bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution in protein interaction networks: co-evolution, rewiring and the role of duplication
Authors: Robertson David L. , Lovell Simon C.
Published: July 2009

Molecular function is the result of proteins working together, mediated by highly specific interactions. Maintenance and change of protein interactions can thus be considered one of the main links between molecular function and mutation. As a consequence, protein interaction datasets can be used to study functional evolution directly. In terms of constraining change, the co-evolution of interacting molecules is a very subtle process. This has implications for the signal being used to predict protein–protein interactions. In terms of functional change, the ‘rewiring’ of interaction networks, gene duplication is critically important. Interestingly, once duplication has occurred, the genes involved have different probabilities of being retained related to how they were generated. In the present paper, we discuss some of our recent work in this area.
Two distinct groups of fungal catalase/peroxidases
Authors: Zámocký Marcel , Furtmüller Paul G. , Obinger Christian
Published: July 2009

Catalase/peroxidases (KatGs) are bifunctional haem b-containing (Class I) peroxidases with overwhelming catalase activity and substantial peroxidase activity with various one-electron donors. These unique oxidoreductases evolved in ancestral bacteria revealing a complex gene-duplicated structure. Besides being found in numerous bacteria of all phyla, katG genes were also detected in genomes of lower eukaryotes, most prominently of sac and club fungi. Phylogenetic analysis demonstrates the occurrence of two distinct groups of fungal KatGs that differ in localization, structural and functional properties. Analysis of lateral gene transfer of bacterial katGs into fungal genomes reveals that the most probable progenitor was a katG from a bacteroidetes predecessor. The putative physiological role(s) of both fungal KatG groups is discussed with respect to known structure–function relationships in bacterial KatGs and is related with the acquisition of (phyto)pathogenicity in fungi.
Differences in the SNARE evolution of fungi and metazoa
Authors: Kienle Nickias , Kloepper Tobias H. , Fasshauer Dirk
Published: July 2009

Proteins of the SNARE (soluble N-ethylmaleimide-sensitive factor-attachment protein receptor) family are key factors in all vesicle-fusion steps in the endocytic and secretory pathways. SNAREs can assemble into a tight four-helix bundle complex between opposing membranes, a process that is thought to pull the two membranes into close proximity. The complex-forming domains are highly conserved, not only between different species, but also between different vesicular trafficking steps. SNARE protein sequences can be classified into four main types (Qa, Qb, Qc and R), each reflecting their position in the four-helix bundle. Further refinement of these main types resulted in the identification of 20 distinct conserved groups, which probably reflect the original repertoire of a proto-eukaryotic cell. We analysed the evolution of the SNARE repertoires in metazoa and fungi and unveiled remarkable differences in both lineages. In metazoa, the SNARE repertoire appears to have undergone a substantial expansion, particularly in the endosomal pathways. This expansion probably occurred during the transition from a unicellular to a multicellular lifestyle. We also observed another expansion that led to a major increase of the secretory SNAREs in the vertebrate lineage. Interestingly, fungi developed multicellularity independently, but in contrast with plants and metazoa, this change was not accompanied by an expansion of the SNARE set. Our findings suggest that the rise of multicellularity is not generally linked to an expansion of the SNARE set. The structural and functional diversity that exists between fungi and metazoa might offer a simple explanation for the distinct evolutionary history of their SNARE repertoires.
Prediction of horizontal gene transfers in eukaryotes: approaches and challenges
Authors: Whitaker John W. , McConkey Glenn A. , Westhead David R.
Published: July 2009

HGT (horizontal gene transfer) is recognized as an important force in bacterial evolution. Now that many eukaryotic genomes have been sequenced, it has become possible to carry out studies of HGT in eukaryotes. The present review compares the different approaches that exist for identifying HGT genes and assess them in the context of studying eukaryotic evolution. The metabolic evolution resource metaTIGER is then described, with discussion of its application in identification of HGT in eukaryotes.
Novel regulatory mechanisms for theCFTRgene
Authors: Ott Christopher J. , Blackledge Neil P. , Leir Shih-Hsing , Harris Ann
Published: July 2009

The CFTR (cystic fibrosis transmembrane conductance regulator) gene, which when mutated causes cystic fibrosis, encompasses nearly 200 kb of genomic DNA at chromosome 7q31.2. It is flanked by two genes ASZ1 [ankyrin repeat, SAM (sterile α-motif) and basic leucine zipper] and CTTNBP2 (cortactin-binding protein 2), which have very different expression profiles. CFTR is expressed primarily in specialized epithelial cells, whereas ASZ1 is transcribed exclusively in the testis and ovary, and CTTNBP2 is highly expressed in the brain, kidney and pancreas, with lower levels of expression in other tissues. Despite its highly regulated pattern of expression, the promoter of the CFTR gene apparently lacks the necessary elements to achieve this. We previously suggested that cis-acting regulatory elements elsewhere in the locus, both flanking the gene and within introns, were required to co-ordinate regulated, tissue-specific expression of CFTR. We identified a number of crucial elements, including enhancer-blocking insulators flanking the locus, intronic tissue-specific enhancers and also characterized some of the interacting proteins. We recently employed a high-resolution method of mapping DHS (DNase I-hypersensitive sites) using tiled microarrays. DHS are often associated with regulatory elements and use of this technique generated cell-specific profiles of potential regulatory sequences in primary cells and cell lines. We characterized a set of cis-acting elements within the CFTR locus and demonstrated direct physical interaction between them and the CFTR promoter, by chromosome conformation capture (3C). These results provide the first insight into the three-dimensional structure of the active CFTR gene.
Cytoplasmic tail of IL-13Rα2 regulates IL-4 signal transduction
Authors: Andrews Allison-Lynn , Nordgren Ida Karin , Kirby Isabelle , Holloway John W. , Holgate Stephen T. , Davies Donna E. , Tavassoli Ali
Published: July 2009

