bluuebunny/crossref_metadata_2025 huggingface dataset:
Revisiting the Processing of Internal and External Features of Unfamiliar Faces: The Headscarf Effect
Authors: Megreya Ahmed M , Bindemann Markus
Published: October 2009

Five experiments are reported in which the relative importance of internal and external features for unfamiliar face identification are examined by a matching task. In experiments 1–3, Egyptian adults showed a robust internal-feature advantage for matching photographs of Egyptian faces. In experiment 4, a cross-cultural comparison between the ability of Egyptian and British adults to match the internal and external features of unfamiliar Egyptian and British faces was made. Once again, Egyptians showed an internal-feature advantage, for all faces. In contrast, British observers—and also Egyptian children in experiment 5—showed external-feature advantages consistent with previous research. We attribute this contrast to the long-term experience of Egyptians in perceiving and recognising faces with headscarves, which might develop more expertise in processing the internal than the external features of unfamiliar faces.
Modulation of Viewpoint Effects in Object Recognition by Shape and Motion Cues
Authors: Vuong Quoc C , Friedman Alinda , Plante Courtney
Published: October 2009

In three experiments, we examined the role of structural similarity and different types of motion on the efficiency of performing same – different shape judgments across changes in viewpoints. In all experiments, participants judged whether two novel, multi-part objects were structurally identical, and they were to ignore any viewpoint or motion differences between the objects. In experiment 1, participants were affected by viewpoint differences more for structurally similar than structurally distinct objects, but this interaction was mitigated by rigid motion. In experiments 2 and 3, we used only structurally similar objects that moved only some of their parts, either in a similar way between objects within a pair or in distinctive ways. Participants' recognition performance was facilitated by this articulated motion relative to both static and scrambled controls. We conclude that coherent motion facilitates generalisation across different views of dynamic objects under some conditions.
Genetic differentiation among and within three red mahoganies (series Annulares), Eucalyptus pellita, E. resinifera and E. scias (Myrtaceae)
Authors: Le Son , Nock Catherine , Henson Michael , Shepherd Mervyn
Published: October 2009

The red mahogany group (Eucalyptus ser. Annulares Blakely) includes some of the most important commercial species (i.e. Eucalyptus urophylla S.T.Blake) worldwide for forestry in the subtropics and tropics. However, the taxonomic status of some species in this group is unclear and the relationship among and genetic structuring within some species is unresolved. The present study examined genetic variation at 13 microsatellite loci in E. pellita F.Muell., E. resinifera Smith and E. scias L.Johnson & K.Hill. Despite close geographical proximity and natural hybridisation in northern Queensland, E. resinifera and E. pellita remain genetically distinct as taxa. Within E. pellita, two genetic groups were clearly resolved, one from New Guinea and one from Queensland (Cape York Peninsula populations were not sampled). Geographic structuring was also evident in E. resinifera, with northern Queensland populations separating from those from Fraser Island southwards. Ecological factors and species disjunctions were implicated in the genetic substructuring of these two taxa because patterns of geographic variation aligned with biogeographical regions. E. scias was indistinguishable from southern E. resinifera and its three subspecies could not be resolved.
A revision of Cassinia (Asteraceae: Gnaphalieae) in Australia. 6. Section Cassinia
Authors: Orchard A. E.
Published: October 2009

The present paper completes a taxonomic revision of Cassinia subg. Cassinia, a group of 35 species separated from subg. Achromolaena by the structure of its inflorescence (capitula arrangement approximately dichasial, giving rise to flat- or round-topped compound inflorescences, as opposed to the irregular or alternate arrangement of capitula in subg. Achromolaena, where the overall shape of the inflorescence is conical or elongate). The seven species of Cassinia sect. Cassinia (C. aculeata, C. thinicola, C. wilsoniae, C. longifolia, C. aureonitens, C. trinerva and C. cinerea) are keyed, described and illustrated, with discussion of ecology, distribution and variation. Cassinia aculeata subsp. nova-anglica Orchard, C. thinicola Orchard, C. wilsoniae Orchard and C. cinerea Orchard are described as new. Cassinia aculeata is a variable and widespread species. Four morphological variants are described and discussed, although not formally named. Previously suggested hybridisation between C. aculeata and Ozothamnus obcordatus is discussed, and dismissed. A new subspecies, narrowly endemic to the New England region of New South Wales (NSW), and separated by 350 km from subsp. aculeata, is described. Cassinia longifolia is similarly widespread and variable, particularly in indumentum and leaf shape. Again, four more or less distinct local morphological variants are described, but they are not formally named because of problems with satisfactory circumscription. Cassinia thinicola is newly segregated from C. aculeata. It is a strikingly distinct species, confined to coastal habitats north and south of Newcastle, distinguished by its (usually) lack of hairs on the upper leaf surface, ochre-coloured inflorescences and compact habit. Cassinia wilsoniae, confined to Wyperfeld National Park in western Victoria, has hitherto been largely overlooked, with specimens assigned to a broadly circumscribed ‘C. uncata’, or C. aculeata or C. longifolia. It is geographically widely separated from all of these taxa. It is unusual in the genus, in being confined largely to the summits of consolidated sand dunes. It has rather small inflorescences with few capitula, and these are ochre-coloured. The leaf margins are strongly revolute, almost completely covering the midrib below, unlike related taxa where the midrib remains uncovered. Cassinia cinerea is a rare species confined to south-eastern Queensland, and hitherto confused with C. laevis and C. collina, both in subg. Achromolaena (and thus with conical inflorescences). It also differs from both in a range of indumentum and leaf characters. The remaining, previously recognised, species are redescribed in detail, and their nomenclature, variation, ecology and distribution are discussed as required.
Fruit availability and utilisation by grey-headed flying foxes (Pteropodidae: Pteropus poliocephalus) in a human-modified environment on the south coast of New South Wales, Australia
Authors: Schmelitschek Emily , French Kristine , Parry-Jones Kerryn
Published: October 2009

