitudes in relation to the value of the rangelands present both threats and opportunities for the inhabitants of the rangelands. It is argued that capitalising on the wider range of values represented by the landscape beyond only production of generic agricultural products and mining presents a more viable path to an ecologically sustainable and socially acceptable future for the Australian rangelands.
Activation of GATA binding protein 6 (
GATA6
) sustains oncogenic lineage-survival in esophageal adenocarcinoma
Authors: Lin Lin , Bass Adam J. , Lockwood William W. , Wang Zhuwen , Silvers Amy L. , Thomas Dafydd G. , Chang Andrew C. , Lin Jules , Orringer Mark B. , Li Weiquan , Glover Thomas W. , Giordano Thomas J. , Lam Wan L. , Meyerson Matthew , Beer David G.
Published: February 2012

Gene amplification is a tumor-specific event during malignant transformation. Recent studies have proposed a lineage-dependency (addiction) model of human cancer whereby amplification of certain lineage transcription factors predisposes a survival mechanism in tumor cells. These tumor cells are derived from tissues where the lineage factors play essential developmental and maintenance roles. Here, we show that recurrent amplification at 18q11.2 occurs in 21% of esophageal adenocarcinomas (EAC). Utilization of an integrative genomic strategy reveals a single gene, the embryonic endoderm transcription factor
GATA6
, as the selected target of the amplification. Overexpression of
GATA6
is found in EACs that contain gene amplification. We find that EAC patients whose tumors carry
GATA6
amplification have a poorer survival. We show that ectopic expression of
GATA6
, together with
FGFR2
isoform IIIb, increases anchorage-independent growth in immortalized Barrett's esophageal cells. Conversely, siRNA-mediated silencing of
GATA6
significantly reduces both cell proliferation and anchorage-independent growth in EAC cells. We further demonstrate that induction of apoptotic/anoikis pathways is triggered upon silencing of
GATA6
in EAC cells but not in esophageal squamous cells. We show that activation of p38α signaling and up-regulation of TNF-related apoptosis-inducing ligand are detected in apoptotic EAC cells upon
GATA6
deprivation. We conclude that selective gene amplification of
GATA6
during EAC development sustains oncogenic lineage-survival of esophageal adenocarcinoma.
A unique series of reversibly switchable fluorescent proteins with beneficial properties for various applications
Authors: Chang Hao , Zhang Mingshu , Ji Wei , Chen Juanjuan , Zhang Yongdeng , Liu Bei , Lu Jingze , Zhang Junlong , Xu Pingyong , Xu Tao
Published: February 2012

Reversibly switchable fluorescent proteins (RSFPs) have attracted widespread interest for emerging techniques including repeated tracking of protein behavior and superresolution microscopy. Among the limited number of RSFPs available, only Dronpa is widely employed for most cell biology applications due to its monomeric and other favorable photochemical properties. Here we developed a series of monomeric green RSFPs with beneficial optical characteristics such as high photon output per switch, high photostability, a broad range of switching rate, and pH-dependence, which make them potentially useful for various applications. One member of this series, mGeos-M, exhibits the highest photon budget and localization precision potential among all green RSFPs. We propose mGeos-M as a candidate to replace Dronpa for applications such as dynamic tracking, dual-color superresolution imaging, and optical lock-in detection.
When Good Fish Make Bad Decisions: Coho Salmon in an Ecological Trap
Authors: Jeffres Carson , Moyle Peter
Published: February 2012

Coho salmon Oncorhynchus kisutch are a threatened species in California. In the Shasta River, they may be caught in an ecological trap that is exacerbating their decline. Adults appear to have equal preferences for spawning habitat that reduces the survival of their young and that of apparently similar quality where survival would be more likely. The primary cause of juvenile mortality is water withdrawals, which degrade summer water quality and create barriers to movement to habitats with more suitable rearing conditions. The situation has been exacerbated by the addition of gravel to support spawning fall-run Chinook salmon O. tshawytscha, creating habitat that is also attractive to spawning coho salmon in locations where juvenile coho salmon survival will be extremely low. The Shasta River acts as a conceptual model of how habitat degradation and ecologically naive restoration actions may combine to create severe ecological traps for nontarget species.

Received March 10, 2011; accepted October 11, 2011
Exercise promotion: An integration of exercise self‐identity, beliefs, intention, and behaviour
Authors: de Bruijn Gert‐Jan , van den Putte Bas
Published: February 2012

We explored the role of exercise self‐identity within the framework of the theory of planned behaviour (TPB). Participants were 538 undergraduate students who completed measures of exercise self‐identity, exercise behaviour, TPB items, and behavioural and control beliefs. Regression analysis showed that self‐identity was the second strongest predictor of exercise behaviour and interacted with exercise intention. Follow‐up analysis showed that the intention–exercise relationship was more than three times stronger at high than at low levels of exercise self‐identity. Results also showed that only a marginal part of the sample with strong exercise identities had a weak exercise intention, whereas a large part of the sample with a strong exercise intention also reported a strong exercise identity. Nevertheless, only a quarter of the sample that reported strong exercise identity and intention were sufficiently active. The results underline the notion that exercise self‐identity may be a useful component for the theory of planned behaviour.
Perceptions of team athletes on the importance of recovery modalities
Authors: Venter Rachel Elizabeth
Published: February 2012