IL (interleukin)-4 and IL-13 are key cytokines in the pathogenesis of allergic inflammatory disease. IL-4 and IL-13 share many functional properties as a result of their utilization of a common receptor complex comprising IL-13Rα1 (IL-13 receptor α-chain 1) and IL-4Rα. The second IL-13R (IL-13 receptor) has been identified, namely IL-13Rα2. This has been thought to be a decoy receptor due to its short cytoplasmic tail and its high binding affinity for IL-13 but not IL-4. IL-13Rα2 exists on the cell membrane, intracellularly and in a soluble form. Recent reports revealed that membrane IL-13Rα2 may have some signalling capabilities, and a soluble form of IL-13Rα2 can be generated in the presence of environmental allergens such as DerP. Interestingly, IL-13Rα2 has also been shown to regulate both IL-13 and IL-4 response in primary airway cells, despite the fact that IL-13Rα2 does not bind IL-4. The regulator mechanism is still unclear but the physical association of IL-13Rα2 with IL-4Rα appears to be a key regulatory step. These results suggest that the cytoplasmic tail of IL-13Rα2 may interfere with the association or activation of signalling molecules, such as JAK1 (Janus kinase 1), on IL-4Rα and thus prevents downstream signal cascade. The receptor has more complicated functions than a simple decoy receptor. In this review, we discuss newly revealed functions of IL-13Rα2.
DNA damage by low-energy ions
Authors: Hunniford C. Adam , McCullough Robert W. , Davies R. Jeremy H. , Timson David J.
Published: July 2009

Ion-beam irradiation provides a promising treatment for some types of cancer. This promise is due mainly to the selective deposition of energy into a relatively small volume (the Bragg peak), thus reducing damage to healthy tissue. Recent observations that electrons with energies below the ionization potential of DNA can cause covalent damage to the bases and backbone have led to investigations into the ability of low-energy (<1 keV·Da−1) ion beams to damage double-stranded DNA. It has been clearly demonstrated that these low-energy ions induce a mixture of single- and double-strand breaks to dried DNA in vacuo. These effects depend upon the number of ions incident upon the DNA, the kinetic energy of the ions and on their charge state. This DNA damage may be important, as all radiotherapies will result in the production of low-energy secondary ions as radiation passes through tissues. Currently, their effects are neglected in treatment planning, and thus more work is required to quantify and understand DNA damage by low-energy ions.
Quantum chemistry of quantum dots: Effects of ligands and oxidation
Authors: Inerbaev Talgat M. , Masunov Artëm E. , Khondaker Saiful I. , Dobrinescu Alexandra , Plamadă Andrei-Valentin , Kawazoe Yoshiyuki
Published: July 2009

We report Gaussian basis set density functional theory (DFT) calculations of the structure and spectra of several colloidal quantum dots (QDs) with a (CdSe)n core (n=6,15,17), that are either passivated by trimethylphosphine oxide ligands, or unpassivated and oxidized. From the ground state geometry optimization results we conclude that trimethylphosphine oxide ligands preserve the wurtzite structure of the QDs. Evaporation of the ligands may lead to surface reconstruction. We found that the number of two-coordinated atoms on the nanoparticle’s surface is the critical parameter defining the optical absorption properties. For (CdSe)15 wurtzite-derived QD this number is maximal among all considered QDs and the optical absorption spectrum is strongly redshifted compared to QDs with threefold coordinated surface atoms. According to the time-dependent DFT results, surface reconstruction is accompanied by a significant decrease in the linear absorption. Oxidation of QDs destroys the perfection of the QD surface, increases the number of two-coordinated atoms and results in the appearance of an infrared absorption peak close to 700 nm. The vacant orbitals responsible for this near infrared transition have strong Se–O antibonding character. Conclusions of this study may be used in optimization of engineered nanoparticles for photodetectors and photovoltaic devices.
Mechanism study on the effects of side assisting gas velocity during CO2 laser welding process
Authors: Zhang Linjie , Zhang Jianxun , Gong Shuili
Published: July 2009

An experimental study on the effects of side assisting gas during CO2 laser welding has been carried out, and it is found that side assisting gas velocity can significantly affect the laser induced plasma and the weld cross-sectional geometry. In order to get better understanding on the associated mechanism, a three dimensional model based on the conservation laws of mass, momentum, and energy has been developed to simulate the spatial distributions of plasma temperature under different side assisting gas velocities. Furthermore, ray-tracing method is employed to investigate the variation of bremsstrahlung absorption and power density distribution on keyhole walls at different side assisting gas velocities with the assumption of conical keyhole shape. The results show that the diminishing of refraction and bremsstrahlung absorption due to an increase in side assisting gas velocity results in an increase in heat transfer efficiency, which contributes to the increase of weld cross-sectional area and penetration depth.
Intrinsically limited mobility of the two-dimensional electron gas in gated AlGaN/GaN and AlGaN/AlN/GaN heterostructures
Authors: Polyakov V. M. , Schwierz F. , Cimalla I. , Kittler M. , Lübbers B. , Schober A.
Published: July 2009