Context. Extensive clearing and modification of habitat is likely to change many facets of the environment including climate and regional food resources. Such changes may result in changes in behaviour in highly mobile fauna, such as flying foxes. Aims.The availability of fruit resources was examined to determine whether grey-headed flying foxes (Pteropus poliocephalus) have feeding preferences related to habitat or dietary items, and whether human usage of the land around the colony site has affected the resources available. Methods. Fruit availability around a colony was monitored from December 2004 to March 2005. Night surveys and faecal analyses were undertaken to determine the distribution of feeding locations, the food species used and the food items consumed by P. poliocephalus. Key results.The amount of food available per hectare in each habitat was similar. However, we found differences in the composition of food trees and the distribution of food resources within each habitat. Ficus species were a major resource with flying foxes observed feeding in figs during every survey and figs identified in droppings over the whole period. Human-modified habitats were used throughout the study period with flying foxes observed in small patches of vegetation and in individual trees without any nearby vegetation. Conclusions. The need for maintaining vegetation, particularly Ficus species, in all areas where flying foxes are found, especially in human-modified habitats and rainforest remnants, is highlighted as this vegetation is of great importance to flying foxes. Other wildlife, such as birds and possums, may also benefit from the maintenance of this vegetation. Implications. Through management of urban resources there is the potential to prevent future conflict situations arising between humans and wildlife, such as can be seen when flying fox colonies are in close proximity to houses.
Bird use of native trees retained in young eucalypt plantations: species richness and use of hollows
Authors: Koch Amelia J. , Munks Sarah A. , Spencer Chris
Published: October 2009

Context. The retention of mature eucalypts in plantation areas is expected to have biodiversity benefits, especially for animals with specific requirements such as hollow-using species. Aims. The aim of the current study was to examine the degree to which retained trees embedded in young (≤3 years old) eucalypt plantation provide habitat for birds, whether as a perching/foraging resource for all bird species or as a potential shelter/breeding site for hollow-using species. Methods. We examined bird use of remnant trees in young eucalypt plantations at five sites in northern Tasmania. Four 20-min surveys were done on 214 trees (101 of these had visible hollows) over two breeding seasons (2007 and 2008). Bird activity at a hollow was recorded during all four surveys, whereas the number of bird species observed in a tree was only recorded during two surveys in the first breeding season. The relationship between both species richness and hollow use with site and tree variables was explored using hierarchical partitioning. Key results. Bird species richness at a tree was most strongly related to which of the five properties the tree was located on. This may be due to differences in soil fertility and/or the amount of forested area within and around the property. Birds were observed investigating 50 hollows on 36 trees. More than one hollow was used in 10 trees and hollow use was most strongly related to hollow abundance in a tree. High re-use of particular trees (n = 15) and hollows (n = 16) indicates that retained trees vary in the type and quality of habitat they provide for hollow-using birds. The most common hollow users observed were the common starling (Sturnus vulgaris) and the striated pardalote (Pardalotus striatus). Conclusions and implications. Retaining trees in plantation areas, particularly trees with special features such as hollows, should be encouraged to provide habitat for birds and help contribute to the maintenance of bird diversity in an area.
Nest-box use by arboreal mammals in a peri-urban landscape
Authors: Durant Rebecca , Luck Gary W. , Matthews Alison
Published: October 2009

Context. Nest boxes provide important nesting, denning and shelter sites for many fauna species worldwide, but we know little about the factors that influence the suitability of nest boxes for particular species. Such information is crucial in urban landscapes where natural hollows are scarce. Aims. The aim of this study was to record the use of nest boxes by sugar gliders (Petaurus breviceps), squirrel gliders (P. norfolcensis) and other fauna in a peri-urban landscape in northern Victoria and examine factors at multiple spatial scales that may influence nest-box use. Methods. We monitored the use of 102 nest boxes over three seasons in 2006. Attributes that may influence nest-box occupancy were measured at five different spatial scales: (i) landscape; (ii) the habitat beyond 20 m of the nest box; (iii) the habitat within 20 m of the nest box; (iv) the tree that the nest box was located in; and (v) the nest box. Key results. At the landscape scale, topography influenced nest-box occupancy with squirrel gliders using boxes in flat or gully areas, and sugar gliders using boxes in gully, mid-slope or ridge areas. For habitat beyond 20 m of the nest box, sugar gliders were more likely to occupy boxes with a higher density of surrounding nest boxes and a higher density of residential dwellings. Within 20 m of the nest box, boxes occupied by sugar gliders were more likely to occur in areas with a higher density of acacia shrubs and lower density of hollow-bearing trees, whereas the presence of acacia did not influence nest-box use by squirrel gliders. At the scale of the nest-box tree, boxes occupied by sugar gliders were more likely to be on smaller trees (based on height and diameter) and on box (e.g. red box Eucalyptus polyanthemos) species. The only nest-box characteristic to have a strong relationship with occupancy was date of establishment, with longer established boxes more likely to be occupied. Conclusions. Our study demonstrates that various factors influence nest-box use at different scales and nest boxes remain an important conservation and management tool in heavily modified landscapes. Implications. Land managers and groups should be aware that nest boxes may help to alleviate some of the negative impacts of the loss of hollow-bearing trees in low density urban areas, but nest-box use will vary depending on landscape context, habitat factors, box design, and the ecological traits of the target species. Each of these factors must be considered to maximise the conservation benefits of nest-box programs.
Imaging the interaction of HIV-1 genomes and Gag during assembly of individual viral particles
Authors: Jouvenet Nolwenn , Simon Sanford M. , Bieniasz Paul D.
Published: October 2009