The aim of this study was to determine how elite team athletes perceive the importance of various recovery modalities. Differences between men and women, players from various team sports and different levels of participation were determined. A total of 890 athletes who volunteered to participate in the study were team players from field hockey (n=213; mean age 21.8±3.3 years), netball (n=215; mean age 22.0±4.0 years), rugby union (n=317; mean age 23.2±3 years) and soccer (n=145; mean age 21.3±2.2 years). The total group of players consisted of 507 (57%) men and 383 (43%) women. At the time of the study, players who participated in the study competed at the highest level of the major competitions and tournaments in their sport, both locally and internationally. Data were collected by means of a questionnaire specifically designed for the study. A one‐page, alphabetical list consisted of 32 words or phrases relating to physiological, psychological, social as well as complimentary and alternative strategies, which could be used for the recovery of athletes. Recovery modalities that were rated as important by all players, regardless of gender, type of sport or level of participation, were sleep, fluid replacement and socialise with friends. Gender differences could play a role in how the importance of recovery modalities was perceived. Men rated an ice bath and supplements as significantly more important (P<0.001) than women. Women rated discussions with their teammates and coaches after training and matches as significantly more important (P<0.001) than men. Significant differences were also found between the different sport codes and levels of participation in regard to the perceived importance of various modalities that could affect recovery of team sport players.
The endosomal adaptor protein APPL1 impairs the turnover of leading edge adhesions to regulate cell migration
Authors: Broussard Joshua A. , Lin Wan-hsin , Majumdar Devi , Anderson Bridget , Eason Brady , Brown Claire M. , Webb Donna J.
Published: February 2012

Cell migration is a complex process that requires the integration of signaling events that occur in distinct locations within the cell. Adaptor proteins, which can localize to different subcellular compartments, where they bring together key signaling proteins, are emerging as attractive candidates for controlling spatially coordinated processes. However, their function in regulating cell migration is not well understood. In this study, we demonstrate a novel role for the adaptor protein containing a pleckstrin-homology (PH) domain, phosphotyrosine-binding (PTB) domain, and leucine zipper motif 1 (APPL1) in regulating cell migration. APPL1 impairs migration by hindering the turnover of adhesions at the leading edge of cells. The mechanism by which APPL1 regulates migration and adhesion dynamics is by inhibiting the activity of the serine/threonine kinase Akt at the cell edge and within adhesions. In addition, APPL1 significantly decreases the tyrosine phosphorylation of Akt by the nonreceptor tyrosine kinase Src, which is critical for Akt-mediated cell migration. Thus, our results demonstrate an important new function for APPL1 in regulating cell migration and adhesion turnover through a mechanism that depends on Src and Akt. Moreover, our data further underscore the importance of adaptor proteins in modulating the flow of information through signaling pathways.
Not seeing is not believing: improving the visibility of your fluorescence images
Authors: Johnson Jayme
Published: February 2012

The digital age has brought both technical advances and ethical quandaries regarding data acquisition and image presentation in the field of cell biology. Image manipulation has drawn considerable attention in the past decade, leading to general guidelines for ethical data processing. However, effective methods of image presentation have been discussed only cursorily and have been largely overlooked. Under standard viewing conditions, the human visual system imposes limitations for readers analyzing fluorescence images. In this paper, I discuss the advantages and limitations of image-manipulation techniques with respect to the human visual system, including contrast stretching, nonlinear grayscale transformations, and pseudocoloring. While online data viewing presents innovative ways to access image information, most images continue to be viewed in static publications, in which image presentation is critical for effective information transmission.
StochSens—matlab package for sensitivity analysis of stochastic chemical systems
Authors: Komorowski Michał , Žurauskienė Justina , Stumpf Michael P.H.
Published: February 2012

Motivation: The growing interest in the role of stochasticity in biochemical systems drives the demand for tools to analyse stochastic dynamical models of chemical reactions. One powerful tool to elucidate performance of dynamical systems is sensitivity analysis. Traditionally, however, the concept of sensitivity has mainly been applied to deterministic systems, and the difficulty to generalize these concepts for stochastic systems results from necessity of extensive Monte Carlo simulations.

Results: Here we present a Matlab package, StochSens, that implements sensitivity analysis for stochastic chemical systems using the concept of the Fisher Information Matrix (FIM). It uses the linear noise approximation to represent the FIM in terms of solutions of ordinary differential equations. This is the first computational tool that allows for quick computation of the Information Matrix for stochastic systems without the need for Monte Carlo simulations.

Availability:  http://www.theosysbio.bio.ic.ac.uk/resources/stns

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  mkomor@ippt.gov.pl; M.Stumpf@imperial.ac.uk
Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations
Authors: Kiryu Hisanori , Asai Kiyoshi
Published: February 2012

Motivation: Measuring the effects of base mutations is a powerful tool for functional and evolutionary analyses of RNA structures. To date, only a few methods have been developed for systematically computing the thermodynamic changes of RNA secondary structures in response to base mutations.