We report on the intrinsically limited low-field mobility of the two-dimensional electron gas (2DEG) in gated AlGaN/GaN and AlGaN/AlN/GaN heterostructures. Monte Carlo transport simulations are carried out to calculate the room-temperature 2DEG mobilities in dependence on the electron sheet density. The simulated 2DEG mobilities are compared to the phonon-limited mobility of bulk GaN. We estimate a maximum 2DEG mobility of about 2700 cm2 V−1 s−1 for an electron sheet density of ∼5×1012 cm−2, which remarkably exceeds the phonon-limited bulk mobility of 1520 cm2 V−1 s−1. By reducing the electron sheet density below 5×1012 cm−2, i.e., in a weak electron quantum confinement regime, the room-temperature 2DEG mobility gradually decreases and approaches the phonon-limited bulk value for vanishing quantum confinement. The insertion of a thin AlN barrier interlayer improves transport properties of the 2DEG and the mobility substantially increases due to a suppression of the alloy scattering.
Modeling the temperature characteristics of InAs/GaAs quantum dot lasers
Authors: Rossetti Marco , Fiore Andrea , Sęk Grzegorz , Zinoni Carl , Li Lianhe
Published: July 2009

A systematic investigation of the temperature characteristics of quantum dot lasers emitting at 1.3 μm is reported. The temperature dependence of carrier lifetime, radiative efficiency, threshold current, differential efficiency, and gain is measured, and compared to the theoretical results based on a rate equation model. The model accurately reproduces all experimental laser characteristics above room temperature. The degradation of laser characteristics with increasing temperature is clearly shown to be associated to the thermal escape of holes from the confined energy levels of the dots toward the wetting layer and the nonradiative recombination therein.
In situ thin film and multilayer structural characterization using x-ray fluorescence induced by reflection high energy electron diffraction
Authors: Chandril Sandeep , Keenan Cameron , Myers T. H. , Lederman David
Published: July 2009

The angular dependence of the x-ray fluorescence from Y and Mn inner K shell ionization induced by a grazing angle incident electron beam in several multilayered Y/Mn structures was analyzed using the distorted-wave approximation. Estimates of structural parameters, thickness, and interfacial roughness were obtained from the x-ray fluorescence measured in the total reflection regime and compared with ex situ x-ray reflectivity results. Although the sensitivity to the surface and interface roughness was relatively low, the thickness values for both single and buried layers were in good agreement with the x-ray reflectivity measurements.
van der Pauw method for measuring resistivity of a plane sample with distant boundaries
Authors: Lim S. H. N. , McKenzie D. R. , Bilek M. M. M.
Published: July 2009

In the paper, we derive an algorithm which follows from the original van der Pauw’s technique for measuring resistivity with the added advantage of allowing contacts to be positioned a distance away from the boundary. For a large sample area, we show that the resistivity calculated by our algorithm is equivalent to the resistivity calculated by the original van der Pauw’s method. In practice, this configuration is easier to achieve and can eliminate errors associated with contacts that are not placed exactly at the edge.
Damage of amorphous carbon induced by soft x-ray femtosecond pulses above and below the critical angle
Authors: Chalupský J. , Hájková V. , Altapova V. , Burian T. , Gleeson A. J. , Juha L. , Jurek M. , Sinn H. , Störmer M. , Sobierajski R. , Tiedtke K. , Toleikis S. , Tschentscher Th. , Vyšín L. , Wabnitz H. , Gaudin J.
Published: July 2009

We present results of damage studies conducted at the Free Electron LASer in Hamburg (FLASH) facility with 13.5 nm (91.8 eV) and 7 nm (177.1 eV) radiations. The laser beam was focused on a sample of 890-nm-thick amorphous carbon coated on a silicon wafer mimicking a x-ray mirror. The fluence threshold for graphitization was determined for different grazing angles above and below the critical angle. The observed angular dependence of Fth is explained by the variation in absorption depth and reflectivity. Moreover, the absorbed local dose needed for the phase transition leading to graphitization is shown to vary with the radiation wavelength.
Nonlinear excitation of short scale turbulence in solar corona by kinetic Alfvén waves
Authors: Kumar Sachin , Sharma R. P. , Singh H. D.
Published: July 2009

The model equations for the nonlinear interaction between kinetic Alfvén waves and ion acoustic waves in the intermediate-β (thermal to background magnetic pressure ratio) plasmas are presented. The nonlinear dynamical equations satisfy the modified Zakharov system of equations by taking the nonadiabatic response of the background density. Numerical solution has been obtained to study this nonlinear process. The localized magnetic filamentary structures are found in solar corona along with the density dips and humps associated with the kinetic Alfvén waves. The power spectra of magnetic field fluctuations indicate that the nonlinear interactions may be redistributing energy among higher wave numbers. The heating of the solar corona observed by Yohkoh and Solar and Heliospheric Observatory may be produced by the coupling of kinetic Alfvén waves and ion acoustic waves via filamentation process.
Aharonov–Bohm oscillations in a nanoscale dopant ring in silicon
Authors: Reusch T. C. G. , Fuhrer A. , Füchsle M. , Weber B. , Simmons M. Y.
Published: July 2009