The incorporation of viral genomes into particles has never previously been imaged in live infected cells. Thus, for many viruses it is unknown how the recruitment and packaging of genomes into virions is temporally and spatially related to particle assembly. Here, we devised approaches to simultaneously image HIV-1 genomes, as well as the major HIV-1 structural protein, Gag, to reveal their dynamics and functional interactions during the assembly of individual viral particles. In the absence of Gag, HIV-1 RNA was highly dynamic, moving in and out of the proximity of the plasma membrane. Conversely, in the presence of Gag, RNA molecules docked at the membrane where their lateral movement slowed and then ceased as Gag assembled around them and they became irreversibly anchored. Viral genomes were not retained at the membrane when their packaging signals were mutated, nor when expressed with a Gag mutant that was not myristoylated. In the presence of a Gag mutant that retained membrane- and RNA-binding activities but could not assemble into particles, the viral RNA docked at the membrane but continued to drift laterally and then often dissociated from the membrane. These results, which provide visualization of the recruitment and packaging of genomes into individual virus particles, demonstrate that a small number of Gag molecules recruit viral genomes to the plasma membrane where they nucleate the assembly of complete virions.
Structure of the lethal phage pinhole
Authors: Pang Ting , Savva Christos G. , Fleming Karen G. , Struck Douglas K. , Young Ry
Published: October 2009

Perhaps the simplest of biological timing systems, bacteriophage holins accumulate during the phage morphogenesis period and then trigger to permeabilize the cytoplasmic membrane with lethal holes; thus, terminating the infection cycle. Canonical holins form very large holes that allow nonspecific release of fully-folded proteins, but a recently discovered class of holins, the pinholins, make much smaller holes, or pinholes, that serve only to depolarize the membrane. Here, we interrogate the structure of the prototype pinholin by negative-stain transmission electron-microscopy, cysteine-accessibility, and chemical cross-linking, as well as by computational approaches. Together, the results suggest that the pinholin forms symmetric heptameric structures with the hydrophilic surface of one transmembrane domain lining the surface of a central channel ≈15 Å in diameter. The structural model also suggests a rationale for the prehole state of the pinholin, the persistence of which defines the duration of the viral latent period, and for the sensitivity of the holin timing system to the energized state of the membrane.
Genetic diagnosis by whole exome capture and massively parallel DNA sequencing
Authors: Choi Murim , Scholl Ute I. , Ji Weizhen , Liu Tiewen , Tikhonova Irina R. , Zumbo Paul , Nayir Ahmet , Bakkaloğlu Ayșin , Özen Seza , Sanjad Sami , Nelson-Williams Carol , Farhi Anita , Mane Shrikant , Lifton Richard P.
Published: October 2009

Protein coding genes constitute only approximately 1% of the human genome but harbor 85% of the mutations with large effects on disease-related traits. Therefore, efficient strategies for selectively sequencing complete coding regions (i.e., “whole exome”) have the potential to contribute to the understanding of rare and common human diseases. Here we report a method for whole-exome sequencing coupling Roche/NimbleGen whole exome arrays to the Illumina DNA sequencing platform. We demonstrate the ability to capture approximately 95% of the targeted coding sequences with high sensitivity and specificity for detection of homozygous and heterozygous variants. We illustrate the utility of this approach by making an unanticipated genetic diagnosis of congenital chloride diarrhea in a patient referred with a suspected diagnosis of Bartter syndrome, a renal salt-wasting disease. The molecular diagnosis was based on the finding of a homozygous missense D652N mutation at a position in
SLC26A3
(the known congenital chloride diarrhea locus) that is virtually completely conserved in orthologues and paralogues from invertebrates to humans, and clinical follow-up confirmed the diagnosis. To our knowledge, whole-exome (or genome) sequencing has not previously been used to make a genetic diagnosis. Five additional patients suspected to have Bartter syndrome but who did not have mutations in known genes for this disease had homozygous deleterious mutations in
SLC26A3
. These results demonstrate the clinical utility of whole-exome sequencing and have implications for disease gene discovery and clinical diagnosis.
Rationale against Preoperative Screening for HIV in Polish Hospitals: A Prevalence Study of Anti-HIV in Contrast to Anti-Hepatitis C Virus and Hepatitis B Surface Antigen
Authors: Gańczak Maria , Szych Zbigniew
Published: October 2009