Results: We have developed algorithms for computing the changes of the ensemble free energy, mean energy and the thermodynamic entropy of RNA secondary structures for exhaustive patterns of single and double mutations. The computational complexities are O(NW  2) (where N is sequence length and W is maximal base pair span) for single mutations and O(N  2  W  2) for double mutations with large constant factors. We show that the changes are relatively insensitive to GC composition and the maximal span constraint. The mean free energy changes are bounded ~7−9 kcal/mol and depend only weakly on position if sequence lengths are sufficiently large. For tRNA sequences, the most stabilizing mutations come from the change of the 5′-most base of the anticodon loop. We also show that most of the base changes in the acceptor stem destabilize the structures, indicating that the nucleotide sequence in the acceptor stem is highly optimized for secondary structure stability. We investigate the 22 tRNA genes in the human mitochondrial genome and show that non-pathogenic polymorphisms tend to cause smaller changes in thermodynamic variables than generic mutations, suggesting that a mutation which largely increases thermodynamic variables has higher possibility to be a pathogenic or lethal mutation.

Availability and implementation: The C++ source code of the Rchange software is available at http://www.ncrna.org/software/rchange/

Contact:  kiryu-h@k.u-tokyo.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Water temperature and timing of capelin spawning determine seabird diets
Authors: Davoren Gail K. , Penton Paulette , Burke Chantelle , Montevecchi William A.
Published: February 2012

Davoren, G. K., Penton, P., Burke, C., and Montevecchi, W. A. 2012. Water temperature and timing of capelin spawning determine seabird diets. – ICES Journal of Marine Science, 69: . The capelin (Mallotus villosus) is the focal forage fish in many northern marine ecosystems. Its capacity to respond to changes in ocean climate is explored and the usefulness of seabird diets as indicators evaluated by integrating the timing of capelin spawning and temperature (0–150 m) during gonadal development (February–June) with colony-based measures of prey deliveries to chicks of common murres (Uria aalge) and northern gannets (Morus bassanus) on the east coast of Newfoundland during the years 1991–1993 and 2003–2010. Great variation was observed in the timing of spawning, with similar annual trends in different regions of coastal Newfoundland. Spawning was later in years of colder-than-average temperature, although the importance of other variables (e.g. fish size) could not be ruled out. The relationship between temperature during gonadal development and timing of spawning was weak at demersal spawning sites, suggesting that timing may be regulated by other factors (e.g. temperature at spawning sites). When spawning was early in warmer years relative to chick-rearing, common murres delivered a lower percentage of energy-rich gravid capelin to their chicks and northern gannets delivered a lower percentage of capelin. Integrating multiple data sources will be important to monitor marine ecosystem health as ocean climate changes.
Fishing intensity metrics for use in overfishing determination
Authors: Cordue P. L.
Published: February 2012

Cordue, P. L. 2012. Fishing intensity metrics for use in overfishing determination. – ICES Journal of Marine Science, 69: 615–623. The issue of constructing a technically correct fishing intensity metric from the output of a stock assessment model is considered. Four metrics of annual overall “fishing intensity” are defined. The metrics are applicable to age- or length-structured stock assessment models, which may, or may not, include complex spatial and temporal structure in the population and the fisheries. Two of the metrics are termed “direct” as they are calculated from the model output in the given year. Equivalent annual U is a number-based exploitation rate, and equivalent annual F is an average fishing mortality rate. The other two metrics, equilibrium stock depletion (ESD) and spawning potential ratio (SPR), measure fishing intensity in terms of the potential long-term effect on the stock (via 1–ESD and 1–SPR). The use of the metrics for overfishing determination is illustrated with a simple, spatial, two-fishery model. Summary statistics, which are sometimes used as a measure of fishing intensity, such as total catch over a reference biomass, or a number-weighted F are shown to be technically invalid for overfishing determination. The common approach, for virtual population analysis assessments, of using an average F over a specified age range is also discussed.
First Report of Stem Canker Disease of Pitaya (Hylocereus undatus and H. polyrhizus) Caused by Neoscytalidium dimidiatum in Taiwan
Authors: Chuang M. F. , Ni H. F. , Yang H. R. , Shu S. L. , Lai S. Y. , Jiang Y. L.
Published: February 2012