We have fabricated a nanoscale ring of phosphorus dopants in silicon using a scanning tunneling microscope to pattern a hydrogen resist layer. Low-temperature magnetotransport measurements reveal both aperiodic universal conductance fluctuations and periodic Aharonov–Bohm oscillations. From the ratio of the h/e and h/2e components of the Aharonov–Bohm oscillations, we estimate a phase coherence length of ≃100 nm at a temperature T=100 mK. This is in agreement with previous results from weak localization measurements on low-dimensional dopant devices in silicon.
The chemisorption of tetracene on Si(100)-2×1 surface
Authors: Mao Hongying , Guan Dandan , Chen Meiliang , Dou Weidong , Song Fei , Zhang Hanjie , Li Haiyang , He Pimo , Bao Shining
Published: July 2009

The adsorption of tetracene on Si(100)-2×1 substrate has been studied by ultraviolet photoemission spectroscopy (UPS). Six features deriving from the organic material are located at 1.22, 2.41, 3.63, 4.67, 7.11, and 8.77 eV below the Fermi level. These features shift in binding energy with increasing the thickness of the organic film. In the case of a monolayer, angle-resolved UPS measurements suggest that the molecular plane is parallel to the substrate. Further theoretical density functional theory calculation reveals the most stable structure of tetracene molecule on Si substrate in which six covalent Si–C chemical bonds are formed between carbon atoms of the tetracene molecule and the Si atoms on the substrate.
Infants Can't Discriminate the Orientation of a Grating Surrounded by an Oblique Square
Authors: Tsuruhara Aki , Kanazawa So , Yamaguchi Masami K
Published: July 2009

We examined whether infants could visually discriminate the orientation of a grating surrounded by an oblique square (experiment 1) and a vertical square (experiment 2). A familiarisation–novelty preference procedure was used. In experiment 1, infants aged 4 to 6 months did not visually distinguish the orientation of a grating surrounded by an oblique square. However, in experiment 2, in which a vertical surrounding square was used, such infants visually distinguished the orientation of a grating. Our results suggest that the external visual frame can affect infants' perception of the orientation of a grating, as it does in adults. In experiment 1, a grating was within an oblique square. Here, the relative orientation with respect to the external visual frame differs from the orientation relative to the retinal/gravitational axes. Such discrepancy appears to cause confusion in infants' perception of orientation.
Improved elongation of Scots pine seedlings under blue light depletion is not dependent on resource acquisition
Authors: Sarala Marian , Taulavuori Erja , Karhu Jouni , Savonen Eira-Maija , Laine Kari , Kubin Eero , Taulavuori Kari
Published: July 2009

Removal of blue light (400–500 nm) induced shoot elongation of 2-year-old Scots pine (Pinus sylvestris L.) seedlings, which was not related to resource acquisition (carbohydrates, C/N ratio and soluble proteins) and frost hardening. The seedlings were grown in northern Finland (64°N) in plexiglass chambers, either orange in colour or transparent, during elongation and cold hardening periods in 2001. The orange chamber removed the blue wavelengths. The results suggest that the growth inhibiting effect of blue light on Scots pine elongation is probably a photomorphogenic regulation response; the removal of blue light did not affect the gas exchange and accumulation of growth resources. In addition, the removal of blue light also did not affect the physiological parameters (pigment composition, chlorophyll fluorescence and lipid peroxidation) measured during the preparation for winter.
Seasonal patterns of leaf H2O2 content: reflections of leaf phenology, or environmental stress?
Authors: Cheeseman John M.
Published: July 2009

H2O2 is an ubiquitous compound involved in signalling, metabolic control, stress responses and development. The compatibility of leaf tissue levels with these functions has, however, often been questioned. The objective here is to document H2O2 levels and variability under natural conditions, and their underlying causes. Using the FOX method, bulk H2O2 concentrations were analysed in leaf samples from 18 species of herbs and trees throughout the 2006 growing season. Sampling addressing targeted predictions was emphasised in 2007 and 2008. H2O2 levels varied 100-fold through the year, with a main peak in spring. Two hypotheses were examined: (H1) that H2O2 reflects seasonally variable responses to environmental stresses, and (H2) that it reflects metabolism associated with leaf development. Based on poor or inappropriate correlations between H2O2 and indicators of light, temperature or drought stress, support for H1 was minimal. H2 was supported both by seasonal patterns and by targeted analyses of concentration changes throughout leaf development. This study concludes that bulk tissue H2O2 concentrations are poor indicators of stress, and are generally too high to reflect either signalling or metabolic control networks. Instead, the linkage of H2O2 and leaf phenology appears to reflect the roles of H2O2 in cell expansion, lignification and wall cross-linking.
The evolutionary development of plant body plans
Authors: Niklas Karl J. , Kutschera Ulrich
Published: July 2009