We describe the prevalence of anti-human immunodeficiency virus (anti-HIV) among a sample of 1,652 surgical and gynecologic patients in Polish hospitals, contrasting it with the prevalence of hepatitis B surface antigen (HBsAg) and anti-hepatitis C virus (anti-HCV) to assess the rationale for preoperative testing. No anti-HIV-positive samples were found; the prevalence of anti-HCV was 0.9%, slightly higher than the prevalence of HBsAg of 0.6%. Universal preoperative screening of hospital patients for HIV is currently not warranted according to the Centers for Disease Control and Prevention guidelines. However, the seroprevalence of HIV should be reassessed periodically.
Phosphatidylinositol 3,4,5-trisphosphate Localization in Recycling Endosomes Is Necessary for AP-1B–dependent Sorting in Polarized Epithelial Cells
Authors: Fields Ian C. , King Shelby M. , Shteyn Elina , Kang Richard S. , Fölsch Heike
Published: October 2009

Polarized epithelial cells coexpress two almost identical AP-1 clathrin adaptor complexes: the ubiquitously expressed AP-1A and the epithelial cell–specific AP-1B. The only difference between the two complexes is the incorporation of the respective medium subunits μ1A or μ1B, which are responsible for the different functions of AP-1A and AP-1B in TGN to endosome or endosome to basolateral membrane targeting, respectively. Here we demonstrate that the C-terminus of μ1B is important for AP-1B recruitment onto recycling endosomes. We define a patch of three amino acid residues in μ1B that are necessary for recruitment of AP-1B onto recycling endosomes containing phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P3]. We found this lipid enriched in recycling endosomes of epithelial cells only when AP-1B is expressed. Interfering with PI(3,4,5)P3 formation leads to displacement of AP-1B from recycling endosomes and missorting of AP-1B–dependent cargo to the apical plasma membrane. In conclusion, PI(3,4,5)P3 formation in recycling endosomes is essential for AP-1B function.
Retrograde Neurotrophic Signaling Requires a Protein Interacting with Receptor Tyrosine Kinases via C2H2 Zinc Fingers
Authors: Fu Xiaoqin , Zang Keling , Zhou Zhiwei , Reichardt Louis F. , Xu Baoji
Published: October 2009

Neurotrophins at axonal terminals signal to cell bodies to regulate neuronal development via signaling endosomes containing activated Trk receptor tyrosine kinases and mitogen-activated protein kinases (MAPKs). Requirements for the formation of signaling endosomes remain, however, poorly characterized. Here we show that a novel Trk-interacting protein, NTRAP (neurotrophic factor receptor–associated protein), plays a crucial role in this signaling process. NTRAP interacts with the Trk intracellular domain through its C2H2 zinc fingers in a kinase-dependent manner. It is associated with vesicles, some of which contain markers for signaling endosomes. Inhibition of NTRAP function suppresses neurotrophin-induced neurite outgrowth in PC12 cells by altering TrkA endocytic traffic, inhibiting the formation of endosomes containing persistently active MAPKs. In compartmentalized sensory neuron cultures, down-regulation of NTRAP abolishes the ability of neurotrophins applied to distal axons to activate the transcription factor adenosine 3′,5′-monophosphate response element-binding protein (CREB) and to promote neuronal survival. We propose that NTRAP regulates retrograde neurotrophic signaling by controlling the formation of signaling endosomes.
Computational protein profile similarity screening for quantitative mass spectrometry experiments
Authors: Kirchner Marc , Renard Bernhard Y. , Köthe Ullrich , Pappin Darryl J. , Hamprecht Fred A. , Steen Hanno , Steen Judith A. J.
Published: October 2009

Motivation: The qualitative and quantitative characterization of protein abundance profiles over a series of time points or a set of environmental conditions is becoming increasingly important. Using isobaric mass tagging experiments, mass spectrometry-based quantitative proteomics deliver accurate peptide abundance profiles for relative quantitation. Associated data analysis workflows need to provide tailored statistical treatment that (i) takes the correlation structure of the normalized peptide abundance profiles into account and (ii) allows inference of protein-level similarity. We introduce a suitable distance measure for relative abundance profiles, derive a statistical test for equality and propose a protein-level representation of peptide-level measurements. This yields a workflow that delivers a similarity ranking of protein abundance profiles with respect to a defined reference. All procedures have in common that they operate based on the true correlation structure that underlies the measurements. This optimizes power and delivers more intuitive and efficient results than existing methods that do not take these circumstances into account.

Results: We use protein profile similarity screening to identify candidate proteins whose abundances are post-transcriptionally controlled by the Anaphase Promoting Complex/Cyclosome (APC/C), a specific E3 ubiquitin ligase that is a master regulator of the cell cycle. Results are compared with an established protein correlation profiling method. The proposed procedure yields a 50.9-fold enrichment of co-regulated protein candidates and a 2.5-fold improvement over the previous method.

Availability: A MATLAB toolbox is available from http://hci.iwr.uni-heidelberg.de/mip/proteomics.

Contact:  hanno.steen@childrens.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing
Authors: Clement Nathan L. , Snell Quinn , Clement Mark J. , Hollenhorst Peter C. , Purwar Jahnvi , Graves Barbara J. , Cairns Bradley R. , Johnson W. Evan
Published: October 2009

Motivation: The advent of next-generation sequencing technologies has increased the accuracy and quantity of sequence data, opening the door to greater opportunities in genomic research.