Pitaya (Hylocereus undatus and H. polyrhizus Britt. & Rose), a perennial succulent plant grown in the tropics, is becoming an emerging and important fruit plant in Taiwan. In September of 2009 and 2010, a number of pitaya plants were found to have a distinctive canker on stems. The disease expanded quickly to most commercial planting areas in Taiwan (e.g., Pintung, Chiayi, and Chunghua). Symptoms on the stem were small, circular, sunken, orange spots that developed into cankers. Pycnidia were erumpent from the surface of the cankers and the stems subsequently rotted. After surface disinfestation with 0.1% sodium hypochloride, tissues adjacent to cankers were placed on acidified potato dextrose agar (PDA) and incubated at room temperature for 1 week, after which colonies with dark gray-to-black aerial mycelium grew. Hyphae were branched, septate, and brown and disarticulated into 0- to 1-septate arthrospores. Sporulation was induced by culturing on sterile horsetail tree (Casuarina equisetifolia) leaves. Conidia (12.79 ± 0.72 × 5.14 ± 0.30 μm) from pycnidia were one-celled, hyaline, and ovate. The internal transcribed spacer (ITS) region of ribosomal DNA was PCR amplified with primers ITS1 and ITS4 (2) and sequenced. The sequence (GenBank Accession No. HQ439174) showed 99% identity to Neoscytalidium dimidiatum (Penz.) Crous & Slippers (GenBank Accession No. GQ330903). On the basis of morphology and nucleotide-sequence identity, the isolates were identified as N. dimidiatum (1). Pathogenicity tests were conducted in two replicates by inoculating six surface-sterilized detached stems of pitaya with either mycelium or conidia. Mycelial plugs from 2-day-old cultures (incubated at 25°C under near UV) were inoculated to the detached stems after wounding with a sterile needle. Conidial suspensions (103 conidia/ml in 200 μl) were inoculated to nonwounded stems. Noninoculated controls were treated with sterile medium or water. Stems were then incubated in a plastic box at 100% relative humidity and darkness at 30°C for 2 days. The symptoms described above were observed on inoculated stems at 6 to 14 days postinoculation, whereas control stems did not develop any symptoms. N. dimidiatum was reisolated from symptomatic tissues. To our knowledge, this is the first report of N. dimidiatum causing stem canker of pitaya.

References: (1) P. W. Crous et al. Stud. Mycol. 55:235, 2006. (2) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds. Academic Press, New York, 1990.
A Systematic Study Reveals that Xylella fastidiosa Strains from Pecan Are Part of X. fastidiosa subsp. multiplex
Authors: Melanson R. A. , Sanderlin R. S. , McTaggart A. R. , Ham J. H.
Published: February 2012

Xylella fastidiosa causes disease in a number of economically important crops, ornamental plants, and shade trees, including grapevine, citrus, oleander, and sycamore. In pecan, X. fastidiosa causes pecan bacterial leaf scorch (PBLS), which leads to defoliation and reduces nut yield. No economically effective treatments are available for PBLS. In order to improve PBLS management practices, it is necessary to determine the subspecies of X. fastidiosa strains that infect pecan so that potential sources of inoculum may be identified. Multiprimer polymerase chain reaction (PCR) and phylogenetic analyses using nucleotide sequence data from the 16S-23S rRNA intergenic transcribed spacer (ITS) region and pglA consistently identified strains of X. fastidiosa isolated from pecan as X. fastidiosa subsp. multiplex. Enterobacterial repetitive intergenic consensus PCR and repetitive extragenic palindromic (REP)-PCR analyses were congruent with phylogenetic analyses. REP-PCR analyses indicated genetic variation within strains of X. fastidiosa from pecan. From these same analyses, X. fastidiosa strains from sycamore, grapevine, and oleander from Louisiana were identified as subsp. multiplex, subsp. fastidiosa, and subsp. sandyi, respectively. This study provides additional information about the host ranges of X. fastidiosa subspecies.
Ant attendance reduces flight muscle and wing size in the aphid
Tuberculatus quercicola
Authors: Yao Izumi
Published: February 2012

In otherwise mutualistic relationships between aphids and ants, attendance by ants often has negative impacts on aphids. For example, in a previous study using traps in the field, the aphid
Tuberculatus quercicola
, which exhibits mutualistic interactions with ants, showed extremely low dispersal rates, despite having long wings. This study investigates whether components of the flight apparatus (mesonotum length, flight muscle and wings) differ between aphids attended by ants and not attended by ants. Randomized block analysis of variance, using body length as a covariate, showed that ant attendance has a negative influence on aphid flight apparatus. This result indicates that aphids produce honeydew at the expense of resource investment in flight apparatus. Since the dispersal of
T. quercicola
is limited under ant attendance, the reduction in flight apparatus could precede a decrease in body size. This study also showed that flight apparatus was more developed in aphids under ant-exclusion conditions. This may imply that
T. quercicola
fly when ants are not available. The maintenance of flight apparatus in
T. quercicola
might therefore be partly explained by gene flow on the rare occasions that this aphid species disperses.
Hermit crabs perceive the extent of their virtual bodies
Authors: Sonoda Kohei , Asakura Akira , Minoura Mai , Elwood Robert W. , Gunji Yukio-P.
Published: February 2012

A flexible body image is required by animals if they are to adapt to body changes and move effectively within a structurally complex environment. Here, we show that terrestrial hermit crabs,
Coenobita rugosus
, which frequently change shells, can modify walking behaviour, dependent on the shape of the shell. Hermit crabs walked along a corridor that had alternating left and right corners; if it was narrow at the corner, crabs rotated their bodies to avoid the wall, indicating an awareness of environmental obstacles. This rotation increased when a plastic plate was attached to the shell. We suggest that the shell, when extended by the plate, becomes assimilated to the hermit crab's own body. While there are cases of a tool being assimilated with the body, our result is the first example of the habitat where an animal lives and/or carries being part of a virtual body.
Dynamics and processing in finite self-similar networks
Authors: DeDeo Simon , Krakauer David C.
Published: February 2012