Evolutionary developmental biology, cladistic analyses, and paleontological insights make it increasingly clear that regulatory mechanisms operating during embryogenesis and early maturation tend to be highly conserved over great evolutionary time scales, which can account for the conservative nature of the body plans in the major plant and animal clades. At issue is whether morphological convergences in body plans among evolutionarily divergent lineages are the result of adaptive convergence or ‘genome recall’ and ‘process orthology’. The body plans of multicellular photosynthetic eukaryotes (‘plants’) are reviewed, some of their important developmental/physiological regulatory mechanisms discussed, and the evidence that some of these mechanisms are phyletically ancient examined. We conclude that endosymbiotic lateral gene transfers, gene duplication and functional divergence, and the co-option of ancient gene networks were key to the evolutionary divergence of plant lineages.
High-affinity lamprey VLRA and VLRB monoclonal antibodies
Authors: Tasumi Satoshi , Velikovsky C. Alejandro , Xu Gang , Gai S. Annie , Wittrup K. Dane , Flajnik Martin F. , Mariuzza Roy A. , Pancer Zeev
Published: July 2009

Lamprey are members of the ancestral vertebrate taxon (jawless fish), which evolved rearranging antigen receptors convergently with the jawed vertebrates. But instead of Ig superfamily domains, lamprey variable lymphocyte receptors (VLRs) consist of highly diverse leucine-rich repeats. Although VLRs represent the only known adaptive immune system not based on Ig, little is known about their antigen-binding properties. Here we report robust plasma VLRB responses of lamprey immunized with hen egg lysozyme and β-galactosidase (β-gal), demonstrating adaptive immune responses against soluble antigens. To isolate monoclonal VLRs, we constructed large VLR libraries from antigen-stimulated and naïve animals in a novel yeast surface-display vector, with the VLR C-terminally fused to the yeast Flo1p surface anchor. We cloned VLRB binders of lysozyme, β-gal, cholera toxin subunit B, R-phycoerythrin, and B-trisaccharide antigen, with dissociation constants up to the single-digit picomolar range, equivalent to those of high-affinity IgG antibodies. We also isolated from a single lamprey 13 anti-lysozyme VLRA clones with affinities ranging from low nanomolar to mid-picomolar. All of these VLRA clones were closely related in sequence, differing at only 15 variable codon positions along the 244-residue VLR diversity region, which augmented antigen-binding affinity up to 100-fold. Thus, VLRs can provide a protective humoral antipathogen shield. Furthermore, the broad range of nominal antigens that VLRs can specifically bind, and the affinities achieved, indicate a functional parallelism between LRR-based and Ig-based antibodies. VLRs may be useful natural single-chain alternatives to conventional antibodies for biotechnology applications.
Evaluation of medial acetabular wall bone stock in patients with developmental dysplasia of the hip using a helical computed tomography multiplanar reconstruction technique
Authors: Liu Rui Yu , Wang Kun Zheng , Wang Chun Sheng , Dang Xiao Qian , Tong Zhi Qin
Published: July 2009

Background: The technique of medialization has been used to reconstruct acetabula at the level of true acetabula in total hip arthroplasty (THA) in patients with developmental dysplasia of the hip (DDH). Appreciation of the bone stock in the medial acetabular wall is significant for making an optimal acetabular reconstruction plan and avoiding complications.

Purpose: To evaluate the bone stock of the medial acetabular wall and its relation to the degree of subluxation in patients with DDH using computed tomography (CT).

Material and Methods: Helical CT scans of 27 hips were obtained from 21 patients with osteoarthritis secondary to DDH who were scheduled for total hip arthroplasty. Eleven hips belonged to Crowe class I, while 16 hips belonged to Crowe class II/III. The raw CT data were reprocessed in various planes by scrolling multiplanar reformation (MPR). Acetabular opening, depth, and medial bone stock, as indicated by the minimum thickness of the medial acetabular wall, were measured in the transverse reformed MPR plane.

Results: The minimum thicknesses of the medial acetabular wall in Crowe-I and Crowe-II/III hips were 3.8±2.1 mm and 7.1±3.1 mm, respectively, with statistically significant differences between the groups ( P<0.05). Furthermore, the bone stock in the medial acetabular wall correlated with the degree of subluxation ( R=0.69) and the acetabular depth ( R= ;− ;0.71).

Conclusion: There was significantly more bone stock in the medial acetabular wall in patients with higher-degree subluxation than there was in the less-severe class. This difference should be taken into consideration when reconstructing acetabula in THA in patients with DDH using the technique of medialization.
Guanine Nucleotide Exchange Factor-H1 Regulates Cell Migration via Localized Activation of RhoA at the Leading Edge
Authors: Nalbant Perihan , Chang Yuan-Chen , Birkenfeld Jörg , Chang Zee-Fen , Bokoch Gary M.
Published: July 2009