Results: In this article, we present GNUMAP (Genomic Next-generation Universal MAPper), a program capable of overcoming two major obstacles in the mapping of reads from next-generation sequencing runs. First, we have created an algorithm that probabilistically maps reads to repeat regions in the genome on a quantitative basis. Second, we have developed a probabilistic Needleman–Wunsch algorithm which utilizes _prb.txt and _int.txt files produced in the Solexa/Illumina pipeline to improve the mapping accuracy for lower quality reads and increase the amount of usable data produced in a given experiment.

Availability: The source code for the software can be downloaded from http://dna.cs.byu.edu/gnumap.

Contact:  nathanlclement@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Nordihydroguaiaretic Acid from Creosote Bush (Larrea tridentata) Mitigates 12‐O‐Tetradecanoylphorbol‐13‐Acetate‐Induced Inflammatory and Oxidative Stress Responses of Tumor Promotion Cascade in Mouse Skin
Authors: Rahman Shakilur , Ansari Rizwan Ahmed , Rehman Hasibur , Parvez Suhel , Raisuddin Sheikh
Published: October 2009

Nordihydroguaiaretic acid (NDGA) is a phenolic antioxidant found in the leaves and twigs of the evergreen desert shrub, Larrea tridentata (Sesse and Moc. ex DC) Coville (creosote bush). It has a long history of traditional medicinal use by the Native Americans and Mexicans. The modulatory effects of topically applied NDGA was studied on acute inflammatory and oxidative stress responses in mouse skin induced by stage I tumor promoting agent, 12‐O‐tetradecanoylphorbol‐13‐acetate (TPA). Double TPA treatment adversely altered many of the marker responses of stage I skin tumor promotion cascade. Pretreatment of NDGA in TPA‐treated mice mitigated cutaneous lipid peroxidation and inhibited production of hydrogen peroxide. NDGA treatment also restored reduced glutathione level and activities of antioxidant enzymes. Elevated activities of myeloperoxidase, xanthine oxidase and skin edema formation in TPA‐treated mice were also lowered by NDGA indicating a restrained inflammatory response. Furthermore, results of histological study demonstrated inhibitory effect of NDGA on cellular inflammatory responses. This study provides a direct evidence of antioxidative and anti‐inflammatory properties of NDGA against TPA‐induced cutaneous inflammation and oxidative stress corroborating its chemopreventive potential against skin cancer.
The Traditional Japanese Medicine Rikkunshito Promotes Gastric Emptying via the Antagonistic Action of the 5‐HT3 Receptor Pathway in Rats
Authors: Tominaga K. , Kido T. , Ochi M. , Sadakane C. , Mase A. , Okazaki H. , Yamagami H. , Tanigawa T. , Watanabe K. , Watanabe T. , Fujiwara Y. , Oshitani N. , Arakawa T.
Published: October 2009

The traditional Japanese medicine rikkunshito ameliorates the nitric oxide‐associated delay in gastric emptying. Whether rikkunshito affects gastric motility associated with 5‐hydroxytryptamine (serotonin: 5‐HT) receptors or dopamine receptors is unknown. We examined the effects of rikkunshito on the delay in gastric emptying induced by 5‐HT or dopamine using the phenol red method in male Wistar rats. 5‐HT (0.01–1.0 mg kg−1, i.p.) dose dependently delayed gastric emptying, similar to the effect of the 5‐HT3 receptor agonist 1‐(3‐chlorophenyl) biguanide (0.01–1.0 mg kg−1, i.p.). Dopamine also dose dependently delayed gastric emptying. The 5‐HT3 receptor antagonist ondansetron (0.04–4.0 mg kg−1) and rikkunshito (125–500 mg kg−1) significantly suppressed the delay in gastric emptying caused by 5‐HT or 1‐(3‐chlorophenyl) biguanide. Hesperidin (the most active ingredient in rikkunshito) suppressed the 5‐HT‐induced delayed gastric emptying in a dose‐dependent manner, the maximum effect of which was similar to that of ondansetron (0.4 mg kg−1). The improvement obtained by rikkunshito or ondansetron in delaying gastric emptying was completely blocked by pretreatment with atropine. Rikkunshito appears to improve delay in gastric emptying via the antagonistic action of the 5‐HT3 receptor pathway.
Correction for Leao
et al.
, Non-random nature of spontaneous mIPSCs in mouse auditory brainstem neurons revealed by recurrence quantification analysis
Authors: Leao R. N. , Leao F. N. , Walmsley B.
Published: October 2009

Correction for ‘Non-random nature of spontaneous mIPSCs in mouse auditory brainstem neurons revealed by recurrence quantification analysis’ by R. N. Leao, F. N. Leao and B. Walmsley (Proc. R. Soc. B
272
, 2551–2559.
(doi:
10.1098/rspb.2005.3258
)).

On p. 2552, line 12 of §2(b) contains an incorrect citation. ‘Bacchereti 2004’ should have read ‘Marwan 2003’, and the former reference not included in the reference list.The complete citation details for Marwan 2003 are as follows:
Correction for Kiel and Goedert, Deep-sea food bonanzas: early Cenozoic whale-fall communities resemble wood-fall rather than seep communities
Authors: Kiel Steffen , Goedert James L.
Published: October 2009

Correction for ‘Deep-sea food bonanzas: early Cenozoic whale-fall communities resemble wood-fall rather than seep communities’ by Steffen Kiel and James L. Goedert (Proc. R. Soc. B
273
, 2625–2631.
(doi:
10.1098/rspb.2006.3620
)).