A common feature of biological networks is the geometrical property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks show self-similar connectivity at multiple scales. We analyse the relationship between topology and signalling in contrasting classes of such topologies. We find that networks differ in their ability to contain or propagate signals between arbitrary nodes in a network depending on whether they possess branching or loop-like features. Networks also differ in how they respond to noise, such that one allows for greater integration at high noise, and this performance is reversed at low noise. Surprisingly, small-world topologies, with diameters logarithmic in system size, have slower dynamical time scales, and may be less integrated (more modular) than networks with longer path lengths. All of these phenomena are essentially mesoscopic, vanishing in the infinite limit but producing strong effects at sizes and time scales relevant to biology.
Dramatic reduction of dimensionality in large biochemical networks owing to strong pair correlations
Authors: Dworkin Michael , Mukherjee Sayak , Jayaprakash Ciriyam , Das Jayajit
Published: February 2012

Large multi-dimensionality of high-throughput datasets pertaining to cell signalling and gene regulation renders it difficult to extract mechanisms underlying the complex kinetics involving various biochemical compounds (e.g. proteins and lipids). Data-driven models often circumvent this difficulty by using pair correlations of the protein expression levels to produce a small number (fewer than 10) of principal components, each a linear combination of the concentrations, to successfully model how cells respond to different stimuli. However, it is not understood if this reduction is specific to a particular biological system or to nature of the stimuli used in these experiments. We study temporal changes in pair correlations, described by the covariance matrix, between concentrations of different molecular species that evolve following deterministic mass-action kinetics in large biologically relevant reaction networks and show that this dramatic reduction of dimensions (from hundreds to less than five) arises from the strong correlations between different species at any time and is insensitive to the form of the nonlinear interactions, network architecture, and to a wide range of values of rate constants and concentrations. We relate temporal changes in the eigenvalue spectrum of the covariance matrix to low-dimensional, local changes in directions of the system trajectory embedded in much larger dimensions using elementary differential geometry. We illustrate how to extract biologically relevant insights such as identifying significant timescales and groups of correlated chemical species from our analysis. Our work provides for the first time, to our knowledge, a theoretical underpinning for the successful experimental analysis and points to a way to extract mechanisms from large-scale high-throughput datasets.
Solution to the eddy-current induction problem in a conducting half-space with a vertical cylindrical borehole
Authors: Skarlatos Anastassios , Theodoulidis Theodoros
Published: February 2012

The eddy-current induction problem in a conducting half-space with a vertical borehole is studied and a solution based on modal techniques is presented. Owing to the particular characteristics of the specific geometry, the straightforward application of the truncated region eigenfunction expansion method (a well-established tool for the analytical solution of such problems) presents significant difficulties. Therefore, a modified truncation approach has been adopted that treats the problem in two steps, each one based on the superposition principle. The approach proves to be very efficient and numerically robust. Results for the coil impedance are in excellent agreement with those obtained with the finite-element method. From the engineering point of view, the geometry simulates the eddy-current inspection of fastener holes in aircraft structures when coil scanning is performed from the surface. The presented solution constitutes an important step towards the development of a complete model for fastener hole crack inspections.
On the dispersal of leatherback turtle hatchlings from Mesoamerican nesting beaches
Authors: Shillinger George L. , Di Lorenzo Emanuele , Luo Hao , Bograd Steven J. , Hazen Elliott L. , Bailey Helen , Spotila James R.
Published: February 2012

So little is known about the early life history of leatherback turtles (
Dermochelys coriacea
) from hatchling to adulthood that this period has been termed the ‘lost years’. For critically endangered eastern Pacific leatherback populations, continued and rapid declines underscore the urgent need to develop conservation strategies across all life stages. We investigate leatherback hatchling dispersal from four Mesoamerican nesting beaches using passive tracer experiments within a regional ocean modelling system. The evolution of tracer distribution from each of the nesting beaches showed the strong influence of eddy transport and coastal currents. Modelled hatchlings from Playa Grande, Costa Rica, were most likely to be entrained and transported offshore by large-scale eddies coincident with the peak leatherback nesting and hatchling emergence period. These eddies potentially serve as ‘hatchling highways’, providing a means of rapid offshore transport away from predation and a productive refuge within which newly hatched turtles can develop. We hypothesize that the most important leatherback nesting beach remaining in the eastern Pacific (Playa Grande) has been evolutionarily selected as an optimal nesting site owing to favourable ocean currents that enhance hatchling survival.
Insights into the phylogeny of systematically controversial haptorian ciliates (Ciliophora, Litostomatea) based on multigene analyses
Authors: Zhang Qianqian , Simpson Alastair , Song Weibo
Published: February 2012