Cell migration involves the cooperative reorganization of the actin and microtubule cytoskeletons, as well as the turnover of cell–substrate adhesions, under the control of Rho family GTPases. RhoA is activated at the leading edge of motile cells by unknown mechanisms to control actin stress fiber assembly, contractility, and focal adhesion dynamics. The microtubule-associated guanine nucleotide exchange factor (GEF)-H1 activates RhoA when released from microtubules to initiate a RhoA/Rho kinase/myosin light chain signaling pathway that regulates cellular contractility. However, the contributions of activated GEF-H1 to coordination of cytoskeletal dynamics during cell migration are unknown. We show that small interfering RNA-induced GEF-H1 depletion leads to decreased HeLa cell directional migration due to the loss of the Rho exchange activity of GEF-H1. Analysis of RhoA activity by using a live cell biosensor revealed that GEF-H1 controls localized activation of RhoA at the leading edge. The loss of GEF-H1 is associated with altered leading edge actin dynamics, as well as increased focal adhesion lifetimes. Tyrosine phosphorylation of focal adhesion kinase and paxillin at residues critical for the regulation of focal adhesion dynamics was diminished in the absence of GEF-H1/RhoA signaling. This study establishes GEF-H1 as a critical organizer of key structural and signaling components of cell migration through the localized regulation of RhoA activity at the cell leading edge.
Role for RACK1 Orthologue Cpc2 in the Modulation of Stress Response in Fission Yeast
Authors: Núñez Andrés , Franco Alejandro , Madrid Marisa , Soto Teresa , Vicente Jero , Gacto Mariano , Cansado José
Published: July 2009

The receptor of activated C kinase (RACK1) is a protein highly conserved among eukaryotes. In mammalian cells, RACK1 functions as an adaptor to favor protein kinase C (PKC)-mediated phosphorylation and subsequent activation of c-Jun NH2-terminal kinase mitogen-activated protein kinase. Cpc2, the RACK1 orthologue in the fission yeast Schizosaccharomyces pombe, is involved in the control of G2/M transition and interacts with Pck2, a PKC-type protein member of the cell integrity Pmk1 mitogen-activated protein kinase (MAPK) pathway. Both RACK1 and Cpc2 are structural components of the 40S ribosomal subunit, and recent data suggest that they might be involved in the control of translation. In this work, we present data supporting that Cpc2 negatively regulates the cell integrity transduction pathway by favoring translation of the tyrosine-phosphatases Pyp1 and Pyp2 that deactivate Pmk1. In addition, Cpc2 positively regulates the synthesis of the stress-responsive transcription factor Atf1 and the cytoplasmic catalase, a detoxificant enzyme induced by treatment with hydrogen peroxide. These results provide for the first time strong evidence that the RACK1-type Cpc2 protein controls from the ribosome the extent of the activation of MAPK cascades, the cellular defense against oxidative stress, and the progression of the cell cycle by regulating positively the translation of specific gene products involved in key biological processes.
Monkey and humans exhibit similar motion-processing mechanisms
Authors: Curran William , Lynn Catherine
Published: July 2009

Single cell recording studies have resulted in a detailed understanding of motion-sensitive neurons in non-human primate visual cortex. However, it is not known to what extent response properties of motion-sensitive neurons in the non-human primate brain mirror response characteristics of motion-sensitive neurons in the human brain. Using a motion adaptation paradigm, the direction aftereffect, we show that changes in the activity of human motion-sensitive neurons to moving dot patterns that differ in dot density bear a strong resemblance to data from macaque monkey. We also show a division-like inhibition between neural populations tuned to opposite directions, which also mirrors neural-inhibitory behaviour in macaque. These findings strongly suggest that motion-sensitive neurons in human and non-human primates share common response and inhibitory characteristics.
Climate change: is the dark Soay sheep endangered?
Authors: Maloney Shane K. , Fuller Andrea , Mitchell Duncan
Published: July 2009

It was recently reported that the proportion of dark-coloured Soay sheep (Ovis aries) in the Hebrides has decreased, despite the fact that dark sheep tend to be larger than lighter sheep, and there exists a selective advantage to large body size. It was concluded that an apparent genetic linkage between loci for the coat colour polymorphism and loci with antagonistic effects on body size explained the decrease. Those results explain why the proportion of dark animals is not increasing, but not why it is decreasing. Between 1985 and 2005 there was a significant increase in mean ambient temperature near the islands. We suggest that, while in the past a dark coat has offset the metabolic costs of thermoregulation by absorbing solar radiation, the selective advantage of a dark coat may be waning as the climate warms in the North Atlantic. In parallel, Bergman's rule may be operating, reducing the selective advantage of large body size in the cold. Either or both of these mechanisms can explain the decrease in the proportion of dark-coloured larger sheep in this population in which smaller (and light-coloured) sheep should be favoured by their lower gross energy demand. If environmental effects are the cause of the decline, then we can expect the proportion of dark-coloured Soay sheep to decrease further.
Internal resonance of vibrational modes in single-walled carbon nanotubes
Authors: Shi M. X. , Li Q. M. , Huang Y.
Published: July 2009

We show, by molecular dynamics simulations, that 2:1 internal resonance may occur between a radial breathing mode (RBM) and a circumferential flexural mode (CFM) in single-walled carbon nanotubes (SWCNTs). When the RBM vibration amplitude is greater than a critical value, automatic transformations between the RBM and CFM with approximately half RBM-frequency are observed. This discovery in the discrete SWCNT atom assembly is similar to the 2:1 internal resonance mechanism observed in continuum shells. A non-local continuum shell model is employed to determine the critical conditions for the occurrence of observed 2:1 internal resonance between the RBM and CFMs based on two non-dimensional parameters and the Mathieu stability diagram.
Hidden levels of phylodiversity in Antarctic green algae: further evidence for the existence of glacial refugia
Authors: De Wever Aaike , Leliaert Frederik , Verleyen Elie , Vanormelingen Pieter , Van der Gucht Katleen , Hodgson Dominic A. , Sabbe Koen , Vyverman Wim
Published: July 2009