On page 2626, seven lines before the end of section 2, the complete list of sites and species is available online, but is not published as electronic supplementary material to this paper.
Exocytosis Precedes and Predicts the Increase in Growth in Oscillating Pollen Tubes
Authors: McKenna Sylvester T. , Kunkel Joseph G. , Bosch Maurice , Rounds Caleb M. , Vidali Luis , Winship Lawrence J. , Hepler Peter K.
Published: October 2009

We examined exocytosis during oscillatory growth in lily (Lilium formosanum and Lilium longiflorum) and tobacco (Nicotiana tabacum) pollen tubes using three markers: (1) changes in cell wall thickness by Nomarski differential interference contrast (DIC), (2) changes in apical cell wall fluorescence in cells stained with propidium iodide (PI), and (3) changes in apical wall fluorescence in cells expressing tobacco pectin methyl esterase fused to green fluorescent protein (PME-GFP). Using PI fluorescence, we quantified oscillatory changes in the amount of wall material from both lily and tobacco pollen tubes. Measurement of wall thickness by DIC was only possible with lily due to limitations of microscope resolution. PME-GFP, a direct marker for exocytosis, only provides information in tobacco because its expression in lily causes growth inhibition and cell death. We show that exocytosis in pollen tubes oscillates and leads the increase in growth rate; the mean phase difference between exocytosis and growth is –98° ± 3° in lily and –124° ± 4° in tobacco. Statistical analyses reveal that the anticipatory increase in wall material predicts, to a high degree, the rate and extent of the subsequent growth surge. Exocytosis emerges as a prime candidate for the initiation and regulation of oscillatory pollen tube growth.
WASP plays a novel role in regulating platelet responses dependent on αIIbβ3 integrin outside‐in signalling
Authors: Shcherbina Anna , Cooley Jessica , Lutskiy Maxim I. , Benarafa Charaf , Gilbert Gary E. , Remold‐O’Donnell Eileen
Published: October 2009

The most consistent feature of Wiskott Aldrich syndrome (WAS) is profound thrombocytopenia with small platelets. The responsible gene encodes WAS protein (WASP), which functions in leucocytes as an actin filament nucleating agent –yet– actin filament nucleation proceeds normally in patient platelets regarding shape change, filopodia and lamellipodia generation. Because WASP localizes in the platelet membrane skeleton and is mobilized by αIIbβ3 integrin outside‐in signalling, we questioned whether its function might be linked to integrin. Agonist‐induced αIIbβ3 activation (PAC‐1 binding) was normal for patient platelets, indicating normal integrin inside‐out signalling. Inside‐out signalling (fibrinogen, JON/A binding) was also normal for wasp‐deficient murine platelets. However, adherence/spreading on immobilized fibrinogen was decreased for patient platelets and wasp‐deficient murine platelets, indicating decreased integrin outside‐in responses. Another integrin outside‐in dependent response, fibrin clot retraction, involving contraction of the post‐aggregation actin cytoskeleton, was also decreased for patient platelets and wasp‐deficient murine platelets. Rebleeding from tail cuts was more frequent for wasp‐deficient mice, suggesting decreased stabilisation of the primary platelet plug. In contrast, phosphatidylserine exposure, a pro‐coagulant response, was enhanced for WASP‐deficient patient and murine platelets. The collective results reveal a novel function for WASP in regulating pro‐aggregatory and pro‐coagulant responses downstream of integrin outside‐in signalling.
Lipid compounds of human Wharton’s jelly and their alterations in preeclampsia
Authors: Romanowicz Lech , Bańkowski Edward
Published: October 2009

Wharton’s jelly is a myxomatous substance which surrounds the umbilical cord vessels protecting them against extension, bending, twisting and compression. Very low number of cells in this tissue produce high amounts of extracellular matrix; collagen, hyaluronate and proteoglycans which bind large quantities of peptide growth factors (PGFs). Preeclampsia (the most common pregnancy‐associated syndrome) is accompanied by a significant reduction in hyaluronate and a concomitant increase in sulphated glycosaminoglycans/proteoglycans content in Wharton’s jelly. Such a phenomenon corresponds to an ‘early ageing’ of this tissue. We have evaluated the lipid composition of Wharton’s jelly and its alteration in preeclampsia. Thin layer chromatography and high‐performance liquid chromatography were employed. It was found that Wharton’s jelly contains free fatty acids (FFA), mono‐, di‐ and triacylglycerols, free cholesterol and its esters. The characteristic feature is the presence of relatively high amounts of unsaturated fatty acids, including those (C18:2 and C18:3) which are nutritionally essential. Preeclampsia is associated with a slight increase in the total fatty acid content in Wharton’s jelly and with marked changes in the proportional relationships between various lipids. A distinct decrease in the amounts of FFA was observed with a concomitant increase in monoacylglycerols and cholesterol esters. At least in some cases the effects exerted by PGFs are mediated by the lipid second messengers. Thus it is possible that alterations in lipid compounds of Wharton’s jelly may participate in the deregulation of various cell functions, including overproduction of sulphated glycosaminoglycans or down‐regulation of enzymes which participate in their degradation.
Phylogeography and phylogeny of the epineritic cosmopolitan bonitos of the genus Sarda (Cuvier): inferred patterns of intra‐ and inter‐oceanic connectivity derived from nuclear and mitochondrial DNA data
Authors: Viñas Jordi , Alvarado Bremer Jaime R. , Pla Carles
Published: October 2009

Aim  To reconstruct the phylogenetic relationships of the four species of the genus Sarda (Sarda sarda, Sarda orientalis, Sarda australis and Sarda chilensis) and their phylogeographic history in the context of historical and ecological biogeography. Also, to reconstruct within‐species phylogenetic relationships to test whether the North Atlantic and Mediterranean populations of Atlantic bonito (S. sarda) warrant subspecies status, and the validity of the allopatric northern and southern populations of eastern Pacific bonito (S. chiliensis), recognized as S. chiliensis lineolata and S. chiliensis chiliensis.