The ciliate subclass Haptoria is a diverse taxon that includes most of the free-living predators in the class Litostomatea. Phylogenetic study of this group was initially conducted using a single molecular marker small-subunit ribosomal RNA (SSU rRNA genes). Multi-gene analysis has been limited because very few other sequences were available. We performed phylogenetic analyses of Haptoria incorporating new SSU rRNA gene sequences from several debated members of the taxon, in particular, the first molecular data from
Cyclotrichium
. We also provided nine large-subunit ribosomal RNA (LSU rRNA) gene sequences and 10 alpha-tubulin sequences from diverse haptorians, and two possible relatives of controversial haptorians (Plagiopylea, Prostomatea). Phylogenies inferred from the different molecules showed the following: (i)
Cyclotrichium
and
Paraspathidium
were clearly separated from the haptorids and even from class Litostomatea, rejecting their high-level taxonomic assignments based on morphology. Both genera branch instead with the classes Plagiopylea, Prostomatea and Oligohymenophora. This raises the possibility that the well-known but phylogenetically problematic cyclotrichiids
Mesodinium
and
Myrionecta
may also have affinities here, rather than with litostomes; (ii) the transfer of
Trachelotractus
to Litostomatea is supported, especially by the analyses of SSU rRNA and LSU rRNA genes, however,
Trachelotractus
and
Chaenea
(more uncertainly) generally form the two deepest lineages within litostomes; and (iii) phylogenies of the new molecular markers are consistent with SSU rRNA gene information in recovering order Pleurostomatida as monophyletic. However, Pleurostomatida branches cladistically within order Haptorida, as does subclass Trichostomatia (on the basis of SSU rRNA phylogenies). Our results suggest that the class-level taxonomy of ciliates is still not resolved, and also that a systematic revision of litostomes is required, beginning at high taxonomic levels (taxa currently ranked as subclasses and orders).
Projected poleward shift of king penguins' (
Aptenodytes patagonicus
) foraging range at the Crozet Islands, southern Indian Ocean
Authors: Péron Clara , Weimerskirch Henri , Bost Charles-André
Published: February 2012

Seabird populations of the Southern Ocean have been responding to climate change for the last three decades and demographic models suggest that projected warming will cause dramatic population changes over the next century. Shift in species distribution is likely to be one of the major possible adaptations to changing environmental conditions. Habitat models based on a unique long-term tracking dataset of king penguin (
Aptenodytes patagonicus
) breeding on the Crozet Islands (southern Indian Ocean) revealed that despite a significant influence of primary productivity and mesoscale activity, sea surface temperature consistently drove penguins' foraging distribution. According to climate models of the Intergovernmental Panel on Climate Change (IPCC), the projected warming of surface waters would lead to a gradual southward shift of the more profitable foraging zones, ranging from 25 km per decade for the B1 IPCC scenario to 40 km per decade for the A1B and A2 scenarios. As a consequence, distances travelled by incubating and brooding birds to reach optimal foraging zones associated with the polar front would double by 2100. Such a shift is far beyond the usual foraging range of king penguins breeding and would negatively affect the Crozet population on the long term, unless penguins develop alternative foraging strategies.
How the type of anthropogenic change alters the consequences of ecological traps
Authors: Fletcher Robert J. , Orrock John L. , Robertson Bruce A.
Published: February 2012

Understanding altered ecological and evolutionary dynamics in novel environments is vital for predicting species responses to rapid environmental change. One fundamental concept relevant to such dynamics is the ecological trap, which arises from rapid anthropogenic change and can facilitate extinction. Ecological traps occur when formerly adaptive habitat preferences become maladaptive because the cues individuals preferentially use in selecting habitats lead to lower fitness than other alternatives. While it has been emphasized that traps can arise from different types of anthropogenic change, the resulting consequences of these different types of traps remain unknown. Using a novel model framework that builds upon the Price equation from evolutionary genetics, we provide the first analysis that contrasts the ecological and evolutionary consequences of ecological traps arising from two general types of perturbations known to trigger traps. Our model suggests that traps arising from degradation of existing habitats are more likely to facilitate extinction than those arising from the addition of novel trap habitat. Importantly, our framework reveals the mechanisms of these outcomes and the substantial scope for persistence via rapid evolution that may buffer many populations from extinction, helping to resolve the paradox of continued persistence of many species in dramatically altered landscapes.
Conserved properties ofDrosophilaand human spermatozoal mRNA repertoires
Authors: Fischer Bettina E. , Wasbrough Elizabeth , Meadows Lisa A. , Randlet Owen , Dorus Steve , Karr Timothy L. , Russell Steven
Published: February 2012

It is now well established that mature mammalian spermatozoa carry a population of mRNA molecules, at least some of which are transferred to the oocyte at fertilization, however, their function remains largely unclear. To shed light on the evolutionary conservation of this feature of sperm biology, we analysed highly purified populations of mature sperm from the fruitfly,Drosophila melanogaster. As with mammalian sperm, we found a consistently enriched population of mRNA molecules that are unlikely to be derived from contaminating somatic cells or immature sperm. Using tagged transcripts for three of the spermatozoal mRNAs, we demonstrate that they are transferred to the oocyte at fertilization and can be detected before, and at least until, the onset of zygotic gene expression. We find a remarkable conservation in the functional annotations associated with fly and human spermatozoal mRNAs, in particular, a highly significant enrichment for transcripts encoding ribosomal proteins (RPs). The substantial functional coherence of spermatozoal transcripts in humans and the fly opens the possibility of using the power ofDrosophilagenetics to address the function of this enigmatic class of molecules in sperm and in the oocyte following fertilization.
Human postmeiotic sex chromatin and its impact on sex chromosome evolution
Authors: Sin Ho-Su , Ichijima Yosuke , Koh Eitetsu , Namiki Mikio , Namekawa Satoshi H.
Published: February 2012