Recent data revealed that metazoans such as mites and springtails have persisted in Antarctica throughout several glacial–interglacial cycles, which contradicts the existing paradigm that terrestrial life was wiped out by successive glacial events and that the current inhabitants are recent colonizers. We used molecular phylogenetic techniques to study Antarctic microchlorophyte strains isolated from lacustrine habitats from maritime and continental Antarctica. The 14 distinct chlorophycean and trebouxiophycean lineages observed point to a wide phylogenetic diversity of apparently endemic Antarctic lineages at different taxonomic levels. This supports the hypothesis that long-term survival took place in glacial refugia, resulting in a specific Antarctic flora. The majority of the lineages have estimated ages between 17 and 84 Ma and probably diverged from their closest relatives around the time of the opening of Drake Passage (30–45 Ma), while some lineages with longer branch lengths have estimated ages that precede the break-up of Gondwana. The variation in branch length and estimated age points to several independent but rare colonization events.
Phylogenetic Analysis of ADP-Glucose Pyrophosphorylase Subunits Reveals a Role of Subunit Interfaces in the Allosteric Properties of the Enzyme
Authors: Georgelis Nikolaos , Shaw Janine R. , Hannah L. Curtis
Published: July 2009

ADP-glucose pyrophosphorylase (AGPase) catalyzes a rate-limiting step in glycogen and starch synthesis in bacteria and plants, respectively. Plant AGPase consists of two large and two small subunits that were derived by gene duplication. AGPase large subunits have functionally diverged, leading to different kinetic and allosteric properties. Amino acid changes that could account for these differences were identified previously by evolutionary analysis. In this study, these large subunit residues were mapped onto a modeled structure of the maize (Zea mays) endosperm enzyme. Surprisingly, of 29 amino acids identified via evolutionary considerations, 17 were located at subunit interfaces. Fourteen of the 29 amino acids were mutagenized in the maize endosperm large subunit (SHRUNKEN-2 [SH2]), and resulting variants were expressed in Escherichia coli with the maize endosperm small subunit (BT2). Comparisons of the amount of glycogen produced in E. coli, and the kinetic and allosteric properties of the variants with wild-type SH2/BT2, indicate that 11 variants differ from the wild type in enzyme properties or in vivo glycogen level. More interestingly, six of nine residues located at subunit interfaces exhibit altered allosteric properties. These results indicate that the interfaces between the large and small subunits are important for the allosteric properties of AGPase, and changes at these interfaces contribute to AGPase functional specialization. Our results also demonstrate that evolutionary analysis can greatly facilitate enzyme structure-function analyses.
Recruitment of Anguilla spp. glass eels in the Waikato River, New Zealand. Evidence of declining migrations?
Authors: Jellyman D. J. , Booker D. J. , Watene E.
Published: July 2009

The timing of Anguilla spp. glass eel recruitment into the Waikato River, North Island, New Zealand, was studied over a 2 year period (2004–2005). While glass eels of both the shortfin eel Anguilla australis and the endemic longfin eel Anguilla dieffenbachii were caught, the former comprised >97% of the species composition. There was a positive correlation of glass eel migrations with spring tides, with peak migration periods typically occurring within a few hours of the peak of high tide, and between 2 and 4 days after the day of spring tide. Both water temperature and discharge had significant inverse relationships with glass eel catches, with temperature explaining >30% of the variance in catch periodicity. Comparison of catch data 30 years apart showed that main migration periods appear to occur several weeks earlier today than previously. Reduced catch per unit effort and duration of runs from recent years' sampling (compared with the 1970s) indicate that a reduction in recruitment may also have occurred during this period, something recorded in other temperate species of Anguilla.
Size selectivity of fyke nets for European eel Anguilla anguilla
Authors: Bevacqua D. , De Leo G. A. , Gatto M. , Melià P.
Published: July 2009

Size selectivity of fyke nets for European eels Anguilla anguilla was investigated by reviewing the results of published experimental studies. A general size selectivity model was then derived that can be easily incorporated into demographic models to simulate population dynamics, assess and monitor abundance and length structure of eel stocks and forecast the consequences of different management options.
Influence of water temperature and feeding regime on otolith growth in Anguilla japonica glass eels and elvers: does otolith growth cease at low temperatures?
Authors: Fukuda N. , Kuroki M. , Shinoda A. , Yamada Y. , Okamura A. , Aoyama J. , Tsukamoto K.
Published: July 2009