Location  Representative samples of all four Sarda species collected world‐wide were analysed.

Methods  Phylogenetic inference was carried out with neighbour‐joining, maximum parsimony and maximum likelihood, employing nucleotide sequences of the mitochondrial DNA (mtDNA) control region I (CR‐I) and of the single‐copy nuclear DNA (nDNA) Tmo‐4c4 gene. Analysis of molecular variance was used on the mtDNA data to estimate the extent of geographic population structuring.

Results  Gene trees derived from mtDNA and nDNA data yielded concordant phylogenies that support the monophyly of the genus Sarda. The following sibling pairs received strong statistical support: striped bonito (S. orientalis) with Australian bonito (S. australis), and Atlantic bonito (S. sarda) with eastern Pacific bonito (S. chiliensis). Furthermore, the origin of S. sarda mtDNA is paraphyletic with respect to S. chiliensis, and these results are indicative of introgression. The analysis of Tmo‐4c4 sequences corroborates the ancestral hybridization between these allopatric species. Comparisons of north‐west Atlantic and Mediterranean populations of S. sarda using mtDNA CR‐I data revealed substantial genetic differentiation. By contrast, no differences between the putative northern and southern allopatric subspecies of S. chiliensis were detected.

Main conclusions  The monophyly of the genus Sarda as indicated by morphology is corroborated using both molecular markers. However, molecular phylogenies depicted a paraphyletic relationship between S. sarda and S. chiliensis. This phylogeographical relationship is better explained by an ancestral introgression facilitated by trans‐Arctic contact during the Pleistocene. The pronounced genetic differentiation between S. sarda samples from the north‐west Atlantic and the Mediterranean is consistent with the differentiation of these two regions, but not with the amphi‐Atlantic speciation hypothesis. Finally, the S. chiliensis lineolata and S. chiliensis chiliensis subspecies status is not supported by the molecular data.
Measuring the importance of competition: a new formulation of the problem
Authors: Damgaard Christian , Fayolle Adeline
Published: October 2009

1. Currently, there is a debate among plant ecologists on the concepts of the intensity of competition and the importance of competition, which is central to many issues of modern plant population ecology and plant community ecology.

2. It is problematic that the current measures of intensity and importance of competition, typically, are reported as dimensionless indices because they hide the fact that both indices are functions of plant density and the level of the environmental gradient.

3. Here, a new formulation of the concepts is suggested, which explicitly highlights the functional dependencies on plant density and the level of the environmental gradient. The new measures are a generalization of the previous indices and correspond to the previous indices in the case of a simple experimental design.

4. The suggested measures of the intensity and importance of competition are exemplified using data from a response surface competition experiment between Agrostis capillaris and Festuca ovina along a herbicide gradient, where the expected clear effect of plant density was demonstrated.

5. Synthesis. As the suggested measures of the intensity and importance of competition explicitly highlight the functional dependencies on plant density and the level of the environmental gradient, we think that they will help to ensure a closer connection between experimental plant ecology and the attempts to model plant populations and communities.
An idealized model for tree–grass coexistence in savannas: the role of life stage structure and fire disturbances
Authors: Baudena Mara , D’Andrea Fabio , Provenzale A.
Published: October 2009

1. We discuss a simple implicit‐space model for the competition of trees and grasses in an idealized savanna environment. The model represents patch occupancy dynamics within the habitat and introduces life stage structure in the tree population, namely adults and seedlings. A tree can be out‐competed by grasses only as long as it is a seedling.

2. The model is able to predict grassland, forest, savanna and bistability between forest and grassland, depending on the different characteristics of the ecosystem, represented by the model’s parameters.

3. The inclusion of stochastic fire disturbances significantly widens the parameter range where coexistence of trees and grasses is found. At the same time, grass‐fire feedback can induce bistability between forest and grassland.

4. Synthesis. These results suggest that tree–grass coexistence in savannas can be either deterministically stable or stabilized by random disturbances, depending on prevailing environmental conditions and on the types of plant species present in the ecosystem.
Direct trade‐off between cyanogenesis and resistance to a fungal pathogen in lima bean (Phaseolus lunatus L.)
Authors: Ballhorn Daniel J. , Pietrowski Andrea , Lieberei Reinhard
Published: October 2009

1. Plants are simultaneously attacked by multiple herbivores and pathogens. While some plant defences act synergistically, others trade‐off against each other. Such trade‐offs among resistances to herbivores and pathogens are usually explained by the costs of resistance, i.e. resource limitations compromising a plant’s overall defence.