Sex chromosome inactivation is essential epigenetic programming in male germ cells. However, it remains largely unclear how epigenetic silencing of sex chromosomes impacts the evolution of the mammalian genome. Here we demonstrate that male sex chromosome inactivation is highly conserved between humans and mice and has an impact on the genetic evolution of human sex chromosomes. We show that, in humans, sex chromosome inactivation established during meiosis is maintained into spermatids with the silent compartment postmeiotic sex chromatin (PMSC). Human PMSC is illuminated with epigenetic modifications such as trimethylated lysine 9 of histone H3 and heterochromatin proteins CBX1 and CBX3, which implicate a conserved mechanism underlying the maintenance of sex chromosome inactivation in mammals. Furthermore, our analyses suggest that male sex chromosome inactivation has impacted multiple aspects of the evolutionary history of mammalian sex chromosomes: amplification of copy number, retrotranspositions, acquisition of de novo genes, and acquisition of different expression profiles. Most strikingly, profiles of escape genes from postmeiotic silencing diverge significantly between humans and mice. Escape genes exhibit higher rates of amino acid changes compared with non-escape genes, suggesting that they are beneficial for reproductive fitness and may allow mammals to cope with conserved postmeiotic silencing during the evolutionary past. Taken together, we propose that the epigenetic silencing mechanism impacts the genetic evolution of sex chromosomes and contributed to speciation and reproductive diversity in mammals.
The contractile system as a negative regulator of the connexin 43 hemichannel
Authors: Ponsaerts Raf , Wang Nan , Himpens Bernard , Leybaert Luc , Bultynck Geert
Published: February 2012

The molecular mechanisms underlying the regulation of gap junction (GJ) channels based on the 43‐kDa connexin isoform (Cx43) have been studied extensively. GJ channels are formed by the docking of opposed hemichannels in adjacent cells. Mounting data indicate that unopposed Cx43 hemichannels are also functional in the plasma membrane. However, our understanding of how Cx43‐hemichannel opening and closing is regulated at the molecular level is only poorly understood. Recent work elucidated that actomyosin contractility inhibits potently Cx43 hemichannels. It is known that intracellular Ca2+ exerts a bell‐shaped‐dependent effect on Cx43‐hemichannel opening. While low‐intracellular [Ca2+] (<500 nM) provokes opening of the channel, high‐intracellular [Ca2+] (> 500 nM) favours closing of the channel. The mechanism underlying this negative regulation of Cx43‐hemichannel activity by high‐intracellular [Ca2+] seems to be dependent on the activation of the actomyosin contractile system. The activity of Cx43 hemichannels is critically controlled by molecular interactions between the intracellular loop and the C‐terminal tail. These interactions are essential for Cx43‐hemichannel opening in response to triggers such as cytosolic [Ca2+] rise or external [Ca2+] lowering. In this review, we present the hypothesis that the actomyosin contractile system can function as an important brake mechanism on Cx43‐hemichannel opening. By controlling loop–tail interactions, the contractile system would prevent aberrant or excessive opening of Cx43 hemichannels.
Killer cell immunoglobulin‐like receptor gene polymorphisms predispose susceptibility to Epstein‐Barr virus associated hemophagocytic lymphohistiocytosis in Chinese children
Authors: Qiang Qin , Zhengde Xie , Chunyan Liu , Zhizhuo Huang , Junmei Xu , Junhong Ai , Zheng Chengyun , Henter Jan‐Inge , Kunling Shen
Published: February 2012

Epstein‐Barr virus associated hemophagocytic lymphohistiocytosis (EBV‐HLH) has a high mortality rate among children. The pathogenesis of, and underlying predisposing factors for, EBV‐HLH are as yet unclear; however, natural killer cells may play a key role in progression of the disease. This study attempted to determine whether killer cell immunoglobulin‐like receptor (KIR) gene polymorphisms are responsible for susceptibility to EBV‐HLH. Of the 125 children with EBV infection studied, 59 had EBV‐HLH and 66 patients had EBV associated infectious mononucleosis (IM) without HLH. The control group was 146 normal children without immune deficiency. KIR polymorphisms were determined by polymerase chain reaction with sequence‐specific primers. KIR polymorphism data were analyzed using the X2 test or Fisher's exact test. The overall observed carrier frequency (OF) of KIR2DS5 was significantly higher in EBV‐HLH patients than in IM patients and normal controls (49.2% versus 31.8%, P = 0.048; 49.2% versus 31.5%, P = 0.018, respectively), and the odds ratios (95% confidence interval) were 2.071 (1.001–4.286) and 2.101(1.132–3.900) respectively. The OF of KIR3DS1 was significantly higher in the EBV‐HLH patients than in the IM patients (47.4% versus 24.6%, P  =  0.012), but not different from normal controls. In summary, KIR polymorphisms may be involved in the development of EBV‐HLH, with KIR2DS5 promoting susceptibility to this disease. The obtained KIR data will enrich the understanding of genetic relationships among diseases associated with EBV infection in children.
Production and properties of lipase of Aeromonas sobria
Authors: Takahashi Eizo , Ito Hidenobu , Kobayashi Hidetomo , Yamanaka Hiroyasu , Takeda Yoshifumi , Balakrish Nair Gopinath , Arimoto Sakae , Negishi Tomoe , Okamoto Keinosuke
Published: February 2012