The influences of water temperature and feeding regime on otolith growth in Anguilla japonica glass eels and elvers were investigated using individuals reared at 5, 10, 15, 20, 25 and 30° C and in fed or unfed conditions at salinity 32 after their otoliths were marked with alizarin complexone (ALC). To eliminate the difficulty of observing the edges of otoliths with optical (OM) or scanning electron (SEM) microscopes, three to 10 individuals were sampled from each tank at 10, 20 and 30 days during the experiment and reared for an additional 10 days at 25° C after their otoliths were marked a second time. Otolith growth and the number of increments were measured using both OM and SEM. Most A. japonica commenced feeding after 10 days at 20–30° C or after 20 days at 15° C, but no feeding occurred at 5 and 10° C. No otolith growth occurred at 5 and 10° C except in two individuals with minimal increment deposition at 10° C. Otolith growth was proportional to water temperature within 15–25° C and not different between 25 and 30° C. At 15, 25 and 30° C, the mean otolith growth rate in fed conditions was higher than in unfed conditions. The number of increments per day was significantly different among water temperatures (0·00–0·01 day−1 at 5 and 10° C, 0·43–0·48 day−1 at 15° C and 0·94–1·07 day−1 at 20–30° C). These results indicated that otolith growth in A. japonica glass eels and elvers was affected by temperature and ceased at ≤10° C under experimental conditions. Hence, future studies analysing the otoliths of wild‐caught A. japonica glass eels and elvers need to carefully consider the water temperatures potentially experienced by the juveniles in the wild.
Differential effects of origin and salinity rearing conditions on growth of glass eels of the American eel Anguilla rostrata: implications for stocking programmes
Authors: Côté C. L. , Castonguay M. , Verreault G. , Bernatchez L.
Published: July 2009

In this study, growth patterns were monitored in controlled fresh and brackish water (BW) conditions for 7 months during Anguilla rostrata glass eel and elver stages. Null hypotheses tested were that there is no significant difference in growth between glass eels (1) collected from two geographic regions typified by different sex ratios, (2) reared in fresh and BW and (3) due to origin × salinity interactions. It was found that young A. rostrata from Mira River (MR, Cape Breton, Nova Scotia, Canada, an area where both males and females occur) grew faster than those from Grande‐Rivière‐Blanche (Québec, Canada, an area where population are highly skewed towards females; 99–100%). Anguilla rostrata from both origins also grew faster in BW, although there was a trend for origin × salinity interactions whereby this effect was more pronounced for fish from the MR. The results support the hypothesis that salinity can influence growth patterns, as possibly can quantitative genetic differences between A. rostrata glass eels from different origins. Possible explanations for these patterns and potential consequences for sex determination and translocation programmes are discussed.
The effects of seasonal and interannual variability of oceanic structure in the western Pacific North Equatorial Current on larval transport of the Japanese eel Anguilla japonica
Authors: Zenimoto K. , Kitagawa T. , Miyazaki S. , Sasai Y. , Sasaki H. , Kimura S.
Published: July 2009

As the North Equatorial Current (NEC)–bifurcation is known to be related to El Niño‐Southern Oscillation (ENSO) events, the influence of the position of the NEC bifurcation on transport success of the larval Japanese eel Anguilla japonica was investigated. Using a Lagrangian modelling approach, larval transport was simulated and the relative influence of El Niño and La Niña events and the NEC‐bifurcation position on the success of particle transport analysed. The number of particles transported from the NEC to the Kuroshio tended to be lowest during El Niño years, and differences between La Niña and regular years were small. The transport success observed in simulations showed some relationships to annual A. japonica glass eel recruitment to Tanegashima Island over 1993 to 2001, but not in 2002. The study shows that particle tracking simulations can be used to improve knowledge of the oceanic migration of A. japonica but further studies are required, including comparisons with the effects on larval survival of fluctuations in temperature and food availability.
High therapy adherence but substantial limitations to daily activities amongst members of the Dutch inflammatory bowel disease patients' organization: a patient empowerment study
Authors: BAARS J. E. , ZELINKOVA Z. , MENSINK P. B. F. , MARKUS T. , LOOMAN C. W. N. , KUIPERS E. J. , VAN DER WOUDE C. J.
Published: July 2009

Aliment Pharmacol Ther 30, 864–872

Background  Adherence is important for successful treatment in inflammatory bowel disease (IBD) patients. Previous studies demonstrated high prevalence of non‐adherence.

Aim  To assess IBD‐patients’ perceptions of therapy adherence and disease‐related functional status in members of the Dutch patients’ association of Crohn’s disease and ulcerative colitis (CCUVN).

Methods  Inflammatory bowel disease‐patients completed anonymously a survey at the website of the CCUVN. Statistical analysis was performed using principal component analysis, univariate and multivariate logistic regression.

Results  The questionnaire was completed by 1067 patients [617 (58%) Crohn’s disease (CD) and 450 (42%) ulcerative colitis (UC)]. Mean age was 43 years (s.d. 13.7); women (66%). Of 920 patients currently using medication, 797 (87%) were adherent. Of the patients using 5‐ASA, 91% were adherent (527/582), vs. 96% using corticosteroids (316/330) and 97% (414/425) using immunosuppressives. CD patients (OR 1.54; 95% CI 1.05–2.27), patients with duration of disease ≤8 years (OR 2.25; 95% CI 1.49–3.39) were more adherent. Fifty percent of patients reported a low functional status and were limited in daily activities.

Conclusion  This population‐based study shows high therapy adherence, but low functional status in Dutch CCUVN‐related IBD‐patients. The high adherence rate in this present study could be an effect of CCUVN membership.
Is intrinsic asthma synonymous with infection?
Authors: Dahlberg P. E. , Busse W. W.
Published: July 2009

Rackemann described the ‘intrinsic asthma’ population over 50 years ago as a unique subgroup that was characterized by onset of progressive loss of lung function beginning later in life, possibly after a respiratory infection. It has also been associated with a female predominance, aspirin‐sensitive bronchospasm, and nasal polyposis. While the aetiology is not understood, we propose that persistent respiratory infections play a central role in the development of intrinsic asthma.