2. Here, we demonstrate that trade‐offs can also result from direct negative interactions among defensive traits. We studied cyanogenesis (release of HCN) of lima bean (Fabaceae: Phaseolus lunatus) and effects of this efficient anti‐herbivore defence on resistance to a fungal pathogen (Melanconiaceae: Colletotrichum gloeosporioides).

3. Leaf tissue destruction by fungal growth was significantly higher on high cyanogenic (HC) lima bean accessions than on low cyanogenic (LC) plants. The susceptibility of HC accessions to the fungal pathogen was strongly correlated to reduced activity of resistance‐associated polyphenol oxidases (PPOs) in leaves of these plants. LC accessions, in contrast, showed high PPO activity, which was correlated with distinct resistance to C. gloeosporioides.

4. Experimentally applied, gaseous HCN reduced PPO activity and significantly increased the size of lesions caused by C. gloeosporioides in LC leaves.

5. Field observations of a wild lima bean population in Mexico revealed a higher infection rate of HC compared to LC plant individuals. The types of lesions observed on the different cyanogenic plants in nature were similar to those observed on HC and LC plants in the laboratory.

6. Synthesis. We suggest that cyanogenesis of lima bean directly trades off with plant defence against fungal pathogens and that the causal mechanism is the inhibition of PPOs by HCN. Our findings provide a functional explanation for the observed phenomenon of the low resistance of HC lima beans in nature.
The effects of sleep and sleep deprivation on task‐switching performance
Authors: COUYOUMDJIAN ALESSANDRO , SDOIA STEFANO , TEMPESTA DANIELA , CURCIO GIUSEPPE , RASTELLINI ELISABETTA , DE GENNARO LUIGI , FERRARA MICHELE
Published: October 2009

Neural systems of the prefrontal cortex (PFC) involved in executive functions are particularly vulnerable to sleep deprivation (SD). In this study, we investigated whether SD selectively affects specific components of the executive control processes involved in task‐switching performance. Two different tasks are performed in rapid and random succession in this procedure, so that the to‐be‐executed task may change from one trial to the next (switch trial), or may be repeated (repetition trial). Task‐switches are usually slower than task repetitions, giving way to the ‘switch cost’. One hundred and eight university students were assigned randomly to the sleep (S) or the SD group. Each of them was tested on a task‐switching paradigm before and after an experimental night (S or SD), and after one recovery night. SD impaired both task‐switching accuracy and speed. A higher proportion of errors and increased switch costs after SD have been observed, compared to normal sleep. Control analyses on switch and repetition trials showed that the SD group was significantly worse only on the switch trials. The effects of SD are reverted by one night of recovery sleep. It is concluded that the ability to adjust behaviour rapidly and flexibly to changing environmental demands, which relies on the functional integrity of the PFC, is impacted negatively by sleep loss.
Morphology of Testes from Transgenic Rabbits: Histological and Ultrastructural Aspects
Authors: Chrenek P. , Makarevich A. V. , Kubovičová E. , Pivko J.
Published: October 2009

The aim of this study was to compare morphological characteristics of testes from transgenic (the WAP‐hFVIII gene) and non‐transgenic rabbits with emphasis on the histological and ultrastructural aspects. Samples of testes from both groups were fixed and embedded into Durcupan ACM for transmission electron microscopy. For histological analysis, semi‐thin toluidine blue‐stained sections were evaluated under a Jenaval light microscope. Male fertility was tested based on egg fecundity and blastocyst yield; transgene transmission was proved using PCR assay. Spermatogenesis in rabbit testes had not been destroyed both in transgenic and non‐transgenic rabbits. No significant differences were found in the occurrence of individual cell organelles of the Sertoli cells in transgenic and non‐transgenic rabbits. The ultrastructure of Leydig cells in testes of transgenic and non‐transgenic rabbits was rather similar. No differences in the occurrence of individual organelles of Leydig cells between transgenic and non‐transgenic males were found. These results were in concert with fertilizing capacity of transgenic spermatozoa. The presented status of organelles in this study indicates functional activity of the analysed cells.
Apoptosis in the Myocardium of the Adult Dromedary Camel: Ultrastructural Characterization
Authors: Osman A.‐H. K. , Sato S. , Caceci T. , Pfeiffer D. C.
Published: October 2009

Apoptosis is a highly regulated mode of cell death that occurs in the absence of inflammation. Light microscopic (LM) examination of the myocardium of apparently healthy camel did not reveal evidence of apoptosis in any samples; however, evidence of apoptosis was apparent by transmission electron microscopy (TEM). The most common apoptotic features observed by TEM included (1) an intact sarcolemma with some bleb formation; (2) nuclear chromatin condensation and margination with nucleolar disruption; (3) mitochondrial swelling and disorganization, accompanied by degeneration or hypercondensation of cristae; and (4) an intercalated disc region with a higher‐than‐normal mitochondrion/myofibril ratio, or surrounded from both sides by asymmetrically contracted sarcomeres. Apoptotic alterations were also noted among the endothelial cells lining the microvasculature of the myocardium. These alterations included (1) marked nuclear chromatin condensation and margination; (2) villous blebs on the adluminal plasmalemma, which projected into the lumen; (3) cytoplasmic vacuolation; (4) presence of intraluminal membrane‐bounded vesicles; and (5) occasional pericapillary edema and accumulations of cellular debris. The results of this study indicate that myocardial apoptosis can occur in apparently healthy camels, in the absence of a clear‐cut etiology.