Aeromonas have been isolated from a wide variety of aquatic environments. However the number of Aeromonas in sea water is extremely small compared to that in fresh water. In in vitro culture, Aeromonas can grow in mediums containing NaCl at a concentration of 3.0%, this concentration corresponding to that of sea water. It is unclear why the number of Aeromonas is low in sea water. Exoproteins of bacteria are thought to be important for bacterial growth and survival in the environment. Previously, the present authors have shown that mediums containing 3.0% NaCl suppress production of two proteases, serine protease and metalloprotease. In this experiment, other exoproteins whose production is influenced by the amount of NaCl in the medium were analyzed. A protein whose production is repressed in medium containing 3.0% NaCl was found and purified. Biological assay of the purified protein showed that it degrades tributyrin and hydrolyzes para‐nitrophenyl‐fatty acylesters. These results show that the protein is a lipase. Subsequently, the nucleotide sequence of the gene encoding the lipase was determined and the amount of mRNA of the lipase gene in the cells measured. It was found that transcription of the gene is not inhibited by NaCl in the medium. This result indicates that the lipase might be synthesized, but the folding process to become an active structure does not progress smoothly in a medium containing 3.0% NaCl.
Inhibition of p53 transcriptional activity by human cytomegalovirus UL44
Authors: Kwon Yejin , Kim Mi‐Na , Young Choi Eun , Heon Kim Jung , Hwang Eung‐Soo , Cha Chang‐Yong
Published: February 2012

Human cytomegalovirus (HCMV) stimulates cellular synthesis of DNA and proteins and induces transition of the cell cycle from G1 to S and G2/M phase, in spite of increased amounts of p53 in the infected cells. The immediate early protein IE2–86  kDa (IE86) tethers a transcriptional repression domain to p53; however, its repression of p53 function is not enough to abrogate the G1 checkpoint function of p53. Other HCMV proteins that suppress the activity of p53 were investigated in this study. Of the HCMV proteins that bind to p53 when assessed by immunoprecipitation and immunoblot analysis, HCMV UL44 was chosen as a candidate protein. It was found that reporter gene containing p53 consensus sequence was activated by transfection with wild type p53, but when plasmids of p53 with IE86 or UL44 were co‐transfected, p53 transcriptional activity was decreased to 3–7% of the p53 control in a dose‐dependent manner. When the deletion mutant of UL44 was co‐transected with p53, the carboxyl one‐third portion of UL44 had little effect on inhibition of p53 transcriptional activity. The amount of mRNA p21 was measured in H1299 by real time PCR after transfection of the combination of p53 and UL44 vectors and it was found that p21 transcription by p53 was inhibited dose‐dependently by UL44. Increased G0/G1 and decreased S phases in p53 wild type‐transfected H1299 cells were recovered to the level of p53 mutant type‐transfected ones by the additional transfection of UL44 in a dose‐dependent manner. In conclusion, the transcriptional activity of p53 is suppressed by UL44 as well as by IE86.
Iron deficiency affects plant defence responses and confers resistance to Dickeya dadantii and Botrytis cinerea
Authors: KIEU NAM PHUONG , AZNAR AUDE , SEGOND DIEGO , RIGAULT MARTINE , SIMOND‐CÔTE ELIZABETH , KUNZ CAROLINE , SOULIE MARIE‐CHRISTINE , EXPERT DOMINIQUE , DELLAGI ALIA
Published: February 2012

Iron is an essential element for most living organisms, and pathogens are likely to compete with their hosts for the acquisition of this element. The bacterial plant pathogen Dickeya dadantii has been shown to require its siderophore‐mediated iron uptake system for systemic disease progression on several host plants, including Arabidopsis thaliana. In this study, we investigated the effect of the iron status of Arabidopsis on the severity of disease caused by D. dadantii. We showed that symptom severity, bacterial fitness and the expression of bacterial pectate lyase‐encoding genes were reduced in iron‐deficient plants. Reduced symptoms correlated with enhanced expression of the salicylic acid defence plant marker gene PR1. However, levels of the ferritin coding transcript AtFER1, callose deposition and production of reactive oxygen species were reduced in iron‐deficient infected plants, ruling out the involvement of these defences in the limitation of disease caused by D. dadantii. Disease reduction in iron‐starved plants was also observed with the necrotrophic fungus Botrytis cinerea. Our data demonstrate that the plant nutritional iron status can control the outcome of an infection by acting on both the pathogen's virulence and the host's defence. In addition, iron nutrition strongly affects the disease caused by two soft rot‐causing plant pathogens with a large host range. Thus, it may be of interest to take into account the plant iron status when there is a need to control disease without compromising crop quality and yield in economically important plant species.